Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 139 of 145
Found at i:45991278 original size:7 final size:7
Alignment explanation
Indices: 45991266--45991360 Score: 60
Period size: 7 Copynumber: 14.0 Consensus size: 7
45991256 AACCCTGAAT
45991266 CCTTAAA
1 CCTTAAA
45991273 CCTTAAA
1 CCTTAAA
*
45991280 CC-TGAA
1 CCTTAAA
45991286 CCTTAAA
1 CCTTAAA
45991293 CCTTAAA
1 CCTTAAA
45991300 -CTCTAAA
1 CCT-TAAA
* *
45991307 TCATTGAA
1 -CCTTAAA
45991315 -CTCTAAA
1 CCT-TAAA
45991322 CC-TAAA
1 CCTTAAA
*
45991328 CTTTAAA
1 CCTTAAA
*
45991335 CC-TCAA
1 CCTTAAA
45991341 CAC-TAAA
1 C-CTTAAA
45991348 -CTTAAA
1 CCTTAAA
45991354 CCTTAAA
1 CCTTAAA
45991361 TCTCAAACCG
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
5 1 0.01
6 21 0.31
7 41 0.60
8 4 0.06
9 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.27
Consensus pattern (7 bp):
CCTTAAA
Found at i:45991291 original size:20 final size:21
Alignment explanation
Indices: 45991259--45991300 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
45991249 AACTTACAAC
45991259 CCTGAATCCTTAAACCTTAAA
1 CCTGAATCCTTAAACCTTAAA
45991280 CCTGAA-CCTTAAACCTTAAA
1 CCTGAATCCTTAAACCTTAAA
45991300 C
1 C
45991301 TCTAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (21 bp):
CCTGAATCCTTAAACCTTAAA
Found at i:45991334 original size:13 final size:13
Alignment explanation
Indices: 45991269--45991360 Score: 55
Period size: 13 Copynumber: 6.8 Consensus size: 13
45991259 CCTGAATCCT
45991269 TAAACCTTAAACC
1 TAAACCTTAAACC
*
45991282 TGAACCTTAAACC
1 TAAACCTTAAACC
*
45991295 TTAAA-CTCTAAATCAT
1 -TAAACCT-TAAA-C-C
*
45991311 TGAA-CTCTAAACC
1 TAAACCT-TAAACC
*
45991324 TAAACTTTAAACC
1 TAAACCTTAAACC
* *
45991337 TCAACAC-TAAACT
1 TAAAC-CTTAAACC
45991350 TAAACCTTAAA
1 TAAACCTTAAA
45991361 TCTCAAACCG
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
12 1 0.02
13 40 0.66
14 9 0.15
15 11 0.18
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (13 bp):
TAAACCTTAAACC
Found at i:45991368 original size:20 final size:18
Alignment explanation
Indices: 45991267--45991360 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 18
45991257 ACCCTGAATC
*
45991267 CTTAAACCTTAAACCTGAAC
1 CTTAAACCTTAAA-CT-AAA
45991287 CTTAAACCTTAAACTCTAAA
1 CTTAAACCTTAAA--CTAAA
*
45991307 TCATTGAA-CTCTAAACCTAAA
1 -C-TTAAACCT-TAAA-CTAAA
*
45991328 CTTTAAACCTCAACACTAAA
1 C-TTAAACCTTAA-ACTAAA
45991348 CTTAAACCTTAAA
1 CTTAAACCTTAAA
45991361 TCTCAAACCG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 10 0.17
20 28 0.47
21 13 0.22
22 8 0.13
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.28
Consensus pattern (18 bp):
CTTAAACCTTAAACTAAA
Found at i:45991592 original size:18 final size:18
Alignment explanation
Indices: 45991569--45991603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45991559 TTGTTTATAA
45991569 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
45991587 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
45991604 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:45993626 original size:15 final size:15
Alignment explanation
Indices: 45993606--45993635 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45993596 ATATTTGATG
45993606 TTAATTTCATTTGTT
1 TTAATTTCATTTGTT
45993621 TTAATTTCATTTGTT
1 TTAATTTCATTTGTT
45993636 AAAATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (15 bp):
TTAATTTCATTTGTT
Found at i:45997030 original size:17 final size:18
Alignment explanation
Indices: 45996998--45997032 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45996988 CCATGATGTT
45996998 CACCCGTGTGGGCCCACA
1 CACCCGTGTGGGCCCACA
45997016 CACCCGTGT-GGCCCACA
1 CACCCGTGTGGGCCCACA
45997033 TGGCCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.46, G:0.26, T:0.11
Consensus pattern (18 bp):
CACCCGTGTGGGCCCACA
Found at i:46019614 original size:15 final size:16
Alignment explanation
Indices: 46019586--46019623 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
46019576 TTTGCATCAT
46019586 ATTTGTTGTTAATTTC
1 ATTTGTTGTTAATTTC
46019602 ATTTGTT-TTAATTTC
1 ATTTGTTGTTAATTTC
46019617 ATTTGTT
1 ATTTGTT
46019624 AAAATATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (16 bp):
ATTTGTTGTTAATTTC
Found at i:46020351 original size:23 final size:23
Alignment explanation
Indices: 46020308--46020350 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46020298 AAAAATAAAT
*
46020308 TATTCTTTTCTTTATTATTTTAC
1 TATTCGTTTCTTTATTATTTTAC
46020331 TATTCGTTTCTTT-TTATTTT
1 TATTCGTTTCTTTATTATTTT
46020351 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTCGTTTCTTTATTATTTTAC
Found at i:46023311 original size:17 final size:17
Alignment explanation
Indices: 46023255--46023312 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
46023245 TTATTTTCAT
*
46023255 ATCATTAAATTAATAATA
1 ATCATTAAATTTA-AATA
*
46023273 CATCATTATATATTTTATATA
1 -ATCATTA-A-A-TTTAAATA
46023294 ATCATTAAATTTAAATA
1 ATCATTAAATTTAAATA
46023311 AT
1 AT
46023313 TACTAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
17 9 0.27
18 1 0.03
19 8 0.24
20 8 0.24
21 4 0.12
22 3 0.09
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
ATCATTAAATTTAAATA
Found at i:46023532 original size:135 final size:138
Alignment explanation
Indices: 46023369--46023632 Score: 419
Period size: 138 Copynumber: 1.9 Consensus size: 138
46023359 AATTATTTTA
46023369 GATTAATAATTAATGTTGTCAAAATTTATTTCAATTAATTTACAAT-T-TAATGTTTTGTAAATT
1 GATTAATAATTAATGTTGTCAAAATTTATTTCAATTAATTTACAATCTATAATGTTTTGTAAATT
** * *
46023432 TTTAATATAAATT-TATATTATTTAAATATATTTTCATAGTTTCAGACTTTTAGAGTTTTAGATT
66 TTTAATAT-AATTATATAACATTTAAACATATTTTCATAATTTCAGACTTTTAGAGTTTTAGATT
46023496 GAATTTATC
130 GAATTTATC
* * *
46023505 GATTAATAA-TAATGTTTTCAAATTTTATTTCAATTAATTTACAATCTAATAATGTTTTGTAGAT
1 GATTAATAATTAATGTTGTCAAAATTTATTTCAATTAATTTACAATCT-ATAATGTTTTGTAAAT
46023569 TTTTAATATAATTATATAACATTTAAACATATTTTCATAATTTCAGACTTTTAGAGTTTTAGAT
65 TTTTAATATAATTATATAACATTTAAACATATTTTCATAATTTCAGACTTTTAGAGTTTTAGAT
46023633 CAAGTTTATC
Statistics
Matches: 117, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
135 34 0.29
136 10 0.09
137 4 0.03
138 69 0.59
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (138 bp):
GATTAATAATTAATGTTGTCAAAATTTATTTCAATTAATTTACAATCTATAATGTTTTGTAAATT
TTTAATATAATTATATAACATTTAAACATATTTTCATAATTTCAGACTTTTAGAGTTTTAGATTG
AATTTATC
Found at i:46025784 original size:315 final size:315
Alignment explanation
Indices: 46025212--46025842 Score: 1244
Period size: 315 Copynumber: 2.0 Consensus size: 315
46025202 ATCTTTCCAA
46025212 TATTAGGTTCTTTGATATCGGTGTGAATAAGATTCAAGGTACTCTTTATACTGACTTAGCAATCA
1 TATTAGGTTCTTTGATATCGGTGTGAATAAGATTCAAGGTACTCTTTATACTGACTTAGCAATCA
46025277 CTATGCCATATGTTGAGTTCTTTTCTGTAAGGGGAAATAAAATCTCCGGACAAATCCCAGTTTCA
66 CTATGCCATATGTTGAGTTCTTTTCTGTAAGGGGAAATAAAATCTCCGGACAAATCCCAGTTTCA
*
46025342 ATATCCAATGCCTCAAATCTGAATGTACTTCAATTTAATGATAATAGACTTGGTGGAAAGGTGCC
131 ATAACCAATGCCTCAAATCTGAATGTACTTCAATTTAATGATAATAGACTTGGTGGAAAGGTGCC
46025407 CTCCCTAGAAAAGCTAGATAAACTATCTACCCTTCAACTAAGTGTAAACCGTTTGGGGCATGGGA
196 CTCCCTAGAAAAGCTAGATAAACTATCTACCCTTCAACTAAGTGTAAACCGTTTGGGGCATGGGA
*
46025472 GAGAAGGTGACTTGAACTTTCTTTGCACTTTAGTCAATAATACCAAACTAGAGTT
261 GAGAAGGTGACTTGAACTTCCTTTGCACTTTAGTCAATAATACCAAACTAGAGTT
46025527 TATTAGGTTCTTTGATATCGGTGTGAATAAGATTCAAGGTACTCTTTATACTGACTTAGCAATCA
1 TATTAGGTTCTTTGATATCGGTGTGAATAAGATTCAAGGTACTCTTTATACTGACTTAGCAATCA
46025592 CTATGCCATATGTTGAGTTCTTTTCTGTAAGGGGAAATAAAATCTCCGGACAAATCCCAGTTTCA
66 CTATGCCATATGTTGAGTTCTTTTCTGTAAGGGGAAATAAAATCTCCGGACAAATCCCAGTTTCA
46025657 ATAACCAATGCCTCAAATCTGAATGTACTTCAATTTAATGATAATAGACTTGGTGGAAAGGTGCC
131 ATAACCAATGCCTCAAATCTGAATGTACTTCAATTTAATGATAATAGACTTGGTGGAAAGGTGCC
46025722 CTCCCTAGAAAAGCTAGATAAACTATCTACCCTTCAACTAAGTGTAAACCGTTTGGGGCATGGGA
196 CTCCCTAGAAAAGCTAGATAAACTATCTACCCTTCAACTAAGTGTAAACCGTTTGGGGCATGGGA
46025787 GAGAAGGTGACTTGAACTTCCTTTGCACTTTAGTCAATAATACCAAACTAGAGTT
261 GAGAAGGTGACTTGAACTTCCTTTGCACTTTAGTCAATAATACCAAACTAGAGTT
46025842 T
1 T
46025843 CTATATATTA
Statistics
Matches: 314, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
315 314 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (315 bp):
TATTAGGTTCTTTGATATCGGTGTGAATAAGATTCAAGGTACTCTTTATACTGACTTAGCAATCA
CTATGCCATATGTTGAGTTCTTTTCTGTAAGGGGAAATAAAATCTCCGGACAAATCCCAGTTTCA
ATAACCAATGCCTCAAATCTGAATGTACTTCAATTTAATGATAATAGACTTGGTGGAAAGGTGCC
CTCCCTAGAAAAGCTAGATAAACTATCTACCCTTCAACTAAGTGTAAACCGTTTGGGGCATGGGA
GAGAAGGTGACTTGAACTTCCTTTGCACTTTAGTCAATAATACCAAACTAGAGTT
Found at i:46029384 original size:16 final size:16
Alignment explanation
Indices: 46029359--46029394 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46029349 TCATTCCAAC
* *
46029359 CAATCTAGTGTTGGTA
1 CAATCGAGTGTTAGTA
46029375 CAATCGAGTGTTAGTA
1 CAATCGAGTGTTAGTA
46029391 CAAT
1 CAAT
46029395 GATAAAAACA
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:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (16 bp):
CAATCGAGTGTTAGTA
Found at i:46030590 original size:115 final size:116
Alignment explanation
Indices: 46030454--46030685 Score: 457
Period size: 115 Copynumber: 2.0 Consensus size: 116
46030444 GGGGCTAAAG
