Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:327746 original size:20 final size:19
Alignment explanation
Indices: 327721--327762 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
327711 ATATATGACA
*
327721 AAATCAAAATCATATCACAC
1 AAATCAAAATCAAATCA-AC
*
327741 AAATCAACATCAAATCAAC
1 AAATCAAAATCAAATCAAC
327760 AAA
1 AAA
327763 CAACATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATCAAAATCAAATCAAC
Found at i:331643 original size:14 final size:15
Alignment explanation
Indices: 331614--331643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
331604 TGGAGCTCTT
331614 AAACACCTCTCAAAG
1 AAACACCTCTCAAAG
331629 AAACACCTC-CAAAG
1 AAACACCTCTCAAAG
331643 A
1 A
331644 CTTCTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.33, G:0.07, T:0.10
Consensus pattern (15 bp):
AAACACCTCTCAAAG
Found at i:337199 original size:13 final size:13
Alignment explanation
Indices: 337181--337206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
337171 AATTTTTTTG
337181 TGTATCGATACAT
1 TGTATCGATACAT
337194 TGTATCGATACAT
1 TGTATCGATACAT
337207 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:340371 original size:155 final size:156
Alignment explanation
Indices: 339839--340639 Score: 783
Period size: 155 Copynumber: 5.1 Consensus size: 156
339829 ATAAATTACG
* * * *
339839 AAAAATGCCCCTAGCG-GGTACCTTTGACTTAGAAGTG-CTCGATACCACT-AAAGACTTAAAAA
1 AAAAATACCCCTAG-GAGATACCTTTGACTTAAAAGTGCCTC-ATACCCCTAAAAGACTTAAAAA
* * * ** * * * *
339901 AGATAATAGATGGGATGAACATGTCCTAAATACTTACCTTTGGCATAAAAGTGAACCCAGTGACA
64 AGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCTAGTGACA
* *
339966 ACCTAGGACTCAATTCTAAAAAAATTAT
129 ACCTAGGACTTAGTTCTAAAAAAATTAT
* * * * * * * *
339994 GAAAATGCCCTTAAGGGATGGATACCTTCGACTTAAAATTGCTTGATACTCCTAAAAGACTTAAA
1 AAAAATACCCCT-A-GGA--GATACCTTTGACTTAAAAGTGCCTCATACCCCTAAAAGACTTAAA
* * * * * **
340059 ATAGATTATAAATGGGATGAACCTATCCTAAATACCAACCTTTGGCATAAAAGTGGACCCGGTGA
62 AAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCTAGTGA
* ** * *
340124 CAACTTAGGACTCGGTTTTGAAAAAATTAT
127 CAACCTAGGACTTAGTTCTAAAAAAATTAT
* * * * * *
340154 AAAAATGCCCCTAGGGGATATCTTTGACTTAGAAGTGCCTGATACCCTTAAAAGACTTAAAAAAG
1 AAAAATACCCCTAGGAGATACCTTTGACTTAAAAGTGCCTCATACCCCTAAAAGACTTAAAAAAG
* * * * *
340219 ATTATAGATGGGATTAACTTATCTTAAATACCCACCTTCGGCATAAAAGCGGGCCTAGTGATAAC
66 ATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCTAGTGACAAC
* *
340284 CTAGGACTTAGTTAT-AAAAAATTAC
131 CTAGGACTTAGTTCTAAAAAAATTAT
* * *
340309 AAAAATACCCCTAGGAGATACCTTCGACTTAAAAGTGCCTCATACCCCCAAAGGACTTAAAAAAG
1 AAAAATACCCCTAGGAGATACCTTTGACTTAAAAGTGCCTCATACCCCTAAAAGACTTAAAAAAG
* * ** * *
340374 ATTATAAATGGGATGAACCTATCCTAAATACCCACTTTCAACACAAAAGCGGA-CTCGGTGACAA
66 ATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCT-AGTGACAA
* * * *
340438 CTTAGGAC-TCGATTTTAAAAAAGTTAT
130 CCTAGGACTTAG-TTCTAAAAAAATTAT
* * * *
340465 GAAAATACCCCTA-GAGGA-ACCTTTGACTT-AAAGTGTCTAATACCCCTAAAGGACTTAAAAAA
1 AAAAATACCCCTAGGA-GATACCTTTGACTTAAAAGTGCCTCATACCCCTAAAAGACTTAAAAAA
* * ** * *
340527 GATTATAGATGGAAAGAACCTATCCTAAATACTTACCTTAGGCATAAAAGAGGACCTAGTGACAA
65 GATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCTAGTGACAA
*
340592 CCTAGAACTTAGTTCTAAAAAAATTAT
130 CCTAGGACTTAGTTCTAAAAAAATTAT
* * *
340619 GAAAATACCCTTAGGGGATAC
1 AAAAATACCCCTAGGAGATAC
340640 TTTCAACATG
Statistics
Matches: 531, Mismatches: 100, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
154 117 0.22
155 154 0.29
156 130 0.24
157 1 0.00
158 2 0.00
159 24 0.05
160 103 0.19
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (156 bp):
AAAAATACCCCTAGGAGATACCTTTGACTTAAAAGTGCCTCATACCCCTAAAAGACTTAAAAAAG
ATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCTAGTGACAAC
CTAGGACTTAGTTCTAAAAAAATTAT
Found at i:341811 original size:22 final size:23
Alignment explanation
Indices: 341786--341833 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
341776 TTGGTGAAAA
341786 TTTG-ATTTTTTTTCTTACTATT
1 TTTGTATTTTTTTTCTTACTATT
* *
341808 TTTGTATTTTTTTTCTTTCTTTT
1 TTTGTATTTTTTTTCTTACTATT
341831 TTT
1 TTT
341834 CTCTATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTGTATTTTTTTTCTTACTATT
Found at i:341968 original size:16 final size:16
Alignment explanation
Indices: 341947--341980 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
341937 TTTCTTCTAA
* *
341947 TTTTTTCTTGTTTTCT
1 TTTTTTATTATTTTCT
341963 TTTTTTATTATTTTCT
1 TTTTTTATTATTTTCT
341979 TT
1 TT
341981 GATAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTATTATTTTCT
Found at i:342061 original size:12 final size:12
Alignment explanation
Indices: 342046--342071 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
342036 TAGCCTAATG
342046 ATTATGAAGATA
1 ATTATGAAGATA
342058 ATTATGAAGATA
1 ATTATGAAGATA
342070 AT
1 AT
342072 ATCAGCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATTATGAAGATA
Found at i:342566 original size:22 final size:21
Alignment explanation
Indices: 342513--342567 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
342503 TTTCAATATC
*
342513 AATAAATGTTTTAGAGTTATG
1 AATAAATGTTTTAGAGTTATA
*
342534 AATAAATGTTTTCGAGCTT-TA
1 AATAAATGTTTTAGAG-TTATA
342555 AATAGAATGTTTT
1 AATA-AATGTTTT
342568 TGAAGTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (21 bp):
AATAAATGTTTTAGAGTTATA
Found at i:342684 original size:20 final size:19
Alignment explanation
Indices: 342659--342731 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
342649 ACCCTTGTAC
* *
342659 GTATCGATACATTATGCTTT
1 GTATCGATACATGAT-CATT
*
342679 GTATCGACACATGATCATT
1 GTATCGATACATGATCATT
*
342698 GTATCGATACATGCA-CAACT
1 GTATCGATACATG-ATC-ATT
342718 GTATCGATACATGA
1 GTATCGATACATGA
342732 AACTGGCAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.37
20 29 0.63
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (19 bp):
GTATCGATACATGATCATT
Found at i:344426 original size:18 final size:18
Alignment explanation
Indices: 344385--344427 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
344375 GATGATAAAG
*
344385 ATAATGATGATGATGATC
1 ATAATGATGAAGATGATC
*
344403 ATAATGATGAAGTTGACTC
1 ATAATGATGAAGATGA-TC
344422 A-AATGA
1 ATAATGA
344428 AGAAATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (18 bp):
ATAATGATGAAGATGATC
Found at i:349196 original size:20 final size:19
Alignment explanation
Indices: 349147--349200 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
349137 TACATCCTGA
**
349147 TGTATCGATACATGATTAT
1 TGTATCGATACATGACAAT
*
349166 TGTATCAATACATGCACAAT
1 TGTATCGATACATG-ACAAT
*
349186 TTTATCGATACATGA
1 TGTATCGATACATGA
349201 AACTGGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGACAAT
Found at i:350333 original size:166 final size:164
Alignment explanation
Indices: 350047--350432 Score: 414
Period size: 166 Copynumber: 2.3 Consensus size: 164
350037 TTTTGGGAAT
* * *
350047 AGAGAAATTTTAAGGAAAAAATGAAAAACTT-ATGAAAAT-AAATGAATTTTTTAAAACTGATTT
1 AGAG-AATTTCAAGG-AAAAATGAAAAA-TTCAT-AAAATAAAAGGAATTTTTTAAAAATGATTT
* * *
350110 ACTGTGAATTAAATGATAATGTTTGATGAATTTTAAAAATTATAAACCAAGGAAAATCTCCT-CG
62 AATGTGAATTAAATAATAATGTATGATGAATTTTAAAAATTATAAA-CAAGGAAAATC-CCTCCG
* *
350174 AAAACATTTATGGAGTAA-AAAACT-CTATATTTTAG-AAACA
125 AAAAAATTTACGGAG-AAGAAAACTCCT-TA-TTTAGAAAACA
*
350214 AGAGAATTTCAAGGAAAACATGAAAAATTCATAAAATAAAAGGAATTTTTCAAAAATGATTTAAT
1 AGAGAATTTCAAGGAAAA-ATGAAAAATTCATAAAATAAAAGGAATTTTTTAAAAATGATTTAAT
* *
350279 GTGAATTAAATAATAATAG-ATGATGAATTTTAAAATTTATAAA-ATAGTGAAAATCCTTCCGAA
65 GTGAATTAAATAATAAT-GTATGATGAATTTTAAAAATTATAAACA-AG-GAAAATCCCTCCGAA
*
350342 AAAATTTACGGAGAAGAAAACTCCTTATTTCGAAAACA
127 AAAATTTACGGAGAAGAAAACTCCTTATTTAGAAAACA
* * * * **
350380 AGAAGAATTCCAA--AAAAATCAATAACTCACGAAATAAAAGGAATTTTTTAAAA
1 AG-AGAATTTCAAGGAAAAATGAAAAATTCATAAAATAAAAGGAATTTTTTAAAA
350433 CTTATTTGAT
Statistics
Matches: 189, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
164 31 0.16
165 25 0.13
166 117 0.62
167 16 0.08
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (164 bp):
AGAGAATTTCAAGGAAAAATGAAAAATTCATAAAATAAAAGGAATTTTTTAAAAATGATTTAATG
TGAATTAAATAATAATGTATGATGAATTTTAAAAATTATAAACAAGGAAAATCCCTCCGAAAAAA
TTTACGGAGAAGAAAACTCCTTATTTAGAAAACA
Found at i:354545 original size:10 final size:10
Alignment explanation
Indices: 354530--354562 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
354520 TTGTCCAGGC
354530 CAATTTTTGA
1 CAATTTTTGA
354540 CAATTTTTGA
1 CAATTTTTGA
354550 CAATTTTTGA
1 CAATTTTTGA
354560 CAA
1 CAA
354563 AAATGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (10 bp):
CAATTTTTGA
Found at i:359888 original size:13 final size:13
Alignment explanation
Indices: 359870--359895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
359860 AATTTTTTTG
359870 TGTATCGATACAT
1 TGTATCGATACAT
359883 TGTATCGATACAT
1 TGTATCGATACAT
359896 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:360634 original size:21 final size:21
Alignment explanation
Indices: 360593--360636 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
360583 CTCCGCTTTA
* *
360593 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
360614 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
360635 TC
