Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 3 of 770
Found at i:644621 original size:27 final size:26
Alignment explanation
Indices: 644544--644631 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
644534 TGGAGGAAGC
* * *
644544 GTTCTGGTGGCTATACCACATATATCT
1 GTTCTGGTGACTCTGCCACAT-TATCT
* *
644571 GTTCTGGTGGCTTTGCCACGATTATCT
1 GTTCTGGTGACTCTGCCAC-ATTATCT
*
644598 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGACTCTGCCACATTATCT
*
644625 ATTCTGG
1 GTTCTGG
644632 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 5 0.09
27 32 0.60
28 16 0.30
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (26 bp):
GTTCTGGTGACTCTGCCACATTATCT
Found at i:646850 original size:18 final size:18
Alignment explanation
Indices: 646827--646882 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
646817 GGTTGAATCA
*
646827 TTTTAATATATTTTTTAT
1 TTTTAATATATTTTTTAG
646845 TTTTAA-A-ATTTTTATGAG
1 TTTTAATATATTTTT-T-AG
646863 TTTTAAT-TATTTATTTAG
1 TTTTAATATATTT-TTTAG
646881 TT
1 TT
646883 ATTGTTGGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 17 0.53
19 5 0.16
20 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAATATATTTTTTAG
Found at i:647574 original size:29 final size:30
Alignment explanation
Indices: 647504--647575 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
647494 AGTATAAGAA
647504 TAGTCACTCAACTATTTAATTTATTCTATT
1 TAGTCACTCAACTATTTAATTTATTCTATT
* * * *
647534 TGGTCATTCAACTA-TTATTTTTTTC-ATTT
1 TAGTCACTCAACTATTTAATTTATTCTA-TT
647563 TAGTCACTCAACT
1 TAGTCACTCAACT
647576 TTTCAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 22 0.63
30 12 0.34
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (30 bp):
TAGTCACTCAACTATTTAATTTATTCTATT
Found at i:647809 original size:7 final size:7
Alignment explanation
Indices: 647794--647842 Score: 80
Period size: 7 Copynumber: 6.9 Consensus size: 7
647784 TTTAAAAAGT
647794 AATTATTA
1 AATT-TTA
*
647802 ATTTTTA
1 AATTTTA
647809 AATTTTA
1 AATTTTA
647816 AATTTTA
1 AATTTTA
647823 AATTTTA
1 AATTTTA
647830 AATTTTA
1 AATTTTA
647837 AATTTT
1 AATTTT
647843 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
7 36 0.92
8 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:649190 original size:25 final size:26
Alignment explanation
Indices: 649129--649190 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
649119 AAAAAGGTTG
* * *
649129 TTTTTGGATTCTATGCTCTTTTCTTT
1 TTTTTGGTTTCGATGCTCTTTTCTTA
** *
649155 TTTTTTCTTTCGAT-CTTTTTTCTTA
1 TTTTTGGTTTCGATGCTCTTTTCTTA
649180 TTTTTGGTTTC
1 TTTTTGGTTTC
649191 AAATCTATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.06, C:0.15, G:0.10, T:0.69
Consensus pattern (26 bp):
TTTTTGGTTTCGATGCTCTTTTCTTA
Found at i:650505 original size:2 final size:2
Alignment explanation
Indices: 650493--650526 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
650483 GTACATACTT
650493 TA TA T- TA TA 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 TA TA TA TA TA T
650527 TAAATCTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:652271 original size:2 final size:2
Alignment explanation
Indices: 652264--652291 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
652254 TTTAAAACTC
652264 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
652292 TCATATACTA
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:655694 original size:2 final size:2
Alignment explanation
Indices: 655689--655722 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
655679 AATACCCATA
655689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
655723 CACTTCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668313 original size:25 final size:25
Alignment explanation
Indices: 668283--668336 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
668273 ATCTTCTTTG
668283 TTATCCTAGGTATTCATTGGAGAGA
1 TTATCCTAGGTATTCATTGGAGAGA
668308 TTATCCTAGGTATTCATTGGAGAGA
1 TTATCCTAGGTATTCATTGGAGAGA
668333 TTAT
1 TTAT
668337 TCACTTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (25 bp):
TTATCCTAGGTATTCATTGGAGAGA
Found at i:673742 original size:12 final size:12
Alignment explanation
Indices: 673725--673755 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
673715 GTCATAAATA
673725 AATGATAAATTG
1 AATGATAAATTG
673737 AATGATAAATTG
1 AATGATAAATTG
673749 AAT-ATAA
1 AATGATAA
673756 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (12 bp):
AATGATAAATTG
Found at i:681024 original size:17 final size:17
Alignment explanation
Indices: 681002--681034 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
680992 GATATGATAC
681002 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
681019 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
681035 AATCAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:681035 original size:18 final size:17
Alignment explanation
Indices: 681002--681035 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
680992 GATATGATAC
*
681002 TAAAATTATTAAAAAAT
1 TAAAATTATAAAAAAAT
681019 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
681036 ATCAGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:681326 original size:22 final size:21
Alignment explanation
Indices: 681291--681366 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
681281 AAAAGGTATC
* *
681291 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
681312 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
681335 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
681354 TGC-AATCATATCT
1 TACAAATCATATCT
681367 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:681383 original size:35 final size:37
Alignment explanation
Indices: 681320--681417 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
681310 ATTACAAAAT
681320 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
681356 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
681391 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
681418 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:681425 original size:17 final size:19
Alignment explanation
Indices: 681327--681417 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
681317 AATCATATCT
681327 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
681346 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
681364 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
681381 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
681400 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
681418 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:681574 original size:21 final size:20
Alignment explanation
Indices: 681536--681575 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
681526 TTGGACTTCG
**
681536 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
681556 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
681576 TCTGGGCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:682620 original size:23 final size:23
Alignment explanation
Indices: 682590--682640 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
682580 AATTGTAAAG
*
682590 TATTTAAACTATAGGTCTAATTT
1 TATTTAAACTATAGGTCCAATTT
682613 TATTTAAACTATAGGTCCAATTT
1 TATTTAAACTATAGGTCCAATTT
682636 TATTT
1 TATTT
682641 TAATAGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (23 bp):
TATTTAAACTATAGGTCCAATTT
Found at i:684118 original size:33 final size:33
Alignment explanation
Indices: 684076--684138 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
684066 GCTCATCTAG
684076 TAGTTTTTAAAACTAAGTTTGGCCTTTTGTCTT
1 TAGTTTTTAAAACTAAGTTTGGCCTTTTGTCTT
684109 TAGTTTTTAAAACTAAGTTTGGCCTTTTGT
1 TAGTTTTTAAAACTAAGTTTGGCCTTTTGT
684139 GTTTTGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (33 bp):
TAGTTTTTAAAACTAAGTTTGGCCTTTTGTCTT
Found at i:687032 original size:19 final size:19
Alignment explanation
Indices: 687008--687045 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
686998 AAAAGAGCCC
687008 ACATTTTAGGAAAACATAT