46030454 TGTAATTTTATTATTATTAATTTAAAATTTTATAAATTAAATAAAAAAAATTTTTCATTAAGCAC
1 TGTAATTTTATTATTATTAATTTAAAATTTTATAAATTAAATAAAAAAAATTTTTCATTAAGCAC
46030519 TGCCAACTTCTCGGCTCCGCCATTGAGTATAATTATAATGAAATATCATGC
66 TGCCAACTTCTCGGCTCCGCCATTGAGTATAATTATAATGAAATATCATGC
46030570 TGTAATTTTA-TATTATTAATTTAAAATTTTATAAATTAAATAAAAAAAATTTTTCATTAAGCAC
1 TGTAATTTTATTATTATTAATTTAAAATTTTATAAATTAAATAAAAAAAATTTTTCATTAAGCAC
46030634 TGCCAACTTCTCGGCTCCGCCATTGAGTATAATTATAATGAAATATCATGC
66 TGCCAACTTCTCGGCTCCGCCATTGAGTATAATTATAATGAAATATCATGC
46030685 T
1 T
46030686 ATTAAGTTAC
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
115 106 0.91
116 10 0.09
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (116 bp):
TGTAATTTTATTATTATTAATTTAAAATTTTATAAATTAAATAAAAAAAATTTTTCATTAAGCAC
TGCCAACTTCTCGGCTCCGCCATTGAGTATAATTATAATGAAATATCATGC
Found at i:46030615 original size:20 final size:21
Alignment explanation
Indices: 46030573--46030615 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
46030563 ATCATGCTGT
* * *
46030573 AATTTTATATTATTAATTTAA
1 AATTTTATATAATTAAATAAA
46030594 AATTTTATA-AATTAAATAAA
1 AATTTTATATAATTAAATAAA
46030614 AA
1 AA
46030616 AAATTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTATATAATTAAATAAA
Found at i:46040953 original size:25 final size:24
Alignment explanation
Indices: 46040925--46040973 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
46040915 AATACACTAA
* *
46040925 ATTTACTAAAAATATTAAAATAAAT
1 ATTTACCAAAAAT-TGAAAATAAAT
*
46040950 ATTTCCCAAAAATTGAAAATAAAT
1 ATTTACCAAAAATTGAAAATAAAT
46040974 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTACCAAAAATTGAAAATAAAT
Found at i:46044671 original size:112 final size:112
Alignment explanation
Indices: 46044474--46044702 Score: 440
Period size: 112 Copynumber: 2.0 Consensus size: 112
46044464 GGTGATTGAA
46044474 CTGTTAACTCAGCTTTGTTTATGTGTACAAGCTTGGTTTACCAAGTTTCAATGTATTAGTGGTAG
1 CTGTTAACTCAGCTTTGTTTATGTGTACAAGCTTGGTTTACCAAGTTTCAATGTATTAGTGGTAG
46044539 TAGGTATTGATTAGGTGACCATATACTGATTTTGACAAGCTGAATGC
66 TAGGTATTGATTAGGTGACCATATACTGATTTTGACAAGCTGAATGC
46044586 CTGTTAACTCAGCTTTGTTTATGTGTACAAGCTTGGTTTACCAAGTTTCAATGTATTAGTGGTAG
1 CTGTTAACTCAGCTTTGTTTATGTGTACAAGCTTGGTTTACCAAGTTTCAATGTATTAGTGGTAG
*
46044651 TAGGTATTGATTAGGTGACCATATACTGATTTTGACAGGCTGAATGC
66 TAGGTATTGATTAGGTGACCATATACTGATTTTGACAAGCTGAATGC
*
46044698 TTGTT
1 CTGTT
46044703 TTTATGGATT
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (112 bp):
CTGTTAACTCAGCTTTGTTTATGTGTACAAGCTTGGTTTACCAAGTTTCAATGTATTAGTGGTAG
TAGGTATTGATTAGGTGACCATATACTGATTTTGACAAGCTGAATGC
Found at i:46055507 original size:21 final size:21
Alignment explanation
Indices: 46055477--46055516 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46055467 TGCTATCAAA
*
46055477 TTACAAAGGAACAAGACAAGG
1 TTACAAAGGAACAAAACAAGG
*
46055498 TTACATAGGAACAAAACAA
1 TTACAAAGGAACAAAACAA
46055517 TCAAAATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.12
Consensus pattern (21 bp):
TTACAAAGGAACAAAACAAGG
Found at i:46061403 original size:23 final size:21
Alignment explanation
Indices: 46061350--46061398 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
46061340 TCACTTCGTT
*
46061350 TCTTTTTATCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
46061371 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
46061392 TCTTTTT
1 TCTTTTT
46061399 TTGTCTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.57
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:46062003 original size:24 final size:26
Alignment explanation
Indices: 46061956--46062004 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
46061946 ACTATTGAAA
*
46061956 TTTTAATTATTTTTGTTGCTCATTTAT
1 TTTTAATTATTTTAGTTGC-CATTTAT
46061983 TTTTAATT-TTTTAGTTG-CATTT
1 TTTTAATTATTTTAGTTGCCATTT
46062005 TCCTCGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
26 8 0.38
27 8 0.38
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67
Consensus pattern (26 bp):
TTTTAATTATTTTAGTTGCCATTTAT
Found at i:46062421 original size:176 final size:176
Alignment explanation
Indices: 46062127--46062478 Score: 704
Period size: 176 Copynumber: 2.0 Consensus size: 176
46062117 GAGTAGATTG
46062127 AAAGTAAAATATATTTTTTAATTGTGTTAGAAAAATATATTATTCGGTTAATGTCATAAAGCATA
1 AAAGTAAAATATATTTTTTAATTGTGTTAGAAAAATATATTATTCGGTTAATGTCATAAAGCATA
46062192 TTATTTTAATAAAATTATTAATATATTATTTTATTTTATTTTATTGTATTACATTTTATAATTTT
66 TTATTTTAATAAAATTATTAATATATTATTTTATTTTATTTTATTGTATTACATTTTATAATTTT
46062257 TTTAAAAGAGCCCGATTTATTGTTTCGTCTAAGGCCCCATAAATAT
131 TTTAAAAGAGCCCGATTTATTGTTTCGTCTAAGGCCCCATAAATAT
46062303 AAAGTAAAATATATTTTTTAATTGTGTTAGAAAAATATATTATTCGGTTAATGTCATAAAGCATA
1 AAAGTAAAATATATTTTTTAATTGTGTTAGAAAAATATATTATTCGGTTAATGTCATAAAGCATA
46062368 TTATTTTAATAAAATTATTAATATATTATTTTATTTTATTTTATTGTATTACATTTTATAATTTT
66 TTATTTTAATAAAATTATTAATATATTATTTTATTTTATTTTATTGTATTACATTTTATAATTTT
46062433 TTTAAAAGAGCCCGATTTATTGTTTCGTCTAAGGCCCCATAAATAT
131 TTTAAAAGAGCCCGATTTATTGTTTCGTCTAAGGCCCCATAAATAT
46062479 CAAGAACAGA
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (176 bp):
AAAGTAAAATATATTTTTTAATTGTGTTAGAAAAATATATTATTCGGTTAATGTCATAAAGCATA
TTATTTTAATAAAATTATTAATATATTATTTTATTTTATTTTATTGTATTACATTTTATAATTTT
TTTAAAAGAGCCCGATTTATTGTTTCGTCTAAGGCCCCATAAATAT
Found at i:46071758 original size:31 final size:31
Alignment explanation
Indices: 46071721--46071786 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
46071711 AACAGCCTAT
46071721 TGACTTAAAT-AAATACTTTCGAATAATTCAA
1 TGACTTAAATGAAA-ACTTTCGAATAATTCAA
* *
46071752 TGACTTAAATGAAAACTTTCTAATAATTTAA
1 TGACTTAAATGAAAACTTTCGAATAATTCAA
46071783 TGAC
1 TGAC
46071787 CATTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCGAATAATTCAA
Found at i:46075316 original size:16 final size:17
Alignment explanation
Indices: 46075285--46075318 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46075275 TTTAGACTCC
*
46075285 TTTAAAGTTTATAAAAA
1 TTTAAAGTTAATAAAAA
46075302 TTTAAA-TTAATAAAAA
1 TTTAAAGTTAATAAAAA
46075318 T
1 T
46075319 AAAATTACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAAAGTTAATAAAAA
Found at i:46075531 original size:127 final size:128
Alignment explanation
Indices: 46075377--46075633 Score: 507
Period size: 127 Copynumber: 2.0 Consensus size: 128
46075367 TTTAAAAATT
46075377 ATAAAGATATAGATATTAAAATAGAAAAATTACTTTTTTACTATCGTAAAATTATACAATTTAAT
1 ATAAAGATATAGATATTAAAATAGAAAAATTACTTTTTTACTATCGTAAAATTATACAATTTAAT
46075442 TTCTGCCCCCTAAAATTTTTTTTTGACTTTGATCCTCCTCGTATTAATCACGCCCGTCAAAAA
66 TTCTGCCCCCTAAAATTTTTTTTTGACTTTGATCCTCCTCGTATTAATCACGCCCGTCAAAAA
46075505 ATAAAGATATAG-TATTAAAATAGAAAAATTACTTTTTTACTATCGTAAAATTATACAATTTAAT
1 ATAAAGATATAGATATTAAAATAGAAAAATTACTTTTTTACTATCGTAAAATTATACAATTTAAT
46075569 TTCTGCCCCCTAAAATTTTTTTTTGACTTTGATCCTCCTCGTATTAATCACGCCCGTCAAAAA
66 TTCTGCCCCCTAAAATTTTTTTTTGACTTTGATCCTCCTCGTATTAATCACGCCCGTCAAAAA
46075632 AT
1 AT
46075634 TTGGAAGATT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 117 0.91
128 12 0.09
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.39
Consensus pattern (128 bp):
ATAAAGATATAGATATTAAAATAGAAAAATTACTTTTTTACTATCGTAAAATTATACAATTTAAT
TTCTGCCCCCTAAAATTTTTTTTTGACTTTGATCCTCCTCGTATTAATCACGCCCGTCAAAAA
Found at i:46080353 original size:16 final size:14
Alignment explanation
Indices: 46080328--46080375 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
46080318 ACCAATCTGA
46080328 TTTTAGTACTTAATT
1 TTTTAGTACTT-ATT
46080343 TTTTCAGTACTTATT
1 TTTT-AGTACTTATT
* *
46080358 TTTTAATAATTATT
1 TTTTAGTACTTATT
46080372 TTTT
1 TTTT
46080376 TAATTTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 12 0.40
15 11 0.37
16 7 0.23
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTAGTACTTATT
Found at i:46082193 original size:625 final size:626
Alignment explanation
Indices: 46080993--46082244 Score: 2497
Period size: 625 Copynumber: 2.0 Consensus size: 626
46080983 TATTTTTAAT
46080993 GTATTTAATATATTATATTTTTTAAATTTATTTTTATATAAAAAAATTTAAATGGACGGATCGAG
1 GTATTTAATATATTATATTTTTTAAATTTATTTTTATATAAAAAAATTTAAATGGACGGATCGAG
46081058 CTTGGGTTTAGCATTTTTTTATCTGAATCAGGTTTGAGCAAAATTTCAAGTCTATTTTTTTTATG
66 CTTGGGTTTAGCATTTTTTTATCTGAATCAGGTTTGAGCAAAATTTCAAGTCTATTTTTTTTATG
46081123 GACCTGAACATAAAAAAACGAACCTAAAATTTTACATTAACTTGACCCAAACTCAATCCGACCTA
131 GACCTGAACATAAAAAAACGAACCTAAAATTTTACATTAACTTGACCCAAACTCAATCCGACCTA
46081188 TAATCAATTCTACTTCCATTCAACAAGCTGATATGTCCACCACTACAAACTCCATTCTTCACCAA
196 TAATCAATTCTACTTCCATTCAACAAGCTGATATGTCCACCACTACAAACTCCATTCTTCACCAA
46081253 ATTTGGGCCCTTGCCCTTTTGGTGTTACCTTTCCTACACTACAGTGTTATTACATGGGAGCAATC
261 ATTTGGGCCCTTGCCCTTTTGGTGTTACCTTTCCTACACTACAGTGTTATTACATGGGAGCAATC
46081318 TAATTATAGCTTATAGCTCCTTAACATGCGTAACCGTGCAAAGTCTCCATGGATTTACTGAGCAC
326 TAATTATAGCTTATAGCTCCTTAACATGCGTAACCGTGCAAAGTCTCCATGGATTTACTGAGCAC
46081383 TTAATAGGTCTGTTTTGATTTCCACTACCGCTTTGTCAAACAAACTGAAGATTACAGCCATGGCC
391 TTAATAGGTCTGTTTTGATTTCCACTACCGCTTTGTCAAACAAACTGAAGATTACAGCCATGGCC
46081448 TGAATCTAAACAACTAATGTACTATTTGATGAAAAAAATTATGATGTATAAAAATAAGATTCAAT
456 TGAATCTAAACAACTAATGTACTATTTGATGAAAAAAATTATGATGTATAAAAATAAGATTCAAT