1 TC
360637 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:362456 original size:13 final size:13
Alignment explanation
Indices: 362438--362463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
362428 ATAATCACCC
362438 TGTATCGATACAA
1 TGTATCGATACAA
362451 TGTATCGATACAA
1 TGTATCGATACAA
362464 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:364562 original size:15 final size:15
Alignment explanation
Indices: 364542--364572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
364532 ATTTCGTTTG
*
364542 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
364557 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
364572 G
1 G
364573 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:366403 original size:21 final size:21
Alignment explanation
Indices: 366374--366418 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
366364 AAGTTTTCAT
*
366374 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
366394 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
366416 TTT
1 TTT
366419 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:368641 original size:13 final size:13
Alignment explanation
Indices: 368623--368648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
368613 AATTTTTTTG
368623 TGTATCGATACAT
1 TGTATCGATACAT
368636 TGTATCGATACAT
1 TGTATCGATACAT
368649 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:370161 original size:23 final size:23
Alignment explanation
Indices: 370125--370169 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
370115 GCCAATGGTC
* *
370125 GAGTGGGGTGGGTAGGTGTGCTT
1 GAGTGGGGTAGGTAGATGTGCTT
*
370148 GAGTGGTGTAGGTAGATGTGCT
1 GAGTGGGGTAGGTAGATGTGCT
370170 AAGCAGTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.04, G:0.51, T:0.31
Consensus pattern (23 bp):
GAGTGGGGTAGGTAGATGTGCTT
Found at i:370531 original size:16 final size:16
Alignment explanation
Indices: 370510--370540 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
370500 GTGGGAATTT
*
370510 GATGATTTTTGTGAGA
1 GATGATGTTTGTGAGA
370526 GATGATGTTTGTGAG
1 GATGATGTTTGTGAG
370541 GTGTGAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (16 bp):
GATGATGTTTGTGAGA
Found at i:372645 original size:33 final size:32
Alignment explanation
Indices: 372602--372665 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
372592 TACAAGCCAA
*
372602 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
* *
372635 TGTATGGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
372666 AATAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:372754 original size:20 final size:21
Alignment explanation
Indices: 372707--372759 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
372697 GCCAATGACC
*
372707 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
372728 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
372748 TGTATCGATACA
1 TGTATCGATACA
372760 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:372765 original size:13 final size:13
Alignment explanation
Indices: 372747--372771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372737 ACATTTGGTC
372747 ATGTATCGATACA
1 ATGTATCGATACA
372760 ATGTATCGATAC
1 ATGTATCGATAC
372772 TATGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:380082 original size:33 final size:32
Alignment explanation
Indices: 380039--380102 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
380029 TACAAGCCAA
*
380039 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
* *
380072 TGTATGGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
380103 AATAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:380191 original size:20 final size:21
Alignment explanation
Indices: 380144--380196 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
380134 GCCAATGACC
*
380144 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
380165 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
380185 TGTATCGATACA
1 TGTATCGATACA
380197 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:380202 original size:13 final size:13
Alignment explanation
Indices: 380184--380208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380174 ACATTTGGTC
380184 ATGTATCGATACA
1 ATGTATCGATACA
380197 ATGTATCGATAC
1 ATGTATCGATAC
380209 TATGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:380859 original size:15 final size:15
Alignment explanation
Indices: 380839--380870 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
380829 TTTCTCCCCC
380839 TTAATCATAAATTTA
1 TTAATCATAAATTTA
380854 TTAATCATAAATTTA
1 TTAATCATAAATTTA
380869 TT
1 TT
380871 TGCAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATCATAAATTTA
Found at i:382695 original size:13 final size:13
Alignment explanation
Indices: 382677--382701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
382667 ATAAACCCTT
382677 TGTATCGATACAC
1 TGTATCGATACAC
382690 TGTATCGATACA
1 TGTATCGATACA
382702 AAGTATCAAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:385423 original size:19 final size:19
Alignment explanation
Indices: 385384--385467 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
385374 TTTGAATGAT
385384 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
385404 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
385423 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
385437 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
385455 TTGTATCGATACA
1 TTGTATCGATACA
385468 ATGTAAGCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 2 0.03
19 29 0.50
20 14 0.24
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:385442 original size:13 final size:13
Alignment explanation
Indices: 385424--385448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385414 ACATAAGTGT
385424 TGTATCGATACAA
1 TGTATCGATACAA
385437 TGTATCGATACA
1 TGTATCGATACA
385449 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:385446 original size:32 final size:32
Alignment explanation
Indices: 385405--385472 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
385395 CATAAAGTGT
385405 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
385437 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
385469 TGTA
1 TGTA
385473 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:385529 original size:13 final size:13
Alignment explanation
Indices: 385511--385535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385501 ATTACTCAAA
385511 TGTATCGATACAT
1 TGTATCGATACAT
385524 TGTATCGATACA
1 TGTATCGATACA
385536 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:385589 original size:52 final size:52
Alignment explanation
Indices: 385544--385672 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
385534 CACTGATCTT
*
385544 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
385596 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
385648 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
385673 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:390200 original size:720 final size:720
Alignment explanation
Indices: 388822--390263 Score: 2866
Period size: 720 Copynumber: 2.0 Consensus size: 720
388812 TTTAACACAT
388822 GCATCACAAACTCTATCACAATCAAATTTGACCTTAGGTAATCCAATTACGAGATTTTTCCTAGA
1 GCATCACAAACTCTATCACAATCAAATTTGACCTTAGGTAATCCAATTACGAGATTTTTCCTAGA
388887 TAACTTAAAGAGTACGCTCATACTTGCATGTCCTAGTTTTCGGTGCCATAGCCAAGGTATGTCAT
66 TAACTTAAAGAGTACGCTCATACTTGCATGTCCTAGTTTTCGGTGCCATAGCCAAGGTATGTCAT
*
388952 TGTTGTCGGCAACACAACGTACGTTTTGGGACCTTAAAACATCTAAATGTACAACATAAATGTTC
131 TGTTGTCGGCAACACAACATACGTTTTGGGACCTTAAAACATCTAAATGTACAACATAAATGTTC
389017 CCTTCCCTATGGCCTAAGAAAGTTGTTTTATTACTACAAACATCAATTACGTGACAATTTTGTGA
196 CCTTCCCTATGGCCTAAGAAAGTTGTTTTATTACTACAAACATCAATTACGTGACAATTTTGTGA
389082 TTGAAAGACTACTTTCATACCTTTGTCACATAATTGACTAATGCTAAGGAGGTTATGCTTAAGAC
261 TTGAAAGACTACTTTCATACCTTTGTCACATAATTGACTAATGCTAAGGAGGTTATGCTTAAGAC
389147 CATTGACATACAAAACATTTTCAATACAAAACACATCTGCCTTGTTTTAACTTAATTTCTGAAAA
326 CATTGACATACAAAACATTTTCAATACAAAACACATCTGCCTTGTTTTAACTTAATTTCTGAAAA
389212 TAAGCTCTTGTCTTCGGTCATATGCCTTGAGCATCCACTATCAAGGTACAAATAATTCTTCTTTG
391 TAAGCTCTTGTCTTCGGTCATATGCCTTGAGCATCCACTATCAAGGTACAAATAATTCTTCTTTG
389277 ATTCTCTTGCCTTGTAGCAATGCTCCACCTCCTATAAACACAAGGATCAAATCTTGTTTATAGGT
456 ATTCTCTTGCCTTGTAGCAATGCTCCACCTCCTATAAACACAAGGATCAAATCTTGTTTATAGGT
389342 ACCCAAATTTTCTTGGGTCCTTTTTCGTTAGTGTTTAACAATTTGATCCTTTCGGAACCCATTTT
521 ACCCAAATTTTCTTGGGTCCTTTTTCGTTAGTGTTTAACAATTTGATCCTTTCGGAACCCATTTT
389407 ATTTCTTTTTCGAAAGTTTCGATTCCTTTAGGCATCCATACTTGTTTAATGATTTTGCCTCTAAA
586 ATTTCTTTTTCGAAAGTTTCGATTCCTTTAGGCATCCATACTTGTTTAATGATTTTGCCTCTAAA
389472 TTTATTTATTTTAGTATTACATGTGTGAAATGTATGGCCATTTTTCTGACATAACGAACACATGT
651 TTTATTTATTTTAGTATTACATGTGTGAAATGTATGGCCATTTTTCTGACATAACGAACACATGT
389537 ACGAG
716 ACGAG
389542 GCATCACAAACTCTATCACAATCAAATTTGACCTTAGGTAATCCAATTACGAGATTTTTCCTAGA
1 GCATCACAAACTCTATCACAATCAAATTTGACCTTAGGTAATCCAATTACGAGATTTTTCCTAGA
389607 TAACTTAAAGAGTACGCTCATACTTGCATGTCCTAGTTTTCGGTGCCATAGCCAAGGTATGTCAT
66 TAACTTAAAGAGTACGCTCATACTTGCATGTCCTAGTTTTCGGTGCCATAGCCAAGGTATGTCAT
389672 TGTTGTCGGCAACACAACATACGTTTTGGGACCTTAAAACATCTAAATGTACAACATAAATGTTC
