Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 46 of 106
Found at i:17347883 original size:22 final size:21
Alignment explanation
Indices: 17347841--17347891 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
17347831 ATATTATTGG
**
17347841 TAATTAAATTATTAATCTTAT
1 TAATTAAATTATTAAAATTAT
17347862 ATAATTAAA-TATATAAAATTAT
1 -TAATTAAATTAT-TAAAATTAT
17347884 TAAATTAA
1 T-AATTAA
17347892 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAAATTATTAAAATTAT
Found at i:17353587 original size:22 final size:22
Alignment explanation
Indices: 17353562--17353610 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
17353552 GAAAAATGGA
*
17353562 TGCTGATATGTTTATGGTACTT
1 TGCTGATATGTTCATGGTACTT
* *
17353584 TGCTTATATGTTCATGGTATTT
1 TGCTGATATGTTCATGGTACTT
17353606 TGCTG
1 TGCTG
17353611 CTGATAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.51
Consensus pattern (22 bp):
TGCTGATATGTTCATGGTACTT
Found at i:17353676 original size:50 final size:50
Alignment explanation
Indices: 17353608--17353715 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 50
17353598 TGGTATTTTG
17353608 CTGCTGATAATTGAATACTTGCTGATATCCTGCTGTTTATGACATTTTAA
1 CTGCTGATAATTGAATACTTGCTGATATCCTGCTGTTTATGACATTTTAA
17353658 CTGCTGATAATTGAATACTTGCTGATATCCTGCTGTTTATGACATTTTAA
1 CTGCTGATAATTGAATACTTGCTGATATCCTGCTGTTTATGACATTTTAA
*
17353708 CTGTTGAT
1 CTGCTGAT
17353716 TGATAAAAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (50 bp):
CTGCTGATAATTGAATACTTGCTGATATCCTGCTGTTTATGACATTTTAA
Found at i:17367004 original size:13 final size:13
Alignment explanation
Indices: 17366969--17367007 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17366959 ATAATGAATG
17366969 CTTGATGATGAATA
1 CTTGATGAT-AATA
* *
17366983 ATTGTTGATAATA
1 CTTGATGATAATA
17366996 CTTGATGATAAT
1 CTTGATGATAAT
17367008 TGAGAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (13 bp):
CTTGATGATAATA
Found at i:17369529 original size:4 final size:4
Alignment explanation
Indices: 17369520--17369544 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17369510 TTATTTGAAG
17369520 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
17369545 CAAATTAATG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:17373786 original size:33 final size:33
Alignment explanation
Indices: 17373749--17373811 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
17373739 TAAAAGTTAG
*
17373749 TGTGGGTTGTGCTTGCTCCAGTGAAAAGGCCAC
1 TGTGGGTTATGCTTGCTCCAGTGAAAAGGCCAC
**
17373782 TGTGGGTTATGCTTGCTCTTGTGAAAAGGC
1 TGTGGGTTATGCTTGCTCCAGTGAAAAGGC
17373812 AATTGTGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.32
Consensus pattern (33 bp):
TGTGGGTTATGCTTGCTCCAGTGAAAAGGCCAC
Found at i:17374553 original size:20 final size:20
Alignment explanation
Indices: 17374525--17374562 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17374515 ATTTTGAGTG
17374525 AAATCTATCGATACATTCCC
1 AAATCTATCGATACATTCCC
* *
17374545 AAATGTATCGATAGATTC
1 AAATCTATCGATACATTC
17374563 TTCACAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
AAATCTATCGATACATTCCC
Found at i:17385380 original size:2 final size:2
Alignment explanation
Indices: 17385373--17385469 Score: 137
Period size: 2 Copynumber: 50.0 Consensus size: 2
17385363 TAATATTACC
* *
17385373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17385415 AT AT A- AT NT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17385456 AA AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
17385470 GAATTTTTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
1 3 0.04
2 81 0.96
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17392355 original size:35 final size:36
Alignment explanation
Indices: 17392300--17392388 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 36
17392290 TACACCACCC
* * *
17392300 CACTTCATTCATCGTCA-TGTGCACTCCCTACTCGCA
1 CACTTCA-ACATCATCAGTGTGCACTCCCTACGCGCA
17392336 CACTTCAACATCATCATGTGTGCACTCCCTACGCGCA
1 CACTTCAACATCATCA-GTGTGCACTCCCTACGCGCA
*
17392373 CACTTCAGCATCATCA
1 CACTTCAACATCATCA
17392389 CACAACATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
35 7 0.15
36 7 0.15
37 33 0.70
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (36 bp):
CACTTCAACATCATCAGTGTGCACTCCCTACGCGCA
Found at i:17392360 original size:37 final size:37
Alignment explanation
Indices: 17392317--17392388 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
17392307 TTCATCGTCA
*
17392317 TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
1 TGTGCACTCCCTACGCGCACACTTCAACATCATCATG
*
17392354 TGTGCACTCCCTACGCGCACACTTCAGCATCATCA
1 TGTGCACTCCCTACGCGCACACTTCAACATCATCA
17392389 CACAACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.24, C:0.39, G:0.12, T:0.25
Consensus pattern (37 bp):
TGTGCACTCCCTACGCGCACACTTCAACATCATCATG
Found at i:17393153 original size:34 final size:34
Alignment explanation
Indices: 17393110--17393180 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
17393100 TTTTTACTCT
*
17393110 TTTGAAATCATCATTATTTCTATTTCCTTCGTCA
1 TTTGAAATCATCATTATTTCTATTTCCTTCATCA
17393144 TTTGAAATCATCATTATTTCTATTTCCTTCATCA
1 TTTGAAATCATCATTATTTCTATTTCCTTCATCA
17393178 TTT
1 TTT
17393181 TATCCTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (34 bp):
TTTGAAATCATCATTATTTCTATTTCCTTCATCA
Found at i:17397121 original size:27 final size:26
Alignment explanation
Indices: 17397065--17397144 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 26
17397055 TTGCAATCAC
17397065 ATATATCAACTCGTGGCCTAGCCACG
1 ATATATCAACTCGTGGCCTAGCCACG
* *
17397091 -TATATCAACTGGTGGCCTTGCCACG
1 ATATATCAACTCGTGGCCTAGCCACG
17397116 TATATATCACAGACT-GTGGCCTAGCCACG
1 -ATATAT--CA-ACTCGTGGCCTAGCCACG
17397145 TCTAACAGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 23 0.50
27 5 0.11
29 15 0.33
30 3 0.07
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (26 bp):
ATATATCAACTCGTGGCCTAGCCACG
Found at i:17400678 original size:25 final size:25
Alignment explanation
Indices: 17400650--17400709 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
17400640 TAATTTAGAT
17400650 AAAGTTTTGAAAAACACCATAATCC
1 AAAGTTTTGAAAAACACCATAATCC
17400675 AAAGTTTTGAAAAACACCATAATCC
1 AAAGTTTTGAAAAACACCATAATCC
17400700 AAAGTTTTGA
1 AAAGTTTTGA
17400710 GTAAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (25 bp):
AAAGTTTTGAAAAACACCATAATCC
Found at i:17402289 original size:18 final size:16
Alignment explanation
Indices: 17402254--17402301 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
17402244 AAATTTAATG
*
17402254 TTATTTATTTTTGTTA
1 TTATTTATTTTTCTTA
17402270 TTATTTATATTTTCTCTA
1 TTATTTAT-TTTTCT-TA
*
17402288 TTAATTTGTTTTTC
1 TT-ATTTATTTTTC
17402302 ATCTGTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 9 0.33
19 5 0.19
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (16 bp):
TTATTTATTTTTCTTA
Found at i:17404451 original size:19 final size:18
Alignment explanation
Indices: 17404429--17404485 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 18
17404419 ATCTTTTTCT
17404429 TCCAGCAGCTTCTTCATTC
1 TCCAGCAGCTTCTTC-TTC
*
17404448 TCCAGCAACTTCTTCTTTC
1 TCCAGCAGCTTCTTC-TTC
*
17404467 TCTAGCAGCTTCTTCTTC
1 TCCAGCAGCTTCTTCTTC
17404485 T
1 T
17404486 TCTTTTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.12
19 30 0.88
ACGTcount: A:0.14, C:0.35, G:0.09, T:0.42
Consensus pattern (18 bp):
TCCAGCAGCTTCTTCTTC
Found at i:17405245 original size:2 final size:2
Alignment explanation
Indices: 17405238--17405288 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17405228 TGTATATTAG
17405238 TA TA TA TA 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 TA
17405280 TA TA TA TA T
1 TA TA TA TA T
17405289 GTTGTGCATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17405447 original size:38 final size:38
Alignment explanation
Indices: 17405405--17405542 Score: 186
Period size: 38 Copynumber: 3.6 Consensus size: 38
17405395 AAAGTGCCCA
*
17405405 TGAGCACGATATGGGGGGATGCGCACGATGACACTAAT
1 TGAGCACGATGTGGGGGGATGCGCACGATGACACTAAT
* *
17405443 TGAGCACGATGTGGAGGGATGCGCACGATGGCACTAAT
1 TGAGCACGATGTGGGGGGATGCGCACGATGACACTAAT
* * **
17405481 TGAGCACGATGTGGGGGGATGCACACGATGACCCTGGCT
1 TGAGCACGATGTGGGGGGATGCGCACGATGACACT-AAT
*
17405520 ATGTGCACGATGTGGGGGGATGC
1 -TGAGCACGATGTGGGGGGATGC
17405543 ACATGAGCTA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 66 0.75
39 1 0.01
40 21 0.24
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (38 bp):
TGAGCACGATGTGGGGGGATGCGCACGATGACACTAAT
Found at i:17405487 original size:19 final size:19
Alignment explanation
Indices: 17405427--17405491 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
17405417 GGGGGGATGC
*
17405427 GCACGATGACACTAATTGA
1 GCACGATGGCACTAATTGA
* *** *
17405446 GCACGATGTGGAGGGA-TGC
1 GCACGATG-GCACTAATTGA
17405465 GCACGATGGCACTAATTGA
1 GCACGATGGCACTAATTGA
17405484 GCACGATG
1 GCACGATG
17405492 TGGGGGGATG
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
18 3 0.09
19 28 0.85
20 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.18
Consensus pattern (19 bp):
GCACGATGGCACTAATTGA
Found at i:17413606 original size:21 final size:20
Alignment explanation
Indices: 17413581--17413640 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
17413571 AGATGTCTAA
*
17413581 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
17413602 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
17413622 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
17413640 A
1 A
17413641 TTCTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:17418654 original size:36 final size:36
Alignment explanation
Indices: 17418609--17418733 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
17418599 TAGCCAAAGT
*
17418609 CATCGTGTGCACCCCCACATCGCGCACAACTAATGC
1 CATCATGTGCACCCCCACATCGCGCACAACTAATGC
* * *
17418645 CATCATGTGCTCCCTCCACATAGCGCACATGGCATATAT-C
1 CATCATGTGCACCC-CCACATCGCGCACA--AC-TA-ATGC
* *
17418685 ATCATCATCGTGTGCACCCCCACATCACGCACAACTAATGT
1 --CATCA---TGTGCACCCCCACATCGCGCACAACTAATGC
17418726 CATCATGT
1 CATCATGT
17418734 CAAGCCCAGC
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
36 15 0.22
37 13 0.19
39 6 0.09