46081513 TATGATTACTCCTAACAGAGTTAAAAAGCATACAAAATTTTAAAATGAAGATGTGTTGGCCCAAT
521 TATGATTACTCCTAACAGAGTTAAAAAGCATACAAAATTTTAAAATGAAGATGTGTTGGCCCAAT
46081578 TAGTTGCTAAATTTAAGTTACGTGCCGGAAGAGTGAAAAAA
586 TAGTTGCTAAATTTAAGTTACGTGCCGGAAGAGTGAAAAAA
46081619 GTATTTAATA-ATTATATTTTTTAAATTTATTTTTATATAAAAAAATTTAAATGGACGGATCGAG
1 GTATTTAATATATTATATTTTTTAAATTTATTTTTATATAAAAAAATTTAAATGGACGGATCGAG
46081683 CTTGGGTTTAGCATTTTTTTATCTGAATCAGGTTTGAGCAAAATTTCAAGTCTATTTTTTTTATG
66 CTTGGGTTTAGCATTTTTTTATCTGAATCAGGTTTGAGCAAAATTTCAAGTCTATTTTTTTTATG
46081748 GACCTGAACATAAAAAAACGAACCTAAAATTTTACATTAACTTGACCCAAACTCAATCCGACCTA
131 GACCTGAACATAAAAAAACGAACCTAAAATTTTACATTAACTTGACCCAAACTCAATCCGACCTA
46081813 TAATCAATTCTACTTCCATTCAACAAGCTGATATGTCCACCACTACAAACTCCATTCTTCACCAA
196 TAATCAATTCTACTTCCATTCAACAAGCTGATATGTCCACCACTACAAACTCCATTCTTCACCAA
46081878 ATTTGGGCCCTTGCCCTTTTGGTGTTACCTTTCCTACACTACAGTGTTATTACATGGGAGCAATC
261 ATTTGGGCCCTTGCCCTTTTGGTGTTACCTTTCCTACACTACAGTGTTATTACATGGGAGCAATC
46081943 TAATTATAGCTTATAGCTCCTTAACATGCGTAACCGTGCAAAGTCTCCATGGATTTACTGAGCAC
326 TAATTATAGCTTATAGCTCCTTAACATGCGTAACCGTGCAAAGTCTCCATGGATTTACTGAGCAC
46082008 TTAATAGGTCTGTTTTGATTTCCACTACCGCTTTGTCAAACAAACTGAAGATTACAGCCATGGCC
391 TTAATAGGTCTGTTTTGATTTCCACTACCGCTTTGTCAAACAAACTGAAGATTACAGCCATGGCC
46082073 TGAATCTAAACAACTAATGTACTATTTGATGAAAAAAATTATGATGTATAAAAATAAGATTCAAT
456 TGAATCTAAACAACTAATGTACTATTTGATGAAAAAAATTATGATGTATAAAAATAAGATTCAAT
46082138 TATGATTACTCCTAACAGAGTTAAAAAGCATACAAAATTTTAAAATGAAGATGTGTTGGCCCAAT
521 TATGATTACTCCTAACAGAGTTAAAAAGCATACAAAATTTTAAAATGAAGATGTGTTGGCCCAAT
46082203 TAGTTGCTAAATTTAAGTTACGTGCCGGAAGAGTGAAAAAA
586 TAGTTGCTAAATTTAAGTTACGTGCCGGAAGAGTGAAAAAA
46082244 G
1 G
46082245 GAATATGTAC
Statistics
Matches: 626, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
625 616 0.98
626 10 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (626 bp):
GTATTTAATATATTATATTTTTTAAATTTATTTTTATATAAAAAAATTTAAATGGACGGATCGAG
CTTGGGTTTAGCATTTTTTTATCTGAATCAGGTTTGAGCAAAATTTCAAGTCTATTTTTTTTATG
GACCTGAACATAAAAAAACGAACCTAAAATTTTACATTAACTTGACCCAAACTCAATCCGACCTA
TAATCAATTCTACTTCCATTCAACAAGCTGATATGTCCACCACTACAAACTCCATTCTTCACCAA
ATTTGGGCCCTTGCCCTTTTGGTGTTACCTTTCCTACACTACAGTGTTATTACATGGGAGCAATC
TAATTATAGCTTATAGCTCCTTAACATGCGTAACCGTGCAAAGTCTCCATGGATTTACTGAGCAC
TTAATAGGTCTGTTTTGATTTCCACTACCGCTTTGTCAAACAAACTGAAGATTACAGCCATGGCC
TGAATCTAAACAACTAATGTACTATTTGATGAAAAAAATTATGATGTATAAAAATAAGATTCAAT
TATGATTACTCCTAACAGAGTTAAAAAGCATACAAAATTTTAAAATGAAGATGTGTTGGCCCAAT
TAGTTGCTAAATTTAAGTTACGTGCCGGAAGAGTGAAAAAA
Found at i:46082796 original size:13 final size:13
Alignment explanation
Indices: 46082778--46082808 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46082768 AGACTCGATC
46082778 TAAATTACCTCAA
1 TAAATTACCTCAA
46082791 TAAATTACCTCAA
1 TAAATTACCTCAA
46082804 TAAAT
1 TAAAT
46082809 ATGATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATTACCTCAA
Found at i:46083343 original size:45 final size:46
Alignment explanation
Indices: 46083276--46083368 Score: 154
Period size: 45 Copynumber: 2.0 Consensus size: 46
46083266 CCCAAAGAAA
46083276 TCCCCCCCCCCCAACCCAAAAAAAAAAAAAAAAAA-ATCTTAATAGT
1 TCCCCCCCCCCCAACCCAAAAAAAAAAAAAAAAAATA-CTTAATAGT
*
46083322 TCCCCCCCCCCCAACCC-AAAAAAAAAAAAAAACATACTTAATAGT
1 TCCCCCCCCCCCAACCCAAAAAAAAAAAAAAAAAATACTTAATAGT
46083367 TC
1 TC
46083369 GTCTCCCCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
45 27 0.60
46 18 0.40
ACGTcount: A:0.49, C:0.34, G:0.02, T:0.14
Consensus pattern (46 bp):
TCCCCCCCCCCCAACCCAAAAAAAAAAAAAAAAAATACTTAATAGT
Found at i:46104239 original size:25 final size:26
Alignment explanation
Indices: 46104210--46104261 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
46104200 TTTTTTTTTT
46104210 TTGAATTTTGACTC-AAAGAAACTTC
1 TTGAATTTTGACTCAAAAGAAACTTC
46104235 TTGAATTTTGACTCAAAAGAAACTTC
1 TTGAATTTTGACTCAAAAGAAACTTC
46104261 T
1 T
46104262 AGATCTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (26 bp):
TTGAATTTTGACTCAAAAGAAACTTC
Found at i:46123359 original size:12 final size:12
Alignment explanation
Indices: 46123342--46123377 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
46123332 TCAATTTATT
46123342 AATTAAATTAAA
1 AATTAAATTAAA
46123354 AATT-AATTAAA
1 AATTAAATTAAA
46123365 ATATTAAATTAAA
1 A-ATTAAATTAAA
46123378 CTAATTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 7 0.32
13 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATTAAATTAAA
Found at i:46131022 original size:35 final size:34
Alignment explanation
Indices: 46130933--46131022 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 34
46130923 AATTTTGTTT
46130933 ATTTTAAAATTTTTT-ATGATTTTTATTTTCTATA
1 ATTTTAAAATTTTTTAAT-ATTTTTATTTTCTATA
* *
46130967 ATTTTAAGAAATTTTGAATATTTTTATGTTT-TATA
1 ATTTTAA-AATTTTTTAATATTTTTAT-TTTCTATA
* *
46131002 GTTTTTAAATTTTTTTAATAT
1 -ATTTTAAAATTTTTTAATAT
46131023 ACCATGTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
34 7 0.15
35 28 0.61
36 11 0.24
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (34 bp):
ATTTTAAAATTTTTTAATATTTTTATTTTCTATA
Found at i:46132006 original size:2 final size:2
Alignment explanation
Indices: 46131999--46132030 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46131989 TTCAAAATAC
46131999 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
46132031 TCAAACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46133487 original size:16 final size:17
Alignment explanation
Indices: 46133466--46133498 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46133456 TTGTAATTAT
46133466 TATTATA-TTTTACTTA
1 TATTATATTTTTACTTA
46133482 TATTATATTTTTACTTA
1 TATTATATTTTTACTTA
46133499 AAAAATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATATTTTTACTTA
Found at i:46141866 original size:16 final size:15
Alignment explanation
Indices: 46141845--46141920 Score: 75
Period size: 16 Copynumber: 4.9 Consensus size: 15
46141835 ATGACCCGAC
46141845 CAAAATAATCTGAACT
1 CAAAATAATCT-AACT
46141861 CAAAATAA-CTTCAACT
1 CAAAATAATC-T-AACT
* *
46141877 TAAAACAATCTAAACT
1 CAAAATAATCT-AACT
46141893 CAAAATTAATC-AACT
1 CAAAA-TAATCTAACT
46141908 CAAAATAATCTAA
1 CAAAATAATCTAA
46141921 AAATTTTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.10
15 12 0.24
16 28 0.56
17 5 0.10
ACGTcount: A:0.54, C:0.20, G:0.01, T:0.25
Consensus pattern (15 bp):
CAAAATAATCTAACT
Found at i:46141918 original size:31 final size:31
Alignment explanation
Indices: 46141845--46141921 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
46141835 ATGACCCGAC
*
46141845 CAAAATAATCTGAACTCAAAATAACTTCAACT
1 CAAAATAATCTAAACTCAAAATAAC-TCAACT
* *
46141877 TAAAACAATCTAAACTCAAAATTAA-TCAACT
1 CAAAATAATCTAAACTCAAAA-TAACTCAACT
46141908 CAAAATAATCTAAA
1 CAAAATAATCTAAA
46141922 AATTTTGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.46
32 18 0.46
33 3 0.08
ACGTcount: A:0.55, C:0.19, G:0.01, T:0.25
Consensus pattern (31 bp):
CAAAATAATCTAAACTCAAAATAACTCAACT
Found at i:46144891 original size:35 final size:35
Alignment explanation
Indices: 46144835--46144929 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 35
46144825 TTATTCGTTG
* *
46144835 GTTTATCTGACCAGCGTTGGGCGCAAC-TTCCGTCA
1 GTTTATCTGACTAGCGCTGGGCGCAACATT-CGTCA
* * * *
46144870 GTTTATCTGACTAGTGCTGGGCAC-ACATTTGTCG
1 GTTTATCTGACTAGCGCTGGGCGCAACATTCGTCA
*
46144904 GTTTATCTGACTAACGCTGGGCGCAA
1 GTTTATCTGACTAGCGCTGGGCGCAA
46144930 ACTCTTCCGT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 26 0.53
35 23 0.47
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (35 bp):
GTTTATCTGACTAGCGCTGGGCGCAACATTCGTCA
Found at i:46174160 original size:16 final size:16
Alignment explanation
Indices: 46174139--46174181 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
46174129 ATTTGGTCAT
*
46174139 ATTAGAGATGATTTGA
1 ATTAGAAATGATTTGA
46174155 ATTAGAAATGATTTGA
1 ATTAGAAATGATTTGA
46174171 ACTTA-AAATGA
1 A-TTAGAAATGA
46174182 CTTAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (16 bp):
ATTAGAAATGATTTGA
Found at i:46177690 original size:19 final size:21
Alignment explanation
Indices: 46177654--46177700 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
46177644 TACAAAATAA
46177654 TCAAAATAATTTTCAAAAA-T
1 TCAAAATAATTTTCAAAAATT
46177674 TCAAAAT-ATTTAT-AAAAATT
1 TCAAAATAATTT-TCAAAAATT
46177694 TCAAAAT
1 TCAAAAT
46177701 TTATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAAAATAATTTTCAAAAATT
Found at i:46180026 original size:14 final size:15
Alignment explanation
Indices: 46180004--46180080 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
46179994 CAATCAAACA
46180004 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
46180018 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
46180033 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
46180053 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
46180067 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
46180081 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:46180045 original size:20 final size:20
Alignment explanation
Indices: 46180020--46180059 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46180010 AATATTTTCC
*
46180020 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