131 TGTTGTCGGCAACACAACATACGTTTTGGGACCTTAAAACATCTAAATGTACAACATAAATGTTC
389737 CCTTCCCTATGGCCTAAGAAAGTTGTTTTATTACTACAAACATCAATTACGTGACAATTTTGTGA
196 CCTTCCCTATGGCCTAAGAAAGTTGTTTTATTACTACAAACATCAATTACGTGACAATTTTGTGA
389802 TTGAAAGACTACTTTCATACCTTTGTCACATAATTGACTAATGCTAAGGAGGTTATGCTTAAGAC
261 TTGAAAGACTACTTTCATACCTTTGTCACATAATTGACTAATGCTAAGGAGGTTATGCTTAAGAC
389867 CATTGACATACAAAACATTTTCAATACAAAACACATCTGCCTTGTTTTAACTTAATTTCTGAAAA
326 CATTGACATACAAAACATTTTCAATACAAAACACATCTGCCTTGTTTTAACTTAATTTCTGAAAA
389932 TAAGCTCTTGTCTTCGGTCATATGCCTTGAGCATCCACTATCAAGGTACAAATAATTCTTCTTTG
391 TAAGCTCTTGTCTTCGGTCATATGCCTTGAGCATCCACTATCAAGGTACAAATAATTCTTCTTTG
389997 ATTCTCTTGCCTTGTAGCAATGCTCCACCTCCTATAAACACAAGGATCAAATCTTGTTTATAGGT
456 ATTCTCTTGCCTTGTAGCAATGCTCCACCTCCTATAAACACAAGGATCAAATCTTGTTTATAGGT
390062 ACCCAAATTTTCTTGGGTCCTTTTTCGTTAGTGTTTAACAATTTGATCCTTTCGGAACCCATTTT
521 ACCCAAATTTTCTTGGGTCCTTTTTCGTTAGTGTTTAACAATTTGATCCTTTCGGAACCCATTTT
*
390127 ATTTCTTTTTCGGAAGTTTCGATTCCTTTAGGCATCCATACTTGTTTAATGATTTTGCCTCTAAA
586 ATTTCTTTTTCGAAAGTTTCGATTCCTTTAGGCATCCATACTTGTTTAATGATTTTGCCTCTAAA
390192 TTTATTTATTTTAGTATTACATGTGTGAAATGTATGGCCATTTTTCTGACATAACGAACACATGT
651 TTTATTTATTTTAGTATTACATGTGTGAAATGTATGGCCATTTTTCTGACATAACGAACACATGT
390257 ACGAG
716 ACGAG
390262 GC
1 GC
390264 GTTCTTATGC
Statistics
Matches: 720, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
720 720 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (720 bp):
GCATCACAAACTCTATCACAATCAAATTTGACCTTAGGTAATCCAATTACGAGATTTTTCCTAGA
TAACTTAAAGAGTACGCTCATACTTGCATGTCCTAGTTTTCGGTGCCATAGCCAAGGTATGTCAT
TGTTGTCGGCAACACAACATACGTTTTGGGACCTTAAAACATCTAAATGTACAACATAAATGTTC
CCTTCCCTATGGCCTAAGAAAGTTGTTTTATTACTACAAACATCAATTACGTGACAATTTTGTGA
TTGAAAGACTACTTTCATACCTTTGTCACATAATTGACTAATGCTAAGGAGGTTATGCTTAAGAC
CATTGACATACAAAACATTTTCAATACAAAACACATCTGCCTTGTTTTAACTTAATTTCTGAAAA
TAAGCTCTTGTCTTCGGTCATATGCCTTGAGCATCCACTATCAAGGTACAAATAATTCTTCTTTG
ATTCTCTTGCCTTGTAGCAATGCTCCACCTCCTATAAACACAAGGATCAAATCTTGTTTATAGGT
ACCCAAATTTTCTTGGGTCCTTTTTCGTTAGTGTTTAACAATTTGATCCTTTCGGAACCCATTTT
ATTTCTTTTTCGAAAGTTTCGATTCCTTTAGGCATCCATACTTGTTTAATGATTTTGCCTCTAAA
TTTATTTATTTTAGTATTACATGTGTGAAATGTATGGCCATTTTTCTGACATAACGAACACATGT
ACGAG
Found at i:392690 original size:19 final size:18
Alignment explanation
Indices: 392666--392728 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
392656 TACAAGCCAA
392666 TGTATCGATACATTTTGTG
1 TGTATCGATACA-TTTGTG
392685 TGTATCGATACA----T-
1 TGTATCGATACATTTGTG
392698 TGTATCGATACATCTTGTG
1 TGTATCGATACAT-TTGTG
392717 TGTATCGATACA
1 TGTATCGATACA
392729 AACAGTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
18 1 0.03
19 24 0.63
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (18 bp):
TGTATCGATACATTTGTG
Found at i:392703 original size:13 final size:13
Alignment explanation
Indices: 392685--392710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
392675 ACATTTTGTG
392685 TGTATCGATACAT
1 TGTATCGATACAT
392698 TGTATCGATACAT
1 TGTATCGATACAT
392711 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:392707 original size:32 final size:32
Alignment explanation
Indices: 392666--392728 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
392656 TACAAGCCAA
*
392666 TGTATCGATACATTTTGTGTGTATCGATACAT
1 TGTATCGATACATCTTGTGTGTATCGATACAT
392698 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGTGTGTATCGATACA
392729 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATCTTGTGTGTATCGATACAT
Found at i:392817 original size:20 final size:21
Alignment explanation
Indices: 392770--392822 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
392760 GCCAATGACC
*
392770 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
392791 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
392811 TGTATCGATACA
1 TGTATCGATACA
392823 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:392828 original size:13 final size:13
Alignment explanation
Indices: 392810--392834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
392800 ACATTTGGTC
392810 ATGTATCGATACA
1 ATGTATCGATACA
392823 ATGTATCGATAC
1 ATGTATCGATAC
392835 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:397992 original size:20 final size:20
Alignment explanation
Indices: 397947--398013 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
397937 GTAACTTAAA
* *
397947 GTATCGATACATTTAGGGA-T
1 GTATCGATACA-TTATGTATT
*
397967 GCATCGATACATTATGTATT
1 GTATCGATACATTATGTATT
*
397987 GTATCGATACATT-TTTATGT
1 GTATCGATACATTATGTAT-T
398007 GTATCGA
1 GTATCGA
398014 CATAAATGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 9 0.22
20 31 0.77
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTATGTATT
Found at i:400686 original size:59 final size:59
Alignment explanation
Indices: 400565--400699 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
400555 ACTTTTTAAT
* *
400565 AATTTC-ATATATTTTAGGGTCATCTAGGTTATTTTACATAATCTAAAGACCATTCAAT
1 AATTTCTATACATTTTAGGGTCATCTAGGTTATTTTACATAATCTAAAGACCATTCAAC
* * * * ** *
400623 AATTTCTATACATTTTAGGGTTATTTAGGTTATTTTATATAGTCTAGGGACTATT-AAGC
1 AATTTCTATACATTTTAGGGTCATCTAGGTTATTTTACATAATCTAAAGACCATTCAA-C
* *
400682 AATTTCTATGCATATTAG
1 AATTTCTATACATTTTAG
400700 AGACCATTGA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 8 0.12
59 56 0.88
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (59 bp):
AATTTCTATACATTTTAGGGTCATCTAGGTTATTTTACATAATCTAAAGACCATTCAAC
Found at i:404019 original size:2 final size:2
Alignment explanation
Indices: 404000--404036 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
403990 TCAATCCGTG
* *
404000 TC TC TC TG TC TC TG TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
404037 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.05, T:0.51
Consensus pattern (2 bp):
TC
Found at i:404600 original size:2 final size:2
Alignment explanation
Indices: 404593--404617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
404583 TTTCTAAAGC
404593 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
404618 CACTTAACTA
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:404997 original size:2 final size:2
Alignment explanation
Indices: 404986--405020 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
404976 AATATCACGT
404986 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
405021 ACAGATGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:407963 original size:2 final size:2
Alignment explanation
Indices: 407956--407986 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
407946 CACCAGTTTC
407956 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 A
407987 CATGTAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:410923 original size:14 final size:14
Alignment explanation
Indices: 410904--410932 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
410894 TGACATACTC
410904 GTTGGAGATTGAAT
1 GTTGGAGATTGAAT
410918 GTTGGAGATTGAAT
1 GTTGGAGATTGAAT
410932 G
1 G
410933 ATTGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (14 bp):
GTTGGAGATTGAAT
Found at i:411102 original size:13 final size:13
Alignment explanation
Indices: 411084--411111 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
411074 ATAATTCTTC
411084 ATGTATCGATACA
1 ATGTATCGATACA
411097 ATGTATCGATACA
1 ATGTATCGATACA
411110 AT
1 AT
411112 ATGCCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:411203 original size:19 final size:19
Alignment explanation
Indices: 411159--411214 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
411149 CTGCTAGTTT
**
411159 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
411179 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
411198 CATGTATCGAAACAATG
1 CATGTATCGATACAATG
411215 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:419957 original size:20 final size:19
Alignment explanation
Indices: 419946--419998 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
419936 TACAATTGTG
419946 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
419965 TATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
419986 -ATGTATCGATACA
1 CATGTATCGATACA
419999 TCTAGATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:420009 original size:20 final size:19
Alignment explanation
Indices: 419947--420020 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
419937 ACAATTGTGC
419947 ATGTATCGATACA-ATGAAT
1 ATGTATCGATACATA-GAAT
* *
419966 ATGTATCGATACAAAGCAT
1 ATGTATCGATACATAGAAT
419985 AATGTATCGATACATCTAG-AT
1 -ATGTATCGATACA--TAGAAT
420006 ATGTATCGATACATA
1 ATGTATCGATACATA
420021 CAAGGGTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.04
19 16 0.33
20 27 0.55
21 2 0.04
22 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACATAGAAT
Found at i:421508 original size:156 final size:156
Alignment explanation
Indices: 420968--421584 Score: 350
Period size: 156 Copynumber: 4.0 Consensus size: 156
420958 CTTTAAGTCC
* * * * * * ** * * *
420968 TTTAAGGGTACCGAGTACTTTTACATCGAAGGTATACCCTAGAGGCATTTTTGTAATTTTTTAGA
1 TTTAGGGGTATCGAGTACTTTTACGTCAAAGGCATCCCCTAGAGGCATTTTCATAATTGTCTAAA
* * * ** * * * * *
421033 ACCGAGTCTTAGGTTATCACTAGGTTCGCTTTTATGCCGAA-AGTAGATATTTAGGATAAGTTCA