1 ACATTTTAGGAAAACATAT
687027 ACATTTTAGGAAAACATAT
1 ACATTTTAGGAAAACATAT
687046 TATTATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
ACATTTTAGGAAAACATAT
Found at i:687260 original size:25 final size:24
Alignment explanation
Indices: 687215--687261 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
687205 TGTCGTAGGA
* *
687215 CAAAAATCAAAACACATCCAAACC
1 CAAAAATCAAAACAAAACCAAACC
687239 CAAAAATCAACAACAAAACCAAA
1 CAAAAATCAA-AACAAAACCAAA
687262 AGAAAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.64, C:0.30, G:0.00, T:0.06
Consensus pattern (24 bp):
CAAAAATCAAAACAAAACCAAACC
Found at i:691716 original size:21 final size:21
Alignment explanation
Indices: 691692--691741 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
691682 TTAAATTGAT
*
691692 GAATATTTACAACAATCTTAC
1 GAATATTCACAACAATCTTAC
691713 GAATATTCACAACAATCTTAC
1 GAATATTCACAACAATCTTAC
691734 GAATATTC
1 GAATATTC
691742 CATATTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (21 bp):
GAATATTCACAACAATCTTAC
Found at i:695439 original size:18 final size:19
Alignment explanation
Indices: 695401--695440 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
695391 GGCACAATAG
695401 CAACGGCGACACCACAAAAA
1 CAACGGCGACA-CACAAAAA
*
695421 CAACGGCGACA-ATAAAAA
1 CAACGGCGACACACAAAAA
695439 CA
1 CA
695441 CAGCAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.53, C:0.30, G:0.15, T:0.03
Consensus pattern (19 bp):
CAACGGCGACACACAAAAA
Found at i:695655 original size:11 final size:11
Alignment explanation
Indices: 695641--695666 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
695631 TATTTTGGGG
695641 ATATTTCCAAA
1 ATATTTCCAAA
695652 ATATTTCCAAA
1 ATATTTCCAAA
695663 ATAT
1 ATAT
695667 AATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATTTCCAAA
Found at i:706117 original size:2 final size:2
Alignment explanation
Indices: 706110--706135 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
706100 ACTTAGGCGC
706110 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
706136 GTTTCAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:710704 original size:19 final size:19
Alignment explanation
Indices: 710650--710696 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
710640 ATAGTGCATA
710650 CTGGTGCACAAAGTGCAAC
1 CTGGTGCACAAAGTGCAAC
*
710669 CTAGTGCACAAAGTGCAAC
1 CTGGTGCACAAAGTGCAAC
710688 CTGGTGCAC
1 CTGGTGCAC
710697 GAACTGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
CTGGTGCACAAAGTGCAAC
Found at i:712415 original size:46 final size:46
Alignment explanation
Indices: 712355--712582 Score: 318
Period size: 46 Copynumber: 5.0 Consensus size: 46
712345 TTTGACATGA
* * * * * *
712355 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *
712401 TGCCATGGTATCTTTCAACCATGGTCTGT--TCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCT-TACACATTTCATATCAGGT
712446 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
712492 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
712538 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTTATATCAGG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
712583 AGCACACTCC
Statistics
Matches: 169, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
44 5 0.03
45 36 0.21
46 127 0.75
47 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:712494 original size:91 final size:91
Alignment explanation
Indices: 712355--712582 Score: 316
Period size: 91 Copynumber: 2.5 Consensus size: 91
712345 TTTGACATGA
* * * * * *
712355 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
*
712419 CCATGGTCTGT-TCATTTCATATCACGT
65 CCATGGTCT-TAACATTTCATATCACGT
712446 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
* *
712511 CATGGTCTTACACATTTTATATCAGGT
66 CATGGTCTTA-ACATTTCATATCACGT
* *
712538 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTTATATCAGG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
712583 AGCACACTCC
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
90 5 0.04
91 62 0.50
92 56 0.46
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (91 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTAACATTTCATATCACGT
Found at i:714734 original size:11 final size:11
Alignment explanation
Indices: 714718--714769 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
714708 TATACTAAAT
714718 AAATAATAATA
1 AAATAATAATA
*
714729 AAATAAT-ATT
1 AAATAATAATA
* *
714739 AAATATCTCATA
1 AAATA-ATAATA
*
714751 AAATATTAATA
1 AAATAATAATA
714762 AAATAATA
1 AAATAATA
714770 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:716601 original size:31 final size:31
Alignment explanation
Indices: 716555--716629 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
716545 TTGCCCTTTT
* *
716555 AACTTGTCCAGAAGTACTTAGTTGGTACTTG
1 AACTTGTCCAAAAGTACTTAGTTGGTACATG
*
716586 AACTTATCCAAAAGTACTTAGTTGGTACATG
1 AACTTGTCCAAAAGTACTTAGTTGGTACATG
716617 AACTTGTCCAAAA
1 AACTTGTCCAAAA
716630 ATTTATACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
AACTTGTCCAAAAGTACTTAGTTGGTACATG
Found at i:716667 original size:19 final size:20
Alignment explanation
Indices: 716629--716667 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
716619 CTTGTCCAAA
*
716629 AATTTATACTTTTTTTAATT
1 AATTTATACTTTTTTAAATT
716649 AATTTATAC-TTTTTAAATT
1 AATTTATACTTTTTTAAATT
716668 TATGCCCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTATACTTTTTTAAATT
Found at i:718799 original size:51 final size:51
Alignment explanation
Indices: 718744--718844 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
718734 TGTTCTTTTA
* * *
718744 TGTTATGTTGTAATT-TCTTTTACATATTTTGTAATTATATTAGGTTGAAAG
1 TGTTACGTTGTAATTAT-TTTTACATATTATATAATTATATTAGGTTGAAAG
* * *
718795 TGTTACGTTTTAATTATTTTTACATATTATATAATTGTATTATGTTGAAA
1 TGTTACGTTGTAATTATTTTTACATATTATATAATTATATTAGGTTGAAA
718845 TGAATGAGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (51 bp):
TGTTACGTTGTAATTATTTTTACATATTATATAATTATATTAGGTTGAAAG
Found at i:719788 original size:23 final size:23
Alignment explanation
Indices: 719762--719806 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
719752 AACTATTGTA
719762 TTATTCCATAT-AACCAAACAAAG
1 TTATTCCAT-TCAACCAAACAAAG
*
719785 TTATTCCATTCAATCAAACAAA
1 TTATTCCATTCAACCAAACAAA
719807 TATGATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (23 bp):
TTATTCCATTCAACCAAACAAAG
Found at i:728010 original size:13 final size:12
Alignment explanation
Indices: 727992--728056 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
727982 TAGATTTTCC
727992 TAAATATTATCA
1 TAAATATTATCA
*
728004 TTAAATAAT-TC-
1 -TAAATATTATCA
728015 TAAATATTATCA
1 TAAATATTATCA
*
728027 CTAAATAAT-TC-
1 -TAAATATTATCA
728038 TAAATATTATCA
1 TAAATATTATCA
728050 GTAAATA
1 -TAAATA
728057 ATTCAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
12 4 0.10
13 20 0.48
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (12 bp):
TAAATATTATCA
Found at i:728021 original size:23 final size:23
Alignment explanation
Indices: 727991--728065 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
727981 TTAGATTTTC
*
727991 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
728014 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
728037 CTAAATATTATCAGTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
728060 CAAAAT
1 CTAAAT
728066 TTAAAAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:728716 original size:12 final size:12
Alignment explanation
Indices: 728699--728731 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
728689 CAGCCCGTTC
728699 ATATTAATTTTT
1 ATATTAATTTTT
728711 ATATT-ATTTTT
1 ATATTAATTTTT
728722 ATA-TAATTTT
1 ATATTAATTTT
728732 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:728890 original size:30 final size:30
Alignment explanation
Indices: 728854--728916 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
728844 ACTTAACAAG
728854 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