40 5 0.07
41 4 0.06
42 6 0.09
44 12 0.17
45 8 0.12
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.22
Consensus pattern (36 bp):
CATCATGTGCACCCCCACATCGCGCACAACTAATGC
Found at i:17419154 original size:28 final size:28
Alignment explanation
Indices: 17419123--17419187 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
17419113 CCGAGCATAA
17419123 GGGTAAAATAGTCATTTTGCCA-CCCTAG
1 GGGTAAAATAGTCATTTTGCCATCCC-AG
*
17419151 GGGTAAAATAGTCATTTTGGCATCCCAG
1 GGGTAAAATAGTCATTTTGCCATCCCAG
*
17419179 GGGCAAAAT
1 GGGTAAAAT
17419188 TATAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (28 bp):
GGGTAAAATAGTCATTTTGCCATCCCAG
Found at i:17424741 original size:2 final size:2
Alignment explanation
Indices: 17424736--17424763 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17424726 AACACACAAC
17424736 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
17424764 TCCAACATAA
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:17427867 original size:7 final size:7
Alignment explanation
Indices: 17427857--17427890 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
17427847 GGAAAGCAAA
17427857 AAGAAAG
1 AAGAAAG
17427864 AAGAAAG
1 AAGAAAG
*
17427871 GAGAAAG
1 AAGAAAG
*
17427878 AAGAAAA
1 AAGAAAG
17427885 AAGAAA
1 AAGAAA
17427891 AGCTTGAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:17427889 original size:14 final size:14
Alignment explanation
Indices: 17427854--17427890 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17427844 AGAGGAAAGC
17427854 AAAAAGAAAGAAGA
1 AAAAAGAAAGAAGA
**
17427868 AAGGAGAAAGAAGA
1 AAAAAGAAAGAAGA
17427882 AAAAAGAAA
1 AAAAAGAAA
17427891 AGCTTGAAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAGA
Found at i:17431755 original size:27 final size:28
Alignment explanation
Indices: 17431702--17431755 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
17431692 TTTTTTAGCA
* * *
17431702 TAGGGGTAAAATAGTCATTTTGTCACCC
1 TAGGGGAAAAATAGTAATTTTGACACCC
*
17431730 TAGGGGAAAAATTGTAATTTT-ACACC
1 TAGGGGAAAAATAGTAATTTTGACACC
17431756 ACCCGACACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (28 bp):
TAGGGGAAAAATAGTAATTTTGACACCC
Found at i:17442905 original size:25 final size:26
Alignment explanation
Indices: 17442877--17442926 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17442867 GTGGGATCTA
17442877 CATCACATACT-TGCATCATATCATT
1 CATCACATACTCTGCATCATATCATT
* * *
17442902 CATCATATACTCTTCATCATCTCAT
1 CATCACATACTCTGCATCATATCAT
17442927 ATGGTATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.38
Consensus pattern (26 bp):
CATCACATACTCTGCATCATATCATT
Found at i:17443003 original size:68 final size:68
Alignment explanation
Indices: 17442920--17443084 Score: 267
Period size: 68 Copynumber: 2.4 Consensus size: 68
17442910 ACTCTTCATC
* * *
17442920 ATCTCATATGGTATATGGAATCTACATTATACGCCTATCATCATATTATTTTTCATGCACCCTCT
1 ATCTCATGTGGTATATGGAATCTACATCATACACCTATCATCATATTATTTTTCATGCACCCTCT
17442985 ATA
66 ATA
* *
17442988 ATCTCATGTGATATATGGAATCTACATCATACACCTATTATCATATTATTTTTCATGCACCCTCT
1 ATCTCATGTGGTATATGGAATCTACATCATACACCTATCATCATATTATTTTTCATGCACCCTCT
*
17443053 ATC
66 ATA
*
17443056 ATCTCATGTGGTATATGAAATCTACATCA
1 ATCTCATGTGGTATATGGAATCTACATCA
17443085 CATAACTAGC
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 89 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (68 bp):
ATCTCATGTGGTATATGGAATCTACATCATACACCTATCATCATATTATTTTTCATGCACCCTCT
ATA
Found at i:17443099 original size:68 final size:68
Alignment explanation
Indices: 17442855--17443099 Score: 242
Period size: 68 Copynumber: 3.6 Consensus size: 68
17442845 CCATTATTGC
* * * * * * ** ** *
17442855 CTCATATGGTATGTGGGATCTACATCACA-TACTTGCATCATATCATTCATCATATACTCT-TCA
1 CTCATGTGGTATATGGAATCTACATCACACAACTAGCATCATATTATTTTTCATGCACCCTCT-A
17442918 TCAT
65 TCAT
* * * ** *
17442922 CTCATATGGTATATGGAATCTACATTATACGCCTATCATCATATTATTTTTCATGCACCCTCTAT
1 CTCATGTGGTATATGGAATCTACATCACACAACTAGCATCATATTATTTTTCATGCACCCTCTAT
*
17442987 AAT
66 CAT
* * * **
17442990 CTCATGTGATATATGGAATCTACATCATACACCTATTATCATATTATTTTTCATGCACCCTCTAT
1 CTCATGTGGTATATGGAATCTACATCACACAACTAGCATCATATTATTTTTCATGCACCCTCTAT
17443055 CAT
66 CAT
* *
17443058 CTCATGTGGTATATGAAATCTACATCACATAACTAGCATCAT
1 CTCATGTGGTATATGGAATCTACATCACACAACTAGCATCAT
17443100 GGTATTCAAC
Statistics
Matches: 148, Mismatches: 28, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
67 25 0.17
68 122 0.82
69 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (68 bp):
CTCATGTGGTATATGGAATCTACATCACACAACTAGCATCATATTATTTTTCATGCACCCTCTAT
CAT
Found at i:17447018 original size:16 final size:19
Alignment explanation
Indices: 17446997--17447034 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
17446987 TTTAAATGAT
17446997 TTGTTGT-GAA-GAA-TTA
1 TTGTTGTCGAAGGAATTTA
17447013 TTGTTGTCGAAGGAATTTA
1 TTGTTGTCGAAGGAATTTA
17447032 TTG
1 TTG
17447035 GCATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 3 0.16
19 6 0.32
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (19 bp):
TTGTTGTCGAAGGAATTTA
Found at i:17447111 original size:25 final size:22
Alignment explanation
Indices: 17447082--17447127 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
17447072 ATATTTGAAA
17447082 GAAATAAGAAGAAATAATGTGGATT
1 GAAATAAG-A-AAATAAT-TGGATT
*
17447107 GAAATTAGAAAATAATTGGAT
1 GAAATAAGAAAATAATTGGAT
17447128 AGATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 1 0.05
25 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (22 bp):
GAAATAAGAAAATAATTGGATT
Found at i:17447848 original size:43 final size:43
Alignment explanation
Indices: 17447801--17447919 Score: 202
Period size: 43 Copynumber: 2.8 Consensus size: 43
17447791 GTTTTGTGAT
*
17447801 GATGATGACCCGGTTATGTGCGAGTAGGGAGTGTGCATAAGCC
1 GATGATGACCCGGCTATGTGCGAGTAGGGAGTGTGCATAAGCC
*
17447844 GATGATGACCCGACTATGTGCGAGTAGGGAGTGTGCATAAGCC
1 GATGATGACCCGGCTATGTGCGAGTAGGGAGTGTGCATAAGCC
* *
17447887 GATGATGACCCGGCTATGTGTGAGTAGAGAGTG
1 GATGATGACCCGGCTATGTGCGAGTAGGGAGTG
17447920 CACATGTCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (43 bp):
GATGATGACCCGGCTATGTGCGAGTAGGGAGTGTGCATAAGCC
Found at i:17452107 original size:18 final size:19
Alignment explanation
Indices: 17452078--17452117 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
17452068 ACAAGAGAAA
17452078 ATTTTTTAAATAAAATAAT
1 ATTTTTTAAATAAAATAAT
17452097 ATTTTTT-AATAAAATAAT
1 ATTTTTTAAATAAAATAAT
17452115 ATT
1 ATT
17452118 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTTAAATAAAATAAT
Found at i:17452759 original size:46 final size:46
Alignment explanation
Indices: 17452697--17452785 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
17452687 AGTCGATTGT
17452697 GAGAAACAGCAAAAGGAAAGCAAA-AGAACA-AAGGAAAGAAAAAGGA
1 GAGAAACAGCAAAAGGAAAG-AAAGAGAA-AGAAGGAAAGAAAAAGGA
** * *
17452743 GAGAAACAGCTGAAGGAGAGAAAGAGAAAGAAGGAAGGAAAAA
1 GAGAAACAGCAAAAGGAAAGAAAGAGAAAGAAGGAAAGAAAAA
17452786 AAAAAAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 4 0.11
46 33 0.89
ACGTcount: A:0.62, C:0.07, G:0.30, T:0.01
Consensus pattern (46 bp):
GAGAAACAGCAAAAGGAAAGAAAGAGAAAGAAGGAAAGAAAAAGGA
Found at i:17453022 original size:34 final size:35
Alignment explanation
Indices: 17452978--17453064 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 35
17452968 TTAGGTTTTG
* * *
17452978 GCTGCCGA-TTTTGAGGGTGAGATGAGCAACTTTA
1 GCTGCTGATTTTTGAGGCTGAAATGAGCAACTTTA
*
17453012 GCTGCTGATTTTTGAAGGCTGAAATGAGTAACTTTA
1 GCTGCTGATTTTTG-AGGCTGAAATGAGCAACTTTA
*
17453048 GCTGTTGATTTTTGAGG
1 GCTGCTGATTTTTGAGG
17453065 TTTTGGCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.15
35 8 0.17
36 31 0.67
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (35 bp):
GCTGCTGATTTTTGAGGCTGAAATGAGCAACTTTA
Found at i:17453050 original size:92 final size:92
Alignment explanation
Indices: 17452926--17453101 Score: 264
Period size: 92 Copynumber: 1.9 Consensus size: 92
17452916 AGAAAGGGTC
** *
17452926 GATTTTTGAAGGCTGAAAAGAGCAGTTTTAGCTGCTGATTTTTTAGGTTTTGGCTGCC-GATTTT
1 GATTTTTGAAGGCTGAAAAGAGCAACTTTAGCTGCTGATTTTTGAGGTTTTGGCTGCCAG-TTTT
*
17452990 GAGGGTGAGATGAGCAACTTTAGCTGCT
65 GAGGGTGAAATGAGCAACTTTAGCTGCT
* * * *
17453018 GATTTTTGAAGGCTGAAATGAGTAACTTTAGCTGTTGATTTTTGAGGTTTTGGCTGTCAGTTTTG
1 GATTTTTGAAGGCTGAAAAGAGCAACTTTAGCTGCTGATTTTTGAGGTTTTGGCTGCCAGTTTTG
17453083 AGGGTGAAATGAGCAACTT
66 AGGGTGAAATGAGCAACTT
17453102 AGACTACTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
92 74 0.99
93 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (92 bp):
GATTTTTGAAGGCTGAAAAGAGCAACTTTAGCTGCTGATTTTTGAGGTTTTGGCTGCCAGTTTTG
AGGGTGAAATGAGCAACTTTAGCTGCT
Found at i:17453144 original size:92 final size:92
Alignment explanation
Indices: 17452927--17453144 Score: 219
Period size: 92 Copynumber: 2.4 Consensus size: 92
17452917 GAAAGGGTCG
* ** ** * * *
17452927 ATTTTTGAAGGCTGAAAAGAGCAGTTTTAGCTGCTGATTTTTTAGGTTTTGGCTGCCGATTTTGA
1 ATTTTTGAAGGCTGAAAGGAAAAAATTTAGCTGTTGATTTTTGAGGTTTTGGCTGCAGATTTTGA
* * *
17452992 GGGTGAGATGAGCAACTTTAGCTGCTG
66 GGGTGAAATGAGCAACTTTAGCTACTA
* ** *
17453019 ATTTTTGAAGGCTGAAATGAGTAACTTTAGCTGTTGATTTTTGAGGTTTTGGCTGTCAG-TTTTG
1 ATTTTTGAAGGCTGAAAGGAAAAAATTTAGCTGTTGATTTTTGAGGTTTTGGCTG-CAGATTTTG
17453083 AGGGTGAAATGAGCAAC-TTAGACTACTA
65 AGGGTGAAATGAGCAACTTTAG-CTACTA
* *
17453111 ATTTTT-TAGGTTGAAAGGGACAAAAATTT-GCTGT
1 ATTTTTGAAGGCTGAAA-GGA-AAAAATTTAGCTGT
17453145 CGGTAGTGAG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
91 12 0.11
92 87 0.82
93 7 0.07
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (92 bp):
ATTTTTGAAGGCTGAAAGGAAAAAATTTAGCTGTTGATTTTTGAGGTTTTGGCTGCAGATTTTGA
GGGTGAAATGAGCAACTTTAGCTACTA
Found at i:17454358 original size:20 final size:21
Alignment explanation
Indices: 17454324--17454369 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
17454314 TATGTATATA
17454324 TATGAATATATGTTGT-TGAT
1 TATGAATATATGTTGTGTGAT
17454344 TGATGAATA-ATGTTGTGTGAT
1 T-ATGAATATATGTTGTGTGAT
17454365 TATGA
1 TATGA
17454370 TGACCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (21 bp):
TATGAATATATGTTGTGTGAT
Found at i:17454475 original size:46 final size:42
Alignment explanation