46180040 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
46180060 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:46180065 original size:34 final size:35
Alignment explanation
Indices: 46180008--46180074 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
46179998 CAAACACCAG
*
46180008 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
46180043 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
46180075 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:46180081 original size:14 final size:14
Alignment explanation
Indices: 46180043--46180082 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46180033 ACAGAAAAGT
*
46180043 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
46180057 AAATCATTTTACGG
1 AAAACATTTTACAG
46180071 AAAACATTTTAC
1 AAAACATTTTAC
46180083 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:46183717 original size:9 final size:9
Alignment explanation
Indices: 46183703--46183739 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46183693 TATAGTTTAA
46183703 TATTCGAAT
1 TATTCGAAT
46183712 TATTCGAAT
1 TATTCGAAT
*
46183721 TATTCGAGT
1 TATTCGAAT
46183730 TATTCGAAT
1 TATTCGAAT
46183739 T
1 T
46183740 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:46192016 original size:31 final size:30
Alignment explanation
Indices: 46191981--46192058 Score: 124
Period size: 28 Copynumber: 2.6 Consensus size: 30
46191971 AGTTCATTGG
46191981 GACAATAAACACAGAATAGATAGTCCATCGC
1 GACAATAAACACAG-ATAGATAGTCCATCGC
*
46192012 GACAATAAATACAGATAG--AGTCCATCGC
1 GACAATAAACACAGATAGATAGTCCATCGC
46192040 GACAATAAACACAGATAGA
1 GACAATAAACACAGATAGA
46192059 GCTTGTCGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 27 0.61
30 4 0.09
31 13 0.30
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (30 bp):
GACAATAAACACAGATAGATAGTCCATCGC
Found at i:46201848 original size:21 final size:22
Alignment explanation
Indices: 46201817--46201860 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
46201807 ATGCTTATGA
46201817 AAGTCGTAAACCTATGCTATAT
1 AAGTCGTAAACCTATGCTATAT
*
46201839 AAGTC-TAAACCTATGTTATAT
1 AAGTCGTAAACCTATGCTATAT
46201860 A
1 A
46201861 TTCGAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
AAGTCGTAAACCTATGCTATAT
Found at i:46202734 original size:2 final size:2
Alignment explanation
Indices: 46202727--46202751 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46202717 CAAAATTGTC
46202727 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
46202752 GTAGGTTCAA
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:46207887 original size:2 final size:2
Alignment explanation
Indices: 46207880--46207904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46207870 GAATATCGCC
46207880 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46207905 TTGTTCTGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46213340 original size:17 final size:18
Alignment explanation
Indices: 46213318--46213355 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
46213308 GAAATAATTT
46213318 TTTTTTTATAATTTTA-A
1 TTTTTTTATAATTTTAGA
* *
46213335 TTTTTTTCTATTTTTAGA
1 TTTTTTTATAATTTTAGA
46213353 TTT
1 TTT
46213356 AGGACCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTTATAATTTTAGA
Found at i:46217149 original size:56 final size:56
Alignment explanation
Indices: 46217082--46217341 Score: 520
Period size: 56 Copynumber: 4.6 Consensus size: 56
46217072 ACCTAATCAC
46217082 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
46217138 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
46217194 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
46217250 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
46217306 AACCTACTACCACTAACAAACTTAGTTGGAATACAA
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAA
46217342 TCAAGTTTAT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 204 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (56 bp):
AACCTACTACCACTAACAAACTTAGTTGGAATACAACTAATCAACTTAAAATACAA
Found at i:46222475 original size:77 final size:77
Alignment explanation
Indices: 46222343--46222493 Score: 257
Period size: 77 Copynumber: 2.0 Consensus size: 77
46222333 CAGAGTTGCT
* * * *
46222343 ATAACCTTCTCCACTATCCTAGCTTCATTGAACTGCTCTCCAAGGAGCCTGATGCTGTTAACCAC
1 ATAACCTTCTCCACTATCCTAGCTTCATTGAACTACTCTCCAAGGAGCATAATGCTATTAACCAC
46222408 AGCCATAATACA
66 AGCCATAATACA
*
46222420 ATAACCTTCTCCACTATCCTAGCTTCCTTGAACTACTCTCCAAGGAGCATAATGCTATTAACCAC
1 ATAACCTTCTCCACTATCCTAGCTTCATTGAACTACTCTCCAAGGAGCATAATGCTATTAACCAC
46222485 AGCCATAAT
66 AGCCATAAT
46222494 CCTGTCAGAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.28
Consensus pattern (77 bp):
ATAACCTTCTCCACTATCCTAGCTTCATTGAACTACTCTCCAAGGAGCATAATGCTATTAACCAC
AGCCATAATACA
Found at i:46223562 original size:54 final size:54
Alignment explanation
Indices: 46223480--46223589 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
46223470 TCAACAAGAA
46223480 AAACATTATTATTTATAATAAGATTCCTTTCTTTGTACTCTACTAAAAACGTCT
1 AAACATTATTATTTATAATAAGATTCCTTTCTTTGTACTCTACTAAAAACGTCT
46223534 AAACATTATTATTTATAATAAGATTCCTTTCTTTGTACTCTACTAAAAACGTCT
1 AAACATTATTATTTATAATAAGATTCCTTTCTTTGTACTCTACTAAAAACGTCT
46223588 AA
1 AA
46223590 TCTCCTAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (54 bp):
AAACATTATTATTTATAATAAGATTCCTTTCTTTGTACTCTACTAAAAACGTCT
Found at i:46223782 original size:29 final size:30
Alignment explanation
Indices: 46223749--46223810 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
46223739 ATGATTCATG
46223749 TTTGGACTATCCG-ACATGTGTGTTCGCCA
1 TTTGGACTATCCGCACATGTGTGTTCGCCA
* ** *
46223778 TTTGGACTGTTTGCCCATGTGTGTTCGCCA
1 TTTGGACTATCCGCACATGTGTGTTCGCCA
46223808 TTT
1 TTT
46223811 ACGCTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (30 bp):
TTTGGACTATCCGCACATGTGTGTTCGCCA
Found at i:46223821 original size:30 final size:29
Alignment explanation
Indices: 46223763--46223829 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
46223753 GACTATCCGA
* *
46223763 CATGTGTGTTCGCCATTTGGACTGTTTGCC
1 CATGTGTGTTCGCCATTTCGACTATTTG-C
46223793 CATGTGTGTTCGCCATTTACG-CTATTTGC
1 CATGTGTGTTCGCCATTT-CGACTATTTGC
46223822 CATGTGTG
1 CATGTGTG
46223830 CTAGCCATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 9 0.26
30 24 0.71
31 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.40
Consensus pattern (29 bp):
CATGTGTGTTCGCCATTTCGACTATTTGC
Found at i:46224008 original size:67 final size:67
Alignment explanation
Indices: 46223900--46224035 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
46223890 TTTTATTTTA
* * *
46223900 TTTTGTATTTTAAGTTGATGTAATGTAACTTGGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
1 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGCTAGTGGTAGTA
46223965 GG
66 GG
46223967 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGCTAGTGGTAGTA
1 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGCTAGTGGTAGTA
46224032 GG
66 GG
46224034 TT
1 TT
46224036 GTGATTAGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (67 bp):
TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGCTAGTGGTAGTA
GG
Found at i:46231146 original size:34 final size:34
Alignment explanation
Indices: 46231108--46231286 Score: 90
Period size: 34 Copynumber: 5.1 Consensus size: 34
46231098 ATATAACTTA
46231108 GTTGTATTTCAACTAAGTTTGTTAGTGGTAGTAG
1 GTTGTATTTCAACTAAGTTTGTTAGTGGTAGTAG
** * *
46231142 GTTGTGATTT-ATTTAAAG-TTGATGTAAT-GTCACTTA-
1 GTTGT-ATTTCAACT-AAGTTTG-T-TAGTGGT-A-GTAG
46231178 GTTGTA-TTCTAACTAAGTTTGTTAGTGGTAGTAG
1 GTTGTATTTC-AACTAAGTTTGTTAGTGGTAGTAG
** * *
46231212 GTTGTGATTT-ATTTAAAG-TTGATGTAAT-GTCACTTA-
1 GTTGT-ATTTCAACT-AAGTTTG-T-TAGTGGT-A-GTAG
46231248 GTTGTA-TTCTAACTAAGTTTGTTAGTGGTAGTAG
1 GTTGTATTTC-AACTAAGTTTGTTAGTGGTAGTAG
46231282 GTTGT
1 GTTGT
46231287 GATTAGGTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 46
0.63 0.10 0.27
Matches are distributed among these distances:
33 4 0.04
34 37 0.35
35 31 0.29
36 30 0.28
37 4 0.04
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.46
Consensus pattern (34 bp):
GTTGTATTTCAACTAAGTTTGTTAGTGGTAGTAG
Found at i:46231161 original size:35 final size:35
Alignment explanation
Indices: 46231118--46231290 Score: 114
Period size: 35 Copynumber: 4.9 Consensus size: 35
46231108 GTTGTATTTC
46231118 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATT-T
1 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATTCT
** * *
46231152 ATTTAAAG-TTGATGTAAT-GTCACTTA-GTTGT-ATTCT
1 AACT-AAGTTTG-T-TAGTGGT-A-GTAGGTTGTGATTCT
46231188 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATT-T
1 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATTCT
** * *
46231222 ATTTAAAG-TTGATGTAAT-GTCACTTA-GTTGT-ATTCT
1 AACT-AAGTTTG-T-TAGTGGT-A-GTAGGTTGTGATTCT
46231258 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATT
1 AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATT
46231291 AGGTTAACCT
Statistics
Matches: 103, Mismatches: 16, Indels: 39
0.65 0.10 0.25
Matches are distributed among these distances:
33 4 0.04
34 29 0.28
35 36 0.35
36 30 0.29
37 4 0.04
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.45