728884 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
728914 CAA
1 CAA
728917 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:728966 original size:14 final size:14
Alignment explanation
Indices: 728947--728976 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
728937 ATCCAAACAA
728947 TAGCAACAAAATAG
1 TAGCAACAAAATAG
*
728961 TAGCAACATAATAG
1 TAGCAACAAAATAG
728975 TA
1 TA
728977 AAATGGTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
TAGCAACAAAATAG
Found at i:734995 original size:18 final size:20
Alignment explanation
Indices: 734957--734996 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
734947 TGAATGTAAC
*
734957 AAAATACGCAATAGTAAATA
1 AAAATACGCAATAGCAAATA
734977 AAAATACGC-A-AGCAAATA
1 AAAATACGCAATAGCAAATA
734995 AA
1 AA
734997 TTGATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAATACGCAATAGCAAATA
Found at i:735716 original size:2 final size:2
Alignment explanation
Indices: 735705--735735 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
735695 AATAATACTT
735705 TA TA -A 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
735736 ATAAAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:736905 original size:38 final size:39
Alignment explanation
Indices: 736853--736932 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
736843 GTTTTGGGTC
736853 TTTAGTGGGCTTTGGGTCTGTTGGGTTTATGGGTAGTTA
1 TTTAGTGGGCTTTGGGTCTGTTGGGTTTATGGGTAGTTA
*
736892 TTTAG-GGGTTTTGGGTCTGTTGGGTTTATGGGTAGTTA
1 TTTAGTGGGCTTTGGGTCTGTTGGGTTTATGGGTAGTTA
736930 TTT
1 TTT
736933 GTTTAGTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 35 0.88
39 5 0.12
ACGTcount: A:0.10, C:0.04, G:0.38, T:0.49
Consensus pattern (39 bp):
TTTAGTGGGCTTTGGGTCTGTTGGGTTTATGGGTAGTTA
Found at i:739944 original size:31 final size:31
Alignment explanation
Indices: 739909--739968 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
739899 GAAAACACTT
*
739909 AACAG-CTAAGTGATTTAAATAAAAACTTTTG
1 AACAGTCTAA-TGACTTAAATAAAAACTTTTG
* *
739940 AACAGTTTAATGACTTAAATGAAAACTTT
1 AACAGTCTAATGACTTAAATAAAAACTTT
739969 CAAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (31 bp):
AACAGTCTAATGACTTAAATAAAAACTTTTG
Found at i:741909 original size:13 final size:14
Alignment explanation
Indices: 741893--741934 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
741883 TTTTAATTTT
741893 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
741906 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
741921 ATTTTAAATAATAT
1 ATTTT-AATAATAT
741935 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:741919 original size:16 final size:16
Alignment explanation
Indices: 741897--741933 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
741887 AATTTTATTT
741897 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
741914 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
741929 TAATA
1 TAATA
741934 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:741983 original size:15 final size:15
Alignment explanation
Indices: 741965--742021 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
741955 TTTCAATATT
741965 AATATTTTAATAATA
1 AATATTTTAATAATA
*
741980 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
741999 AATATATTAATAATA
1 AATATTTTAATAATA
*
742014 AATGTTTT
1 AATATTTT
742022 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:746274 original size:18 final size:19
Alignment explanation
Indices: 746253--746290 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
746243 TATAAGTATT
746253 TCAAATATAAAAT-ATTTA
1 TCAAATATAAAATAATTTA
* *
746271 TCAACTATGAAATAATTTA
1 TCAAATATAAAATAATTTA
746290 T
1 T
746291 TCTTTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
TCAAATATAAAATAATTTA
Found at i:746322 original size:22 final size:22
Alignment explanation
Indices: 746290--746339 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
746280 AAATAATTTA
* *
746290 TTCTTTACTTTGTAGCATGCTT
1 TTCTTTACTTTATAGCACGCTT
* *
746312 TTCTTTGCTTTATAGCACGTTT
1 TTCTTTACTTTATAGCACGCTT
746334 TTCTTT
1 TTCTTT
746340 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (22 bp):
TTCTTTACTTTATAGCACGCTT
Found at i:747030 original size:119 final size:120
Alignment explanation
Indices: 746813--747038 Score: 409
Period size: 119 Copynumber: 1.9 Consensus size: 120
746803 ATGGTGGCAA
*
746813 AGCAGCTAGGTAATTTTATTGGGGTGTTCCTTGAGTATGATGTGAAAGTTGTTTCATTGGGGTAT
1 AGCAGCTAGGTAATTTTATTGGGGTGTTCCTTAAGTATGATGTGAAAGTTGTTTCATTGGGGTAT
* *
746878 AAAGGAATAATGCGAGTTAGAGTTCGACTTGATATTCGAAAATTGCTAAAGTGTG
66 AAAGGAATAACGCGAGTTAGAGTTCGACTTGATATTAGAAAATTGCTAAAGTGTG
746933 AGCAG-TAGGTAATTTTATTGGGGTGTTCCTTAAGTATGATGTGAAAGTTGTTTCATTGGGGTAT
1 AGCAGCTAGGTAATTTTATTGGGGTGTTCCTTAAGTATGATGTGAAAGTTGTTTCATTGGGGTAT
*
746997 AAAGGAATAACGCGAGTTAGAGTTTGACTTGATATTAGAAAA
66 AAAGGAATAACGCGAGTTAGAGTTCGACTTGATATTAGAAAA
747039 CCACTAAAGT
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 97 0.95
120 5 0.05
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.35
Consensus pattern (120 bp):
AGCAGCTAGGTAATTTTATTGGGGTGTTCCTTAAGTATGATGTGAAAGTTGTTTCATTGGGGTAT
AAAGGAATAACGCGAGTTAGAGTTCGACTTGATATTAGAAAATTGCTAAAGTGTG
Found at i:747334 original size:35 final size:35
Alignment explanation
Indices: 747295--747409 Score: 90
Period size: 35 Copynumber: 3.1 Consensus size: 35
747285 GACGGTAATA
*
747295 ATTTGAGCCTAGCTCTAGTTGGATAAACCAACAAT
1 ATTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
* ** ** *
747330 ATTTGCA-CCCAG-TGCTAGTTAGATTGACTGACGATTGT
1 ATTTG-AGCCCAGCT-CTAGTTGGATAAACCAAC-A--AT
747368 AATTTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
1 -A-TTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
747405 ATTTG
1 ATTTG
747410 CACCCAGTGC
Statistics
Matches: 58, Mismatches: 13, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
34 1 0.02
35 26 0.45
36 3 0.05
37 1 0.02
38 1 0.02
39 3 0.05
40 22 0.38
41 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (35 bp):
ATTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
Found at i:747361 original size:74 final size:75
Alignment explanation
Indices: 747266--747424 Score: 250
Period size: 75 Copynumber: 2.1 Consensus size: 75
747256 AGTTGTGTCA
* *
747266 AGTGCTAGTCAGATTATCTGACGGTAATAA-TTTGAGCCTAGCTCTAGTTGGATAAACCAACAAT
1 AGTGCTAGTCAGATTATCTGACGATAATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
747330 ATTTGCACCC
66 ATTTGCACCC
* **
747340 AGTGCTAGTTAGATTGA-CTGACGATTGTAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACAA
1 AGTGCTAGTCAGATT-ATCTGACGATAATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACAA
747404 TATTTGCACCC
65 TATTTGCACCC
747415 AGTGCTAGTC
1 AGTGCTAGTC
747425 GAATTAACCG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
74 24 0.31
75 53 0.69
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (75 bp):
AGTGCTAGTCAGATTATCTGACGATAATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACAAT
ATTTGCACCC
Found at i:747423 original size:35 final size:35
Alignment explanation
Indices: 747309--747423 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 35
747299 GAGCCTAGCT
747309 CTAGTTGGATAAACCAACAATATTTGCACCCAGTG
1 CTAGTTGGATAAACCAACAATATTTGCACCCAGTG
* ** ** *
747344 CTAGTTAGATTGACTGACGATTGTAATTTTG-AGCCCAGCT-
1 CTAGTTGGATAAACCAAC-A--AT-A-TTTGCA-CCCAG-TG
747384 CTAGTTGGATAAACCAACAATATTTGCACCCAGTG
1 CTAGTTGGATAAACCAACAATATTTGCACCCAGTG
747419 CTAGT
1 CTAGT
747424 CGAATTAACC
Statistics
Matches: 59, Mismatches: 12, Indels: 18
0.66 0.13 0.20
Matches are distributed among these distances:
34 1 0.02
35 27 0.46
36 3 0.05
37 1 0.02
38 1 0.02
39 3 0.05
40 22 0.37
41 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (35 bp):
CTAGTTGGATAAACCAACAATATTTGCACCCAGTG
Found at i:747442 original size:75 final size:75
Alignment explanation
Indices: 747296--747442 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 75
747286 ACGGTAATAA
* * * *
747296 TTTGAGCCTAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTTAGATTGACTGA
1 TTTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTGAGATTAACCGA
*
747361 CGATTGTAAT
66 CAATTGTAAT
747371 TTTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTCGA-ATTAACCG
1 TTTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGT-GAGATTAACCG
747435 ACAATTGT
65 ACAATTGT
747443 GTGCCTAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 65 0.98
76 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (75 bp):
TTTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTGAGATTAACCGA
CAATTGTAAT
Found at i:748250 original size:21 final size:18
Alignment explanation
Indices: 748211--748252 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 18
748201 TAGCATTATA
748211 TCTTCAAAAACATAAATT
1 TCTTCAAAAACATAAATT
748229 TCTTGCAAAAATCATCAAATT
1 TCTT-CAAAAA-CAT-AAATT
748250 TCT
1 TCT
748253 GTAACATCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 3 0.14
21 8 0.38
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (18 bp):
TCTTCAAAAACATAAATT
Found at i:749196 original size:42 final size:42
Alignment explanation
Indices: 749136--749259 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
749126 CGTTTTCTCG
** * *
749136 ATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT-A
1 ATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-ATCA
* * *
749178 ATGCCATAGCCCAGCTATGGTCTTGCACATATTCATATATCG
1 ATGCCATAGCCCAGCTATGGTCTTACACATATTCACATATCA
749220 ATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATATC
1 ATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATATC
749260 TCACTGATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
41 10 0.14
42 60 0.85
43 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAGCTATGGTCTTACACATATTCACATATCA
Found at i:749325 original size:47 final size:46
Alignment explanation
Indices: 749218--749341 Score: 140
Period size: 47 Copynumber: 2.7 Consensus size: 46
749208 ATTCATATAT
* * * * *
749218 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * *
749264 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
* *
749311 CGATGCCACATCCCAAATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
749342 GAAATCACTT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 26 0.41
47 38 0.59
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:749394 original size:31 final size:31
Alignment explanation
Indices: 749359--749538 Score: 263
Period size: 31 Copynumber: 5.8 Consensus size: 31
749349 CTTGTCACTT
*
749359 GTAGCTGAAGCTACCACTATTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* * * *
749390 GTAGCCGGAGCTACCATTTTTCACTGATCGG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
*
749421 GTAGCTGGAGCTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
*
749452 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAG-CTGAAGCTACCACTTTTCACTGATCAG
* *
749483 TTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
749514 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCTGAAGCTACCACTTTTCACT
749539 TGTCATTTGT
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.03
31 126 0.95
32 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCTGAAGCTACCACTTTTCACTGATCAG
Found at i:749621 original size:50 final size:51
Alignment explanation
Indices: 749514--749642 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
749504 CACTGATCAG
* * *
749514 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
* *
749565 GGAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
749615 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
749643 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 44 0.63
51 26 0.37
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:751826 original size:33 final size:33
Alignment explanation
Indices: 751763--751826 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
751753 TACTATATCT
** **
751763 TTTATTTCTTCTTCTTCTTATTATTTTCTTAAC
1 TTTATTTCTTCTTCTAATTATTATAATCTTAAC
751796 TTTATTTCTT-TTCTAATATATTATAATCTTA
1 TTTATTTCTTCTTCTAAT-TATTATAATCTTA
751827 TAATACTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTATTTCTTCTTCTAATTATTATAATCTTAAC
Found at i:751867 original size:20 final size:20
Alignment explanation
Indices: 751842--751881 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
751832 CTAATAAAGG
751842 AGATTGAAACCATCCACTAT
1 AGATTGAAACCATCCACTAT
751862 AGATTGAAACCATCCACTAT
1 AGATTGAAACCATCCACTAT
751882 CTAATATATA
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:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (20 bp):
AGATTGAAACCATCCACTAT
Found at i:758308 original size:75 final size:75
Alignment explanation
Indices: 758135--758309 Score: 269
Period size: 75 Copynumber: 2.3 Consensus size: 75
758125 TGCGTTCAGC
* * **
758135 GCTAGTCGGATTAACTGATGGTAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATT
1 GCTAGTCGGATTAACCGATGATTGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATT
758200 TGCACCCAAT
66 TGCACCCAAT
* * *
758210 GCTAGTTGAATTAACCGATGATTGTAATTGTGAGCCTAGCTCTAGTTGGATAAACCAACAATATT
1 GCTAGTCGGATTAACCGATGATTGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATT
*
758275 TGCACCCAGT
66 TGCACCCAAT
*
758285 GCTAGTCGGATTAACCGACGATTGT
1 GCTAGTCGGATTAACCGATGATTGT
758310 GTGGCCAGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 89 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (75 bp):
GCTAGTCGGATTAACCGATGATTGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATT
TGCACCCAAT
Found at i:759046 original size:19 final size:19
Alignment explanation
Indices: 759022--759058 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
759012 TCCATGGAAA
759022 CTCTCAAAATTTCCATTCG
1 CTCTCAAAATTTCCATTCG
759041 CTCTCAAAATTTCCATTC
1 CTCTCAAAATTTCCATTC
759059 ATAGCATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.03, T:0.38
Consensus pattern (19 bp):
CTCTCAAAATTTCCATTCG
Found at i:762658 original size:126 final size:125
Alignment explanation
Indices: 762428--762735 Score: 350
Period size: 126 Copynumber: 2.5 Consensus size: 125
762418 AGCCAACGGT
* * * * * * *
762428 AAATCGAAACCCAGCACAATTGGGTACGATTTATTGAATTTCCAAATACGAAACATTGCTTCATT
1 AAATCGAAACCCAGCACGATTGGGTACGATCTCTCGAACTTCCAAATACGAAATATTGCCTCATT
** * ** * *
762493 TTAATTTAAGAAAACATGGGTGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGGA
66 TTAATTTAAGAAAACATGGACGAAAATTCAAAAGGATATTCCGTATTTTAGTCGAACGAA
* * *
762553 AAATCGAAACCTAGCACGACTGGGTACGATCTCTCAAACTTCCAAAATACGAAATATTGCCTCAT
1 AAATCGAAACCCAGCACGATTGGGTACGATCTCTCGAACTTCC-AAATACGAAATATTGCCTCAT
* * *
762618 TTTAATTTTAA-AAAGCATGGACGAAAATTCCAAAGGATATTCCGTATTTTAGTTGAACGAA
65 TTTAA-TTTAAGAAAACATGGACGAAAATTCAAAAGGATATTCCGTATTTTAGTCGAACGAA
* * * * *
762679 AAATTGAAACCCAGCACGATTGGGCACGACCCCTCGAAC-TCCTAAACACGAAATATT
1 AAATCGAAACCCAGCACGATTGGGTACGATCTCTCGAACTTCC-AAATACGAAATATT
762736 TCCTTATGTT
Statistics
Matches: 152, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
125 51 0.34
126 96 0.63
127 5 0.03
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (125 bp):
AAATCGAAACCCAGCACGATTGGGTACGATCTCTCGAACTTCCAAATACGAAATATTGCCTCATT
TTAATTTAAGAAAACATGGACGAAAATTCAAAAGGATATTCCGTATTTTAGTCGAACGAA
Found at i:765166 original size:44 final size:44
Alignment explanation
Indices: 765117--765214 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 44
765107 CTACCTCAGA
765117 GAGATAAGACT-G-ATGGCTTAAATCTGCTCCATAGCCGATACATG
1 GAGATAAGACTCGCAT--CTTAAATCTGCTCCATAGCCGATACATG
* * * *
765161 GAGATAAGACTCGCCATTTTCAATCTGTTCCATAGCCGATATATG
1 GAGATAAGACTCG-CATCTTAAATCTGCTCCATAGCCGATACATG
765206 GAGATAAGA
1 GAGATAAGA
765215 TCTGCAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 11 0.23
45 34 0.72
47 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
GAGATAAGACTCGCATCTTAAATCTGCTCCATAGCCGATACATG
Found at i:765193 original size:45 final size:45
Alignment explanation
Indices: 765137--765234 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
765127 TGATGGCTTA