Indices: 17454366--17454493 Score: 166
Period size: 43 Copynumber: 2.9 Consensus size: 42
17454356 TTGTGTGATT
* * *
17454366 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACCC-GTTATGTGCGAGTAGGGAGTGCACATGAGCCG
*
17454409 ATGATGACCCGTCTATGTGCGAGTAGGGAGTGCACATGAGCTAATG
1 ATGATGACCCGT-TATGTGCGAGTAGGGAGTGCACATGAGC---CG
17454455 ATGATGACCGCGTTATGTGCGAGTAGGGAGTGCACATGA
1 ATGATGACC-CGTTATGTGCGAGTAGGGAGTGCACATGA
17454494 TGATGAATGA
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
42 1 0.01
43 36 0.47
46 36 0.47
47 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (42 bp):
ATGATGACCCGTTATGTGCGAGTAGGGAGTGCACATGAGCCG
Found at i:17455699 original size:33 final size:33
Alignment explanation
Indices: 17455639--17455703 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
17455629 TGACATGCTA
* **
17455639 ATATATCATAATTGATGATGATGTGATATGTTG
1 ATATATCATAATTGATGATAACATGATATGTTG
17455672 ATATATCATAATTGATGATAACATGATATGTT
1 ATATATCATAATTGATGATAACATGATATGTT
17455704 AATTATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (33 bp):
ATATATCATAATTGATGATAACATGATATGTTG
Found at i:17465665 original size:33 final size:34
Alignment explanation
Indices: 17465622--17465687 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
17465612 AATAATTTAT
* *
17465622 TTTATGGTATTAGGTAAAG-TAATAACAATTAAC
1 TTTATCGTATTAAGTAAAGATAATAACAATTAAC
17465655 TTTATCGTATTAAGTAAAGATAATAACAATTAA
1 TTTATCGTATTAAGTAAAGATAATAACAATTAA
17465688 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (34 bp):
TTTATCGTATTAAGTAAAGATAATAACAATTAAC
Found at i:17469190 original size:6 final size:7
Alignment explanation
Indices: 17469175--17469199 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17469165 ATGTGCTTAG
17469175 TTTTGTT
1 TTTTGTT
17469182 TTTTGTT
1 TTTTGTT
17469189 TTTTGTT
1 TTTTGTT
17469196 TTTT
1 TTTT
17469200 TTGTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:17480751 original size:31 final size:35
Alignment explanation
Indices: 17480716--17480787 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
17480706 GTTAATCCAA
*
17480716 TTAATTCG-ATCCA-AATATT-TT-ATTAATTGAT
1 TTAATTCGAAACCACAATATTATTCATTAATTGAT
*
17480747 TTAA-TCGAAACCATCAATTTTATTCATTAATTGAT
1 TTAATTCGAAACCA-CAATATTATTCATTAATTGAT
17480782 TTAATT
1 TTAATT
17480788 AGATTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
30 3 0.09
31 8 0.24
33 5 0.15
34 2 0.06
35 14 0.42
36 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (35 bp):
TTAATTCGAAACCACAATATTATTCATTAATTGAT
Found at i:17482039 original size:15 final size:15
Alignment explanation
Indices: 17482022--17482052 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
17482012 TTAAGAAAAT
17482022 AAAATAAATAATAATA
1 AAAAT-AATAATAATA
17482038 AAAATAATAATAATA
1 AAAATAATAATAATA
17482053 GTAATGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:17482352 original size:13 final size:14
Alignment explanation
Indices: 17482329--17482357 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17482319 AATGTCGGCC
17482329 AAAGAAGAAGAAGA
1 AAAGAAGAAGAAGA
17482343 AAAG-AGAAGAAGA
1 AAAGAAGAAGAAGA
17482356 AA
1 AA
17482358 TAAAGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGAAGA
Found at i:17482375 original size:13 final size:15
Alignment explanation
Indices: 17482331--17482375 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
17482321 TGTCGGCCAA
17482331 AGAAGAAGAAGAAAAG
1 AGAAGAAGAA-AAAAG
17482347 AGAAGAAGAAATAAAG
1 AGAAGAAGAAA-AAAG
17482363 AGAA-AA-AAAAAAG
1 AGAAGAAGAAAAAAG
17482376 TCAGCTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.14
14 3 0.11
15 3 0.11
16 18 0.64
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (15 bp):
AGAAGAAGAAAAAAG
Found at i:17483044 original size:56 final size:55
Alignment explanation
Indices: 17482958--17483063 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 55
17482948 AAGCTGCTCC
17482958 CCATATAAGTGTGTGATTAAGTATATTGGGTTTAAATTGTTGTTAGGAAACTTGT
1 CCATATAAGTGTGTGATTAAGTATATTGGGTTTAAATTGTTGTTAGGAAACTTGT
17483013 NCCATATAAGTGTGTGATTAAGTATATTGGGTTTAAATTGTTGTTAGGAAA
1 -CCATATAAGTGTGTGATTAAGTATATTGGGTTTAAATTGTTGTTAGGAAA
17483064 GTTTGTCGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (55 bp):
CCATATAAGTGTGTGATTAAGTATATTGGGTTTAAATTGTTGTTAGGAAACTTGT
Found at i:17486716 original size:73 final size:73
Alignment explanation
Indices: 17486634--17486837 Score: 207
Period size: 73 Copynumber: 2.8 Consensus size: 73
17486624 GAAGATGGCC
* * *
17486634 AGTTCAGAAACAAAACCAACTTAATCGACTAAGA-GATATTGTTAGTCGACTAAGTGCTTACTGC
1 AGTTCAGAAACAAAACCAACTTAATCGACTAAGAGGA-ATCGTTAGTCAACTAAGAGCTTACTGC
17486698 CAGAAGTCG
65 CAGAAGTCG
* * **
17486707 AGTTTAGAAACAGAACTGACTTAATCGACTAAGAGGAATCGTTAGTCAACTAAGAGCTTACTGCC
1 AGTTCAGAAACAAAACCAACTTAATCGACTAAGAGGAATCGTTAGTCAACTAAGAGCTTACTGCC
* *
17486772 TGAA-ACTG
66 AGAAGTC-G
* * * * * * * *
17486780 GGATCAAAAGACAAAACTAACTTAATCGACTAAGAAGTAT-ATTAATCAACTAAGAGCT
1 AGTTCAGAA-ACAAAACCAACTTAATCGACTAAGAGGAATCGTTAGTCAACTAAGAGCT
17486838 CTCTGTCTGA
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
72 1 0.01
73 80 0.73
74 28 0.26
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (73 bp):
AGTTCAGAAACAAAACCAACTTAATCGACTAAGAGGAATCGTTAGTCAACTAAGAGCTTACTGCC
AGAAGTCG
Found at i:17493946 original size:43 final size:43
Alignment explanation
Indices: 17493898--17494098 Score: 314
Period size: 43 Copynumber: 4.7 Consensus size: 43
17493888 CAGCTCATGT
** * *
17493898 GCACTCCCTACTCGCACATGGCTGGGTCATCACCGAGTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
*
17493941 ACACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
17493984 GCACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
*
17494027 GCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATCAC-CGGGTTATGC
* *
17494070 GCACTCCCTACTCGCACATAGCCGAGTCA
1 GCACTCCCTACTCGCACATAACCGGGTCA
17494099 ACATAATTAC
Statistics
Matches: 148, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 1 0.01
43 147 0.99
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.21
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAACCGGGTCATCACCGGGTTATGC
Found at i:17498633 original size:73 final size:71
Alignment explanation
Indices: 17498483--17498683 Score: 188
Period size: 73 Copynumber: 2.7 Consensus size: 71
17498473 GATGGCCAGT
* * * *
17498483 TCAGAAACAGAACCAACTTAATCGACTAAGAGATATTATTAGTTGACTAAGTGCTTATTACCAGA
1 TCAGAAACAGAACCAACTTAATCGACTAAGAGA-A-TATTAGTAGACTAAGAGCTTACTACCAAA
* *
17498548 AGTCGAGT
64 ACTCGAGA
* * * *
17498556 TCAGAAATAGAACCGATTTAATCGACTAAGAGGAATCATTAGTAGACTAAGAGCTTACTGCCTAA
1 TCAGAAACAGAACCAACTTAATCGACTAAGA-GAAT-ATTAGTAGACTAAGAGCTTACTACC-AA
*
17498621 AACT-GGGA
63 AACTCGAGA
** * * *
17498629 TCAGAAGACAGAATTAACTTAATCGACTAAGAAGTATGTTAGTCGACTAAGAGCT
1 TCAGAA-ACAGAACCAACTTAATCGACTAAG-AGAATATTAGTAGACTAAGAGCT
17498684 CTCTGTTTGA
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
72 1 0.01
73 74 0.71
74 28 0.27
75 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (71 bp):
TCAGAAACAGAACCAACTTAATCGACTAAGAGAATATTAGTAGACTAAGAGCTTACTACCAAAAC
TCGAGA
Found at i:17499142 original size:34 final size:34
Alignment explanation
Indices: 17499095--17499163 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
17499085 GTTATTTTTG
* *
17499095 GGTTTTGGTTGATCCCG-TGAAAAACCATTGTAAA
1 GGTTGTGGCTGATCCCGCT-AAAAACCATTGTAAA
* *
17499129 GGTTGTGGCTGATCCTGCTAAAAGCCATTGTAAA
1 GGTTGTGGCTGATCCCGCTAAAAACCATTGTAAA
17499163 G
1 G
17499164 CTTGGTGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (34 bp):
GGTTGTGGCTGATCCCGCTAAAAACCATTGTAAA
Found at i:17520823 original size:23 final size:23
Alignment explanation
Indices: 17520797--17520844 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
17520787 GATAGGGTGC
17520797 ATAA-ACAATGAGATC-AGTAAAAA
1 ATAAGACAAT-AGATCAAG-AAAAA
*
17520820 ATAAGGCAATAGATCAAGAAAAA
1 ATAAGACAATAGATCAAGAAAAA
17520843 AT
1 AT
17520845 CCAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.17
Consensus pattern (23 bp):
ATAAGACAATAGATCAAGAAAAA
Found at i:17522341 original size:743 final size:742
Alignment explanation
Indices: 17520722--17522362 Score: 2354
Period size: 743 Copynumber: 2.2 Consensus size: 742
17520712 GTTTTTTTGT
* * * *
17520722 AAGAATAAGAGAAAAATGGCTAATTGAACCTTACGTACATGTCATTAACAAAA-TCTTCAA-TGG
1 AAGAATAAGAGAAAAATGGCTAATTGAACCCTACCTACATGTCATTAACAAAACT-TTCAACAGA
* *
17520785 ATGATAGGGTGCATAAACAATGAGATC-AGTAAAAAATAAGGCAATAGATCAAGAAAAAATCCAA
65 ACGATAGGGTGCATAAACAATGAGATCAAATAAAAAATAAGGCAATAGATCAAGAAAAAAT-CAA
** *
17520849 AAAAAAATTCAATTGCA-TCAATATTGAAGTAATAAAAAATCCTTTTATTTCATTTATGATTTAA
129 AAAAAAATTTGATTG-AGTCAATATTGAAGTAATAAAAAATCCTTTTATTTCATTTATGATATAA
* *
17520913 ATCAGATGACCAAAACACATGTAAAAAAAAGTCTACTGGATTCAAAAATTAAGTAATCACTACAT
193 ATCAGATGACCAAAACACAAGTAAAAAAAAGTCTACTGGATTCAAAAATTAAGTAATCAATACAT
* * * * *
17520978 TAGTAAAATACCCACTAAGTGAAACTACAAAAATTTGATTTATTTTGGTTTAATATTTTCTATCT
258 TAGCAAAATAACCACTAAGTAAAACTACAAAAATTTGATTTATTCTAGTTTAATATTTTCTATCT
*
17521043 AACTTCATTGCATGTCAATCCAAAAATTGACATCTCTCCAGAAAATATGGGTAGGAATAAGACTA
323 AACTTCATTGCATGTCAATCCAAAAATTGACATCTCTCCAGAAAATATAGGTAGGAATAAGACTA
* * *
17521108 CTAGCAAGCAACGAACCGCAATATTACAAAAGATATTATCAAAAATTAGCTTTAGCATTTAATTT
388 CTAGCAAGCAACGAACCACAATATTACAAAAGATATTATCAAAAATTACCTTTAGCATTTAACTT
* * *
17521173 TGTTCATCCTTTGCTCCACAGAATTCCTACAAAAGACACTTTTGTCATTAATTTTATGTGGAACA
453 TATTCATCCTTTGCTCCACAAAATTCCTACAAAAGACACTTTTGTCATTAATTTTATGGGGAACA
*
17521238 AATATATCATATGGACTTAATCAAGACGAAACAAAATAGTAAAGAAATAAAATAAAACCTCATTC
518 AATATATCAGATGGACTTAATCAAGACGAAACAAAATAGTAAAGAAATAAAATAAAACCT-ATTC
* * *
17521303 CTTTGCATCAAGTTCACCCAGATGCTCAATTCATTTTGTAAGCAGATTTTGTTTACTTCTAATAA
582 CTTTGCATCAAGTTCACCCAGATGCTCAATTCATTTTCTAAGCAGATTTTATTTACTTATAATAA
* **
17521368 GTAAAAATGAATAAACCAAAAAGGGAACAACAACTAATTTTGCCACATAACAACTTAAATGTTTT
647 GTAAAAATGAATAAACCAAAAAGGGAAAAACAACTAATTTCCCCACATAACAACTTAAATGTTTT
*
17521433 TTGTAAAAATATTTTACAACTATAGAGGGAA
712 TTGTAAAAATATTTTACAACTACAGAGGGAA
* * * ** * * *
17521464 AA-AAGAAGAGAAAAATGGCTAACTCAATGCTACCTTCATGTCATTAACAAAACCTTCAACGGAA
1 AAGAATAAGAGAAAAATGGCTAATTGAACCCTACCTACATGTCATTAACAAAACTTTCAACAGAA