Consensus pattern (35 bp):
AACTAAGTTTGTTAGTGGTAGTAGGTTGTGATTCT
Found at i:46231192 original size:70 final size:70
Alignment explanation
Indices: 46231079--46231290 Score: 390
Period size: 70 Copynumber: 3.0 Consensus size: 70
46231069 TGTTTTATTT
* *
46231079 TTTATTTAAAGTTGATGTAATATAACTTAGTTGTATT-TCAACTAAGTTTGTTAGTGGTAGTAGG
1 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCT-AACTAAGTTTGTTAGTGGTAGTAGG
46231143 TTGTGA
65 TTGTGA
46231149 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCTAACTAAGTTTGTTAGTGGTAGTAGGT
1 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCTAACTAAGTTTGTTAGTGGTAGTAGGT
46231214 TGTGA
66 TGTGA
46231219 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCTAACTAAGTTTGTTAGTGGTAGTAGGT
1 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCTAACTAAGTTTGTTAGTGGTAGTAGGT
46231284 TGTGA
66 TGTGA
46231289 TT
1 TT
46231291 AGGTTAACCT
Statistics
Matches: 139, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
70 138 0.99
71 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.46
Consensus pattern (70 bp):
TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCTAACTAAGTTTGTTAGTGGTAGTAGGT
TGTGA
Found at i:46236356 original size:70 final size:70
Alignment explanation
Indices: 46236270--46236481 Score: 399
Period size: 70 Copynumber: 3.0 Consensus size: 70
46236260 AGGTTAACCT
*
46236270 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACTTTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
46236335 AAATA
66 AAATA
46236340 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
46236405 AAATA
66 AAATA
46236410 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGCT-ACATTACATCAACTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAG-TGACATTACATCAACTT
46236474 TAAATA
65 TAAATA
46236480 AA
1 AA
46236482 AAATAAAACA
Statistics
Matches: 140, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
70 139 0.99
71 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (70 bp):
AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
AAATA
Found at i:46236368 original size:35 final size:35
Alignment explanation
Indices: 46236329--46236438 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 35
46236319 ACTTTACATC
46236329 AACTTTAAATAAATCACAACCTACTACCACTAACA
1 AACTTTAAATAAATCACAACCTACTACCACTAACA
** * * *
46236364 AAC-TTAGTTGGAAT-ACAA-CTAAGTGA-CA-TTACA
1 AACTTTAAAT-AAATCACAACCT-ACT-ACCACTAACA
46236397 TCAACTTTAAATAAATCACAACCTACTACCACTAACA
1 --AACTTTAAATAAATCACAACCTACTACCACTAACA
46236434 AACTT
1 AACTT
46236439 AGTTGGAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 6 0.11
34 12 0.22
35 19 0.35
36 12 0.22
37 6 0.11
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (35 bp):
AACTTTAAATAAATCACAACCTACTACCACTAACA
Found at i:46236418 original size:36 final size:36
Alignment explanation
Indices: 46236308--46236418 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
46236298 TAGTTGGAAT
*
46236308 ACAACTAAGTGACTTTACATCAACTTTAAATAAATC
1 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
* * ** *
46236344 ACAACCT-ACT-ACCACTA-A-CAAAC-TTAGTTGGAAT-
1 ACAA-CTAAGTGA-CATTACATC-AACTTTAAAT-AAATC
46236378 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
1 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
46236414 ACAAC
1 ACAAC
46236419 CTACTACCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 20
0.64 0.13 0.24
Matches are distributed among these distances:
33 2 0.04
34 15 0.28
35 16 0.30
36 19 0.35
37 2 0.04
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (36 bp):
ACAACTAAGTGACATTACATCAACTTTAAATAAATC
Found at i:46240779 original size:34 final size:34
Alignment explanation
Indices: 46240741--46240849 Score: 91
Period size: 34 Copynumber: 3.1 Consensus size: 34
46240731 TAACCTAATC
46240741 ACAACCTACTACCACTAACAAACTTAGTTGGAAT
1 ACAACCTACTACCACTAACAAACTTAGTTGGAAT
* * ** *
46240775 ACAA-CTAAGTGA-CA-TTACATCAACTTTAAAT-AAAT
1 ACAACCT-ACT-ACCACTAACA--AAC-TTAGTTGGAAT
46240810 CACAACCTACTACCACTAACAAACTTAGTTGGAAT
1 -ACAACCTACTACCACTAACAAACTTAGTTGGAAT
46240845 ACAAC
1 ACAAC
46240850 TAAGTTACAT
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 6 0.11
34 17 0.31
35 14 0.25
36 12 0.22
37 6 0.11
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (34 bp):
ACAACCTACTACCACTAACAAACTTAGTTGGAAT
Found at i:46240800 original size:35 final size:34
Alignment explanation
Indices: 46240761--46240870 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 34
46240751 ACCACTAACA
46240761 AACTTAGTTGGAATACAACTAAGTGACATTACATC
1 AACTTAGTTGGAATACAACTAAGT-ACATTACATC
** * * *
46240796 AACTTTAAAT-AAATCACAACCT-ACTACCACTA-A-C
1 AAC-TTAGTTGGAAT-ACAA-CTAAGTA-CATTACATC
46240830 AAACTTAGTTGGAATACAACTAAGTTACATTACATC
1 -AACTTAGTTGGAATACAACTAAG-TACATTACATC
46240866 AACTT
1 AACTT
46240871 TAAATAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 2 0.04
34 14 0.25
35 22 0.40
36 15 0.27
37 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (34 bp):
AACTTAGTTGGAATACAACTAAGTACATTACATC
Found at i:46240823 original size:70 final size:70
Alignment explanation
Indices: 46240737--46240877 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
46240727 AGGTTAACCT
46240737 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
46240802 AAATA
66 AAATA
*
46240807 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTTACATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
46240872 AAATA
66 AAATA
46240877 A
1 A
46240878 TAATAAAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (70 bp):
AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
AAATA
Found at i:46261687 original size:192 final size:188
Alignment explanation
Indices: 46261360--46261907 Score: 622
Period size: 190 Copynumber: 2.9 Consensus size: 188
46261350 CTTTTGAATA
* * * * * * * * *
46261360 CTTGAG-CAGCTCATCTTTAACATCTGAAGATTATTTAGAGAGTCTAAAGACAAAGTCACTTCCT
1 CTTGAGCCA-CTCATATCTAACGTCTGAAGATTACTTAGAGAGTCGAGAGACAAGGACACAT-CT
* * * *
46261424 T-AATTTGAG-TCCTAAATAAATTCAATTTTCTTAAGCTTCTTGGGATTTCTGGGAATTCTGTC-
64 TCAATTTGAGTTCC-AGATAAGTTAAATTTT-TTAAGCTTCTTGGGATTTC-GGGAATT-TGACT
46261486 ATTGGGCAATGACTAAGATTCAGATCACGAAGGGCGATTTCCATCTTGATCGATACA-GTTTTTA
125 ATTGGGCAATGACTAAGATTCAGATCACGAA-GG-GA-TTCCATCTTGATCGATACATGTTTTTA
46261550 CC
187 CC
* * * *
46261552 CTTGAGCCACTCATATCTAATGTTTGAAGATTACCTAGAGAGTCGAGAGACAAGGACACCTCTTC
1 CTTGAGCCACTCATATCTAACGTCTGAAGATTACTTAGAGAGTCGAGAGACAAGGACACATCTTC
*
46261617 AATTTGAGTTCCAGATAAGTTTAATTTTATTAAAG-TTCTTGGGATTTCGGGAAATTTGACTATT
66 AATTTGAGTTCCAGATAAGTTAAATTTT-TT-AAGCTTCTTGGGATTTCGGG-AATTTGACTATT
* * *
46261681 GGGCAATGACTAAGATTCAGGTCACGAAGGGATTCCATCTTGATGGATACATTTTTTTACC
128 GGGCAATGACTAAGATTCAGATCACGAAGGGATTCCATCTTGATCGATACATGTTTTTACC
* * *
46261742 CTTGAGCCACTCATATCTAACGTCTGAAGATTACTTGGAGTGTCGAGAGACAAGCACACATCTTC
1 CTTGAGCCACTCATATCTAACGTCTGAAGATTACTTAGAGAGTCGAGAGACAAGGACACATCTTC
* * * * * *
46261807 AATTTGAGTTTCAGATAAGTTAAATTCTGTCAAGCTTCTTGGGATTATTGGGAATTCGGCTATTG
66 AATTTGAGTTCCAGATAAGTTAAATT-TTTTAAGCTTCTTGGGATT-TCGGGAATTTGACTATTG
* * * *
46261872 GGCAATGACTAAGATCCATATCATGAAGTGATTCCA
129 GGCAATGACTAAGATTCAGATCACGAAGGGATTCCA
46261908 ACTTTGAAAT
Statistics
Matches: 307, Mismatches: 39, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
189 21 0.07
190 146 0.48
191 16 0.05
192 116 0.38
193 8 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (188 bp):
CTTGAGCCACTCATATCTAACGTCTGAAGATTACTTAGAGAGTCGAGAGACAAGGACACATCTTC
AATTTGAGTTCCAGATAAGTTAAATTTTTTAAGCTTCTTGGGATTTCGGGAATTTGACTATTGGG
CAATGACTAAGATTCAGATCACGAAGGGATTCCATCTTGATCGATACATGTTTTTACC
Found at i:46262061 original size:20 final size:20
Alignment explanation
Indices: 46262036--46262077 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
46262026 TATAATAGGA
46262036 AAGTGTTTTGGGACCACGGG
1 AAGTGTTTTGGGACCACGGG
46262056 AAGTGTTTTGGGACCACGGG
1 AAGTGTTTTGGGACCACGGG
46262076 AA
1 AA
46262078 ACGTCTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.24
Consensus pattern (20 bp):
AAGTGTTTTGGGACCACGGG
Found at i:46268397 original size:12 final size:12
Alignment explanation
Indices: 46268380--46268406 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46268370 AGCCCCAACT
46268380 CAATACCTAACC
1 CAATACCTAACC
46268392 CAATACCTAACC
1 CAATACCTAACC
46268404 CAA
1 CAA
46268407 CACTACCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATACCTAACC
Found at i:46269794 original size:24 final size:26
Alignment explanation
Indices: 46269741--46269792 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
46269731 CTCATTTGAG
* *
46269741 TTAATAAATTCTCTCTGGGTTTCTTT
1 TTAAGAAATTCTCTCTGAGTTTCTTT
*
46269767 TTAAGAAATTCTCTGT-AGTTTCTTT
1 TTAAGAAATTCTCTCTGAGTTTCTTT
46269792 T
1 T
46269793 AAAAGAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.54
Consensus pattern (26 bp):
TTAAGAAATTCTCTCTGAGTTTCTTT
Found at i:46270030 original size:18 final size:18
Alignment explanation
Indices: 46269990--46270030 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
46269980 TTAATCTTTG
46269990 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
46270007 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