* *
765137 AATCTGCTCCATAGCCGATACATGGAGATAAGA-CTCGCCATTTTC
1 AATCTGTTCCATAGCCGATACATGGAGATAAGATCT-GCAATTTTC
*
765182 AATCTGTTCCATAGCCGATATATGGAGATAAGATCTGCAATTTTC
1 AATCTGTTCCATAGCCGATACATGGAGATAAGATCTGCAATTTTC
*
765227 AGTCTGTT
1 AATCTGTT
765235 ACCCTACTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 46 0.96
46 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
AATCTGTTCCATAGCCGATACATGGAGATAAGATCTGCAATTTTC
Found at i:765226 original size:177 final size:177
Alignment explanation
Indices: 764920--765524 Score: 721
Period size: 177 Copynumber: 3.4 Consensus size: 177
764910 AACTTTAACT
* *
764920 TGCTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
1 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATAGCCGATACATGG
* * * * *
764985 AGATAAGACTCATCA-TATCTGATCTACTCCATAGTCTG-TACATGGAGATAATATCTGTAATTT
66 AGATAAGACTCACCATTTTC-GATCTGCTCCATAG-CCGATACATGGAGATAAGATCTGTAATTT
* ** *
765048 TCAGCCCATTACCCTACTGCTTAGGAGGTTAAGGCTTGTATCTTCAACC
129 TCAGTCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCGTATCTTCAACC
* *
765097 TGCTCTCTTGCTACCTCAGAGAGATAAGACTGATGGCTTAAATCTGCTCCATAGCCGATACATGG
1 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATAGCCGATACATGG
* * * * *
765162 AGATAAGACTCGCCATTTTCAATCTGTTCCATAGCCGATATATGGAGATAAGATCTGCAATTTTC
66 AGATAAGACTCACCATTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTC
* *
765227 AGTCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCATCTTCAACC
131 AGTCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCGTATCTTCAACC
* * * * * * * * * * *
765274 TGCTCTCTTGCTATCTTAGAGAGATAAGGCCGGTAGCTTAAATATGCTCTAGAGCTGATACATAG
1 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATAGCCGATACATGG
* * * *
765339 AGATAAGACTCACCATTTTCGATCAGCTCCATAGCCGATACATAGAGATAAGATCTATAATTTGC
66 AGATAAGACTCACCATTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTC
* * * * * * * * * *
765404 AATCTGTTTCCTTGCTACCTCAGGAAGATAAGACTCGTATCCTCAACC
131 AGTCTGTTACCCTACT-GCTTAGGAGGTTAAGGCTCGTATCTTCAACC
* * *
765452 TACTCTCTTGCTACCTCAAAGAGATAAGGCT-AGTGGCTAAAATCTGTTCCATAGCCGATACATG
1 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGA-TGGCTAAAATCTGCTCCATAGCCGATACATG
765516 GAGATAAGA
65 GAGATAAGA
765525 TCTATAATTT
Statistics
Matches: 358, Mismatches: 66, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
176 2 0.01
177 272 0.76
178 84 0.23
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (177 bp):
TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATAGCCGATACATGG
AGATAAGACTCACCATTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTC
AGTCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCGTATCTTCAACC
Found at i:765531 original size:133 final size:133
Alignment explanation
Indices: 765364--765657 Score: 446
Period size: 133 Copynumber: 2.2 Consensus size: 133
765354 TTTTCGATCA
765364 GCTCCATAGCCGATACATAGAGATAAGATCTATAATTTGCAATCTGT-TTCCTTGCTACCTCAGG
1 GCTCCATAGCCGATACATAGAGATAAGATCTATAATTTGCAATCT-TCTTCCTTGCTACCTCAGG
*
765428 AAGATAAGACTCGTATCCTCAACCTACTCTCTTGCTACCTCAAAGAGATAAGGCTAGTGGCTAAA
65 AAGATAAGACTCATATCCTCAACCTACTCTCTTGCTACCTCAAAGAGATAAGGCTAGTGGCTAAA
765493 ATCT
130 ATCT
* * * *
765497 GTTCCATAGCCGATACATGGAGATAAGATCTATAATTTGCAGTCTTCTTCCTTGTTACCTCAGGA
1 GCTCCATAGCCGATACATAGAGATAAGATCTATAATTTGCAATCTTCTTCCTTGCTACCTCAGGA
* * * * * *
765562 AGATAAGACTCATATCTTTAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTTGGTGGCTAAAA
66 AGATAAGACTCATATCCTCAACCTACTCTCTTGCTACCTCAAAGAGATAAGGCTAGTGGCTAAAA
*
765627 TTT
131 TCT
* *
765630 GCTCCATAGTCGATAGATAGAGATAAGA
1 GCTCCATAGCCGATACATAGAGATAAGA
765658 CTCGCCATTT
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 1 0.01
133 143 0.99
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (133 bp):
GCTCCATAGCCGATACATAGAGATAAGATCTATAATTTGCAATCTTCTTCCTTGCTACCTCAGGA
AGATAAGACTCATATCCTCAACCTACTCTCTTGCTACCTCAAAGAGATAAGGCTAGTGGCTAAAA
TCT
Found at i:765919 original size:64 final size:64
Alignment explanation
Indices: 765818--765945 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
765808 TCACGTATTT
*
765818 ATGCTTATGCCGAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAGGTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAGGTAGATGTG
* * *
765882 ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTTCTAGTTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAGGTAGATGTG
765946 CTGCAGAATG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAGGTAGATGTG
Found at i:765927 original size:32 final size:32
Alignment explanation
Indices: 765830--765928 Score: 80
Period size: 32 Copynumber: 3.1 Consensus size: 32
765820 GCTTATGCCG
765830 AATAATTAGGATGCTATGATCAAAATGAATCA
1 AATAATTAGGATGCTATGATCAAAATGAATCA
** * * **
765862 AATGCTCCTAGG-TAGATGTGATGC-TTATG--TCA
1 AATAAT--TAGGAT-GCTATGAT-CAAAATGAATCA
765894 AATAATTAGGATGCTATGATCAAAATGAATCA
1 AATAATTAGGATGCTATGATCAAAATGAATCA
765926 AAT
1 AAT
765929 GCTTCTAGTT
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
29 1 0.02
30 13 0.28
31 1 0.02
32 17 0.36
33 1 0.02
34 13 0.28
35 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (32 bp):
AATAATTAGGATGCTATGATCAAAATGAATCA
Found at i:774688 original size:16 final size:17
Alignment explanation
Indices: 774653--774688 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
774643 CCTAATTCTC
774653 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
774669 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
774684 CCTTC
1 CCTTC
774689 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:781018 original size:23 final size:21
Alignment explanation
Indices: 780980--781061 Score: 128
Period size: 21 Copynumber: 3.8 Consensus size: 21
780970 AACACATAAA
* *
780980 GTGCCTAAAACGACACACGAG
1 GTGCCTGATACGACACACGAG
781001 GTGCCTGATACGACACACGAG
1 GTGCCTGATACGACACACGAG
781022 GTGCCTGATACGACACACGAG
1 GTGCCTGATACGACACACGAG
781043 GTGCCTGAAATACGACACA
1 GTGCCTG--ATACGACACA
781062 TAAAGTGCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 47 0.82
23 10 0.18
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.13
Consensus pattern (21 bp):
GTGCCTGATACGACACACGAG
Found at i:785962 original size:125 final size:126
Alignment explanation
Indices: 785828--786104 Score: 306
Period size: 126 Copynumber: 2.2 Consensus size: 126
785818 CCCAAACAGT
* ** **
785828 AAATCGAAACCCAGCACGATTGGGCACGATTTATTGAA-TTTCCAAATACAAAACATTGCCTCAT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTATCAAACTCCCCAAATACAAAACATTGCCTCAT
** * * ** * *
785892 TTTAA-TTTAAGAAAACATGGGTGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGGA
66 TTTAATTTTAA-AAAACATGGACGAAAATTCAAAAGAATATTCCGTATTTTAGTCGAACGAA
* * * * * * * *
785953 AGATTGAAACCCAGCAAGATTAGACACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTATCAAACTCCCCAAATACAAAACATTGCCTCAT
** * *
786018 TTTAATTTTAAAAAGTATGGACGAAAATTCCAAAGAATATTCCGTATTTTAGTTGAACGAA
66 TTTAATTTTAAAAAACATGGACGAAAATTCAAAAGAATATTCCGTATTTTAGTCGAACGAA
786079 AAATCGAAACCCAGCACGATTGGGCA
1 AAATCGAAACCCAGCACGATTGGGCA
786105 TGACCCCTCG
Statistics
Matches: 120, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
125 29 0.24
126 86 0.72
127 5 0.04
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (126 bp):
AAATCGAAACCCAGCACGATTGGGCACGATCTATCAAACTCCCCAAATACAAAACATTGCCTCAT
TTTAATTTTAAAAAACATGGACGAAAATTCAAAAGAATATTCCGTATTTTAGTCGAACGAA
Found at i:786058 original size:126 final size:125
Alignment explanation
Indices: 785869--786135 Score: 293
Period size: 126 Copynumber: 2.1 Consensus size: 125
785859 TATTGAATTT
* * ** * * *
785869 CCAAATACAAAACATTGCCTCATTTTAATTTAAGAAAACATGGGTGAAATTTCAAAAGGATATTT
1 CCAAATACGAAATATTGCCTCATTTTAATTTAAGAAAACATGGACGAAAATTCAAAAGAATATTC
* * * * * * *
785934 TGTATTTTAGTCGAATGGAAGATTGAAACCCAGCAAGATTAGACACGATCTCTCAAACTCC
66 CGTATTTTAGTCGAACGAAAAATCGAAACCCAGCAAGATTAGACACGACCCCTCAAACT-C
** *
785995 CCAAATACGAAATATTGCCTCATTTTAATTTTAA-AAAGTATGGACGAAAATTCCAAAGAATATT