17521528 CGATAGGGTGCATAAACAATGAGATCAAATAAAAAATAAGGCAATAGATCAAGAAAAAATCCAAA
66 CGATAGGGTGCATAAACAATGAGATCAAATAAAAAATAAGGCAATAGATCAAGAAAAAAT-C-AA
* *
17521593 AAAAAAATTTGATTGAGTCAATATTGAAGTAATAAAAGATCCTTTTATTTCATTTATGATATGAA
129 AAAAAAATTTGATTGAGTCAATATTGAAGTAATAAAAAATCCTTTTATTTCATTTATGATATAAA
* * *
17521658 TCCGATGACC-AAACACAAGTAAAAAAAAGTCTACTGGATTCTAAAATTAAGTAATCAATGCATT
194 TCAGATGACCAAAACACAAGTAAAAAAAAGTCTACTGGATTCAAAAATTAAGTAATCAATACATT
* *
17521722 AGCAAAATAATCACTAAGTAAAACTACAAAAATTTGATTTATTCTAGTTTAATTTTTTCTATCTA
259 AGCAAAATAACCACTAAGTAAAACTACAAAAATTTGATTTATTCTAGTTTAATATTTTCTATCTA
* * ** *
17521787 GCTTCATTGCATGTCAATCCAAAATTTGACATCTCTTTAGAAAATATAGGTAGGAATAAGGCTA-
324 ACTTCATTGCATGTCAATCCAAAAATTGACATCTCTCCAGAAAATATAGGTAGGAATAAGACTAC
* * * * * *
17521851 TAAGCAAGCAATGAACCATAATATTATAGAAGATATTATTAAAAATTACCTTTAGCATTTGACTT
389 T-AGCAAGCAACGAACCACAATATTACAAAAGATATTATCAAAAATTACCTTTAGCATTTAACTT
*
17521916 TATTCATCCTTTGCTCCACAAAATTCCTACAGAACCA-ACACTTTTGTTATTAATTTTATGGGGA
453 TATTCATCCTTTGCTCCACAAAATTCCTACA-AA--AGACACTTTTGTCATTAATTTTATGGGGA
* *
17521980 ACAAATATATCAGATGGACTTCATCAGGACGAAACAAAATAGTAAAGAAATAAAATAAAATTCCT
515 ACAAATATATCAGATGGACTTAATCAAGACGAAACAAAATAGTAAAGAAATAAAATAAAA--CCT
*
17522045 -TTCCTTTGCATCAAGTTCACCTAGATGCTCAATTCATTTTCTAAGCTA-ATTTTTATTTACTTA
578 ATTCCTTTGCATCAAGTTCACCCAGATGCTCAATTCATTTTCTAAGC-AGA-TTTTATTTACTTA
* * *
17522108 TAATAAGTAAAAATGAATAAA-CAAATAAGGGAAAAATAGCTGATTTCCCCACATAACAACTTAA
641 TAATAAGTAAAAATGAATAAACCAAA-AAGGGAAAAACAACTAATTTCCCCACATAACAACTTAA
17522172 ATGTTTTTTGTAAAAATATTTTACAACTACAGA-GGAA
705 ATGTTTTTTGTAAAAATATTTTACAACTACAGAGGGAA
* * * * *
17522209 AAGAATAAAAGAACAATGGCTGATTGAGCCCTACCTACATGTCGTTAACAAAACTTTCAACAGAA
1 AAGAATAAGAGAAAAATGGCTAATTGAACCCTACCTACATGTCATTAACAAAACTTTCAACAGAA
* * * ** * *
17522274 CAATATGGTGCAAAAACAATGAGATCAAATAAAAAATAAGATAATAGATCAAGAAAACAT-TAAA
66 CGATAGGGTGCATAAACAATGAGATCAAATAAAAAATAAGGCAATAGATCAAGAAAAAATCAAAA
* *
17522338 AAAAATTTGATGGAGACAATATTGA
131 AAAAATTTGATTGAGTCAATATTGA
17522363 CATAAGAAAA
Statistics
Matches: 799, Mismatches: 85, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
741 47 0.06
742 30 0.04
743 310 0.39
744 71 0.09
745 137 0.17
746 201 0.25
747 3 0.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (742 bp):
AAGAATAAGAGAAAAATGGCTAATTGAACCCTACCTACATGTCATTAACAAAACTTTCAACAGAA
CGATAGGGTGCATAAACAATGAGATCAAATAAAAAATAAGGCAATAGATCAAGAAAAAATCAAAA
AAAAATTTGATTGAGTCAATATTGAAGTAATAAAAAATCCTTTTATTTCATTTATGATATAAATC
AGATGACCAAAACACAAGTAAAAAAAAGTCTACTGGATTCAAAAATTAAGTAATCAATACATTAG
CAAAATAACCACTAAGTAAAACTACAAAAATTTGATTTATTCTAGTTTAATATTTTCTATCTAAC
TTCATTGCATGTCAATCCAAAAATTGACATCTCTCCAGAAAATATAGGTAGGAATAAGACTACTA
GCAAGCAACGAACCACAATATTACAAAAGATATTATCAAAAATTACCTTTAGCATTTAACTTTAT
TCATCCTTTGCTCCACAAAATTCCTACAAAAGACACTTTTGTCATTAATTTTATGGGGAACAAAT
ATATCAGATGGACTTAATCAAGACGAAACAAAATAGTAAAGAAATAAAATAAAACCTATTCCTTT
GCATCAAGTTCACCCAGATGCTCAATTCATTTTCTAAGCAGATTTTATTTACTTATAATAAGTAA
AAATGAATAAACCAAAAAGGGAAAAACAACTAATTTCCCCACATAACAACTTAAATGTTTTTTGT
AAAAATATTTTACAACTACAGAGGGAA
Found at i:17523665 original size:2 final size:2
Alignment explanation
Indices: 17523660--17523699 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17523650 TATATATATA
17523660 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17523700 NGGTCGTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17523765 original size:2 final size:2
Alignment explanation
Indices: 17523760--17523801 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17523750 TATATATATA
17523760 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17523802 CATGGATGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17523963 original size:38 final size:40
Alignment explanation
Indices: 17523912--17524014 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
17523902 AAAGTGCTCG
* *
17523912 TGTGCACGATGTGGGGGGATGCACACAATGGC-ACTAAT-
1 TGTGCACGATGTGGGGGGATGCACACAATGACTACGAATA
* * **
17523950 TGTGCACGATGTGGGGGGATGCACACGATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGACTACGAATA
17523990 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
17524015 TGAGCTAGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 30 0.53
39 2 0.04
40 25 0.44
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.20
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACAATGACTACGAATA
Found at i:17526907 original size:73 final size:73
Alignment explanation
Indices: 17526788--17526935 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
17526778 CACTTTAATT
*
17526788 GAAACTAATCTAGAAAAACCACAAGAGAAAGATTTCAACATACTTGACAGTTTGATGTCTACTTT
1 GAAACTAATATAGAAAAACCACAAGAGAAAGATTTCAACATACTTGACAGTTTGATGTCTACTTT
17526853 CTTTGGTG
66 CTTTGGTG
* *
17526861 GAAACTAATATAGAAAAACCACAAGAGAAAGATTTCGACATACTTGATAGTTTGATGTCTACTTT
1 GAAACTAATATAGAAAAACCACAAGAGAAAGATTTCAACATACTTGACAGTTTGATGTCTACTTT
17526926 CTTTGGTG
66 CTTTGGTG
17526934 GA
1 GA
17526936 GTCCTCCTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (73 bp):
GAAACTAATATAGAAAAACCACAAGAGAAAGATTTCAACATACTTGACAGTTTGATGTCTACTTT
CTTTGGTG
Found at i:17535502 original size:19 final size:19
Alignment explanation
Indices: 17535478--17535519 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
17535468 CTTCTTCTCC
17535478 TTCATGCTCCCACGCCATT
1 TTCATGCTCCCACGCCATT
*
17535497 TTCATGCTCCCATGCCATT
1 TTCATGCTCCCACGCCATT
17535516 TTCA
1 TTCA
17535520 CCTTACCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.38, G:0.10, T:0.36
Consensus pattern (19 bp):
TTCATGCTCCCACGCCATT
Found at i:17536203 original size:42 final size:42
Alignment explanation
Indices: 17536137--17536216 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
17536127 AGCACACGCC
17536137 GATGATATATGCCATGTACAGTGTGGGAGAGCACATGATGAT
1 GATGATATATGCCATGTACAGTGTGGGAGAGCACATGATGAT
* * * * *
17536179 GATGATATATGTCGTGTGCGGTGTGGGAGTGCACATGA
1 GATGATATATGCCATGTACAGTGTGGGAGAGCACATGA
17536217 CGGTGACGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.35, T:0.28
Consensus pattern (42 bp):
GATGATATATGCCATGTACAGTGTGGGAGAGCACATGATGAT
Found at i:17536571 original size:22 final size:22
Alignment explanation
Indices: 17536546--17536598 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
17536536 TATTTTAACC
17536546 TTATATAAATAA-TTTTTAATAA
1 TTATATAAATAACTTTTT-ATAA
* * *
17536568 TTATTTTAATAACTTTTTTTAA
1 TTATATAAATAACTTTTTATAA
*
17536590 TTTTATAAA
1 TTATATAAA
17536599 AGGTATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATAAATAACTTTTTATAA
Found at i:17538183 original size:12 final size:11
Alignment explanation
Indices: 17538174--17538230 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
17538164 TTCCTCTCTT
17538174 TTTCTTTCTCC
1 TTTCTTTCTCC
17538185 TTTCTTTCT--
1 TTTCTTTCTCC
*
17538194 TTCCTTTCTCC
1 TTTCTTTCTCC
17538205 TTTCTTTCT--
1 TTTCTTTCTCC
*
17538214 TTCCTTTCTCC
1 TTTCTTTCTCC
17538225 TTTCTT
1 TTTCTT
17538231 CCAACTGATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.42
11 22 0.58
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCTTTCTCC
Found at i:17538202 original size:20 final size:20
Alignment explanation
Indices: 17538177--17538230 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
17538167 CTCTCTTTTT
17538177 CTTTCTCCTTTCTTTCTTTC
1 CTTTCTCCTTTCTTTCTTTC
17538197 CTTTCTCCTTTCTTTCTTTC
1 CTTTCTCCTTTCTTTCTTTC
17538217 CTTTCTCCTTTCTT
1 CTTTCTCCTTTCTT
17538231 CCAACTGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTCCTTTCTTTCTTTC
Found at i:17538232 original size:15 final size:15
Alignment explanation
Indices: 17538156--17538232 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 15
17538146 CCAAGCTTTT
*
17538156 TTTCTTCCTTCCTCTC
1 TTTCTTCCTTTCTC-C
17538172 TTT-TT-CTTTCTCC
1 TTTCTTCCTTTCTCC
*
17538185 TTTCTTTC-TT-TCC
1 TTTCTTCCTTTCTCC
17538198 TTTC-TCC-TT-T-C
1 TTTCTTCCTTTCTCC
17538209 TTTCTTTCCTTTCTCC
1 TTTC-TTCCTTTCTCC
17538225 TTTCTTCC
1 TTTCTTCC
17538233 AACTGATCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
11 5 0.10
12 5 0.10
13 14 0.27
14 12 0.23
15 8 0.15
16 8 0.15
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCTTCCTTTCTCC
Found at i:17541076 original size:21 final size:21
Alignment explanation
Indices: 17541052--17541091 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17541042 TCAGAAAATA
17541052 TGATAGTCTT-ATCCTAAAACC
1 TGATAGTCTTCATCC-AAAACC
17541073 TGATAGTCTTCATCCAAAA
1 TGATAGTCTTCATCCAAAA
17541092 TACCCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
TGATAGTCTTCATCCAAAACC
Found at i:17549054 original size:41 final size:41
Alignment explanation
Indices: 17549009--17549090 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
17548999 TAACAAATTG
*
17549009 AGTTATT-AGATTGAACTATTGA-GATGTAATATATTATGATA
1 AGTTATTGAG-TTGAACTATT-ACGATATAATATATTATGATA
* * *
17549050 AGTTATTGAGTTGGACTGTTACGATATAATATGTTATGATA
1 AGTTATTGAGTTGAACTATTACGATATAATATATTATGATA
17549091 TATTTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
40 1 0.03
41 32 0.91
42 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (41 bp):
AGTTATTGAGTTGAACTATTACGATATAATATATTATGATA
Found at i:17549873 original size:30 final size:29
Alignment explanation
Indices: 17549810--17549888 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
17549800 AAGAATTTAT
17549810 AAAAAAATTTAAAAATTTTGTATAATATC
1 AAAAAAATTTAAAAATTTTGTATAATATC
17549839 AAAAAAATTTAAAAATTTTGTATAATATC
1 AAAAAAATTTAAAAATTTTGTATAATATC
17549868 AAAAAAATTTAATAAATTTTG
1 AAAAAAATTTAA-AAATTTTG
17549889 GGTGGCCATG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 41 0.84
30 8 0.16
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAAAAATTTAAAAATTTTGTATAATATC
Found at i:17550646 original size:55 final size:55
Alignment explanation
Indices: 17550572--17550771 Score: 204
Period size: 55 Copynumber: 3.6 Consensus size: 55
17550562 GCGTATTGTG
* *
17550572 GGTTAACTAGTTTTTTGGGTTGTTAGCGTGTTACGACTGTTCCTGGAGTGTCATA
1 GGTTAACTGGTTTTTTGGGTTGTTAGCGTGTCACGACTGTTCCTGGAGTGTCATA
* * * * * * * *
17550627 GGTTAACTGGATTTATGGGTTTTTGGCGTGTCACGGCTGTTCCTTGCGTGTCATG
1 GGTTAACTGGTTTTTTGGGTTGTTAGCGTGTCACGACTGTTCCTGGAGTGTCATA