66 ACCAAGTCCTAGGTTGTCACCGGGTTCGCTTTAATGCCGAAGA-TGGGTATGTAGGATAGGTTCA
* * *
421097 TCTCATCTATT---ATCCTTTTTTA-AGTCC
130 CCCCAT-T-TTGAAATCC-TTTTTAGA-TCT
* * * * *
421124 TCTAGGGGTA-CTGGGTACTTTTACGTCAAAGGTATCCCCTAG-GAGCATTTTCGTAATT-TTTC
1 TTTAGGGGTATC-GAGTACTTTTACGTCAAAGGCATCCCCTAGAG-GCATTTTCATAATTGTCT-
** * * * * * * * * * * *
421186 AAAA-TTAGTCCTATGTTCTCATCGGGTCCACTTTTATGTCGAAGGTAGATATTTAGGATAGGTT
63 AAAACCAAGTCCTAGGTTGTCACCGGGTTCGCTTTAATGCCGAAGATGGGTATGTAGGATAGGTT
* * * *
421250 CATCTCGTCTATT---AT-CTTCTTTA-AGTCC
128 CACCCCAT-T-TTGAAATCCTT-TTTAGA-TCT
* * * * * * * *
421278 TTTAGGGGTATCGAGTATTTTTACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGA
1 TTTAGGGGTATCGAGTACTTTTACGTCAAAGGCATCCCCTAGAGGCATTTTCATAATTGTCTAAA
* ** * * *
421343 ACCGAGTCCTCA-GTTGTCATTGGGTTCGCTTTCATGCCGAAGATGTGTATGTAGGATAGGTTTA
66 ACCAAGTCCT-AGGTTGTCACCGGGTTCGCTTTAATGCCGAAGATGGGTATGTAGGATAGGTTCA
421407 CCCCAATTTT-AAATCCTTTTTAGATCT
130 CCCC-ATTTTGAAATCCTTTTTAGATCT
* **
421434 TTTAGGGGTATTCGAGTACTTTTATGTCAAAGGCATCCCCTA-AGGCATTTTTGTAATTGTCTAA
1 TTTAGGGGTA-TCGAGTACTTTTACGTCAAAGGCATCCCCTAGAGGCATTTTCATAATTGTCTAA
* * * * *
421498 AACTAAGTCCTAGGTTGTCACCGGGTTCGTTTTAATGCTGATGATGGGTATTTAGGATAGGTTCA
65 AACCAAGTCCTAGGTTGTCACCGGGTTCGCTTTAATGCCGAAGATGGGTATGTAGGATAGGTTCA
* *
421563 TCCCATTTTGTAATCCTTTTTA
130 CCCCATTTTGAAATCCTTTTTA
421585 TGTCTTTAGT
Statistics
Matches: 372, Mismatches: 71, Indels: 36
0.78 0.15 0.08
Matches are distributed among these distances:
153 2 0.01
154 63 0.17
155 125 0.34
156 151 0.41
157 31 0.08
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (156 bp):
TTTAGGGGTATCGAGTACTTTTACGTCAAAGGCATCCCCTAGAGGCATTTTCATAATTGTCTAAA
ACCAAGTCCTAGGTTGTCACCGGGTTCGCTTTAATGCCGAAGATGGGTATGTAGGATAGGTTCAC
CCCATTTTGAAATCCTTTTTAGATCT
Found at i:421591 original size:156 final size:155
Alignment explanation
Indices: 420952--421805 Score: 599
Period size: 155 Copynumber: 5.5 Consensus size: 155
420942 CATCATTACC
* * * * * *
420952 AATCCTCTTTAAGTCCTTTAAGGGTACCGAGTACTTTTACATCGAAGGTATACCCTAGAGGCATT
1 AATCCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCAAAGGTATCCCCTAGAGGCATT
* * * * **
421017 TTTGTAATTTTTTAGAACCGAGTCTTAGGTTATCACTAGGTTCGCTTTTATGCCGAA-AGTAGAT
66 TTCGTAATTTTTTAAAACCGAGTCCTAGGTTGTCACCGGGTTCG-TTTTATGCCGAAGA-TAGAT
* *
421081 ATTTAGGATAAGTTCATCTCATCTATT
129 ATTTAGGATAGGTTCATCCCATCTATT
* *
421108 -ATCCTTTTTTAAGTCCTCTAGGGGTA-CTGGGTACTTTTACGTCAAAGGTATCCCCTAG-GAGC
1 AATCC-TTTTTAAGTCCTTTAGGGGTATC-GAGTACTTTTACGTCAAAGGTATCCCCTAGAG-GC
* ** * * * * * * *
421170 ATTTTCGTAATTTTTCAAAA-TTAGTCCTATGTTCTCATCGGGTCCACTTTTATGTCGAAGGTAG
63 ATTTTCGTAATTTTTTAAAACCGAGTCCTAGGTTGTCACCGGGTTC-GTTTTATGCCGAAGATAG
* *
421234 ATATTTAGGATAGGTTCATCTCGTCTATT
127 ATATTTAGGATAGGTTCATCCCATCTATT
* * * *
421263 -AT-CTTCTTTAAGTCCTTTAGGGGTATCGAGTATTTTTACGTCGAAGGTATCCCCTAGGGGTAT
1 AATCCTT-TTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCAAAGGTATCCCCTAGAGGCAT
* * ** *
421326 TTTCATAATTTTTTAGAACCGAGTCCTCA-GTTGTCATTGGGTTCGCTTTCATGCCGAAGAT-GT
65 TTTCGTAATTTTTTAAAACCGAGTCCT-AGGTTGTCACCGGGTTCG-TTTTATGCCGAAGATAG-
* * * *
421389 GTATGTAGGATAGGTTTACCCCAAT-T-TT
127 ATATTTAGGATAGGTTCATCCC-ATCTATT
* * *
421417 AAATCCTTTTT-AGATCTTTTAGGGGTATTCGAGTACTTTTATGTCAAAGGCATCCCCTA-AGGC
1 -AATCCTTTTTAAG-TCCTTTAGGGGTA-TCGAGTACTTTTACGTCAAAGGTATCCCCTAGAGGC
* * * ** * * *
421480 ATTTTTGTAATTGTCTAAAACTAAGTCCTAGGTTGTCACCGGGTTCGTTTTAATGCTGATGATGG
63 ATTTTCGTAATTTTTTAAAACCGAGTCCTAGGTTGTCACCGGGTTCGTTTT-ATGCCGAAGATAG
* *
421545 GTATTTAGGATAGGTTCATCCCAT-TTTGT
127 ATATTTAGGATAGGTTCATCCCATCTAT-T
* * * * * * * ** * * * * *
421574 AATCCTTTTTATGT-CTTTAGTGATAT-TAGGCACTTCTATGTTGAAGATATCTCTTAGGGGTAT
1 AATCCTTTTTAAGTCCTTTAGGGGTATCGA-GTACTTTTACGTCAAAGGTATCCCCTAGAGGCAT
* * * * * * * * * *
421637 TTTGGTAATTTTCTAAAATCGAATCCTAGGTTGTCAGCAGGTCCAGTTTTAGGCCGAAGGTAGGT
65 TTTCGTAATTTTTTAAAACCGAGTCCTAGGTTGTCACCGGGTTC-GTTTTATGCCGAAGATAGAT
* * * * *
421702 ACTTAGGATTGGTTTATCTCATCTA-C
129 ATTTAGGATAGGTTCATCCCATCTATT
* * * * * * *
421728 AATCCTTTTTAAGTCCTTTAGAGGTATCAAGTACTTTTACTTCGAAGTTATCCCTTAGGGGCATT
1 AATCCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCAAAGGTATCCCCTAGAGGCA-T
*
421793 TTTTGTAATTTTT
65 TTTCGTAATTTTT
421806 CTTGAATTTA
Statistics
Matches: 549, Mismatches: 118, Indels: 62
0.75 0.16 0.09
Matches are distributed among these distances:
153 3 0.01
154 100 0.18
155 234 0.43
156 179 0.33
157 33 0.06
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (155 bp):
AATCCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCAAAGGTATCCCCTAGAGGCATT
TTCGTAATTTTTTAAAACCGAGTCCTAGGTTGTCACCGGGTTCGTTTTATGCCGAAGATAGATAT
TTAGGATAGGTTCATCCCATCTATT
Found at i:425831 original size:14 final size:15
Alignment explanation
Indices: 425814--425842 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
425804 AAATTAAAAA
425814 CAAAATTT-TCTTTT
1 CAAAATTTATCTTTT
425828 CAAAATTTATCTTTT
1 CAAAATTTATCTTTT
425843 TTATTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
CAAAATTTATCTTTT
Found at i:429077 original size:20 final size:19
Alignment explanation
Indices: 429033--429086 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
429023 GTTAGAAGCA
429033 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
*
429053 TTGTATCGATACAATGTTC-C
1 ATGTATCGATACAA--TTCAC
*
429073 ATGTATTGATACAA
1 ATGTATCGATACAA
429087 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 26 0.90
22 3 0.10
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:429161 original size:19 final size:19
Alignment explanation
Indices: 429119--429167 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
429109 CAGTTTCATG
* * *
429119 TATCGATACAATTGTACATG
1 TATCGATAC-AGTGAACATA
429139 TATCGATACAGTGAACATA
1 TATCGATACAGTGAACATA
*
429158 TATCAATACA
1 TATCGATACA
429168 TTGTATCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (19 bp):
TATCGATACAGTGAACATA
Found at i:434810 original size:95 final size:93
Alignment explanation
Indices: 434677--434897 Score: 264
Period size: 95 Copynumber: 2.3 Consensus size: 93
434667 GAGATACTTT
* *
434677 AACCCCATTCTTCTGAGGGATACTCCAACCCCGTTTTTAAACTCGTCAAGATTTAAATATTATTT
1 AACCCCATTCTTCCGAGGGAAACTCCAA--CCGTTTTTAAACTCGTCAAGATTTAAATATTATTT
* * *
434742 TTGCTTAAATTGTCATCAAC-GGGATACTCC
64 TTGCCTAAATTGTC-TCAACAGAGACACTCC
* * * *
434772 AACCCCATTCTTCCGAGGGAAAATCCAACTGTAATTTTAAACTTGTCAAGATTTAAATCTTATTT
1 AACCCCATTCTTCCGAGGGAAACTCCAACCGT--TTTTAAACTCGTCAAGATTTAAATATTATTT
* *
434837 TTGCCTAAATTGTCTCATCAGAGACACTCT
64 TTGCCTAAATTGTCTCAACAGAGACACTCC
* *
434867 AACCCTATTCCTCCGAGGGAATACTCCAACC
1 AACCCCATTCTTCCGAGGGAA-ACTCCAACC
434898 TCACTTTTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
93 3 0.03
94 4 0.04
95 93 0.87
96 7 0.07
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (93 bp):
AACCCCATTCTTCCGAGGGAAACTCCAACCGTTTTTAAACTCGTCAAGATTTAAATATTATTTTT
GCCTAAATTGTCTCAACAGAGACACTCC
Found at i:437293 original size:7 final size:7
Alignment explanation
Indices: 437281--437307 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
437271 TCAAATACAT
437281 AATTTTG
1 AATTTTG
437288 AATTTTG
1 AATTTTG
437295 AATTTTG
1 AATTTTG
437302 AATTTT
1 AATTTT
437308 TACAATTTAG
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:439513 original size:150 final size:153
Alignment explanation
Indices: 439210--439530 Score: 370
Period size: 150 Copynumber: 2.1 Consensus size: 153
439200 ATCGAGATGT
* * *
439210 ATTTTGGTAATTTTTTTTAGAATCTAGTCTAATATAGTCACCGGGATGTTTTTATGTCGAAAGTG
1 ATTTT-GTAATTTTTTTTAGAACCTAGTCTAATATAGTCACC--GA-GCTTTTATGTCCAAAGTG
* * ** * *
439275 GTGCATTTAGGGTAGGTTCACCCATTTATGGTTACTTTTCAGTCCTTTAGGGTTATCAAGATATT
62 GTGCATTAAGGATAGGTTCACCCATTTACAGCTACTTTTCAGTCCTTTAAGGTTATCAAGATATT
439340 TTCATATTGAAGATATACCTCAAAGGC
127 TTCATATTGAAGATATACCTCAAAGGC
*
439367 ATTTTGATAATTTTTTTTAGAACCTAGTCTAATATAGTCACC-A-CTTTTATG-CCAAAG-GTTG
1 ATTTTG-TAATTTTTTTTAGAACCTAGTCTAATATAGTCACCGAGCTTTTATGTCCAAAGTGGTG
* * * *
439428 CATTAAGGATAGGTTTACCCTTTTACAGCTA-TTTTCAAGTCTTTTAAGGTTA-CCAGA-ATGCT
65 CATTAAGGATAGGTTCACCCATTTACAGCTACTTTTC-AGTCCTTTAAGGTTATCAAGATAT--T
439490 TTCATATTGAA-AGTATACCTCAAAGGC
127 TTCATATTGAAGA-TATACCTCAAAGGC
439517 ATTTTCGTAATTTT
1 ATTTT-GTAATTTT
439531 GCATTAGAAC
Statistics
Matches: 144, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
148 2 0.01
149 10 0.07
150 78 0.54
151 6 0.04
152 7 0.05
154 1 0.01
156 1 0.01
157 39 0.27
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (153 bp):
ATTTTGTAATTTTTTTTAGAACCTAGTCTAATATAGTCACCGAGCTTTTATGTCCAAAGTGGTGC
ATTAAGGATAGGTTCACCCATTTACAGCTACTTTTCAGTCCTTTAAGGTTATCAAGATATTTTCA
TATTGAAGATATACCTCAAAGGC
Found at i:440374 original size:4 final size:4
Alignment explanation
Indices: 440365--440389 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
440355 TGGCCTCTAG
440365 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
440390 TAAAATAGTG
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:446857 original size:76 final size:78
Alignment explanation
Indices: 446756--446959 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
446746 GAGATAATAA
* * * * *
446756 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
