Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold154
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: 1945843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 156 characters in sequence are not A, C, G, or T
File 12 of 12
Found at i:1780114 original size:43 final size:43
Alignment explanation
Indices: 1780032--1780119 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
1780022 AGAAGGATGA
* * *
1780032 TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
* * *
1780075 TAAAGGTGCCAATGTGCTGATTCTAGGCCAACGACATTGGGCT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
1780118 TA
1 TA
1780120 GAAGAAGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
Found at i:1780400 original size:96 final size:96
Alignment explanation
Indices: 1780112--1780660 Score: 759
Period size: 96 Copynumber: 5.8 Consensus size: 96
1780102 CCAACGACAT
* * * * *
1780112 TGGGCTTAGAAGAAGATT-CCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACCAACTTGTGT
1 TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGT
* * * * *
1780176 AGGCTTTTGAAAGGGTTACCATCGACTTGTG
66 GGGCTTTAGAAAGGGTTGCCACCAACTTGTG
* * *
1780207 TGGCCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGG-AGGGGTTGCCACTGACTTGTGT
1 TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGT
** * *
1780271 AAGCTTTAGAAAGGGTTGCCACCAGCTTATG
66 GGGCTTTAGAAAGGGTTGCCACCAACTTGTG
* *
1780302 TGGGCTTTGGAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAA-AGTTGCCACCGACTTGTG
1 TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGA-AAGGGTTGCCACCGACTTGTG
1780366 TGGGCTTTAGGAAA-GGTTGCCACCAACTTGTG
65 TGGGCTTTA-GAAAGGGTTGCCACCAACTTGTG
* *
1780398 TGGGCTTTGAAGAA-ATTGCCACCAAGCTTGTGTGGGCATTGGAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAGAAGGTTGCCACC-AGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTG
* *
1780462 TGAGCTTTAGAAAAGGTTGCCACCAACTTGTG
65 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTG
* * *
1780494 TGGGTTTTGAAGAAAGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCATCGACTTGTGT
1 TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGT
* *
1780559 GGGTTTTAGAAAGGGTTGCCACCAACTTCTG
66 GGGCTTTAGAAAGGGTTGCCACCAACTTGTG
* *
1780590 TGGGCTTTGAAGAAGGTTGCCA-CAACTTGTGTGGGCTTTGGAAAGGGTTGCCACCAACTTGTGT
1 TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGT
1780654 GGGCTTT
66 GGGCTTT
1780661 GAAGAAGGTT
Statistics
Matches: 403, Mismatches: 43, Indels: 16
0.87 0.09 0.03
Matches are distributed among these distances:
95 157 0.39
96 233 0.58
97 13 0.03
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (96 bp):
TGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGT
GGGCTTTAGAAAGGGTTGCCACCAACTTGTG
Found at i:1780661 original size:32 final size:32
Alignment explanation
Indices: 1780130--1780661 Score: 593
Period size: 32 Copynumber: 16.7 Consensus size: 32
1780120 GAAGAAGATT
*
1780130 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
* * *
1780162 CCACCAACTTGTGTAGGCTTTTGAAAGGGTTA
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
* * * *
1780194 CCATCGACTTGTGTGGCCTTT-GAAGAAGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAA-AGGGTTG