46270026 -TTTAT
1 ATTTAT
46270031 CTAACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:46271904 original size:15 final size:15
Alignment explanation
Indices: 46271884--46271912 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46271874 TGTATGATAA
46271884 GTTAAAAAATTAAAT
1 GTTAAAAAATTAAAT
46271899 GTTAAAAAATTAAA
1 GTTAAAAAATTAAA
46271913 AAATTAAAAT
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:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
GTTAAAAAATTAAAT
Found at i:46271911 original size:8 final size:8
Alignment explanation
Indices: 46271885--46271927 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
46271875 GTATGATAAG
46271885 TTAAAAAA
1 TTAAAAAA
**
46271893 TT-AAATG
1 TTAAAAAA
46271900 TTAAAAAA
1 TTAAAAAA
46271908 TTAAAAAA
1 TTAAAAAA
*
46271916 TTAAAATA
1 TTAAAAAA
46271924 TTAA
1 TTAA
46271928 GTATTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
TTAAAAAA
Found at i:46271921 original size:15 final size:15
Alignment explanation
Indices: 46271885--46271927 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
46271875 GTATGATAAG
**
46271885 TTAAAAAATTAAATG
1 TTAAAAAATTAAAAA
46271900 TTAAAAAATTAAAAAA
1 TTAAAAAATT-AAAAA
*
46271916 TTAAAATATTAA
1 TTAAAAAATTAA
46271928 GTATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TTAAAAAATTAAAAA
Found at i:46273485 original size:14 final size:14
Alignment explanation
Indices: 46273465--46273514 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
46273455 TCTTTGGCTT
46273465 AAAGAAAATCAGGC
1 AAAGAAAATCAGGC
* **
46273479 CAAGAAAATC--TT
1 AAAGAAAATCAGGC
46273491 AAAGAAAATCAGGC
1 AAAGAAAATCAGGC
*
46273505 TAAGAAAATC
1 AAAGAAAATC
46273515 TTCCTTAGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
12 9 0.33
14 18 0.67
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (14 bp):
AAAGAAAATCAGGC
Found at i:46273493 original size:26 final size:26
Alignment explanation
Indices: 46273462--46273516 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
46273452 AAATCTTTGG
46273462 CTTAAAGAAAATCAGGCCAAGAAAAT
1 CTTAAAGAAAATCAGGCCAAGAAAAT
*
46273488 CTTAAAGAAAATCAGGCTAAGAAAAT
1 CTTAAAGAAAATCAGGCCAAGAAAAT
46273514 CTT
1 CTT
46273517 CCTTAGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (26 bp):
CTTAAAGAAAATCAGGCCAAGAAAAT
Found at i:46292500 original size:142 final size:141
Alignment explanation
Indices: 46292199--46292724 Score: 701
Period size: 141 Copynumber: 3.8 Consensus size: 141
46292189 CTCTACCCTG
* * * *
46292199 TTAACCCATCATTATCTATATTGAGATGTTACAATGATTCTACTTTCATCACCAAAATATTTAAC
1 TTAACCCATCTTTATCTATTTTGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
* * *
46292264 ACCTATACAATCTA-CTAATCTAGGTCATT-ATCATCATCAATGAAAACAAAAGACCTGAAGAAA
66 ACCCATACAATCTATCTAATCTGGGTCATTAAT-ATCATCAATGACAAC-AAAGACCTGAAGAAA
*
46292327 GTCCTTTACCCTA
129 GTCCTTTACCTTA
*
46292340 TTAACCCATCTTTATCTATTTTGGGATGTTACAATGATTCTACTTTCATCATCACTAAAATATTT
1 TTAACCCATCTTTATCTATTTTGAGATGTTACAATGATTCTAC-TTC--CATCACTAAAATATTT
*
46292405 AACACCCATACAATCTATCTAATCTGGGTCATTAATATCATCAAGGACAAC-AA-ACCTGAAGAA
63 AACACCCATACAATCTATCTAATCTGGGTCATTAATATCATCAATGACAACAAAGACCTGAAGAA
*
46292468 AGTCCTTTTCCTTA
128 AGTCCTTTACCTTA
* * *
46292482 TTAACCCATCTTTGTCTATCTCGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
1 TTAACCCATCTTTATCTATTTTGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
* * *
46292547 ACCCATACAATCTATCAAATATGGGTCATTAACATCATCAATGACAACAAAAGACCT-AAGAAAG
66 ACCCATACAATCTATCTAATCTGGGTCATTAATATCATCAATGACAAC-AAAGACCTGAAGAAAG
*
46292611 TCCTTTACCTTG
130 TCCTTTACCTTA
46292623 TTAACCCATC--T-T-TATTTTGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
1 TTAACCCATCTTTATCTATTTTGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
*
46292684 A--C-T-C-A--TA--TAATCTGGGTCATTAACATCATCAATGACAACAA
66 ACCCATACAATCTATCTAATCTGGGTCATTAATATCATCAATGACAACAA
46292725 TCAGTTTTTT
Statistics
Matches: 352, Mismatches: 25, Indels: 30
0.86 0.06 0.07
Matches are distributed among these distances:
127 2 0.01
128 30 0.09
130 2 0.01
132 1 0.00
133 1 0.00
134 1 0.00
135 1 0.00
137 48 0.14
138 1 0.00
139 64 0.18
141 72 0.20
142 67 0.19
143 2 0.01
144 31 0.09
145 27 0.08
146 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (141 bp):
TTAACCCATCTTTATCTATTTTGAGATGTTACAATGATTCTACTTCCATCACTAAAATATTTAAC
ACCCATACAATCTATCTAATCTGGGTCATTAATATCATCAATGACAACAAAGACCTGAAGAAAGT
CCTTTACCTTA
Found at i:46312296 original size:39 final size:39
Alignment explanation
Indices: 46312253--46312342 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
46312243 GCACATTTCT
46312253 TGATCTTCATCCGATGCATCACTGCTCGTCTCATCAATC
1 TGATCTTCATCCGATGCATCACTGCTCGTCTCATCAATC
* *
46312292 TGATCTTCATCGGATGCCTCACTGCTCGTCTCATCAATC
1 TGATCTTCATCCGATGCATCACTGCTCGTCTCATCAATC
46312331 TGATCTTCATCC
1 TGATCTTCATCC
46312343 ACATAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.34
Consensus pattern (39 bp):
TGATCTTCATCCGATGCATCACTGCTCGTCTCATCAATC
Found at i:46313168 original size:13 final size:13
Alignment explanation
Indices: 46313150--46313174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46313140 ATTTCTGGTC
46313150 TTTACTCAAGTTT
1 TTTACTCAAGTTT
46313163 TTTACTCAAGTT
1 TTTACTCAAGTT
46313175 CTTAAGCTGA
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:46322931 original size:23 final size:23
Alignment explanation
Indices: 46322905--46322956 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
46322895 ATTCAAAAAC
*
46322905 AAAAAAAATCAAA-TTACAAATTT
1 AAAAAAAATAAAATTTA-AAATTT
*
46322928 AAAAAAATTAAAATTTAAAATTT
1 AAAAAAAATAAAATTTAAAATTT
46322951 AAAAAA
1 AAAAAA
46322957 CCAACATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAAAAATAAAATTTAAAATTT
Found at i:46322943 original size:16 final size:17
Alignment explanation
Indices: 46322915--46322947 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
46322905 AAAAAAAATC
46322915 AAATTACAAATTTAAAA
1 AAATTACAAATTTAAAA
46322932 AAATTA-AAATTTAAAA
1 AAATTACAAATTTAAAA
46322948 TTTAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTACAAATTTAAAA
Found at i:46332991 original size:7 final size:7
Alignment explanation
Indices: 46332979--46333005 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46332969 AATCCACACA
46332979 CTGCACC
1 CTGCACC
46332986 CTGCACC
1 CTGCACC
46332993 CTGCACC
1 CTGCACC
46333000 CTGCAC
1 CTGCAC
46333006 ATCCATAATC
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:0.56, G:0.15, T:0.15
Consensus pattern (7 bp):
CTGCACC
Found at i:46334526 original size:23 final size:24
Alignment explanation
Indices: 46334486--46334533 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
46334476 AAACATTTAT
46334486 ATATAATTATAACCAAAATA-AAA
1 ATATAATTATAACCAAAATATAAA
*
46334509 ATATAATTATATA-TAAAATATAAA
1 ATATAATTATA-ACCAAAATATAAA
46334533 A
1 A
46334534 CAAAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATAATTATAACCAAAATATAAA
Found at i:46360400 original size:18 final size:18
Alignment explanation
Indices: 46360377--46360411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46360367 AATTTAATTT
46360377 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
* *
46360395 TAATTAATTTTTTTAAA
1 TAATTAAATTATTTAAA
46360412 TTATAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:46360631 original size:7 final size:7
Alignment explanation
Indices: 46360611--46360715 Score: 62
Period size: 7 Copynumber: 15.4 Consensus size: 7
46360601 TTTAGGATTT
*
46360611 AGGTTTG
1 AGGTTTA
*
46360618 AGATTTA
1 AGGTTTA
46360625 AGGTTTA
1 AGGTTTA
46360632 A-GTTT-
1 AGGTTTA
*
46360637 A-GTGTTG
1 AGGT-TTA
46360644 AGGTTTA
1 AGGTTTA
*
46360651 AAGTTT-
1 AGGTTTA
46360657 AGGTTT-
1 AGGTTTA
*
46360663 AGAGTTCA
1 AG-GTTTA
*
46360671 ATGATTT-
1 A-GGTTTA
46360678 AGAGTTTA
1 AG-GTTTA
46360686 AGGTTTA
1 AGGTTTA
*
46360693 AGG-TTC
1 AGGTTTA
46360699 AGGTTTA
1 AGGTTTA
46360706 AGGTTTA
1 AGGTTTA
46360713 AGG
1 AGG
46360716 ATTCAGGGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
5 3 0.04
6 19 0.25
7 47 0.61
8 7 0.09
9 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.29, T:0.42
Consensus pattern (7 bp):
AGGTTTA
Found at i:46360631 original size:20 final size:20
Alignment explanation
Indices: 46360597--46360636 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46360587 CTTAAACCTC
*
46360597 GAGATTTAGGATTTAGGTTT
1 GAGATTTAGGATTTAAGTTT
46360617 GAGATTTAAGG-TTTAAGTTT
1 GAGATTT-AGGATTTAAGTTT
46360637 AGTGTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (20 bp):
GAGATTTAGGATTTAAGTTT
Found at i:46360637 original size:13 final size:13
Alignment explanation
Indices: 46360621--46360715 Score: 61
Period size: 13 Copynumber: 7.0 Consensus size: 13
46360611 AGGTTTGAGA
46360621 TTTAAGGTTTAA-G
1 TTTAA-GTTTAAGG
*
46360634 TTT-AGTGTTGAGG
1 TTTAAGT-TTAAGG
46360647 TTTAAAGTTT-AGG
1 TTT-AAGTTTAAGG
* *
46360660 TTTAGAGTTCAATGA
1 TTTA-AGTTTAA-GG
46360675 TTTAGAGTTTAAGG
1 TTTA-AGTTTAAGG
* *
46360689 TTTAAGGTTCAGG
1 TTTAAGTTTAAGG
46360702 TTTAAGGTTTAAGG
1 TTTAA-GTTTAAGG
46360716 ATTCAGGGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
11 2 0.03
12 5 0.08
13 29 0.45
14 14 0.22