1 CCAAATACGAAATATTGCCTCATTTTAA-TTTAAGAAAACATGGACGAAAATTCAAAAGAATATT
* * * * * *
786059 CCGTATTTTAGTTGAACGAAAAATCGAAACCCAGCACGATTGGGCATGACCCCTCGAACTC
65 CCGTATTTTAGTCGAACGAAAAATCGAAACCCAGCAAGATTAGACACGACCCCTCAAACTC
*
786120 CCAAACACGAAATATT
1 CCAAATACGAAATATT
786136 TCCTTATGTT
Statistics
Matches: 116, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
125 16 0.14
126 95 0.82
127 5 0.04
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (125 bp):
CCAAATACGAAATATTGCCTCATTTTAATTTAAGAAAACATGGACGAAAATTCAAAAGAATATTC
CGTATTTTAGTCGAACGAAAAATCGAAACCCAGCAAGATTAGACACGACCCCTCAAACTC
Found at i:793545 original size:32 final size:32
Alignment explanation
Indices: 793504--793568 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
793494 CTTCAAAAGA
793504 AAAACATTTTTTCCGCTTAATTTTTCTCTGTC
1 AAAACATTTTTTCCGCTTAATTTTTCTCTGTC
793536 AAAACATTTTTTCCGCTTAATTTTTCTCTGTC
1 AAAACATTTTTTCCGCTTAATTTTTCTCTGTC
793568 A
1 A
793569 GTGAGAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49
Consensus pattern (32 bp):
AAAACATTTTTTCCGCTTAATTTTTCTCTGTC
Found at i:797257 original size:32 final size:32
Alignment explanation
Indices: 797196--797257 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
797186 TTTATTTTAT
* *
797196 ATAGCAAAAATAAAATATAAAGGCTAAAGTTA
1 ATAGCAAAAATAAAACATAAAGGCCAAAGTTA
* *
797228 ATAGCAAAAATAAAGCATATAGGCCAAAGT
1 ATAGCAAAAATAAAACATAAAGGCCAAAGT
797258 GCTAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (32 bp):
ATAGCAAAAATAAAACATAAAGGCCAAAGTTA
Found at i:809990 original size:46 final size:46
Alignment explanation
Indices: 809930--810240 Score: 415
Period size: 46 Copynumber: 6.9 Consensus size: 46
809920 TTTGACGTGA
* * * * * *
809930 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * **
809976 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACCT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
810022 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
810068 TGCCATGGTATCTTTCAACAATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
810114 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
810160 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
810198 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
810241 AAGAGCACAC
Statistics
Matches: 237, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
38 32 0.14
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.02
46 191 0.81
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:810209 original size:38 final size:38
Alignment explanation
Indices: 810158--810230 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
810148 TTCATATCAA
810158 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
810196 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
810231 TTTCATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:814823 original size:21 final size:19
Alignment explanation
Indices: 814799--814837 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
814789 TTTGAGTTAA
814799 AAGGAAGAAGATGAAAAAAAC
1 AAGGAAG-AGA-GAAAAAAAC
*
814820 AAGGGAGAGAGAAAAAAA
1 AAGGAAGAGAGAAAAAAA
814838 AAAGAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.28, T:0.03
Consensus pattern (19 bp):
AAGGAAGAGAGAAAAAAAC
Found at i:815171 original size:30 final size:29
Alignment explanation
Indices: 815109--815171 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
815099 AACTTGCAAA
*
815109 TAAATATTAATAACTTTATTTAAATATAAT
1 TAAATATTAATAAC-TTATTTAAATAAAAT
*
815139 TAAATATTAATTA-TTATTATAAATAAATAT
1 TAAATATTAATAACTTATT-TAAATAAA-AT
815169 TAA
1 TAA
815172 TAACTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 7 0.24
30 17 0.59
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAATATTAATAACTTATTTAAATAAAAT
Found at i:820219 original size:2 final size:2
Alignment explanation
Indices: 820212--820242 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
820202 GTCACATTTC
820212 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
820243 AATACACATG
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:820466 original size:2 final size:2
Alignment explanation
Indices: 820459--820489 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
820449 ATCTTTCAAA
820459 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
820490 ATCGAAGTAA
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:823340 original size:22 final size:22
Alignment explanation
Indices: 823315--823356 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
823305 TATCCAAACA
823315 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
823337 ATAATAGTAAAATGGTAGCA
1 ATAACAATAAAATAGTAGCA
823357 CACTAGGGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:825021 original size:2 final size:2
Alignment explanation
Indices: 825014--825038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
825004 ACACATTATC
825014 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
825039 CTTTATAATA
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:832236 original size:21 final size:21
Alignment explanation
Indices: 832210--832252 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
832200 TTGAAAACCC
832210 AGACACATGAAGCCTATTAGA
1 AGACACATGAAGCCTATTAGA
832231 AGACACATGAAGCCTATTAGA
1 AGACACATGAAGCCTATTAGA
832252 A
1 A
832253 TGCATCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
AGACACATGAAGCCTATTAGA
Found at i:832860 original size:12 final size:12
Alignment explanation
Indices: 832829--832862 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
832819 TATTTAATTA
832829 TTTATAATTTTT
1 TTTATAATTTTT
*
832841 TTGA-AATTTTT
1 TTTATAATTTTT
832852 TTTATAATTTT
1 TTTATAATTTT
832863 ATATATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTATAATTTTT
Found at i:838453 original size:17 final size:17
Alignment explanation
Indices: 838428--838468 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
838418 AGGCGCGACC
*
838428 TATTTTTTTAATAATAT
1 TATTTTTTAAATAATAT
*
838445 ATATTTTTTAAATATTAT
1 -TATTTTTTAAATAATAT
838463 TATTTT
1 TATTTT
838469 ATTATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTTAAATAATAT
Found at i:838722 original size:12 final size:12
Alignment explanation
Indices: 838691--838715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
838681 GCAAAGAGAG
838691 AAAAGAAGAAGA
1 AAAAGAAGAAGA
838703 AAAAGAAGAAGA
1 AAAAGAAGAAGA
838715 A
1 A
838716 GGAGAAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAGA
Found at i:839828 original size:11 final size:11
Alignment explanation
Indices: 839793--839820 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
839783 GAGAATAAGA
839793 AATTTTAATGT
1 AATTTTAATGT
839804 AATTTTAATGT
1 AATTTTAATGT
839815 AATTTT
1 AATTTT
839821 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:841034 original size:27 final size:27
Alignment explanation
Indices: 840996--841056 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
840986 TAAGGGAGTT
840996 ACGCCTCTGCAGCAGGAGCGACTGGTC
1 ACGCCTCTGCAGCAGGAGCGACTGGTC
*
841023 ACGCCTCTGCAGTAGGAGCGACTGGTC
1 ACGCCTCTGCAGCAGGAGCGACTGGTC
*
841050 GCGCCTC
1 ACGCCTC
841057 CGGGTCTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (27 bp):
ACGCCTCTGCAGCAGGAGCGACTGGTC
Found at i:842235 original size:9 final size:9
Alignment explanation
Indices: 842221--842280 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
842211 TGAGAAATAT
842221 ATTTTTAAA
1 ATTTTTAAA
*
842230 ATTTTTTATAT
1 A-TTTTTA-AA
842241 ATTTTT-AA
1 ATTTTTAAA
842249 A-TTTTAAA
1 ATTTTTAAA
*
842257 TTTTTTAAA
1 ATTTTTAAA
* *
842266 ATTTATATA
1 ATTTTTAAA
842275 ATTTTT
1 ATTTTT
842281 TAGAACTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
7 4 0.10
8 4 0.10
9 19 0.47
10 11 0.28
11 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:842277 original size:26 final size:28
Alignment explanation
Indices: 842217--842279 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
842207 TTATTGAGAA
* *
842217 ATATATTTTTAAAATTTTTTATATATTT