* *
1780226 CCACCAGCTTGTGTGGGCTTTGG-AGGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
** ** *
1780257 CCACTGACTTGTGTAAGCTTTAGAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
* *
1780289 CCACCAGCTTATGTGGGCTTTGGAGAA-GGTTG
1 CCACCAACTTGTGTGGGCTTTGGA-AAGGGTTG
* *
1780321 CCACCAGCTTGTGTGGGCTTTGGAGAA-AGTTG
1 CCACCAACTTGTGTGGGCTTTGGA-AAGGGTTG
*
1780353 CCACCGACTTGTGTGGGCTTTAGGAAA-GGTTG
1 CCACCAACTTGTGTGGGCTTT-GGAAAGGGTTG
1780385 CCACCAACTTGTGTGGGCTTTGAAGAAA---TTG
1 CCACCAACTTGTGTGGGCTTTG--GAAAGGGTTG
*
1780416 CCACCAAGCTTGTGTGGGCATTGGAAAGGGTTG
1 CCACCAA-CTTGTGTGGGCTTTGGAAAGGGTTG
* * * *
1780449 CCACCGACTTGTGTGAGCTTTAGAAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
*
1780481 CCACCAACTTGTGTGGGTTTTGAAGAAA--GTTG
1 CCACCAACTTGTGTGGGCTTTG--GAAAGGGTTG
*
1780513 CCACCAGCTTGTGTGGGCTTTGGAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
* * * *
1780545 CCATCGACTTGTGTGGGTTTTAGAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
* *
1780577 CCACCAACTTCTGTGGGCTTT-GAAGAAGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAA-AGGGTTG
1780609 CCA-CAACTTGTGTGGGCTTTGGAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
1780640 CCACCAACTTGTGTGGGCTTTG
1 CCACCAACTTGTGTGGGCTTTG
1780662 AAGAAGGTTT
Statistics
Matches: 424, Mismatches: 58, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
30 8 0.02
31 64 0.15
32 329 0.78
33 19 0.04
34 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (32 bp):
CCACCAACTTGTGTGGGCTTTGGAAAGGGTTG
Found at i:1780848 original size:33 final size:32
Alignment explanation
Indices: 1780804--1780987 Score: 110
Period size: 34 Copynumber: 5.8 Consensus size: 32
1780794 TAGAGGAAGG
1780804 TGCCACGGAGTTGTGGGCTTAAAAGGAACAAAA
1 TGCCACGGAGTTGTGGGCTTAAAAGGAA-AAAA
* * ** *
1780837 TGCCACAGAGTTGTGGACTTTGAAGGAAAAGA
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAA
** * *
1780869 TGCCACGGAGTAATGGGCTTCGCAAA-GAAAAAGT
1 TGCCACGGAGTTGTGGGCTT--AAAAGGAAAAA-A
* * *
1780903 TACCACGGAGTTGTGGACTTAAAAGG-----G
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAA
** * *
1780930 TGCCACAAAGTTATGGACTTAAAAGGAAAAAGA
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAA-A
* *
1780963 GTGCCACGAAGTTGTGGACTTAAAA
1 -TGCCACGGAGTTGTGGGCTTAAAA
1780988 AAGAAAAAGG
Statistics
Matches: 114, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
27 22 0.19
32 22 0.19
33 30 0.26
34 40 0.35
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (32 bp):
TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAA
Found at i:1780967 original size:34 final size:33
Alignment explanation
Indices: 1780923--1781180 Score: 136
Period size: 34 Copynumber: 7.8 Consensus size: 33
1780913 TTGTGGACTT
* *
1780923 AAAAGGGTGCCACAAAGTTATGGACTTAAAAGG
1 AAAAAGGTGCCACAAAGTTGTGGACTTAAAAGG
* *
1780956 AAAAAGAGTGCCACGAAGTTGTGGACTTAAAAAAG
1 AAAAAG-GTGCCACAAAGTTGTGGACTT-AAAAGG
* * * * *
1780991 AAAAAGGTGCCATAGAGTCGTGGACTTTGAAGGG
1 AAAAAGGTGCCACAAAGTTGTGGAC-TTAAAAGG
* * * *
1781025 AACAAGGTGCCATAGAGTTGTGAACTTAAAAGG
1 AAAAAGGTGCCACAAAGTTGTGGACTTAAAAGG
* *** *
1781058 -AAAATGTGCCATGGAGTTGTGGACTTGAAGAGG