446820 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
446832 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
446897 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
446911 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
446960 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:446951 original size:28 final size:28
Alignment explanation
Indices: 446911--446982 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
446901 GGAATAAAGC
** *
446911 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
446939 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
446967 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
446983 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:447040 original size:52 final size:50
Alignment explanation
Indices: 446971--447139 Score: 189
Period size: 52 Copynumber: 3.3 Consensus size: 50
446961 AAATAACGAG
* * *
446971 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
447023 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGAAATAAAACC-GGA
*
447075 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
447126 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
447140 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
50 2 0.02
51 43 0.43
52 45 0.45
53 9 0.09
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:447085 original size:51 final size:51
Alignment explanation
Indices: 447004--447139 Score: 161
Period size: 51 Copynumber: 2.6 Consensus size: 51
446994 AAATTGGTAT
* *
447004 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTGGCG
1 TTTT-GAAATAAAACCGGAGTTGGAGTATCCCCGATT-AAGGAAAAATTAGCG
** *
447056 TTTTGAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTTTGAAATAAAACC-GGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
447107 TTTT-AACGATAAAACCGGAGTTGGAGTATCCCC
1 TTTTGAA--ATAAAACCGGAGTTGGAGTATCCCC
447140 TCGAAAATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
50 4 0.05
51 42 0.57
52 28 0.38
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (51 bp):
TTTTGAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
Found at i:447158 original size:28 final size:28
Alignment explanation
Indices: 447113--447194 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
447103 AGTGTTTTAA
* *
447113 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
447140 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
447167 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
447195 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:449630 original size:13 final size:13
Alignment explanation
Indices: 449612--449637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
449602 ACAAAGATCC
449612 ATGTATCGATACA
1 ATGTATCGATACA
449625 ATGTATCGATACA
1 ATGTATCGATACA
449638 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:449633 original size:33 final size:33
Alignment explanation
Indices: 449591--449657 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
449581 AAAATTTCCA
***
449591 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
449624 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
449657 A
1 A
449658 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:449701 original size:19 final size:18
Alignment explanation
Indices: 449677--449744 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
449667 CAGTAGCTAA
449677 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
449696 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
449711 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
449728 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
449745 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:449717 original size:13 final size:13
Alignment explanation
Indices: 449699--449723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449689 ACAATACTTA
449699 TGTATCGATACAT
1 TGTATCGATACAT
449712 TGTATCGATACA
1 TGTATCGATACA
449724 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:449721 original size:32 final size:32
Alignment explanation
Indices: 449680--449742 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
449670 TAGCTAATTA
*
449680 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
449712 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
449743 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:449824 original size:21 final size:21
Alignment explanation
Indices: 449800--449856 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
449790 CATTTGTAGG
449800 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
449821 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
449842 ATGTATCGATACATT
1 ATGTATCGATACATT
449857 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:449884 original size:20 final size:20
Alignment explanation
Indices: 449859--449900 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
449849 GATACATTTA
449859 AATTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTC
449879 AATTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTC
449899 AA
1 AA
449901 ACACTTTATC
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:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (20 bp):
AATTTTTTTTTTTTTTTTTC
Found at i:454136 original size:20 final size:20
Alignment explanation
Indices: 454113--454192 Score: 63
Period size: 25 Copynumber: 3.7 Consensus size: 20
454103 TACACATGAA
454113 AATGTATCGATACATATTGC
1 AATGTATCGATACATATTGC
*
454133 AATGTATAGATACGATACACCTTGC
1 AATGTATCGATAC-AT--A--TTGC
*
454158 AATGCATCGATACATTATGTG-
1 AATGTATCGATACA-TAT-TGC
*
454179 AAAGTATCGATACA
1 AATGTATCGATACA
454193 AGTCATTGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
20 12 0.25
21 15 0.31
22 2 0.04
23 2 0.04
24 1 0.02
25 16 0.33
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATATTGC
Found at i:454157 original size:25 final size:25
Alignment explanation
Indices: 454120--454170 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
454110 GAAAATGTAT
* *
454120 CGATACATATTGCAATGTATAGATA
1 CGATACACATTGCAATGCATAGATA
* *
454145 CGATACACCTTGCAATGCATCGATA
1 CGATACACATTGCAATGCATAGATA
454170 C
1 C
454171 ATTATGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (25 bp):
CGATACACATTGCAATGCATAGATA
Found at i:454533 original size:38 final size:38
Alignment explanation
Indices: 454482--454560 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
454472 ACAAGAGAAA
*
454482 TTCTATCATACAACATCAAGGAGCTAAAAATCAAGTTC
1 TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
* *
454520 TTCTATCATACAACATCAAAGAGTTGAAAATCAAGTTC
1 TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
454558 TTC
1 TTC
454561 ATTTGTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (38 bp):
TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
Found at i:455189 original size:55 final size:54
Alignment explanation
Indices: 455105--455727 Score: 905
Period size: 55 Copynumber: 11.3 Consensus size: 54
455095 ATAAATTGTA
* * * * *
455105 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
455160 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
455215 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
455270 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
455325 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
455380 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
455435 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
455490 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
455545 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
455600 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
455655 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
455710 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
455728 AAAAAGCGGA
Statistics
Matches: 531, Mismatches: 25, Indels: 24
0.92 0.04 0.04
Matches are distributed among these distances:
54 19 0.04
55 500 0.94
56 10 0.02
57 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:455400 original size:26 final size:26
Alignment explanation
Indices: 455371--455460 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
455361 GTGTGGGCTT
455371 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
455397 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
455424 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
455452 TGAAAGGTG
1 TGAAAGGTG
455461 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:455489 original size:29 final size:29
Alignment explanation
Indices: 455401--455489 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
455391 GAGGACTGAA
455401 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
455430 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
455456 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
455485 AGGTG
1 AGGTG
455490 TCCTGCTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:456729 original size:26 final size:25
Alignment explanation
Indices: 456692--456754 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
456682 GCTTAAGTAG
456692 GTTTTTTCTTTTCTCTCTTTTTCTTT
1 GTTTTTT-TTTTCTCTCTTTTTCTTT
* * * *
456718 GTTTTGTTTTTTTTGTTTTTTTTTTT
1 GTTTT-TTTTTTCTCTCTTTTTCTTT
456744 GTTTTTTTTTT
1 GTTTTTTTTTT