1 ATATAATTTTAAAATTTTTTATAAATTT
*
842245 TTA-AATTTT-AAATTTTTTA-AAATTT
1 ATATAATTTTAAAATTTTTTATAAATTT
842270 ATATAATTTT
1 ATATAATTTT
842280 TTAGAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 7 0.23
26 16 0.53
27 5 0.17
28 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATAATTTTAAAATTTTTTATAAATTT
Found at i:842298 original size:36 final size:35
Alignment explanation
Indices: 842218--842299 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
842208 TATTGAGAAA
*
842218 TATATTTTTAAAATTTTTTATATATTTTTAAATTT
1 TATATTTTTAAAATTTTATATATATTTTTAAATTT
*
842253 TAAATTTTTTAAAA-TTTATATA-ATTTTTTAGAACTTT
1 TATA-TTTTTAAAATTTTATATATA-TTTTTA-AA-TTT
842290 TATATTTTTA
1 TATATTTTTA
842300 GTTTTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
34 1 0.03
35 16 0.40
36 17 0.43
37 6 0.15
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (35 bp):
TATATTTTTAAAATTTTATATATATTTTTAAATTT
Found at i:842300 original size:17 final size:16
Alignment explanation
Indices: 842218--842298 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 16
842208 TATTGAGAAA
*
842218 TATATTTTTAAAATTTTT
1 TATATTTTTTAAA--TTT
842236 TATATATTTTTAAATTT
1 TATAT-TTTTTAAATTT
*
842253 TAAATTTTTTAAAATTT
1 TATATTTTTT-AAATTT
842270 ATATAATTTTTTAGAACTTT
1 -TAT-ATTTTTTA-AA-TTT
842290 TATATTTTT
1 TATATTTTT
842299 AGTTTTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 14 0.26
19 19 0.35
20 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
TATATTTTTTAAATTT
Found at i:842403 original size:22 final size:22
Alignment explanation
Indices: 842378--842427 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
842368 ATTTAAAAAA
842378 TATATA-TTTGTATTGTATTTTT
1 TATATACTTT-TATTGTATTTTT
* *
842400 TATATACTTTTTTTTTATTTTT
1 TATATACTTTTATTGTATTTTT
842422 TGATAT
1 T-ATAT
842428 TGTCTAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (22 bp):
TATATACTTTTATTGTATTTTT
Found at i:848138 original size:13 final size:13
Alignment explanation
Indices: 848120--848150 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
848110 CAACATCAAA
848120 CAAAACACAACAG
1 CAAAACACAACAG
848133 CAAAACACAACAG
1 CAAAACACAACAG
848146 CAAAA
1 CAAAA
848151 AAAGAAAAAG
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:0.65, C:0.29, G:0.06, T:0.00
Consensus pattern (13 bp):
CAAAACACAACAG
Found at i:853388 original size:25 final size:25
Alignment explanation
Indices: 853335--853422 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
853325 GATACACCAC
* **
853335 AGCTCGTATGAGCTTCCCGATTTGC
1 AGCTCGTATGAGCTTACCGATTTAT
*
853360 AGCTCGTATGAGCTTACCGATTCAT
1 AGCTCGTATGAGCTTACCGATTTAT
* *
853385 AGCTCGTGA-GAGCATACTGATTTAT
1 AGCTCGT-ATGAGCTTACCGATTTAT
* *
853410 AGCTTGCATGAGC
1 AGCTCGTATGAGC
853423 ATACATGTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTTAT
Found at i:853613 original size:30 final size:30
Alignment explanation
Indices: 853574--853635 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
853564 TACATGAAAT
853574 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
853605 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
853634 AC
1 AC
853636 TTGCTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:856496 original size:2 final size:2
Alignment explanation
Indices: 856484--856525 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
856474 AGGATGAAGT
*
856484 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
856525 T
1 T
856526 GTGTGCCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:857937 original size:2 final size:2
Alignment explanation
Indices: 857926--857964 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
857916 ATTTCCTAAC
857926 TA TA -A TA TA 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 TA TA
857965 CATTTGGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:862870 original size:16 final size:16
Alignment explanation
Indices: 862849--862885 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
862839 ATAGGGGTAT
862849 AGTAAAATATTAAAAA
1 AGTAAAATATTAAAAA
862865 AGT-AAATATTAAAAA
1 AGTAAAATATTAAAAA
862880 AG-AAAA
1 AGTAAAA
862886 GAAAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (16 bp):
AGTAAAATATTAAAAA
Found at i:867344 original size:26 final size:25
Alignment explanation
Indices: 867314--867362 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
867304 GATCATTTAG
*
867314 TTACATATCAGAGTCATACAGATGAA
1 TTACAGATCA-AGTCATACAGATGAA
* *
867340 TTACAGATCAAGTTATTCAGATG
1 TTACAGATCAAGTCATACAGATG
867363 CAGAACAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (25 bp):
TTACAGATCAAGTCATACAGATGAA
Found at i:873622 original size:142 final size:141
Alignment explanation
Indices: 873361--873645 Score: 464
Period size: 142 Copynumber: 2.0 Consensus size: 141
873351 GTACAAGTTC
873361 ATTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAAAAATCAATTTTGG
1 ATTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAAAAATCAATTTTGG
* * * * *
873426 GAGGCCAAGATCTCTGCCTGCATCTCTTCAGATTCGCCTCTGCAAGGTGGAAAGAAGTTGGCCAT
66 GAGGCCAAAACCTCTGCCTGCATCCCTTCAGATTCGCCTCTACAAGGAGGAAAGAAGTTGGCCAT
873491 GCAAGGACTTA
131 GCAAGGACTTA
*
873502 ATTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAAAAAATTAATTTTG
1 ATTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTAAATTG-AAAAAAAATCAATTTTG
* *
873567 AGG-GGCCAAAACCTCTGCCTGCCTCCCTTCAGATTCGCCTCTACAAGGAGGAAAGAAGTTGGTC
65 -GGAGGCCAAAACCTCTGCCTGCATCCCTTCAGATTCGCCTCTACAAGGAGGAAAGAAGTTGGCC
*
873631 ATGCAAGGATTTA
129 ATGCAAGGACTTA
873644 AT
1 AT
873646 GGTAGGTGGT
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
141 47 0.35
142 84 0.63
143 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (141 bp):
ATTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAAAAATCAATTTTGG
GAGGCCAAAACCTCTGCCTGCATCCCTTCAGATTCGCCTCTACAAGGAGGAAAGAAGTTGGCCAT
GCAAGGACTTA
Found at i:879328 original size:57 final size:58
Alignment explanation
Indices: 879222--879343 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 58
879212 TGAAAATGGA
* * * *
879222 GAAAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTCTTATCCAAAATAAAAAT
1 GAAAATGGAGAAATAGGAAACATTTGAAAATGAATATGATCTTACCCAAAATAAAAAT
* * * *
879280 GAAAATGGAGAAAT-GGAATCATTTGAAAATGAATGTGAAT-TTCCCCAAAATGAAAAT
1 GAAAATGGAGAAATAGGAAACATTTGAAAATGAATATG-ATCTTACCCAAAATAAAAAT
879337 GAAAATG
1 GAAAATG
879344 AAAATGAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 40 0.73
58 15 0.27
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (58 bp):
GAAAATGGAGAAATAGGAAACATTTGAAAATGAATATGATCTTACCCAAAATAAAAAT
Found at i:879335 original size:6 final size:6
Alignment explanation
Indices: 879326--879359 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
879316 GAATTTCCCC
879326 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
879360 ATGACCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:880243 original size:40 final size:40
Alignment explanation
Indices: 880189--880267 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
880179 TTTCCGTTGT
880189 GCAAGAAAACTATTTTCAAA-TCGAATTTTTTCCAACATGA
1 GCAAGAAAACTATTTTCAAACT-GAATTTTTTCCAACATGA
*
880229 GCAAGAAAACTATTTTCAAACTGGATTTTTTCCAACATG
1 GCAAGAAAACTATTTTCAAACTGAATTTTTTCCAACATG
880268 TGTATATGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (40 bp):
GCAAGAAAACTATTTTCAAACTGAATTTTTTCCAACATGA
Found at i:894637 original size:35 final size:35
Alignment explanation
Indices: 894557--894637 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
894547 TCATATTAGC
* **
894557 AATTAATT-ATTTTTTAAAAATATAATTTTTAATT
1 AATTAATTAATTTTTTAAAAATATAAATTTTAAAA
** * * *
894591 TGTTAAATAATTTTTTAAAATTTTAAATTTTAAAA
1 AATTAATTAATTTTTTAAAAATATAAATTTTAAAA
894626 AATTAATTAATT
1 AATTAATTAATT
894638 AACACTGATG
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
34 5 0.14
35 30 0.86
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (35 bp):
AATTAATTAATTTTTTAAAAATATAAATTTTAAAA