1 AAAAAGGTGCCACAAAGTTGTGGACTT-AAAAGG
* * **
1781091 ----AGATGCCACCAAA-TCGTGGACTTGGAA-G
1 AAAAAGGTGCCA-CAAAGTTGTGGACTTAAAAGG
* ** *
1781119 AAAAAGGATGCCACTAAGTCATGGACTTAGAAGG
1 AAAAAGG-TGCCACAAAGTTGTGGACTTAAAAGG
* * *
1781153 -AAAAGGATGGCACTAAGTCGTGGACTTA
1 AAAAAGG-TGCCACAAAGTTGTGGACTTA
1781181 GAGAAGAGAT
Statistics
Matches: 177, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 15 0.08
31 1 0.01
32 27 0.15
33 59 0.33
34 60 0.34
35 13 0.07
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (33 bp):
AAAAAGGTGCCACAAAGTTGTGGACTTAAAAGG
Found at i:1781015 original size:68 final size:65
Alignment explanation
Indices: 1780943--1781083 Score: 149
Period size: 66 Copynumber: 2.1 Consensus size: 65
1780933 CACAAAGTTA
*
1780943 TGGACTTAAAAGGAAAAAGAGTGCCACGA-AGTTGTGGACTTAAAAAAGAAAAAGGTGCCATAGA
1 TGGACTTAAAAGGAAAAAG-GTGCCA-GAGAGTTGTGAACTT--AAAAGAAAAAGGTGCCATAGA
1781007 GTCG
62 GTCG
* * * * * * * *
1781011 TGGACTTTGAAGGGAACAAGGTGCCATAGAGTTGTGAACTTAAAAGGAAAATGTGCCATGGAGTT
1 TGGAC-TTAAAAGGAAAAAGGTGCCAGAGAGTTGTGAACTTAAAAGAAAAAGGTGCCATAGAGTC
1781076 G
65 G
1781077 TGGACTT
1 TGGACTT
1781084 GAAGAGGAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
65 2 0.03
66 26 0.42
67 1 0.02
68 22 0.35
69 11 0.18
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (65 bp):
TGGACTTAAAAGGAAAAAGGTGCCAGAGAGTTGTGAACTTAAAAGAAAAAGGTGCCATAGAGTCG
Found at i:1781110 original size:30 final size:30
Alignment explanation
Indices: 1781071--1781299 Score: 226
Period size: 30 Copynumber: 7.4 Consensus size: 30
1781061 ATGTGCCATG
* * *
1781071 GAGTTGTGGACTTGAAGAGGAGATGCCACC
1 GAGTCGTGGACTTGAAGAAGAGATGCCACT
* * *
1781101 AAATCGTGGACTTGGAAGAAAAAGGATGCCACT
1 GAGTCGTGGACTT-GAAG-AAGA-GATGCCACT
* * * *
1781134 AAGTCATGGACTTAGAAGGAAAAGGATGGCACT
1 GAGTCGTGGACTT-GAA-GAAGA-GATGCCACT
*
1781167 AAGTCGTGGACTT-AGAGAAGAGATGCCACT
1 GAGTCGTGGACTTGA-AGAAGAGATGCCACT
* * *
1781197 GAGTCGTGGACTTAAAGAAAAGATGCCACG
1 GAGTCGTGGACTTGAAGAAGAGATGCCACT
* *
1781227 GAGTCGTAGACTTGGAGAAGAGATGCCACT
1 GAGTCGTGGACTTGAAGAAGAGATGCCACT
* *
1781257 GAGTTGTGGACTTGGAGAAGAGATGCCACT
1 GAGTCGTGGACTTGAAGAAGAGATGCCACT
1781287 GAGTCGTGGACTT
1 GAGTCGTGGACTT
1781300 TGGGAAAGGT
Statistics
Matches: 169, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
30 108 0.64
31 10 0.06
32 3 0.02
33 47 0.28
34 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (30 bp):
GAGTCGTGGACTTGAAGAAGAGATGCCACT
Found at i:1781282 original size:90 final size:96
Alignment explanation
Indices: 1781048--1781299 Score: 277
Period size: 90 Copynumber: 2.7 Consensus size: 96
1781038 AGAGTTGTGA
* * * * ** *
1781048 ACTTAAAAGGAAAATG-TGCCA-TGGAGTTGTGGACTTGAAGAGGAGATGCCACCAAATCGTGGA
1 ACTTAGAAGGAAAAGGATGCCACT-GAGTTGTGGACTTGGAGAAGAGATGCCACTGAGTCGTGGA
* * *
1781111 CTTGGAAGAAAAAGGATGCCACTAAGTCATGG
65 CTTGAAAGAAAAAGGATGCCACGAAGTCATAG
* * * *
1781143 ACTTAGAAGGAAAAGGATGGCACTAAGTCGTGGACTTAGAGAAGAGATGCCACTGAGTCGTGGAC
1 ACTTAGAAGGAAAAGGATGCCACTGAGTTGTGGACTTGGAGAAGAGATGCCACTGAGTCGTGGAC
* *
1781208 TT-AAAG-AAAA-GATGCCACGGAGTCGTAG
66 TTGAAAGAAAAAGGATGCCACGAAGTCATAG
* *
1781236 ACTT-GGA-GAAGA-GATGCCACTGAGTTGTGGACTTGGAGAAGAGATGCCACTGAGTCGTGGAC