15 15 0.23
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.43
Consensus pattern (13 bp):
TTTAAGTTTAAGG
Found at i:46360706 original size:20 final size:21
Alignment explanation
Indices: 46360681--46360722 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
46360671 ATGATTTAGA
46360681 GTTTAAGGTTTAAGG-TTCAG
1 GTTTAAGGTTTAAGGATTCAG
46360701 GTTTAAGGTTTAAGGATTCAG
1 GTTTAAGGTTTAAGGATTCAG
46360722 G
1 G
46360723 GTTGTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.26, C:0.05, G:0.31, T:0.38
Consensus pattern (21 bp):
GTTTAAGGTTTAAGGATTCAG
Found at i:46367648 original size:33 final size:33
Alignment explanation
Indices: 46367606--46367669 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
46367596 CATCTCGCTT
*
46367606 TATTAGCTGTAT-ATCGCAGCCACGTTGCAAGCC
1 TATTAGCTGTATGAT-GCAGCCACGATGCAAGCC
*
46367639 TATTAGCTGTGTGATGCAGCCACGATGCAAG
1 TATTAGCTGTATGATGCAGCCACGATGCAAG
46367670 TCTGCTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (33 bp):
TATTAGCTGTATGATGCAGCCACGATGCAAGCC
Found at i:46370131 original size:23 final size:23
Alignment explanation
Indices: 46370093--46370138 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46370083 TTTCGCCCTG
** *
46370093 GGCCCAGGCAGGCCCAATTACAA
1 GGCCCAGGCAAACCCAAATACAA
46370116 GGCCCAGGCAAACCCAAATACAA
1 GGCCCAGGCAAACCCAAATACAA
46370139 CCCAAACCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.35, G:0.22, T:0.07
Consensus pattern (23 bp):
GGCCCAGGCAAACCCAAATACAA
Found at i:46371120 original size:3 final size:3
Alignment explanation
Indices: 46371114--46371175 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
46371104 CTTTTTTTAG
*
46371114 TAT TAT TAT TAT TAT TAT TAT TATT TAT TA- TAT TAT TGT TACT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT
*
46371160 CA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
46371176 CATAATAGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.82
4 6 0.12
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:46371227 original size:4 final size:4
Alignment explanation
Indices: 46371220--46371247 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
46371210 ACTTCTATAA
46371220 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
46371248 CCTCTTGTAT
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:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:46371977 original size:24 final size:24
Alignment explanation
Indices: 46371945--46371991 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
46371935 TACATCTTTG
*
46371945 TAATATATATGTACATATATTTTA
1 TAATATATATATACATATATTTTA
*
46371969 TAATTTATATATACATATATTTT
1 TAATATATATATACATATATTTT
46371992 TGTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
TAATATATATATACATATATTTTA
Found at i:46372051 original size:4 final size:4
Alignment explanation
Indices: 46372044--46372071 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
46372034 ACTTCTATAA
46372044 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
46372072 CCTCTTGTAT
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:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:46382146 original size:189 final size:189
Alignment explanation
Indices: 46381826--46382293 Score: 708
Period size: 189 Copynumber: 2.5 Consensus size: 189
46381816 TTATCACAAT
* * * * *
46381826 GACACTTCTTCAATTTGAGTGCGAGATAAATCTAAATGTGTTAAGCTTCTTGGGACGTT-TGGAA
1 GACACTTCTTCAATTTGAGTGCCAGATAAATTTAATTCTGTTAAGCTTCTTGGGA-TTTCTGGAA
* * * *
46381890 ATTAGACCATTGGGCAACCACTAAGATCCAGTTTACGAAGGGATTCCAACCTTATCGATACATTT
65 ATTTGATCATTGGGCAATCACTAAGATCCAGTTTACGAAGAGATTCCAACCTTATCGATACATTT
* * * *
46381955 TTGACTGCTGAGCCACTCATATTTAAGAT-CTGAAGATTACATAGAGAGTCGAAAGGTAAG
130 TTGACTACTGAGCCACTCATATTTAAG-TCCTGAAGATTACATAGAGAGTCAAAAGGCAAC
*
46382015 GACACTTCTTCAATTTGAGTGCCAGATAAATTTAATTCTATTAAGCTTCTTGGGATTTCTGGAAA
1 GACACTTCTTCAATTTGAGTGCCAGATAAATTTAATTCTGTTAAGCTTCTTGGGATTTCTGGAAA
* *
46382080 TTTGATCATTGGGCAATCACTAAGATTCAGTTTATGAAGAGATTCCAA-CTTGATCGATACATTT
66 TTTGATCATTGGGCAATCACTAAGATCCAGTTTACGAAGAGATTCCAACCTT-ATCGATACATTT
46382144 TTGACTACTGAGCCACTCATATTTAAGTCCTGAAGATTACATAGAGAGTCAAAAGGCAAC
130 TTGACTACTGAGCCACTCATATTTAAGTCCTGAAGATTACATAGAGAGTCAAAAGGCAAC
* * *
46382204 GACACTTCTTCAATTTGAGTGCCAGATAAGTTTAATTTTGTTAAGCTTTTTGGGATTTCTGGAAA
1 GACACTTCTTCAATTTGAGTGCCAGATAAATTTAATTCTGTTAAGCTTCTTGGGATTTCTGGAAA
*
46382269 TTTGATCATTGGGCAATTACTAAGA
66 TTTGATCATTGGGCAATCACTAAGA
46382294 ACCAATTCAC
Statistics
Matches: 255, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
188 6 0.02
189 249 0.98
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (189 bp):
GACACTTCTTCAATTTGAGTGCCAGATAAATTTAATTCTGTTAAGCTTCTTGGGATTTCTGGAAA
TTTGATCATTGGGCAATCACTAAGATCCAGTTTACGAAGAGATTCCAACCTTATCGATACATTTT
TGACTACTGAGCCACTCATATTTAAGTCCTGAAGATTACATAGAGAGTCAAAAGGCAAC
Found at i:46385880 original size:16 final size:16
Alignment explanation
Indices: 46385856--46385893 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
46385846 TATTTAATAC
*
46385856 ATTATTTTTAAATAAA
1 ATTAATTTTAAATAAA
46385872 ATTAATTTTAAATAAA
1 ATTAATTTTAAATAAA
46385888 ATTAAT
1 ATTAAT
46385894 CTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTTTAAATAAA
Found at i:46400336 original size:13 final size:13
Alignment explanation
Indices: 46400313--46400345 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
46400303 CTTCCATTAC
46400313 TAAATTAACGATAT
1 TAAA-TAACGATAT
46400327 TAAATAACGATAT
1 TAAATAACGATAT
46400340 TAAATA
1 TAAATA
46400346 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (13 bp):
TAAATAACGATAT
Found at i:46412499 original size:29 final size:29
Alignment explanation
Indices: 46412457--46412514 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
46412447 AGGGCAGGTG
*
46412457 AATGTTTTGTTTTACTTTATAATTTTGAT
1 AATGTTTTGTTTTACTATATAATTTTGAT
46412486 AATGTTTTGTTTTACTATATAATTTTGAT
1 AATGTTTTGTTTTACTATATAATTTTGAT
46412515 CTTTTTCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.60
Consensus pattern (29 bp):
AATGTTTTGTTTTACTATATAATTTTGAT
Found at i:46416277 original size:16 final size:16
Alignment explanation
Indices: 46416236--46416270 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
46416226 TTCAATTACT
46416236 ATCAATATTAACAAGC
1 ATCAATATTAACAAGC
46416252 ATCAATATTAACAAGC
1 ATCAATATTAACAAGC
46416268 ATC
1 ATC
46416271 CCAATTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (16 bp):
ATCAATATTAACAAGC
Found at i:46420971 original size:15 final size:15
Alignment explanation
Indices: 46420951--46421002 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
46420941 CCCTTGGTGT
46420951 GGGATATCCCCATGC
1 GGGATATCCCCATGC
** * **
46420966 GGGATAAGCGCATAAT
1 GGGATATCCCCAT-GC
46420982 GGGATATCCCCATGC
1 GGGATATCCCCATGC
46420997 GGGATA
1 GGGATA
46421003 AGCGCGAGAG
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (15 bp):
GGGATATCCCCATGC
Found at i:46421057 original size:21 final size:21
Alignment explanation
Indices: 46421033--46421072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
46421023 CCGGGCTCAT
46421033 AAAACAACAGAACCGGTCACC
1 AAAACAACAGAACCGGTCACC
*
46421054 AAAACAGCAGAACCGGTCA
1 AAAACAACAGAACCGGTCA
46421073 GCTAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.30, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAACAACAGAACCGGTCACC
Found at i:46421453 original size:80 final size:80
Alignment explanation
Indices: 46421320--46421479 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
46421310 AAATCAGCTG
46421320 TATAATAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGTTTA
1 TATAATAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGTTTA
46421385 ACGGATTATTAACTT
66 ACGGATTATTAACTT
*
46421400 TATAATAAATGGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGTTTA
1 TATAATAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGTTTA
46421465 ACGGATTATTAACTT
66 ACGGATTATTAACTT
46421480 GAAAGCTTCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (80 bp):
TATAATAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGTTTA
ACGGATTATTAACTT
Found at i:46423496 original size:26 final size:26
Alignment explanation
Indices: 46423467--46423518 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
46423457 AATTATATAT
*
46423467 ATTTCT-TTAACATTTTTGTTACTTAA
1 ATTTCTATTAACA-TTTTGGTACTTAA
* *
46423493 ATTTTTATTCACATTTTGGTACTTAA
1 ATTTCTATTAACATTTTGGTACTTAA
46423519 TTATCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (26 bp):
ATTTCTATTAACATTTTGGTACTTAA
Found at i:46424058 original size:25 final size:26
Alignment explanation
Indices: 46424003--46424059 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
46423993 ATGCTTAGAT
*
46424003 CAAAGATAAAGAAACAAAAATTAAAG
1 CAAAGAAAAAGAAACAAAAATTAAAG
* *
46424029 C-AAGAAAAATAAACAAAATTTAAA-
1 CAAAGAAAAAGAAACAAAAATTAAAG
46424053 CAAAGAA
1 CAAAGAA
46424060 GAAAAAGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.93
26 1 0.04
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (26 bp):
CAAAGAAAAAGAAACAAAAATTAAAG
Found at i:46424215 original size:7 final size:7
Alignment explanation
Indices: 46424203--46424248 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