* * * * * * *
17550682 GGTTAACTGGTTTTTTGGGTT-TTGGGCGTGTCATGGCTGTTCTTGGCGTGTTATG
1 GGTTAACTGGTTTTTTGGGTTGTT-AGCGTGTCACGACTGTTCCTGGAGTGTCATA
* * *
17550737 GGTAAACTGGTTTTTTGGGTTTTTAGCATGTCACG
1 GGTTAACTGGTTTTTTGGGTTGTTAGCGTGTCACG
17550772 GTTGTTGGTG
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
54 2 0.02
55 119 0.97
56 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.32, T:0.42
Consensus pattern (55 bp):
GGTTAACTGGTTTTTTGGGTTGTTAGCGTGTCACGACTGTTCCTGGAGTGTCATA
Found at i:17550745 original size:110 final size:110
Alignment explanation
Indices: 17550537--17550777 Score: 279
Period size: 110 Copynumber: 2.2 Consensus size: 110
17550527 GTTAGCGTTA
* **
17550537 TTTTAGTGTGTCACGGCTGTTCTTGGCGTATTGTGGGTTAACTAGTTTTTTGGGTTGTTAGCGTG
1 TTTTAGCGTGTCACGGCTGTTCTTGGCGTATCATGGGTTAACTAGTTTTTTGGGTTGTTAGCGTG
* *
17550602 TTACGACTGTTCCTGGAGTGTCATAGGTTAACTGGATTTATGGGT
66 TCACGACTGTTCCTGGAGTGTCATAGGTAAACTGGATTTATGGGT
* * * *
17550647 TTTTGGCGTGTCACGGCTGTTCCTT-GCGTGTCATGGGTTAACTGGTTTTTTGGGTT-TTGGGCG
1 TTTTAGCGTGTCACGGCTGTT-CTTGGCGTATCATGGGTTAACTAGTTTTTTGGGTTGTT-AGCG
* * * * * * * *
17550710 TGTCATGGCTGTTCTTGGCGTGTTATGGGTAAACTGGTTTTTTGGGT
64 TGTCACGACTGTTCCTGGAGTGTCATAGGTAAACTGGATTTATGGGT
* *
17550757 TTTTAGCATGTCACGGTTGTT
1 TTTTAGCGTGTCACGGCTGTT
17550778 GGTGTAACGA
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
109 2 0.02
110 104 0.95
111 3 0.03
ACGTcount: A:0.12, C:0.13, G:0.32, T:0.44
Consensus pattern (110 bp):
TTTTAGCGTGTCACGGCTGTTCTTGGCGTATCATGGGTTAACTAGTTTTTTGGGTTGTTAGCGTG
TCACGACTGTTCCTGGAGTGTCATAGGTAAACTGGATTTATGGGT
Found at i:17553838 original size:23 final size:23
Alignment explanation
Indices: 17553812--17553859 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
17553802 GTCGGGCTTG
*
17553812 ACAACAGTGATGCATGGCGTGTC
1 ACAACACTGATGCATGGCGTGTC
*
17553835 ACAATACTGATGCATGGCGTGTC
1 ACAACACTGATGCATGGCGTGTC
17553858 AC
1 AC
17553860 GACATTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (23 bp):
ACAACACTGATGCATGGCGTGTC
Found at i:17553879 original size:31 final size:31
Alignment explanation
Indices: 17553844--17553949 Score: 133
Period size: 31 Copynumber: 3.4 Consensus size: 31
17553834 CACAATACTG
17553844 ATGCATGGCGTGTCACGACATTTGACTTGAT
1 ATGCATGGCGTGTCACGACATTTGACTTGAT
* *
17553875 ATGCATGGCGTGTCAGGACATTGGACTTGAT
1 ATGCATGGCGTGTCACGACATTTGACTTGAT
* * * * *
17553906 ATGCATGGCATGTTACAACGTTTTACGTT-AT
1 ATGCATGGCGTGTCACGACATTTGAC-TTGAT
17553937 ATGCATGGCGTGT
1 ATGCATGGCGTGT
17553950 AACAACATGA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 62 0.97
32 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (31 bp):
ATGCATGGCGTGTCACGACATTTGACTTGAT
Found at i:17555379 original size:37 final size:37
Alignment explanation
Indices: 17555329--17555447 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 37
17555319 TGTTGGGTGG
* * *
17555329 TGATGTTGAAGTGTGCAAGGAGGGAGTGCACACATGA
1 TGATGATGGAGTGTGCAAGTAGGGAGTGCACACATGA
*
17555366 TGATGATGGAGTGTGCCAGTAGGGAGTGCACACATGA
1 TGATGATGGAGTGTGCAAGTAGGGAGTGCACACATGA
**
17555403 TGATGACAGAGTGTGCAAGTAGGGAGTGCACACATGA
1 TGATGATGGAGTGTGCAAGTAGGGAGTGCACACATGA
*
17555440 TGACGATG
1 TGATGATG
17555448 TATGTATATG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (37 bp):
TGATGATGGAGTGTGCAAGTAGGGAGTGCACACATGA
Found at i:17559314 original size:31 final size:31
Alignment explanation
Indices: 17559279--17559365 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
17559269 CTAAGTGCAA
* *
17559279 TCAGACTTATAGCGTGACATGCTGAGTTAAT
1 TCAGACTTATAGTGTGACATGCTGAATTAAT
*
17559310 TCAGACTTATTGTGTGACATGCTGAATTAAT
1 TCAGACTTATAGTGTGACATGCTGAATTAAT
* * *
17559341 GCAGACTTATGGTGTGACACGCTGA
1 TCAGACTTATAGTGTGACATGCTGA
17559366 CTTCTTACAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (31 bp):
TCAGACTTATAGTGTGACATGCTGAATTAAT
Found at i:17559614 original size:16 final size:16
Alignment explanation
Indices: 17559593--17559626 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17559583 AAAATCAAAT
*
17559593 AATTAATTAAAACTAA
1 AATTAACTAAAACTAA
*
17559609 AATTAACTAAAATTAA
1 AATTAACTAAAACTAA
17559625 AA
1 AA
17559627 CCAACAAGAA
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAACTAAAACTAA
Found at i:17560572 original size:31 final size:31
Alignment explanation
Indices: 17560520--17560886 Score: 383
Period size: 31 Copynumber: 11.8 Consensus size: 31
17560510 CTGGGCAAAN
*
17560520 TTATGCATGGAGTGTCACAACGTTTAACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * * *
17560551 TTATGCGTGGCATGTCCCAACGTTTAACTTA
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
*
17560582 TTATGCATGGTGTGTCACAACGTTTAACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * **
17560613 TTATGCATGGCGTGTCAGAACATTTTGCTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
*
17560644 TTATGCATGACGTGTCACAACGTTTAACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * * **
17560675 TTATGCATGGTGTGTCAGAACATTTTGCTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * *
17560706 TTATCCATGGCTTGTCACAACGTTTAACATG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * * *
17560737 TTATGCATGGCGTGTGAGAACATTTTACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * * * ** *
17560768 TTATGCATGGCATGTGAGAACATTTTGCTTA
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
** *
17560799 TTATGCATGGCGTGTCACAATATTTTACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
* * * * *
17560830 ATATGCACGGCGTGTTACAACATTTTACTTG
1 TTATGCATGGCGTGTCACAACGTTTAACTTG
*
17560861 TTATGCATGGCGTGTCACAACATTTA
1 TTATGCATGGCGTGTCACAACGTTTA
17560887 TTCCTTATTT
Statistics
Matches: 278, Mismatches: 58, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 278 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (31 bp):
TTATGCATGGCGTGTCACAACGTTTAACTTG
Found at i:17561682 original size:31 final size:31
Alignment explanation
Indices: 17561647--17562065 Score: 469
Period size: 31 Copynumber: 13.5 Consensus size: 31
17561637 AATAAGGAAT
17561647 AAATGTTGTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
17561678 AAATGTTGTAACACGCCGTGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
17561709 AAATATTGTGACACGCCATGCATAATAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
17561740 AAATGTTCTCACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
17561771 AAATGTTCTCACACGCCATGCATAACATGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
17561802 AAACGTTGTGACAAGCCATGGATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
17561833 AAATGTTCTGACACACCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
17561864 AAACGTTGTGACACGTCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
17561895 AAATGTTCTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
17561926 AAACGTTGTGACACACCATGCATAATAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * * *
17561957 AAACGTTGGGACATGCCACGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
17561988 AAACGTTGTGACACTCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
17562019 AATTGTTCTAACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
17562050 AAATGTTGTCACACGC
1 AAATGTTGTGACACGC
17562066 TAACGCTGAC
Statistics
Matches: 320, Mismatches: 68, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 320 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:17562907 original size:31 final size:30
Alignment explanation
Indices: 17562840--17562973 Score: 108
Period size: 31 Copynumber: 4.3 Consensus size: 30
17562830 AAGTGGAAGC
* *
17562840 AGATTTATGGGCTAACACGCTGAGTG-TCAGT
1 AGATTTATGGG-TGACACGCTGATTGCT-AGT
* *
17562871 GGATTTATGGCGTGACACGCTGATTGCTTGT
1 AGATTTATGG-GTGACACGCTGATTGCTAGT
* * *
17562902 AGATTTATGGGTTGACACGCTAAGTGCAAGT
1 AGATTTATGGG-TGACACGCTGATTGCTAGT
* * * * *
17562933 AGATGTATGTGGGGACACGCTGACTGGTAGC
1 AGATTTATG-GGTGACACGCTGATTGCTAGT
17562964 AGATTTATGG
1 AGATTTATGG
17562974 CATCACACGC
Statistics
Matches: 82, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
30 2 0.02
31 76 0.93
32 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (30 bp):
AGATTTATGGGTGACACGCTGATTGCTAGT
Found at i:17562950 original size:62 final size:62
Alignment explanation
Indices: 17562837--17562973 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 62
17562827 GCAAAGTGGA
* * * * *
17562837 AGCAGATTTATGGGCTAACACGCTGAGTGTCAGTGGATTTATGGCGTGACACGCTGATTGCT
1 AGCAGATTTATGGGCTAACACGCTAAGTGTCAGTAGATGTATGGCGGGACACGCTGACTGCT
* * * * *
17562899 TGTAGATTTATGGGTTGACACGCTAAGTG-CAAGTAGATGTATGTG-GGGACACGCTGACTGGT
1 AGCAGATTTATGGGCTAACACGCTAAGTGTC-AGTAGATGTATG-GCGGGACACGCTGACTGCT
17562961 AGCAGATTTATGG
1 AGCAGATTTATGG
17562974 CATCACACGC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
61 1 0.02
62 59 0.97
63 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (62 bp):
AGCAGATTTATGGGCTAACACGCTAAGTGTCAGTAGATGTATGGCGGGACACGCTGACTGCT
Found at i:17563093 original size:19 final size:20
Alignment explanation
Indices: 17563051--17563093 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
17563041 TTCTTCGTAT
17563051 AAAATTAATTGTGTATAGGCAAA
1 AAAATTAATTGTGTAT--G-AAA
17563074 AAAATTAATTGTGTAT-AAA
1 AAAATTAATTGTGTATGAAA
17563093 A
1 A
17563094 TTAATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
23 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATTAATTGTGTATGAAA
Found at i:17563104 original size:14 final size:16
Alignment explanation
Indices: 17563074--17563219 Score: 66
Period size: 16 Copynumber: 9.1 Consensus size: 16
17563064 TATAGGCAAA
17563074 AAAATTAATTGTGTAT
1 AAAATTAATTGTGTAT
* *
17563090 AAAATTAATTGTATAA
1 AAAATTAATTGTGTAT
* * ** *
17563106 AATATATTATTTATACAAA
1 AA-A-ATTAATTGT-GTAT
*
17563125 AATAATTAATTCTGTAT
1 AA-AATTAATTGTGTAT
* *
17563142 ACAATGAA-T-TGTAT
1 AAAATTAATTGTGTAT
* *
17563156 AAAATAAATTATGTAT
1 AAAATTAATTGTGTAT
**
17563172 ACAAAAAAATTGTGTAT
1 A-AAATTAATTGTGTAT
*
17563189 AAAATTAA-T-TATAT
1 AAAATTAATTGTGTAT
* *
17563203 AAAAATAATTCTGTAT
1 AAAATTAATTGTGTAT
17563219 A
1 A
17563220 TGAAAAAAAT
Statistics
Matches: 100, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
14 22 0.22
15 4 0.04
16 37 0.37
17 17 0.17
18 14 0.14
19 6 0.06