Found at i:895641 original size:13 final size:13
Alignment explanation
Indices: 895625--895685 Score: 79
Period size: 13 Copynumber: 4.7 Consensus size: 13
895615 ACCAAATTTT
895625 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
895638 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
895651 TCCATAA-CACTTC
1 T-CAAAAGCACTTC
*
895664 TCAAAAGCACTTT
1 TCAAAAGCACTTC
895677 TCAAAAGCA
1 TCAAAAGCA
895686 TTACCAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
12 4 0.10
13 33 0.80
14 4 0.10
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:897669 original size:11 final size:11
Alignment explanation
Indices: 897653--897705 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
897643 ATACGATATT
*
897653 TAATATATACG
1 TAATATATACA
*
897664 TAATATGT--A
1 TAATATATACA
*
897673 TAATA-A-AAA
1 TAATATATACA
897682 TAATATATACA
1 TAATATATACA
897693 TAATATATACA
1 TAATATATACA
897704 TA
1 TA
897706 CATAAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 11 0.32
10 1 0.03
11 22 0.65
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (11 bp):
TAATATATACA
Found at i:898051 original size:3 final size:3
Alignment explanation
Indices: 898045--898112 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
898035 TTACTACTGC
898045 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
898093 CAA TAA TAG TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TA
898113 GTATAAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:898610 original size:20 final size:19
Alignment explanation
Indices: 898563--898610 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
898553 AAAAACAGAA
*
898563 GAGGAGGGAGAGAAAAGAGG
1 GAGG-GGGAAAGAAAAGAGG
*
898583 GAGCGGGGAAAGAAGAGAGGG
1 GAG-GGGGAAAGAAAAGA-GG
898604 GAGGGGG
1 GAGGGGG
898611 GAGCTCCGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.60, T:0.00
Consensus pattern (19 bp):
GAGGGGGAAAGAAAAGAGG
Found at i:898744 original size:12 final size:12
Alignment explanation
Indices: 898711--898747 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
898701 ATTTTTTTTG
898711 TTTATTATTT-T
1 TTTATTATTTAT
898722 TGTTATT-TTTAT
1 T-TTATTATTTAT
898734 TTTATTATTTAT
1 TTTATTATTTAT
898746 TT
1 TT
898748 ATTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:898753 original size:26 final size:25
Alignment explanation
Indices: 898700--898751 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
898690 TAAAAAATTA
*
898700 TATTTTTTTTGTTTATTATTTTTGT
1 TATTTTTTTTGTTTATTATTTATGT
*
898725 TA-TTTTTAT-TTTATTATTTAT-T
1 TATTTTTTTTGTTTATTATTTATGT
898747 TATTT
1 TATTT
898752 ATATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 13 0.54
24 6 0.25
25 2 0.08
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (25 bp):
TATTTTTTTTGTTTATTATTTATGT
Found at i:899260 original size:26 final size:26
Alignment explanation
Indices: 899223--899280 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
899213 AGTAGGTTTA
899223 GTTA-TTGGGTTTTGGGGTTTAATGG
1 GTTAGTTGGGTTTTGGGGTTTAATGG
899248 GTTAGTTGGGTTTTGGGGTTTAATGG
1 GTTAGTTGGGTTTTGGGGTTTAATGG
899274 GTTAGTT
1 GTTAGTT
899281 TAGGATGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (26 bp):
GTTAGTTGGGTTTTGGGGTTTAATGG
Found at i:899531 original size:28 final size:32
Alignment explanation
Indices: 899474--899543 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 32
899464 GTATCTGATA
*
899474 ATTTAAATATAAATTATTCAATTTATATTT-T
1 ATTTATATATAAATTATTCAATTTATATTTAT
899505 ATTTTATATATAAA-TATTC-A-TT-TATTTAT
1 A-TTTATATATAAATTATTCAATTTATATTTAT
899534 ATTTATATAT
1 ATTTATATAT
899544 TTGTTAGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 14 0.39
29 4 0.11
30 1 0.03
31 6 0.17
32 11 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTATATATAAATTATTCAATTTATATTTAT
Found at i:899535 original size:22 final size:23
Alignment explanation
Indices: 899502--899544 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
899492 CAATTTATAT
899502 TTTATTTTATATATAAATATTCA
1 TTTATTTTATATATAAATATTCA
* *
899525 TTTA-TTTATATTTATATATT
1 TTTATTTTATATATAAATATT
899545 TGTTAGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTCA
Found at i:899544 original size:14 final size:14
Alignment explanation
Indices: 899494--899545 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
899484 AAATTATTCA
899494 ATTTATAT-TTTAT
1 ATTTATATATTTAT
**
899507 -TTTATATATAAAT
1 ATTTATATATTTAT
* *
899520 ATTCATTTATTTAT
1 ATTTATATATTTAT
899534 ATTTATATATTT
1 ATTTATATATTT
899546 GTTAGTCAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
14 19 0.66
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:899746 original size:86 final size:86
Alignment explanation
Indices: 899656--899959 Score: 418
Period size: 86 Copynumber: 3.5 Consensus size: 86
899646 TATTTTGAGA
* *
899656 TTTATTACATTTTTTATTTTGTTTCCAAACAAGTATTAAAATTAAATAAAATATGTTTC-AGGAT
1 TTTATTTCATTTTTTATTTTGTTTCCAAACGAGTATTAAAATTAAATAAAATATGTTTCGA-GAT
899720 TTATTCCCGCCGTTCAACAGAT
65 TTATTCCCGCCGTTCAACAGAT
* *
899742 TTTA-TTCTATTTTTTTATTTT-TTTCCAAACTAGTATTAAAATTAAATAAAATTTGTTTCGAGA
1 TTTATTTC-A-TTTTTTATTTTGTTTCCAAACGAGTATTAAAATTAAATAAAATATGTTTCGAGA
* *
899805 TTTATTCCCGCCATTTAACAGAT
64 TTTATTCCCGCCGTTCAACAGAT
* * *
899828 TTTATTTCATTTTTTATTTTGTTTCCAAACGAGTATTAAAACTAAATAAAATCTGTTTTGAGATT
1 TTTATTTCATTTTTTATTTTGTTTCCAAACGAGTATTAAAATTAAATAAAATATGTTTCGAGATT
* *
899893 TATTCCTGTCGTTCAACAGAT
66 TATTCCCGCCGTTCAACAGAT
* * * *
899914 TTTATTTTATTTTTTATTTTATTTCCAAATGAGTGTTAAAA-TAAAT
1 TTTATTTCATTTTTTATTTTGTTTCCAAACGAGTATTAAAATTAAAT
899960 CCCGTAGTTC
Statistics
Matches: 196, Mismatches: 17, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
85 18 0.09
86 163 0.83
87 15 0.08
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.48
Consensus pattern (86 bp):
TTTATTTCATTTTTTATTTTGTTTCCAAACGAGTATTAAAATTAAATAAAATATGTTTCGAGATT
TATTCCCGCCGTTCAACAGAT
Found at i:899930 original size:12 final size:12
Alignment explanation
Indices: 899913--899937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
899903 GTTCAACAGA
899913 TTTTATTTTATT
1 TTTTATTTTATT
899925 TTTTATTTTATT
1 TTTTATTTTATT
899937 T
1 T
899938 CCAAATGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:901842 original size:7 final size:7
Alignment explanation
Indices: 901832--901863 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
901822 TGGAAAATGG
*
901832 AAATTGT
1 AAATAGT
901839 AAATAGT
1 AAATAGT
901846 AAATAGT
1 AAATAGT
901853 AAATAGT
1 AAATAGT
901860 AAAT
1 AAAT
901864 GTTTTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (7 bp):
AAATAGT
Found at i:902323 original size:23 final size:22
Alignment explanation
Indices: 902273--902323 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
902263 TACATTTGTG
902273 TATTTAAATTAATTTTTACAAA
1 TATTTAAATTAATTTTTACAAA
*
902295 TAATTTATATTAATTGTCTTA-AAA
1 T-ATTTAAATTAATT-T-TTACAAA
902319 TATTT
1 TATTT
902324 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 16 0.64
24 5 0.20
25 3 0.12
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTTAAATTAATTTTTACAAA
Found at i:902550 original size:16 final size:17
Alignment explanation
Indices: 902513--902547 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
902503 AATTTAAATG
902513 AAATATATTGAAATTCA
1 AAATATATTGAAATTCA
902530 AAATATA-T-AAATTCA
1 AAATATATTGAAATTCA
902545 AAA
1 AAA
902548 ATAATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATATATTGAAATTCA
Found at i:903966 original size:47 final size:47
Alignment explanation
Indices: 903897--903988 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 47
903887 TGCCTGTCGA
* *
903897 ATCATGGCTAATTGTGTTAATAATTATGGATCATTTTAGTAAGAGTG
1 ATCATAGCTAATTGTGTTAATAATTATGGATCATTTTAGAAAGAGTG
* * * *
903944 ATCATAGCTTATTGTGTTAATAATTCTTGATTATTTTAGAAAGAG
1 ATCATAGCTAATTGTGTTAATAATTATGGATCATTTTAGAAAGAG
903989 ATGTTTCTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (47 bp):
ATCATAGCTAATTGTGTTAATAATTATGGATCATTTTAGAAAGAGTG
Done.