456755 TGAAGAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 6 0.19
26 24 0.75
27 2 0.06
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (25 bp):
GTTTTTTTTTTCTCTCTTTTTCTTT
Found at i:456741 original size:12 final size:12
Alignment explanation
Indices: 456709--456756 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
456699 CTTTTCTCTC
*
456709 TTTTTCTTTGTTT
1 TTTTTTTTTG-TT
456722 TGTTTTTTTTGTT
1 T-TTTTTTTTGTT
456735 TTTTTTTTTGTT
1 TTTTTTTTTGTT
456747 TTTTTTTTTG
1 TTTTTTTTTG
456757 AAGAGAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 21 0.64
13 4 0.12
14 8 0.24
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:456745 original size:21 final size:23
Alignment explanation
Indices: 456710--456752 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
456700 TTTTCTCTCT
456710 TTTTCTTTGTTTTGTTTTTTTTG
1 TTTTCTTTGTTTTGTTTTTTTTG
456733 TTTT-TTT-TTTTGTTTTTTTT
1 TTTTCTTTGTTTTGTTTTTTTT
456753 TTTGAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.88
Consensus pattern (23 bp):
TTTTCTTTGTTTTGTTTTTTTTG
Found at i:469263 original size:76 final size:78
Alignment explanation
Indices: 469162--469365 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
469152 GAGATAATAA
* * * * *
469162 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
469226 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
469238 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
469303 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
469317 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
469366 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:469357 original size:28 final size:28
Alignment explanation
Indices: 469317--469388 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
469307 GGAATAAAGC
** *
469317 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
469345 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
469373 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
469389 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:469446 original size:52 final size:50
Alignment explanation
Indices: 469377--469546 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
469367 AAATAACGAG
* * *
469377 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
469429 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
469482 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
469533 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
469547 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:469565 original size:28 final size:28
Alignment explanation
Indices: 469520--469601 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
469510 AGTGTTTTAA
* *
469520 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
469547 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
469574 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
469602 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:472037 original size:13 final size:13
Alignment explanation
Indices: 472019--472044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472009 ACAAAGATCC
472019 ATGTATCGATACA
1 ATGTATCGATACA
472032 ATGTATCGATACA
1 ATGTATCGATACA
472045 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:472040 original size:33 final size:33
Alignment explanation
Indices: 471998--472064 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
471988 AAAATTTCCA
***
471998 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
472031 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
472064 A
1 A
472065 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:472108 original size:19 final size:18
Alignment explanation
Indices: 472084--472151 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
472074 CAGTAGCTAA
472084 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
472103 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
472118 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
472135 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
472152 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:472124 original size:13 final size:13
Alignment explanation
Indices: 472106--472130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
472096 ACAATACTTA
472106 TGTATCGATACAT
1 TGTATCGATACAT
472119 TGTATCGATACA
1 TGTATCGATACA
472131 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:472128 original size:32 final size:32
Alignment explanation
Indices: 472087--472149 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
472077 TAGCTAATTA
*
472087 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
472119 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
472150 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:472231 original size:21 final size:21
Alignment explanation
Indices: 472207--472263 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
472197 CATTTGTAGG
472207 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
472228 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
472249 ATGTATCGATACATT
1 ATGTATCGATACATT
472264 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:472292 original size:21 final size:21
Alignment explanation
Indices: 472266--472305 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
472256 GATACATTTA
472266 AATTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTC
472287 AATTTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTTT
472306 CAAACACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (21 bp):
AATTTTTTTTTTTTTTTTTTC
Found at i:472294 original size:20 final size:20
Alignment explanation
Indices: 472269--472308 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
472259 ACATTTAAAT
472269 TTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTCAA
472289 TTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTCAA
472309 ACACTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTCAA
Found at i:476545 original size:20 final size:20
Alignment explanation
Indices: 476522--476601 Score: 63
Period size: 25 Copynumber: 3.7 Consensus size: 20
476512 TACACATGAA
476522 AATGTATCGATACATATTGC
1 AATGTATCGATACATATTGC
*
476542 AATGTATAGATACGATACACCTTGC
1 AATGTATCGATAC-AT--A--TTGC
*
476567 AATGCATCGATACATTATGTG-
1 AATGTATCGATACA-TAT-TGC
*
476588 AAAGTATCGATACA
1 AATGTATCGATACA
476602 AGTCATTGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
20 12 0.25
21 15 0.31
22 2 0.04
23 2 0.04
24 1 0.02
25 16 0.33
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATATTGC
Found at i:476566 original size:25 final size:25
Alignment explanation
Indices: 476529--476579 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
476519 GAAAATGTAT
* *
476529 CGATACATATTGCAATGTATAGATA
1 CGATACACATTGCAATGCATAGATA
* *
476554 CGATACACCTTGCAATGCATCGATA
1 CGATACACATTGCAATGCATAGATA
476579 C
1 C
476580 ATTATGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (25 bp):
CGATACACATTGCAATGCATAGATA
Found at i:476942 original size:38 final size:38
Alignment explanation
Indices: 476891--476969 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
476881 ACAAGAGAAA
*
476891 TTCTATCATACAACATCAAGGAGCTAAAAATCAAGTTC
1 TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
* *
476929 TTCTATCATACAACATCAAAGAGTTGAAAATCAAGTTC
1 TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
476967 TTC
1 TTC
476970 ATTTGTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (38 bp):
TTCTATCATACAACATCAAAGAGCTAAAAATCAAGTTC
Found at i:479964 original size:22 final size:23
Alignment explanation
Indices: 479939--479988 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
479929 AGTTAGAAAT
*
479939 ATGTATGGGT-TTAATT-AAGTTC
1 ATGTATAGGTCTTAATTGAA-TTC
479961 ATGTATAGGTCTTAATTGAATTC
1 ATGTATAGGTCTTAATTGAATTC
479984 ATGTA
1 ATGTA
479989 ACTAGCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
23 14 0.56
24 2 0.08
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (23 bp):
ATGTATAGGTCTTAATTGAATTC
Found at i:483313 original size:23 final size:24
Alignment explanation
Indices: 483286--483350 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
483276 TAGTTTTCTA
483286 TTTCTTTCTTTATTTTTCCTCT-T
1 TTTCTTTCTTTATTTTTCCTCTCT
483309 TTTCTTTCTTT-TTTCTT-CTCTCT
1 TTTCTTTCTTTATTT-TTCCTCTCT
* *
483332 TTTCTCTC-TAATTTTTCCT
1 TTTCTTTCTTTATTTTTCCT
483351 ACTAGCTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTCTTTCTTTATTTTTCCTCTCT
Found at i:484086 original size:164 final size:162
Alignment explanation
Indices: 483692--484105 Score: 435
Period size: 165 Copynumber: 2.5 Consensus size: 162
483682 AAAATAATTC
* * * * *
483692 AAAATTCATG-AAATAATTTGAATTTTTCAAAATTGATTTAATTTGAATTAAATGATAATATTAG
1 AAAATTCATGAAAATAA-ATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTG
* * * * **
483756 ATGAATTCT-AAAAGTTTTAAACCAAGAAAAATCCCCTCAAAAATGTTTATGGAGTAGGAAACTC
65 ATGAATTTTGAAAA---TTAAA--AAAAAAAATCCCCTCAAAAATATTTACGGAGTAAAAAACTC
*
483820 AGTTTTTCAGGAAAAAGAGAATTTCAAGGAAAAAATGA
125 AGTTTTTCAGGAAAAAGAGAATTTCAAGGAAAAAAGGA
* * * * * *
483858 AAAATTTACGAAAATAAATGAA-TTTTGAAAACTAATTTAACATGAATCAAATAATAATATTTGA
1 AAAATTCATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGA
* * *
483922 TGAATTTTGAAAATTAAAAATAAAAAATCTCCTCGAAAATATTTACGGAGTAAAAAACTCCGTAT
66 TGAATTTTGAAAATTAAAAA-AAAAAATCCCCTCAAAAATATTTACGGAGTAAAAAACTCAGT-T
* *
483987 TTT-A-GAAATATAG-GCATTTTAAGGAAAACAAGGA
129 TTTCAGGAAA-A-AGAGAATTTCAAGGAAAA-AAGGA
* *
484021 AAAACTCATGAAAATAAATGAATTTTTTAAAACTGATTTAATATGAATTAAATAATAATATTTGA
1 AAAATTCATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGA
* *
484086 TAAATTTTAGAAATTTAAAA
66 TGAATTTT-GAAAATTAAAA
484106 TCGATGAAAA
Statistics
Matches: 207, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
161 6 0.03
162 49 0.24
163 34 0.16
164 45 0.22
165 51 0.25
166 16 0.08
167 6 0.03
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (162 bp):
AAAATTCATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGA
TGAATTTTGAAAATTAAAAAAAAAAATCCCCTCAAAAATATTTACGGAGTAAAAAACTCAGTTTT
TCAGGAAAAAGAGAATTTCAAGGAAAAAAGGA
Found at i:485356 original size:84 final size:83
Alignment explanation
Indices: 485268--485453 Score: 216
Period size: 84 Copynumber: 2.2 Consensus size: 83
485258 ACTAGGATAA
* * * *
485268 AATCGATAAGTTAACAAAGGAT-AAAGAAATTTACTC-GGGACTAAGCCGACAGGTAAATAAGGG
1 AATCGATAAGTTAACAAAGGATAAAAG-AATTTAC-CAAGGACTAAGCCGACAAGTAAAGAA-AG
485331 AT-AAAAGGTTAACCAGGGCTG
63 ATGAAAA-GTTAACCAGGGCTG
* * * *
485352 AATCGATAAGTTAACAAAGGGTAAAAGAGTTTACCAAGGACTGAGCTGACAAGTAAAGAAAGATG
1 AATCGATAAGTTAACAAAGGATAAAAGAATTTACCAAGGACTAAGCCGACAAGTAAAGAAAGATG
**
485417 AAAAGTTGCCCAGGGCTG
66 AAAAGTTAACCAGGGCTG
*
485435 AACCGATAAGTTAACAAAG
1 AATCGATAAGTTAACAAAG
485454 AGTAAAGGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
83 34 0.39
84 50 0.57
85 4 0.05
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (83 bp):
AATCGATAAGTTAACAAAGGATAAAAGAATTTACCAAGGACTAAGCCGACAAGTAAAGAAAGATG
AAAAGTTAACCAGGGCTG
Found at i:485454 original size:40 final size:42
Alignment explanation
Indices: 485330--485459 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 42
485320 GTAAATAAGG
* *
485330 GATAAAAG-G-TTAACCAGGGCTGAATCGATAAGTTAACAAA
1 GATAAAAGAGTTTACCCAGGGCTGAACCGATAAGTTAACAAA
* * * * * * * *
485370 GGGTAAAAGAGTTTACCAAGGACTGAGCTGACAAGTAAAGAAA
1 -GATAAAAGAGTTTACCCAGGGCTGAACCGATAAGTTAACAAA
* *
485413 GATGAAA-AG-TTGCCCAGGGCTGAACCGATAAGTTAACAAA
1 GATAAAAGAGTTTACCCAGGGCTGAACCGATAAGTTAACAAA
485453 GAGTAAA
1 GA-TAAA
485460 GGTATTCACT
Statistics
Matches: 65, Mismatches: 21, Indels: 6
0.71 0.23 0.07
Matches are distributed among these distances:
40 25 0.38
41 12 0.18
42 6 0.09
43 22 0.34
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (42 bp):
GATAAAAGAGTTTACCCAGGGCTGAACCGATAAGTTAACAAA
Found at i:485504 original size:83 final size:84
Alignment explanation
Indices: 485333--485552 Score: 207
Period size: 83 Copynumber: 2.6 Consensus size: 84
485323 AATAAGGGAT
* * *
485333 AAAAGGTTAACCAGGGCTGAATCGATAAGTTAACAAAGGGTAAAAGAGTTTACCAAGGACTGAGC
1 AAAAGGTTGACCAGGGCTGAACCGATAAGTTAACAAAGAGTAAAAGAGTTTACCAAGGACTGAGC
* * *
485398 TGACAAGTAAAGAAAGATG
66 TCAAAAGTAAACAAAGATG
* *
485417 AAAA-GTTGCCCAGGGCTGAACCGATAAGTTAACAAAGAGT-AAAG-GTATTCACTAAGGACTGA
1 AAAAGGTTGACCAGGGCTGAACCGATAAGTTAACAAAGAGTAAAAGAGT-TT-ACCAAGGACTGA
* * *
485479 TC-CAAAAGGTGAACAAGCGAT-
64 GCTCAAAA-GTAAACAA-AGATG
* ** ** * *
485500 AAAAGGTTGACTAGGGCTGAACTAATAAGTCGACAAAGTGTAAATGAGTTTAC
1 AAAAGGTTGACCAGGGCTGAACCGATAAGTTAACAAAGAGTAAAAGAGTTTAC
485553 GAGAGACTGA
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
81 2 0.02
82 9 0.08
83 54 0.49
84 38 0.35
85 5 0.05
86 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (84 bp):
AAAAGGTTGACCAGGGCTGAACCGATAAGTTAACAAAGAGTAAAAGAGTTTACCAAGGACTGAGC
TCAAAAGTAAACAAAGATG
Found at i:485839 original size:44 final size:44
Alignment explanation
Indices: 485791--486045 Score: 157
Period size: 44 Copynumber: 5.8 Consensus size: 44
485781 TTGAAAAGAG
* * *
485791 TTTGACTAGGTTGATAACCATACGTCAAACAGAAAAAAGGCAGA
1 TTTGACCAGGGTGGTAACCATACGTCAAACAGAAAAAAGGCAGA
* ** * ** *
485835 TTTGACTAGGGTGGTAAGTATATGTCAAATTGAAATGAAAAG-A-A
1 TTTGACCAGGGTGGTAACCATACGTCAAACAGAAA--AAAGGCAGA
* * *
485879 TTTGACCAGGGTGGTAACCATACGTCACACTA-AAATAA-GAAGA
1 TTTGACCAGGGTGGTAACCATACGTCAAAC-AGAAAAAAGGCAGA
* * * * **
485922 GTTTGGCCAGGGTGATAACCATACATCAAACAGGAAGGAGGCAGA
1 -TTTGACCAGGGTGGTAACCATACGTCAAACAGAAAAAAGGCAGA
* * * **
485967 TTTGACCAGGTTGGTAACTATACATCAAATCCAAGTGAAAA-G-A-A
1 TTTGACCAGGGTGGTAACCATACGTCAAA--C-AGAAAAAAGGCAGA
* *
486011 TCTGATCAGGGTGGTAACCATACGTCAAAC-GAAAA
1 TTTGACCAGGGTGGTAACCATACGTCAAACAGAAAA
486046 TGAGAAGAGT
Statistics
Matches: 161, Mismatches: 39, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
40 3 0.02
41 1 0.01
42 4 0.02
43 2 0.01
44 135 0.84
45 6 0.04
46 6 0.04
47 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (44 bp):
TTTGACCAGGGTGGTAACCATACGTCAAACAGAAAAAAGGCAGA
Found at i:485893 original size:132 final size:132
Alignment explanation
Indices: 485786--486064 Score: 369
Period size: 132 Copynumber: 2.1 Consensus size: 132
485776 CCGACTTGAA
* * * *
485786 AAGAGTTTGACTAGGTTGATAACCATACGTCAAACAGAAAAAAGGCAGATTTGACTAGGGTGGTA
1 AAGAGTTTGACCAGGGTGATAACCATACATCAAACAGAAAAAAGGCAGATTTGACCAGGGTGGTA
* ** ** * *
485851 AGTATATGTCAAATTGAAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCACACTAAAATA
66 ACTATACATCAAATCCAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCACACCAAAATA
485916 AG
131 AG
* * ** *
485918 AAGAGTTTGGCCAGGGTGATAACCATACATCAAACAGGAAGGAGGCAGATTTGACCAGGTTGGTA
1 AAGAGTTTGACCAGGGTGATAACCATACATCAAACAGAAAAAAGGCAGATTTGACCAGGGTGGTA
* * * * *
485983 ACTATACATCAAATCCAAGTGAAAAGAATCTGATCAGGGTGGTAACCATACGTCAAACGAAAATG
66 ACTATACATCAAATCCAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCACACCAAAATA
486048 AG
131 AG
486050 AAGAGTTTGACCAGG
1 AAGAGTTTGACCAGG
486065 ACCTAACACC
Statistics
Matches: 126, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
132 126 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (132 bp):
AAGAGTTTGACCAGGGTGATAACCATACATCAAACAGAAAAAAGGCAGATTTGACCAGGGTGGTA
ACTATACATCAAATCCAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCACACCAAAATA
AG
Found at i:486108 original size:48 final size:48
Alignment explanation
Indices: 486053--486166 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
486043 AAATGAGAAG
*
486053 AGTTTGACCAGGACCTAACACCAATACAATCAAAC-AAGGGATAAAAAA
1 AGTTTGACCAGGTCCTAACACCAATACAATCAAACGAA-GGATAAAAAA
* * *
486101 AGTTTGACCAGGTCGTAACACCAATACAATCAAACGAAGGATGAAAAG
1 AGTTTGACCAGGTCCTAACACCAATACAATCAAACGAAGGATAAAAAA
*
486149 AGTTTGACTAGGTCCTAA
1 AGTTTGACCAGGTCCTAA
486167 TGTCAATGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 57 0.97
49 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.18
Consensus pattern (48 bp):
AGTTTGACCAGGTCCTAACACCAATACAATCAAACGAAGGATAAAAAA
Found at i:486412 original size:14 final size:14
Alignment explanation
Indices: 486188--486406 Score: 212
Period size: 14 Copynumber: 15.7 Consensus size: 14
486178 TTGAATGATG
486188 GATGAAAAG-GTTT
1 GATGAAAAGAGTTT
* *
486201 GAAGGAAAGAGTTT
1 GATGAAAAGAGTTT
*
486215 AATGAAAAGAGTTT
1 GATGAAAAGAGTTT
* *
486229 AATGAAAAGAATTT
1 GATGAAAAGAGTTT
*
486243 GGTGAAAAGAGTTT
1 GATGAAAAGAGTTT
*
486257 GATG-AAGGAAGTTT
1 GATGAAAAG-AGTTT
* *
486271 GACGAAAATAGTTT
1 GATGAAAAGAGTTT
*
486285 AATGAAAAGAGTTT
1 GATGAAAAGAGTTT
* * *
486299 GGTGAAAAAAGATT
1 GATGAAAAGAGTTT
* *
486313 GGTGAAAAAAGTTT
1 GATGAAAAGAGTTT
486327 GATGAAAAGAGTTT
1 GATGAAAAGAGTTT
* *
486341 GGTGAAAAGAGATT
1 GATGAAAAGAGTTT
486355 -AGTGAAAAGAGTTT
1 GA-TGAAAAGAGTTT
* *
486369 GGTGAAAAGAGATT
1 GATGAAAAGAGTTT
486383 -AGTGAAAAGAGTTT
1 GA-TGAAAAGAGTTT
486397 GATGAAAAGA
1 GATGAAAAGA
486407 AGTTGACGAG
Statistics
Matches: 167, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.06
14 154 0.92
15 3 0.02
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
GATGAAAAGAGTTT
Found at i:486498 original size:48 final size:49
Alignment explanation
Indices: 486419--486513 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 49
486409 TTGACGAGGG
* *
486419 TAAAAACAGTTTGACCAGGCCCTAACCCCAATATAGTCAAAC-AAGAGA
1 TAAAAACAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAAGAGA
* * *
486467 TAAAAAGAGTTTGACCAGGTCTTAACACCAATACAGTCAAACGAAGA
1 TAAAAACAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAAGA
486514 AGATTTGACT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 37 0.90
49 4 0.10
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (49 bp):
TAAAAACAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAAGAGA
Found at i:487791 original size:12 final size:12
Alignment explanation
Indices: 487774--487799 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
487764 CTTAAATAGG
487774 AATTTTTGGATT
1 AATTTTTGGATT
487786 AATTTTTGGATT
1 AATTTTTGGATT
487798 AA
1 AA
487800 ATAGAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
AATTTTTGGATT
Found at i:494505 original size:23 final size:23
Alignment explanation
Indices: 494479--494522 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
494469 TAGAAACGAC
494479 AAATTTATTTGATGAAATAAGGT
1 AAATTTATTTGATGAAATAAGGT
494502 AAATTTATTTGATGAAATAAG
1 AAATTTATTTGATGAAATAAG
494523 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (23 bp):