1 ACTTAGAAGGAAAAGGATGCCACTGAGTTGTGGACTTGGAGAAGAGATGCCACTGAGTCGTGGAC
1781298 TT
66 TT
1781300 TGGGAAAGGT
Statistics
Matches: 133, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
90 48 0.36
91 4 0.03
92 2 0.02
93 18 0.14
94 4 0.03
95 17 0.13
96 39 0.29
97 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.20
Consensus pattern (96 bp):
ACTTAGAAGGAAAAGGATGCCACTGAGTTGTGGACTTGGAGAAGAGATGCCACTGAGTCGTGGAC
TTGAAAGAAAAAGGATGCCACGAAGTCATAG
Found at i:1781430 original size:74 final size:74
Alignment explanation
Indices: 1781342--1781493 Score: 277
Period size: 74 Copynumber: 2.1 Consensus size: 74
1781332 GAAAAAGATT
1781342 TGAAAGATTGAGATGTAGTCCACTAAGGATTAATGTGAGTAAGAGTAGTGCTATGACGACATATG
1 TGAAAGATTGAGATGTAGTCCACTAAGGATTAATGTGAGTAAGAGTAGTGCTATGACGACATATG
1781407 GTAATGATG
66 GTAATGATG
* * *
1781416 TGAAAGATTGAGATGTAGTCCATTAAGGATTGATGTGAGTAAGAGTAGTGCTATGATGACATATG
1 TGAAAGATTGAGATGTAGTCCACTAAGGATTAATGTGAGTAAGAGTAGTGCTATGACGACATATG
1781481 GTAATGATG
66 GTAATGATG
1781490 TGAA
1 TGAA
1781494 TGCATGATGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (74 bp):
TGAAAGATTGAGATGTAGTCCACTAAGGATTAATGTGAGTAAGAGTAGTGCTATGACGACATATG
GTAATGATG
Found at i:1781451 original size:35 final size:34
Alignment explanation
Indices: 1781342--1781453 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 34
1781332 GAAAAAGATT
*
1781342 TGAAAGATTGAGATGTAGTCCACTAAGGATTAATG
1 TGAAAGATTGAGATGTAGTCCA-TAAGGATTGATG
* * * *
1781377 TGAGTAAGAGT-AG-TGCTATGACGACATATGGTAATGATG
1 TGA--AAGATTGAGATG-TA-GTC--CATAAGG-ATTGATG
1781416 TGAAAGATTGAGATGTAGTCCATTAAGGATTGATG
1 TGAAAGATTGAGATGTAGTCCA-TAAGGATTGATG
1781451 TGA
1 TGA
1781454 GTAAGAGTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
35 16 0.28
36 8 0.14
37 14 0.24
38 8 0.14
39 12 0.21
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (34 bp):
TGAAAGATTGAGATGTAGTCCATAAGGATTGATG
Found at i:1782620 original size:16 final size:16
Alignment explanation
Indices: 1782601--1782635 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1782591 CCTTTTTAAT
1782601 TTTTTGTTGTTTTTTC
1 TTTTTGTTGTTTTTTC
* *
1782617 TTTTTTTTTTTTTTTC
1 TTTTTGTTGTTTTTTC
1782633 TTT
1 TTT
1782636 CTTTGACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (16 bp):
TTTTTGTTGTTTTTTC
Found at i:1782625 original size:20 final size:20
Alignment explanation
Indices: 1782600--1782639 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1782590 GCCTTTTTAA
*
1782600 TTTTTTGTTGTTT-TTTCTT
1 TTTTTTTTTGTTTCTTTCTT
*
1782619 TTTTTTTTTTTTTCTTTCTT
1 TTTTTTTTTGTTTCTTTCTT
1782639 T
1 T
1782640 GACTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTGTTTCTTTCTT
Found at i:1789946 original size:87 final size:88
Alignment explanation
Indices: 1789776--1789991 Score: 326
Period size: 87 Copynumber: 2.5 Consensus size: 88
1789766 CATCTTCTTC
* *
1789776 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTCAAGACCAATGTCACT
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTAGCACCTTTATCTTCAAGACCAATGTCACT
*
1789841 GGCCTTGAATCAGTACATTGGCA
66 GGCCTTGAATCAGCACATTGGCA
* * * *
1789864 TAAGTCCGATATCGCTGGCCTTGAATCAACATATTAGCTCC-TTGTCTTTAAGACCAATGTCACT