46424193 AGTAAAAGAA
46424203 CCAAGCC
1 CCAAGCC
46424210 CCAAGCC
1 CCAAGCC
*
46424217 CCTAAAACC
1 CC--AAGCC
46424226 CCAAGCC
1 CCAAGCC
46424233 CCAAGCC
1 CCAAGCC
46424240 CCAAGCC
1 CCAAGCC
46424247 CC
1 CC
46424249 TAACACCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 29 0.83
9 6 0.17
ACGTcount: A:0.30, C:0.57, G:0.11, T:0.02
Consensus pattern (7 bp):
CCAAGCC
Found at i:46424263 original size:15 final size:15
Alignment explanation
Indices: 46424209--46424263 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
46424199 AGAACCAAGC
*
46424209 CCCAAGCCCCTAAAA
1 CCCAAGCCCCTAACA
46424224 CCCCAAGCCCC-AAGC-
1 -CCCAAGCCCCTAA-CA
46424239 CCCAAGCCCCTAACA
1 CCCAAGCCCCTAACA
*
46424254 CCCAAACCCC
1 CCCAAGCCCC
46424264 CCAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 11 0.32
15 13 0.38
16 10 0.29
ACGTcount: A:0.33, C:0.56, G:0.07, T:0.04
Consensus pattern (15 bp):
CCCAAGCCCCTAACA
Found at i:46431906 original size:55 final size:56
Alignment explanation
Indices: 46431822--46431927 Score: 205
Period size: 55 Copynumber: 1.9 Consensus size: 56
46431812 ATAATTTATT
46431822 AAAATGTTTTCATTTGTAATCTTTATG-AAAAAACCAATAAAAGAAAGTGTACCTG
1 AAAATGTTTTCATTTGTAATCTTTATGAAAAAAACCAATAAAAGAAAGTGTACCTG
46431877 AAAATGTTTTCATTTGTAATCTTTATGAAAAAAACCAATAAAAGAAAGTGT
1 AAAATGTTTTCATTTGTAATCTTTATGAAAAAAACCAATAAAAGAAAGTGT
46431928 CATTTTCTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 27 0.54
56 23 0.46
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (56 bp):
AAAATGTTTTCATTTGTAATCTTTATGAAAAAAACCAATAAAAGAAAGTGTACCTG
Found at i:46437882 original size:19 final size:20
Alignment explanation
Indices: 46437858--46437902 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
46437848 CAAAAATTAC
46437858 AAAAAATAGAAACAG-AAAA
1 AAAAAATAGAAACAGCAAAA
46437877 AAAAAATAGAAACAGCAAAA
1 AAAAAATAGAAACAGCAAAA
46437897 AAAAAA
1 AAAAAA
46437903 ACTGAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAATAGAAACAGCAAAA
Found at i:46440573 original size:16 final size:15
Alignment explanation
Indices: 46440552--46440609 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
46440542 ACCCCAAGCC
46440552 GGGATATCCCTATAAT
1 GGGATATCCCTA-AAT
**
46440568 GGGATATCCC-AAGGC
1 GGGATATCCCTAA-AT
46440583 GGGATATCCCTAGAAT
1 GGGATATCCCTA-AAT
*
46440599 AGGATATCCCT
1 GGGATATCCCT
46440610 GACTGGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 21 0.62
17 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (15 bp):
GGGATATCCCTAAAT
Found at i:46440586 original size:31 final size:31
Alignment explanation
Indices: 46440544--46440608 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
46440534 ACCCCTAGAC
* *
46440544 CCCAAGCCGGGATATCCCTATAATGGGATAT
1 CCCAAGCCGGGATATCCCTAGAATAGGATAT
*
46440575 CCCAAGGCGGGATATCCCTAGAATAGGATAT
1 CCCAAGCCGGGATATCCCTAGAATAGGATAT
46440606 CCC
1 CCC
46440609 TGACTGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (31 bp):
CCCAAGCCGGGATATCCCTAGAATAGGATAT
Found at i:46440681 original size:21 final size:21
Alignment explanation
Indices: 46440657--46440706 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
46440647 CGTTAAAAAT
46440657 TGAACCGGCCACCAAAACTGC
1 TGAACCGGCCACCAAAACTGC
46440678 TGAACCGGCCACCAAAACTGC
1 TGAACCGGCCACCAAAACTGC
46440699 TGAACCGG
1 TGAACCGG
46440707 GACGGGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.36, G:0.22, T:0.10
Consensus pattern (21 bp):
TGAACCGGCCACCAAAACTGC
Found at i:46444304 original size:78 final size:78
Alignment explanation
Indices: 46444175--46444325 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
46444165 GTACACAAAG
* * *
46444175 TCCATGGTGATCGCTATCAACATGATCACCAACTCTCCTAGCTGATGAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
46444240 TTAATGGTCGAAC
66 TTAATGGTCGAAC
* * *
46444253 TCCATGGTGATCATTATCAACATGATCACCGACTCTCCCAGCTGGTAAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
46444318 TTAATGGT
66 TTAATGGT
46444326 AGAATATGAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (78 bp):
TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
TTAATGGTCGAAC
Found at i:46463008 original size:2 final size:2
Alignment explanation
Indices: 46463001--46463033 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46462991 GTGTTTGTGG
46463001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46463034 ATACAAGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46471484 original size:80 final size:80
Alignment explanation
Indices: 46471347--46471510 Score: 294
Period size: 80 Copynumber: 2.1 Consensus size: 80
46471337 TTACATGTAT
*
46471347 TAAA-AGGAAATCATATTATGAATGAGAAAAGCTTCATGTATAATGTAATCAACTTAAAATTTAA
1 TAAATAGGAAATCAAATTATGAATGAGAAAAGCTTCATGTATAATGTAATCAACTTAAAATTTAA
46471411 GATAGAATTAGGTAA
66 GATAGAATTAGGTAA
* *
46471426 TAAATAGGAAATCAAATTATGAATGAGAAAAGCTTTATGTATGATGTAATCAACTTAAAATTTAA
1 TAAATAGGAAATCAAATTATGAATGAGAAAAGCTTCATGTATAATGTAATCAACTTAAAATTTAA
46471491 GATAGAATTAGGTAA
66 GATAGAATTAGGTAA
46471506 TAAAT
1 TAAAT
46471511 TTCAGCCTAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 4 0.05
80 77 0.95
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.31
Consensus pattern (80 bp):
TAAATAGGAAATCAAATTATGAATGAGAAAAGCTTCATGTATAATGTAATCAACTTAAAATTTAA
GATAGAATTAGGTAA
Found at i:46472290 original size:50 final size:51
Alignment explanation
Indices: 46472202--46472303 Score: 161
Period size: 50 Copynumber: 2.0 Consensus size: 51
46472192 AGAAAGAAAG
* * *
46472202 AATATATCAAAATAATATATATATATGCACATTTCACTTACAGATGCATGCA
1 AATATACCAAAAGAATATATACATA-GCACATTTCACTTACAGATGCATGCA
46472254 AATATACCAAAAGAATATATACATA-CACATTTCACTTACAGATGCATGCA
1 AATATACCAAAAGAATATATACATAGCACATTTCACTTACAGATGCATGCA
46472304 GCGAAATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 25 0.53
52 22 0.47
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (51 bp):
AATATACCAAAAGAATATATACATAGCACATTTCACTTACAGATGCATGCA
Found at i:46477636 original size:2 final size:2
Alignment explanation
Indices: 46477629--46477653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46477619 ATTCTAAAGA
46477629 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
46477654 CGTGCATGTA
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:46484215 original size:30 final size:30
Alignment explanation
Indices: 46484181--46484241 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
46484171 ATTATCACCA
46484181 TTCATATATCATATTAAACGGATAATTTAT
1 TTCATATATCATATTAAACGGATAATTTAT
46484211 TTCATATATCATATTAAACGGATAATTTAT
1 TTCATATATCATATTAAACGGATAATTTAT
46484241 T
1 T
46484242 CGATGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (30 bp):
TTCATATATCATATTAAACGGATAATTTAT
Found at i:46494263 original size:5 final size:5
Alignment explanation
Indices: 46494253--46494290 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
46494243 AAGGATCCGA
46494253 GTCAT GTCAT GTCAT GTCAT GTCAT GTCAT GTCAT GTC
1 GTCAT GTCAT GTCAT GTCAT GTCAT GTCAT GTCAT GTC
46494291 TGGTTCTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (5 bp):
GTCAT
Found at i:46504159 original size:2 final size:2
Alignment explanation
Indices: 46504152--46504179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46504142 GTATAATCTC
46504152 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
46504180 CTAATCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46505635 original size:14 final size:15
Alignment explanation
Indices: 46505616--46505644 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46505606 TATTTAGCTC
46505616 TTTTC-TTTTGTTCT
1 TTTTCTTTTTGTTCT
46505630 TTTTCTTTTTGTTCT
1 TTTTCTTTTTGTTCT
46505645 GTCGATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTGTTCT
Found at i:46506981 original size:5 final size:5
Alignment explanation
Indices: 46506973--46506997 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46506963 AACTCTATTC
46506973 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
46506998 ATTTCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:46507006 original size:15 final size:16
Alignment explanation
Indices: 46506969--46507006 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
46506959 TACTAACTCT
46506969 ATTCTAATTTAATTTA
1 ATTCTAATTTAATTTA
46506985 ATT-TAATTTAA-TTA
1 ATTCTAATTTAATTTA
*
46506999 TTTCTAAT
1 ATTCTAAT
46507007 AATACAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 12 0.60
16 3 0.15
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTCTAATTTAATTTA
Found at i:46514445 original size:50 final size:51
Alignment explanation
Indices: 46514385--46514489 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 51
46514375 GTCCCTATCA
*
46514385 AAAAACTCCAAATGCATTTGCCATTAGCTCAAATAACTCAACACAGACGCT
1 AAAAACTCCAAATGCATTTGCCATTAGCCCAAATAACTCAACACAGACGCT
46514436 AAAAA-TCCAAATGCATTTGCCATTAGCCCAAATAACTCAACACAGACGCT
1 AAAAACTCCAAATGCATTTGCCATTAGCCCAAATAACTCAACACAGACGCT
46514486 AAAA
1 AAAA
46514490 TACTTGTTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 48 0.91
51 5 0.09
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (51 bp):
AAAAACTCCAAATGCATTTGCCATTAGCCCAAATAACTCAACACAGACGCT
Done.