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (16 bp):
AAAATTAATTGTGTAT
Found at i:17563152 original size:52 final size:51
Alignment explanation
Indices: 17563047--17563182 Score: 182
Period size: 52 Copynumber: 2.6 Consensus size: 51
17563037 AAAATTCTTC
* * * *
17563047 GTATAAAATTAATTGTGTATAGGCAAAAAAATTAATTGTGTATAAAATTAATT
1 GTATAAAATAAATTATGTATA--CAAAAAAATTAATTCTGTATAAAATGAATT
* * *
17563100 GTATAAAATATATTATTTATACAAAAATAATTAATTCTGTATACAATGAATT
1 GTATAAAATAAATTATGTATACAAAAA-AATTAATTCTGTATAAAATGAATT
17563152 GTATAAAATAAATTATGTATACAAAAAAATT
1 GTATAAAATAAATTATGTATACAAAAAAATT
17563183 GTGTATAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 10 0.14
52 46 0.63
53 17 0.23
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (51 bp):
GTATAAAATAAATTATGTATACAAAAAAATTAATTCTGTATAAAATGAATT
Found at i:17563187 original size:17 final size:16
Alignment explanation
Indices: 17563151--17563229 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
17563141 TACAATGAAT
*
17563151 TGTATAAAATAAATTA
1 TGTATAAAAAAAATTA
*
17563167 TGTATACAAAAAAATTG
1 TGTATA-AAAAAAATTA
**
17563184 TGTATAAAATTAATTA
1 TGTATAAAAAAAATTA
* *
17563200 --TATAAAAATAATTC
1 TGTATAAAAAAAATTA
17563214 TGTATATGAAAAAAAT
1 TGTATA--AAAAAAAT
17563230 GTACAAACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.24
16 17 0.34
17 14 0.28
18 7 0.14
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (16 bp):
TGTATAAAAAAAATTA
Found at i:17563195 original size:29 final size:30
Alignment explanation
Indices: 17563161--17563219 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
17563151 TGTATAAAAT
*
17563161 AAATT-ATGTATACAAAAA-AATTGTGTATA
1 AAATTAAT-TATACAAAAATAATTCTGTATA
*
17563190 AAATTAATTATATAAAAATAATTCTGTATA
1 AAATTAATTATACAAAAATAATTCTGTATA
17563220 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (30 bp):
AAATTAATTATACAAAAATAATTCTGTATA
Found at i:17565071 original size:93 final size:93
Alignment explanation
Indices: 17564912--17565174 Score: 339
Period size: 93 Copynumber: 2.8 Consensus size: 93
17564902 AATAAGGAAT
* * * * * *
17564912 AAATGTTGTGAAACGCCATGCATAATAAGCAAAATGTTGTGACACGCTATGCATAGCAAG-CAAA
1 AAATGTTATGACACGCCATGCATATTAAGTAAAATGTTGTGACACGTTATGCATATCAAGTC-AA
17564976 ATGTTGTGACACGCCATGCATAACAAGTA
65 ATGTTGTGACACGCCATGCATAACAAGTA
*
17565005 AAATGTTTTGACACGCCATGCATATTAAGTAAAATGTTGTGACACGTTATGCATATCAAGTCAAA
1 AAATGTTATGACACGCCATGCATATTAAGTAAAATGTTGTGACACGTTATGCATATCAAGTCAAA
** * * *
17565070 TGTTGTGACACGTTATGCATATCGAGTC
66 TGTTGTGACACGCCATGCATAACAAGTA
* * * * * *
17565098 AAATGTTATGACACGCCATGCATATCAAGTCAAATTTTGTGACATGTCATGCATATCGAGTCAAA
1 AAATGTTATGACACGCCATGCATATTAAGTAAAATGTTGTGACACGTTATGCATATCAAGTCAAA
*
17565163 TGTTGTCACACG
66 TGTTGTGACACG
17565175 TTAACAATGC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 149 0.99
94 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (93 bp):
AAATGTTATGACACGCCATGCATATTAAGTAAAATGTTGTGACACGTTATGCATATCAAGTCAAA
TGTTGTGACACGCCATGCATAACAAGTA
Found at i:17565153 original size:31 final size:31
Alignment explanation
Indices: 17564912--17565174 Score: 307
Period size: 31 Copynumber: 8.5 Consensus size: 31
17564902 AATAAGGAAT
*
17564912 AAATGTTGTGAAACGCCATGCATAAT-AAG-C
1 AAATGTTGTGACACGCCATGCAT-ATCAAGTC
* *
17564942 AAAATGTTGTGACACGCTATGCATAGCAAG-C
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
* *
17564973 AAAATGTTGTGACACGCCATGCATAACAAGTA
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
17565005 AAATGTTTTGACACGCCATGCATATTAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTC
**
17565036 AAATGTTGTGACACGTTATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
** *
17565067 AAATGTTGTGACACGTTATGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
17565098 AAATGTTATGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* * * *
17565129 AAATTTTGTGACATGTCATGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
17565160 AAATGTTGTCACACG
1 AAATGTTGTGACACG
17565175 TTAACAATGC
Statistics
Matches: 203, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
30 1 0.00
31 202 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTC
Found at i:17565689 original size:29 final size:29
Alignment explanation
Indices: 17565656--17565711 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17565646 GCTGTTCAAC
17565656 CAATGCCATGTCACACACTCTAAACCAAG
1 CAATGCCATGTCACACACTCTAAACCAAG
* *
17565685 CAATGTCGTGTCACACACTCTAAACCA
1 CAATGCCATGTCACACACTCTAAACCA
17565712 TGGCATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.20
Consensus pattern (29 bp):
CAATGCCATGTCACACACTCTAAACCAAG
Found at i:17565768 original size:23 final size:25
Alignment explanation
Indices: 17565653--17565779 Score: 81
Period size: 23 Copynumber: 5.1 Consensus size: 25
17565643 TCAGCTGTTC
* *
17565653 AACCAATGCCATGTCACACACTCTA
1 AACCAATGGCGTGTCACACACTCTA
*
17565678 AACCAAGCAATGTCGTGTCACACACTCTA
1 AA-C---CAATGGCGTGTCACACACTCTA
*
17565707 AACC-ATGGCATGT-A-A-ACT-TAA
1 AACCAATGGCGTGTCACACACTCT-A
* *
17565728 CAAGCAATGCCGTGTCACACACTCTA
1 -AACCAATGGCGTGTCACACACTCTA
17565754 AA-C-ATGGCGTGTCAC-CAACTCTA
1 AACCAATGGCGTGTCACAC-ACTCTA
17565777 AAC
1 AAC
17565780 TTTGGCTTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 5 0.06
23 27 0.33
24 9 0.11
25 6 0.07
26 5 0.06
27 1 0.01
28 1 0.01
29 22 0.27
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.20
Consensus pattern (25 bp):
AACCAATGGCGTGTCACACACTCTA
Found at i:17565838 original size:47 final size:47
Alignment explanation
Indices: 17565756--17565982 Score: 258
Period size: 47 Copynumber: 4.8 Consensus size: 47
17565746 ACACTCTAAA
* * * ** * *
17565756 CATGGCGTGTCACCAACTCTAAACTTTGGCTTGTCACAGCTTCTCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTC
*
17565803 CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAAATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTC
* * ** **
17565850 CATGGTGTCTCACCAACTTTGAAAGCTAAAGTGTCACAGATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTC
* * * *
17565897 CATGCCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTC
* *
17565944 CATGGCATCTCACCAACTCTGAACGCT-GACGTGTCACAG
1 CATGGCGTCTCACCAACTCTGAACTCTGGA-GTGTCACAG
17565983 TCGTGTCACA
Statistics
Matches: 148, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
46 1 0.01
47 147 0.99
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.27
Consensus pattern (47 bp):
CATGGCGTCTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTC
Found at i:17568300 original size:25 final size:26
Alignment explanation
Indices: 17568252--17568301 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
17568242 ATCTTAATTA
* *
17568252 TGGTCAAATTTACCATTTTGCCTTTT
1 TGGTCAAATTGACCATTTTACCTTTT
*
17568278 TGGTCAAA-TGACTATTTTACCTTT
1 TGGTCAAATTGACCATTTTACCTTT
17568302 ATAAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (26 bp):
TGGTCAAATTGACCATTTTACCTTTT
Found at i:17573555 original size:36 final size:35
Alignment explanation
Indices: 17573423--17573644 Score: 189
Period size: 36 Copynumber: 6.3 Consensus size: 35
17573413 TCTCAAGCAC
*
17573423 TTGATTAAAATTGTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* * * * *
17573456 TTAATTAAATTATTTAATAAAGTCATTGGACCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* **** *
17573491 TTAATTAAATTAAACAATTAAGTTATTGGGTCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *
17573526 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAG
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* * *
17573562 TTGACTAAAATTGTTTAATTAAATTATTGGGCTTAA
1 TTGA-TTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *** *
17573598 TTAATTAAATTGTTGGGCTTAAGTTATTGGACCTAA
1 TTGATTAAATTGTT-TAATTAAGTTATTGGGCCTAA
17573634 TTGATTAAATT
1 TTGATTAAATT
17573645 AAACATTAAG
Statistics
Matches: 149, Mismatches: 34, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
32 14 0.09
33 5 0.03
35 53 0.36
36 73 0.49
37 4 0.03
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:17573604 original size:22 final size:22
Alignment explanation
Indices: 17573576--17573619 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17573566 CTAAAATTGT
17573576 TTAATTAAATTATTGGGCTTAA
1 TTAATTAAATTATTGGGCTTAA
*
17573598 TTAATTAAATTGTTGGGCTTAA
1 TTAATTAAATTATTGGGCTTAA
17573620 GTTATTGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (22 bp):
TTAATTAAATTATTGGGCTTAA
Found at i:17575057 original size:180 final size:180
Alignment explanation
Indices: 17574788--17575111 Score: 472
Period size: 180 Copynumber: 1.8 Consensus size: 180
17574778 AAAGCAGTCC
* * *
17574788 AGCTCACTGTTATGACATGAATTTCAGTTTTAATTAACAAGAAAGTCTTGGAAATTAATTCTGAA
1 AGCTCACTGTTATGACATGAATTTCAGCTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGAA
* *
17574853 AAATTCCAAGAAACTTATCTTTATTAAAATGTTTAATAAGGATTATTTCTGGAAAA-TATCATGG
66 AAATTCCAAGAAAATTATCTTTATTAAAATGTTCAATAAGGATTATTTCT-GAAAATTATCATGG
* * *
17574917 TCAAATATGCTGATTCCGAGCAAGAAAGTTGGTGCAAATATAAATATGTCA
130 CCAAACAAGCTGATTCCGAGCAAGAAAGTTGGTGCAAATATAAATATGTCA
* * * * *
17574968 AGCTTACTGTTTTGGCATGAATTTCAGCTTTAATTGACAGGAAACTCTTGAAAATTAATTCTGAA
1 AGCTCACTGTTATGACATGAATTTCAGCTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGAA
* * *
17575033 AAATTTC-AGAAAAATTATCTTTATTAAAATGTTCAATGAGGATTATTTCTGAAAATTTTCATGG
66 AAATTCCAAG-AAAATTATCTTTATTAAAATGTTCAATAAGGATTATTTCTGAAAATTATCATGG
17575097 CCAAACAAGCTGATT
130 CCAAACAAGCTGATT
17575112 TAGGCATCAA
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
179 7 0.06
180 119 0.94
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (180 bp):
AGCTCACTGTTATGACATGAATTTCAGCTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGAA
AAATTCCAAGAAAATTATCTTTATTAAAATGTTCAATAAGGATTATTTCTGAAAATTATCATGGC
CAAACAAGCTGATTCCGAGCAAGAAAGTTGGTGCAAATATAAATATGTCA
Found at i:17577957 original size:13 final size:13
Alignment explanation
Indices: 17577939--17577964 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17577929 ATGTTTCAAG
17577939 TTTGAATAATTAT
1 TTTGAATAATTAT
17577952 TTTGAATAATTAT
1 TTTGAATAATTAT
17577965 GTCATATTTA
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:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTGAATAATTAT
Found at i:17578029 original size:17 final size:17
Alignment explanation
Indices: 17578004--17578037 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17577994 TATCCTTGCA
*
17578004 ATGATATTTGATCAATT
1 ATGAAATTTGATCAATT
*
17578021 ATGAAATTTGTTCAATT
1 ATGAAATTTGATCAATT
17578038 GATCAAAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (17 bp):
ATGAAATTTGATCAATT
Found at i:17579984 original size:36 final size:35
Alignment explanation
Indices: 17579859--17580049 Score: 208
Period size: 35 Copynumber: 5.5 Consensus size: 35
17579849 CACTTGATTA
*
17579859 AAATTGTTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
17579891 AAATTATTTAATTAAGTCTTTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * *
17579926 AAATTAAATAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
17579961 AAATTTGTTTAATTATGTCATTGGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** *
17579997 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
17580033 AAATTGTTTAATTAAGT
1 AAATTGTTTAATTAAGT
17580050 TATTAAGCCT
Statistics
Matches: 133, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
32 15 0.11
35 64 0.48
36 51 0.38
37 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.46
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:17580034 original size:107 final size:103
Alignment explanation
Indices: 17579852--17580053 Score: 253
Period size: 107 Copynumber: 1.9 Consensus size: 103
17579842 TCTCAAGCAC
* *
17579852 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTATTTAATTAAGTCTTTGGGCC
1 TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATCTTTGGGCC
17579917 TAATTAATTAAATTAAATAATTAAGTTATTGGGCCTAA
66 TAATTAATTAAATTAAATAATTAAGTTATTGGGCCTAA
* * * * *
17579955 TTGATTAAATTTGTTTAATTATGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAAT-TGTT
1 TTGATTAAAATTGTTTAATTAAG---TTGGGCCTAATTAATT-AAATTATTTAATTAAATCT-TT
* ***
17580019 GGGCTTAATTAATTAAATTGTTTAATTAAGTTATT
61 GGGCCTAATTAATTAAATTAAATAATTAAGTTATT
17580054 AAGCCTNNNN
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
103 21 0.25
106 14 0.17
107 48 0.58
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (103 bp):
TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATCTTTGGGCC
TAATTAATTAAATTAAATAATTAAGTTATTGGGCCTAA
Found at i:17584942 original size:43 final size:43
Alignment explanation
Indices: 17584894--17585061 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
17584884 TGGTGTGATA
* *
17584894 ATGATGACCCAGCTATGTGCAATGT-GGGAGTGCATATGAGCTG
1 ATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCACATGAGCTG
* * *
17584937 ATGATGACCAAGCTATGTTCGATGTA-GGAGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCACATGAGCTG
* * * * *
17584980 ATGATGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTG
* *
17585023 ATGATGACCCGGCCATGTGCGAGTAGGGAGTGCACATGA
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGA
17585062 CGATGAATGA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 3 0.03
43 103 0.97
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTG
Found at i:17585357 original size:22 final size:22
Alignment explanation
Indices: 17585323--17585385 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
17585313 CCAGACCTGT
*
17585323 TTCTCGCTACAGCGAAAAAGAA
1 TTCTCGCTGCAGCGAAAAAGAA
* * *
17585345 TTCTCGTTGCAGCGAAAATGGA
1 TTCTCGCTGCAGCGAAAAAGAA
* *
17585367 TTTTCGCTGCAGCCAAAAA
1 TTCTCGCTGCAGCGAAAAA
17585386 CTCTCGGGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (22 bp):
TTCTCGCTGCAGCGAAAAAGAA
Found at i:17586492 original size:81 final size:77
Alignment explanation
Indices: 17586404--17586633 Score: 190
Period size: 81 Copynumber: 3.0 Consensus size: 77
17586394 GCTATGACAT
*
17586404 GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAATATGTGAGACGGCATAGTGAACATATGT
1 GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAATATGTGAGACGGCATGGTGAACATATGT
17586469 GACACTATTGTCACAC
66 GACAC-A-TGT--CAC
* * * * * ** * * * *
17586485 GGTAGGGTTCAAAGTTTGTGACAAGCCAT-GAAAGGAATCTGTGACACGACACGGTGAGA-ATAT
1 GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGA-GAATATGTGAGACGGCATGGTGA-ACATAT
17586548 GTG--ACA--T---
64 GTGACACATGTCAC
* * *
17586555 GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAAAATGTTAGATGGCATGGTGAACATATGT
1 GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAATATGTGAGACGGCATGGTGAACATATGT
17586620 GACACGACTGTCAC
66 GACAC-A-TGTCAC
17586634 TCAACAAGGT
Statistics
Matches: 110, Mismatches: 26, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
69 1 0.01
70 47 0.43
71 2 0.02
72 2 0.02
73 1 0.01
75 1 0.01
76 1 0.01
78 1 0.01
79 2 0.02
80 2 0.02
81 49 0.45
82 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (77 bp):
GGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAATATGTGAGACGGCATGGTGAACATATGT
GACACATGTCAC
Found at i:17586702 original size:151 final size:151
Alignment explanation
Indices: 17586398--17586682 Score: 444
Period size: 151 Copynumber: 1.9 Consensus size: 151
17586388 GGCATGGCTA
*
17586398 TGACATGGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAATATGTGAGACGGCATAGTGAAC
1 TGACATGGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAAAATGTGAGACGGCATAGTGAAC
* * *** *
17586463 ATATGTGACACTATTGTCACACGGTAGGGTTCAAAGTTTGTGACAAGCCATGAAAGGAATCTGTG
66 ATATGTGACACGACTGTCACACAACAAGGTTCAAAGTTTGTGACAAGCCATGAAAGGAATCTGTG
17586528 ACACGACACGGTGAGAATATG
131 ACACGACACGGTGAGAATATG
* * *
17586549 TGACATGGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAAAATGTTAGATGGCATGGTGAAC
1 TGACATGGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAAAATGTGAGACGGCATAGTGAAC
* * * *
17586614 ATATGTGACACGACTGTCACTCAACAAGGTTCAGAGTTTGTGACATGCCATGGAAGGAATCTGTG
66 ATATGTGACACGACTGTCACACAACAAGGTTCAAAGTTTGTGACAAGCCATGAAAGGAATCTGTG
17586679 ACAC
131 ACAC
17586683 AGCAGGGTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 120 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (151 bp):
TGACATGGCAGGGTTTAGAGTTGGTGACACGCCATGGTGAGAAAATGTGAGACGGCATAGTGAAC
ATATGTGACACGACTGTCACACAACAAGGTTCAAAGTTTGTGACAAGCCATGAAAGGAATCTGTG
ACACGACACGGTGAGAATATG
Found at i:17586804 original size:23 final size:23
Alignment explanation
Indices: 17586778--17586844 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
17586768 GGTGAGAATG
*
17586778 TGTGACACGGCATGGCTTGAACA
1 TGTGACACGCCATGGCTTGAACA
* * * *
17586801 TGTGAAACACCATGGGTTGAATA
1 TGTGACACGCCATGGCTTGAACA
* * *
17586824 TGTGACATGTCATGGTTTGAA
1 TGTGACACGCCATGGCTTGAA
17586845 ATAGAAAAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (23 bp):
TGTGACACGCCATGGCTTGAACA
Found at i:17587447 original size:87 final size:87
Alignment explanation
Indices: 17587299--17587484 Score: 257
Period size: 87 Copynumber: 2.1 Consensus size: 87
17587289 AGGTTTTTAA
* * * * ** *
17587299 CATGTCACTACATTGGTTATTTTAAGGCAGTTCGTGTAATGATTCAGTAATTATAGTGATTGGTG
1 CATGTCACCACATTGGGTATTTTAAGGCAATTCGTGTAAGGAGACAGTAATTATAGTGATTGGGG
*
17587364 TGTCACGACATGCCATGGTTGG
66 TGTCACGACACGCCATGGTTGG
* *
17587386 CGTGTCACCACATTGGGTATATTT-AGGTAATTCGTGTAAGGAGACAGTAATTATAGTGATTGGG
1 CATGTCACCACATTGGGTAT-TTTAAGGCAATTCGTGTAAGGAGACAGTAATTATAGTGATTGGG
*
17587450 GTGTCATGACACGCCATGGTTGG
65 GTGTCACGACACGCCATGGTTGG
17587473 CATGTCACCACA
1 CATGTCACCACA
17587485 CTGCTCAGCA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 83 0.97
88 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (87 bp):
CATGTCACCACATTGGGTATTTTAAGGCAATTCGTGTAAGGAGACAGTAATTATAGTGATTGGGG
TGTCACGACACGCCATGGTTGG
Found at i:17587534 original size:31 final size:31
Alignment explanation
Indices: 17587496--17587606 Score: 204
Period size: 31 Copynumber: 3.6 Consensus size: 31
17587486 TGCTCAGCAT
17587496 TGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
17587527 TGGCGTGTAACAACATTTGACTTGGTATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
17587558 TGGCGTGTAACAATATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
17587589 TGGCGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
17587607 ATTTCATTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACTTGATATGCA
Found at i:17591767 original size:22 final size:23
Alignment explanation
Indices: 17591701--17591875 Score: 194
Period size: 23 Copynumber: 7.7 Consensus size: 23
17591691 TCAGTCATGT
* *
17591701 TGTTACACGTCATTTTTAAAAAA
1 TGTTACACGCCATGTTTAAAAAA
*
17591724 TGTTACACGCCATGTTTAAAAAT
1 TGTTACACGCCATGTTTAAAAAA
*
17591747 TGTTACACGTCATGTTTAAAAAA
1 TGTTACACGCCATGTTTAAAAAA
*
17591770 TGTTACACGCCATG-TTCAAAAA
1 TGTTACACGCCATGTTTAAAAAA
* * *
17591792 TGTTACAC-CCAAG-TTCAAAAT
1 TGTTACACGCCATGTTTAAAAAA
*** *
17591813 TGTTACACGCCATGTTCCCAACA
1 TGTTACACGCCATGTTTAAAAAA
*
17591836 TGTTACACGCCATGTTAAATAAAAA
1 TGTTACACGCCATGTT-TA-AAAAA
17591861 TGTTACACGCCATGT
1 TGTTACACGCCATGT
17591876 GCTAACACAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
21 19 0.15
22 19 0.15
23 74 0.57
25 18 0.14
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (23 bp):
TGTTACACGCCATGTTTAAAAAA
Found at i:17591821 original size:66 final size:68
Alignment explanation
Indices: 17591701--17591872 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 68
17591691 TCAGTCATGT
* * * * *
17591701 TGTTACACGTCATTTTTAAAAAATGTTACACGCCATGTTTAAAAATTGTTACACGTCATGTTTAA
1 TGTTACACGCCA-TGTTAAAAAATGTTACACGCCAAGTTTAAAAATTGTTACACGCCATGTTCAA
17591766 AAAA
65 AAAA
* * **
17591770 TGTTACACGCCATGTTCAAAAATGTTACAC-CCAAG-TTCAAAATTGTTACACGCCATGTTCCCA
1 TGTTACACGCCATGTTAAAAAATGTTACACGCCAAGTTTAAAAATTGTTACACGCCATGTTCAAA
*
17591833 ACA
66 AAA
17591836 TGTTACACGCCATGTTAAATAAAAATGTTACACGCCA
1 TGTTACACGCCATGTT--A-AAAAATGTTACACGCCA
17591873 TGTGCTAACA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
66 41 0.47
67 4 0.05
68 16 0.18
69 24 0.27
70 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (68 bp):
TGTTACACGCCATGTTAAAAAATGTTACACGCCAAGTTTAAAAATTGTTACACGCCATGTTCAAA
AAA
Found at i:17592210 original size:63 final size:63
Alignment explanation
Indices: 17592106--17592227 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
17592096 ACCATAGCAC
* * * * *
17592106 GATGATGATGGTGCTCAACAGAGAGTTGACAGAGCTCATACAGTTCAGAGAGTTGAGAGCGCT