AAATTTATTTGATGAAATAAGGT
Found at i:494530 original size:23 final size:23
Alignment explanation
Indices: 494479--494533 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
494469 TAGAAACGAC
*
494479 AAATTTATTTGATGAAATAAGGT
1 AAATTTATTTGATGAAATAAGAT
494502 AAATTTATTTGATGAAATAAGAT
1 AAATTTATTTGATGAAATAAGAT
**
494525 TTATTTATT
1 AAATTTATT
494534 GTTACGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (23 bp):
AAATTTATTTGATGAAATAAGAT
Found at i:495454 original size:22 final size:23
Alignment explanation
Indices: 495408--495454 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
495398 TAGTTTTCTA
495408 TTTCCTTCTTTATTTTTCCTCTT
1 TTTCCTTCTTTATTTTTCCTCTT
*
495431 TTTCTTTCTTT-TTTCTT-CTCTT
1 TTTCCTTCTTTATTT-TTCCTCTT
495453 TT
1 TT
495455 CTCTCTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTCCTTCTTTATTTTTCCTCTT
Found at i:497383 original size:20 final size:20
Alignment explanation
Indices: 497358--497424 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
497348 GTAATATACC
497358 GATACATTTTTCATTGTATT
1 GATACATTTTTCATTGTATT
*
497378 GATACATTCTT-AGTT-T-TT
1 GATACATTTTTCA-TTGTATT
** *
497396 GACCCAAATTTTCATTGTATT
1 GATAC-ATTTTTCATTGTATT
497417 GATACATT
1 GATACATT
497425 CTTGGTTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 16 0.47
21 5 0.15
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
GATACATTTTTCATTGTATT
Found at i:497413 original size:39 final size:39
Alignment explanation
Indices: 497365--497443 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
497355 ACCGATACAT
497365 TTTTCATTGTATTGATACATTCTTAGTTTTTGACCCAAA
1 TTTTCATTGTATTGATACATTCTTAGTTTTTGACCCAAA
*
497404 TTTTCATTGTATTGATACATTCTTGGTTTTTGACCCAAA
1 TTTTCATTGTATTGATACATTCTTAGTTTTTGACCCAAA
497443 T
1 T
497444 GTATCAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (39 bp):
TTTTCATTGTATTGATACATTCTTAGTTTTTGACCCAAA
Found at i:498578 original size:115 final size:115
Alignment explanation
Indices: 498373--498720 Score: 570
Period size: 115 Copynumber: 3.0 Consensus size: 115
498363 AATTACCTTA
* * *
498373 ACAGCCCTTGATCATGCATTTCGTACCATGTTCCATGCATTTTAACATGTCCAGCATCTCCAAGA
1 ACAGCCCTTGATCATGCATTTCGTACCATGTTCCATGCATTTTTACAAGTCCAACATCTCCAAGA
*
498438 ATGTCACTCATTATTTTCTTACATGTTCATCATGTTTTCCTTGTCAAAAT
66 ATGTCACTCATTATTTTCTTGCATGTTCATCATGTTTTCCTTGTCAAAAT
** * *
498488 ATTGCCCTTGATCATGCCTTTCGTACCATGTTCCATGTATTTTTACAAGTCCAACATCTCCAAGA
1 ACAGCCCTTGATCATGCATTTCGTACCATGTTCCATGCATTTTTACAAGTCCAACATCTCCAAGA
* * *
498553 ATGTCACTCATTATTTTCTTGCATGTTCATCATATTTTCTTTATCAAAAT
66 ATGTCACTCATTATTTTCTTGCATGTTCATCATGTTTTCCTTGTCAAAAT
* * *
498603 ACAACCCTCGATCATGCATTTCGTACCATGTTCCATGCATTTTTACAAGTCCAATATCTCCAAGA
1 ACAGCCCTTGATCATGCATTTCGTACCATGTTCCATGCATTTTTACAAGTCCAACATCTCCAAGA
498668 ATGTCACTCATTATTTTCTTGCATGTTCATCATGTTTTCCTTGTCAAAAT
66 ATGTCACTCATTATTTTCTTGCATGTTCATCATGTTTTCCTTGTCAAAAT
498718 ACA
1 ACA
498721 TGCTAGTTTG
Statistics
Matches: 212, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 212 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (115 bp):
ACAGCCCTTGATCATGCATTTCGTACCATGTTCCATGCATTTTTACAAGTCCAACATCTCCAAGA
ATGTCACTCATTATTTTCTTGCATGTTCATCATGTTTTCCTTGTCAAAAT
Found at i:501953 original size:51 final size:51
Alignment explanation
Indices: 501884--501998 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
501874 GAAAATAACG
* * * ***
501884 GGGTTAGAGAATCCTCGATGGTGAAAAATTGGTATTTT-GAAAATAAAACCA
1 GGGTTGGAGTATCATCGATGGTGAAAAATCAATATTTTAG-AAATAAAACCA
***
501935 GGGTTGGAGTATCATCGATGGTGAAAAATCAATATTTTAGAAATAAAATTG
1 GGGTTGGAGTATCATCGATGGTGAAAAATCAATATTTTAGAAATAAAACCA
501986 GGGTTGGAGTATC
1 GGGTTGGAGTATC
501999 CCTTCGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 53 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCATCGATGGTGAAAAATCAATATTTTAGAAATAAAACCA
Found at i:502018 original size:79 final size:78
Alignment explanation
Indices: 501935--502328 Score: 350
Period size: 79 Copynumber: 5.0 Consensus size: 78
501925 AATAAAACCA
* * *
501935 GGGTTGGAGTATCATCGATGGTGAAAAATCAATATTTTAGAAATAAAATTGGGGTTGGAGTATCC
1 GGGTTAGAGTATC-TCGATGGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCC
502000 CTTCGAAAATAATG
65 CTTCGAAAATAATG
** * * * *
502014 GGGTTATTGTATCCCCGATGGTGAAAAATTGATATTTT-GAAAATAAAAATGAGGATGGAGTATC
1 GGGTTAGAGTAT-CTCGATGGTGAAAAATCGATATTTTAG-AAATAAAAATGGGGTTGGAGTATC
* *
502078 CCCTCTG-AAATAACG
64 CCTTC-GAAAATAATG
* * ** * * *
502093 GGATTAGAGTATCTCCGATAGTGAAATTTTGATATTTTAGAAATAAAAACGGGGTTGGAATATCC
1 GGGTTAGAGTATCT-CGATGGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCC
**
502158 C--CGATGGTGATAAT-
65 CTTCGA---AAATAATG
* * *
502172 GGGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTTA-AAATAAAACTGGGGTTGGAGTATC
1 GGGTTAGAGTATCTC-GATGGTGAAAAATCGATA-TTTTAGAAATAAAAATGGGGTTGGAGTATC
* *
502236 TCATCAGAAAATAATG
64 CCTTC-GAAAATAATG
** * * *
502252 GTATTGGAGTATCCTCGATGGTGAAAAATCGATATTTTGGAAATAAAAATGGGGTTGAAGTATCC
1 GGGTTAGAGTAT-CTCGATGGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCC
* *
502317 TTTCGCAAATAA
65 CTTCGAAAATAA
502329 CAGGATTGAA
Statistics
Matches: 248, Mismatches: 50, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
78 3 0.01
79 176 0.71
80 62 0.25
81 3 0.01
82 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (78 bp):
GGGTTAGAGTATCTCGATGGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCCC
TTCGAAAATAATG
Found at i:502073 original size:130 final size:130
Alignment explanation
Indices: 501826--502077 Score: 355
Period size: 130 Copynumber: 1.9 Consensus size: 130
501816 TTTCTCGATG
* **
501826 GAAAAATTTAATATTTTAGGGATAAAAATAGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAG
1 GAAAAATTCAATATTTTAGAAATAAAAATAGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAG
* * *
501891 AGAATCCTCGATGGTGAAAAATTGGTATTTTGAAAATAAAACCAGGGTTGGAGTATCATCGATGG
66 AGAATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAA-CAGGGATGGAGTATCATCGATGG
501956 T
130 T
* * * *
501957 GAAAAA-TCAATATTTTAGAAATAAAATTGGGGTTGGAGTATCCCTTCGAAAATAATGGGGTTAT
1 GAAAAATTCAATATTTTAGAAATAAAAATAGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAG
* *
502021 TGTATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAA-ATGAGGATGGAGTATC
66 AGAATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAACA-G-GGATGGAGTATC
502078 CCCTCTGAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
128 1 0.01
129 1 0.01
130 99 0.93
131 6 0.06
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.30
Consensus pattern (130 bp):
GAAAAATTCAATATTTTAGAAATAAAAATAGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAG
AGAATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAACAGGGATGGAGTATCATCGATGGT
Found at i:502151 original size:158 final size:158
Alignment explanation
Indices: 501941--502328 Score: 433
Period size: 158 Copynumber: 2.4 Consensus size: 158
501931 ACCAGGGTTG
* * * *
501941 GAGTATCATCGATGGTGAAAAATCAATATTTTAGAAATAAAATTGGGGTTGGAGTATCCCTTCGA
1 GAGTATCCTCGATAGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCTTCGA
** *
502006 AAATAATGGGGTTATTGTATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAAATGAGGATG
66 AAATAAT-GGGTTAAAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAATGAGGATG
* *
502071 GAGTATCCCCTCTG-AAATAACGGGATTA
130 GAGTATCCCATCAGAAAATAACGGGATTA
** * * *
502099 GAGTAT-CTCCGATAGTGAAATTTTGATATTTTAGAAATAAAAACGGGGTTGGAATATCCC--CG
1 GAGTATCCT-CGATAGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCTTCG
** * * * *
502161 ATGGTGATAATGGGTTAAAGTATCCCTGATGGTGAAAAATCGATATTTTTAAAATAAAACTGGGG
65 A---AAATAATGGGTTAAAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAATGAGG
* * * * *
502226 TTGGAGTATCTCATCAGAAAATAATGGTATTG
127 ATGGAGTATCCCATCAGAAAATAACGGGATTA
* * * * *
502258 GAGTATCCTCGATGGTGAAAAATCGATATTTTGGAAATAAAAATGGGGTTGAAGTATCCTTTCGC
1 GAGTATCCTCGATAGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCTTCGA
502323 AAATAA
66 AAATAA
502329 CAGGATTGAA
Statistics
Matches: 185, Mismatches: 37, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
156 3 0.02
157 1 0.01
158 113 0.61
159 64 0.35
160 2 0.01
161 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (158 bp):
GAGTATCCTCGATAGTGAAAAATCGATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCTTCGA
AAATAATGGGTTAAAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAATGAGGATGG
AGTATCCCATCAGAAAATAACGGGATTA
Found at i:503111 original size:22 final size:21
Alignment explanation
Indices: 503086--503129 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
503076 ATTTTTAGGG
503086 AAAAATATTAAAAATTTTGAAA
1 AAAAATATTAAAAATTTT-AAA
* * *
503108 AAAATTATTTAATATTTTAAA
1 AAAAATATTAAAAATTTTAAA
503129 A
1 A
503130 TAATATTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATATTAAAAATTTTAAA
Found at i:503112 original size:21 final size:20
Alignment explanation
Indices: 503086--503136 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
503076 ATTTTTAGGG
503086 AAAAATATTAAAAATTTTGAA
1 AAAAATATTAAAAATTTT-AA
* *
503107 AAAAATTATTTAATATTTTAA
1 AAAAA-TATTAAAAATTTTAA
*
503128 AATAATATT
1 AAAAATATT
503137 CAAGCTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATATTAAAAATTTTAA
Done.