1 GATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTCATACAGTTCAAAGAGCTGAGAGCGCT
* * *
17592169 GATGACGATGGTGCTTAACAAAGAGTTGACAAAGTTGATACAGTTCAAAGAGCTGAGAG
1 GATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTCATACAGTTCAAAGAGCTGAGAG
17592228 AGAGCGAGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (63 bp):
GATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTCATACAGTTCAAAGAGCTGAGAGCGCT
Found at i:17593912 original size:107 final size:106
Alignment explanation
Indices: 17593754--17593964 Score: 323
Period size: 107 Copynumber: 2.0 Consensus size: 106
17593744 AATTGAATTG
17593754 TTTAATTAAATCATCAGGCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTA
1 TTTAATTAAATCATCAGGCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTA
17593819 AATTAAATAATTAAGTTATTGGGCCCAATTGATTAAATTTA
66 AATTAAATAATTAAGTTATTGGGCCCAATTGATTAAATTTA
* ** * * * *
17593860 TTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTATTGGGCTTAATTAATT
1 TTTAATTAAATCATCAGGCCTAATTAATT-AAATTGTTTAATTAAATCATTGGGCCTAATTAATT
** *
17593925 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
65 AAATTAAATAATTAAGTTATTGGGCCCAATTGATTAAATT
17593965 AAACAATTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
106 24 0.26
107 70 0.74
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (106 bp):
TTTAATTAAATCATCAGGCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTA
AATTAAATAATTAAGTTATTGGGCCCAATTGATTAAATTTA
Found at i:17593973 original size:35 final size:35
Alignment explanation
Indices: 17593709--17593985 Score: 263
Period size: 35 Copynumber: 7.9 Consensus size: 35
17593699 TATCAAGCAC
* *
17593709 TTGATTAAAATTGTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTATTTAATTAAGTTATTGGGCCTAA
* * * * * **
17593742 TTAATTGAATTGTTTAATTAAATCATCAGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* * * *
17593777 TTAATTAAATTGTTTAATTAAATCATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* ** *
17593812 TTAATTAAATTAAATAATTAAGTTATTGGGCCCAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* *
17593847 TTGATTAAATTTATTTAATTAAGTCATTGGGCCTAG
1 TTGATTAAA-TTATTTAATTAAGTTATTGGGCCTAA
* * *
17593883 TTGATTAAAATTGTTTAATTAAATTATTGGGCTTAA
1 TTGATT-AAATTATTTAATTAAGTTATTGGGCCTAA
*
17593919 TTAATTAAATTATTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
***
17593954 TTGATTAAATTAAACAATTAAGTTATTTGGGC
1 TTGATTAAATTATTTAATTAAGTTA-TTGGGC
17593986 TTCTTAAGGA
Statistics
Matches: 204, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
32 14 0.07
33 5 0.02
35 123 0.60
36 59 0.29
37 3 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (35 bp):
TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
Found at i:17593986 original size:71 final size:70
Alignment explanation
Indices: 17593774--17593987 Score: 284
Period size: 71 Copynumber: 3.0 Consensus size: 70
17593764 TCATCAGGCC
* * *
17593774 TAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTAAATAATTAAGTTATT
1 TAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAATTAAATAATTAAGTTATT
*
17593839 GGGCC
66 GGGCT
* * * *** *
17593844 CAATTGATTAAATTTATTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTA
1 TAATTAATTAAA-TTATTTAATTAAGTCATTGGGCCTAATTGATT-AAATTAAATAATTAAGTTA
17593909 TTGGGCT
64 TTGGGCT
* *
17593916 TAATTAATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAAGTTATT
1 TAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAATTAAATAATTAAGTTA-T
17593981 TGGGCT
65 TGGGCT
17593987 T
1 T
17593988 CTTAAGGACT
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
70 24 0.20
71 66 0.55
72 31 0.26
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (70 bp):
TAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAATTAAATAATTAAGTTATT
GGGCT
Found at i:17604276 original size:2 final size:2
Alignment explanation
Indices: 17604269--17604305 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17604259 TTGGCACTGT
*
17604269 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17604306 CAAACTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17604378 original size:41 final size:42
Alignment explanation
Indices: 17604306--17604386 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
17604296 AAGAAAGAGA
17604306 CAAACTAAATGTAGTAAATATTTACATTAG-TTTTTGTGTNAG
1 CAAACTAAATGTAGTAAATATTTACATTAGTTTTTTGTGT-AG
17604348 CAAACTAAATGT-GTAAATATTTTACA-TAGTTTTTTGTGT
1 CAAACTAAATGTAGTAAATA-TTTACATTAGTTTTTTGTGT
17604387 TCATACCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (42 bp):
CAAACTAAATGTAGTAAATATTTACATTAGTTTTTTGTGTAG
Found at i:17607699 original size:17 final size:19
Alignment explanation
Indices: 17607663--17607701 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
17607653 GTTCTTTGCT
*
17607663 TTGTCTTCAAGATCCTTCA
1 TTGTCTTCAACATCCTTCA
17607682 TTGTCTTC-ACAT-CTTCA
1 TTGTCTTCAACATCCTTCA
17607699 TTG
1 TTG
17607702 ATTACCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.18, C:0.26, G:0.10, T:0.46
Consensus pattern (19 bp):
TTGTCTTCAACATCCTTCA
Found at i:17608553 original size:16 final size:16
Alignment explanation
Indices: 17608507--17608565 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
17608497 TGGTTCATAG
*
17608507 AATAAAATAAAAT-AA
1 AATAAAATAAAGTAAA
* *
17608522 AATAAATATTATGTAAA
1 AATAAA-ATAAAGTAAA
17608539 AATAAAATAAAGTAAA
1 AATAAAATAAAGTAAA
*
17608555 AATAGAATAAA
1 AATAAAATAAA
17608566 AATGATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.17
16 22 0.61
17 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
AATAAAATAAAGTAAA
Found at i:17608565 original size:27 final size:28
Alignment explanation
Indices: 17608503--17608568 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
17608493 TAATTGGTTC
17608503 ATAGAAT-AAAATAAAATAAAATAAATA
1 ATAGAATAAAAATAAAATAAAATAAATA
* *
17608530 TTATG--TAAAAATAAAATAAAGTAAA-A
1 ATA-GAATAAAAATAAAATAAAATAAATA
17608556 ATAGAATAAAAAT
1 ATAGAATAAAAAT
17608569 GATATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 26 0.81
28 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (28 bp):
ATAGAATAAAAATAAAATAAAATAAATA
Found at i:17608757 original size:22 final size:21
Alignment explanation
Indices: 17608732--17608798 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
17608722 TTTTATTTAT
17608732 TTTATTTTTTAAATATTAATAA
1 TTTA-TTTTTAAATATTAATAA
*
17608754 TTTA-TTTAAAATATTAATAA
1 TTTATTTTTAAATATTAATAA
* * *
17608774 TTGATAATTTAATTATTAAT-A
1 TTTAT-TTTTAAATATTAATAA
17608795 TTTA
1 TTTA
17608799 AAAATATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 18 0.49
21 4 0.11
22 15 0.41
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTATTTTTAAATATTAATAA
Found at i:17608770 original size:27 final size:27
Alignment explanation
Indices: 17608740--17608831 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
17608730 ATTTTATTTT
*
17608740 TTAAATATTAATAATTTATTTAAAATA
1 TTAAATATTAATAATTTATTTATAATA
* *
17608767 TT-AATAATTGATAATTTAATTATTAATA
1 TTAAAT-ATTAATAATTTATTTA-TAATA
*
17608795 TTTAAAAATATTAATATTTTATTTATAAT-
1 -TT--AAATATTAATAATTTATTTATAATA
17608824 TTAAATAT
1 TTAAATAT
17608832 CTTTATGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
26 9 0.17
27 16 0.30
28 6 0.11
29 2 0.04
30 4 0.08
31 13 0.25
32 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAAATATTAATAATTTATTTATAATA
Found at i:17608812 original size:22 final size:21
Alignment explanation
Indices: 17608763--17608812 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
17608753 ATTTATTTAA
* *
17608763 AATATTAATAATTGATAATTT
1 AATATTAATAATTAAAAATTT
*
17608784 AATTATTAATATTTAAAAATATT
1 AA-TATTAATAATTAAAAAT-TT
17608807 AATATT
1 AATATT
17608813 TTATTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 18 0.75
23 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATTAATAATTAAAAATTT
Found at i:17620073 original size:20 final size:20
Alignment explanation
Indices: 17620049--17620097 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17620039 ATAAATATAA
17620049 ATAACATAAAACAAAC-TTT
1 ATAACATAAAACAAACATTT
* *
17620068 ATTAACTTAAAATAAACATTT
1 A-TAACATAAAACAAACATTT
17620089 A-AACATAAA
1 ATAACATAAA
17620098 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAACATAAAACAAACATTT
Found at i:17620638 original size:35 final size:35
Alignment explanation
Indices: 17620585--17620656 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
17620575 CCTTAAAGTA
* *
17620585 AGCTCACCTTTTTTCACATTAATTAAAGCTCGAGT
1 AGCTCACCTTTTTCCACATCAATTAAAGCTCGAGT
17620620 AGCTCATCC-TTTTCCACATCAATTAAAGCTCGAGT
1 AGCTCA-CCTTTTTCCACATCAATTAAAGCTCGAGT
17620655 AG
1 AG
17620657 TTTTCAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
AGCTCACCTTTTTCCACATCAATTAAAGCTCGAGT
Found at i:17621566 original size:21 final size:21
Alignment explanation
Indices: 17621524--17621591 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
17621514 TTGAATAGAG
* *
17621524 GCATCAGTCCTTGTTA-GAAAT
1 GCATTAGTCTTTGTTATG-AAT
17621545 GCATTAGTCTTTGTTATGAAT
1 GCATTAGTCTTTGTTATGAAT
* * *
17621566 GTATTAGTTTTTGTCATGAATT
1 GCATTAGTCTTTGTTATGAA-T
17621588 GCAT
1 GCAT
17621592 GAGCATATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (21 bp):
GCATTAGTCTTTGTTATGAAT
Found at i:17623047 original size:24 final size:24
Alignment explanation
Indices: 17623020--17623072 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17623010 AATTTATATA
*
17623020 ATTCACAAAACCACAATTTTAGCC
1 ATTCACAAAACCACAATTTCAGCC
****
17623044 ATTCATGCTACCACAATTTCAGCC
1 ATTCACAAAACCACAATTTCAGCC
17623068 ATTCA
1 ATTCA
17623073 TGCTACCACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.28
Consensus pattern (24 bp):
ATTCACAAAACCACAATTTCAGCC
Found at i:17623073 original size:24 final size:24
Alignment explanation
Indices: 17623029--17623088 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
17623019 AATTCACAAA
*
17623029 ACCACAATTTTAGCCATTCATGCT
1 ACCACAATTTCAGCCATTCATGCT
17623053 ACCACAATTTCAGCCATTCATGCT
1 ACCACAATTTCAGCCATTCATGCT
17623077 ACCACAATTTCA
1 ACCACAATTTCA
17623089 TAAGCCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.30
Consensus pattern (24 bp):
ACCACAATTTCAGCCATTCATGCT
Done.