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTAGCACCTTTATCTTCAAGACCAATGTCACT
1789928 GGCCTTGAATCAGCACATTGGCA
66 GGCCTTGAATCAGCACATTGGCA
* * * *
1789951 CAAGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACC
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTAGCACC
1789992 ACCATCTTTA
Statistics
Matches: 115, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 78 0.68
88 37 0.32
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (88 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAACATATTAGCACCTTTATCTTCAAGACCAATGTCACT
GGCCTTGAATCAGCACATTGGCA
Found at i:1789971 original size:39 final size:39
Alignment explanation
Indices: 1789917--1790214 Score: 157
Period size: 39 Copynumber: 6.9 Consensus size: 39
1789907 GTCTTTAAGA
* * *
1789917 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
* * *
1789956 CCAATATCGTTGGCCTTGAATCAACATATTGGCACCA-C
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
* *
1789994 CATCTTTAAATCTGATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGA
1 C--C-----A----ATATCGCTGGCCTTGAATCAGCATATTGGCA------C---AAGC
* * *
1790053 CCAATGTCGCTGGCCTTGAATAAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
*
1790092 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGCCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATT-G----G-CA-C---AAGC
* * * * *
1790141 CCAATGTAGTTGGCCTTGAATCAGCACATTAGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
*
1790180 CCAATATCGCTAGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1790215 CTTCATCTTT
Statistics
Matches: 198, Mismatches: 30, Indels: 62
0.68 0.10 0.21
Matches are distributed among these distances:
38 2 0.01
39 93 0.47
40 2 0.01
42 2 0.01
43 2 0.01
44 2 0.01
45 3 0.02
46 1 0.01
48 27 0.14
49 59 0.30
52 1 0.01
55 1 0.01
57 1 0.01
58 1 0.01
59 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAGC
Found at i:1790033 original size:136 final size:136
Alignment explanation
Indices: 1789871--1790138 Score: 473
Period size: 136 Copynumber: 2.0 Consensus size: 136
1789861 GCATAAGTCC
*
1789871 GATATCGCTGGCCTTGAATCAACATATTAGCTCCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
1 GATATCGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
* *
1789936 ATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCACCATCTTT
66 ATAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTT
1790001 AAATCT
131 AAATCT
* *
1790007 GATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
1 GATATCGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
* *
1790072 ATAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGCCATCTTT
66 ATAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTT
1790137 AA
131 AA
1790139 GACCAATGTA
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (136 bp):
GATATCGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
ATAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTT
AAATCT
Found at i:1790155 original size:136 final size:136
Alignment explanation
Indices: 1789872--1790175 Score: 457
Period size: 136 Copynumber: 2.2 Consensus size: 136
1789862 CATAAGTCCG
* *
1789872 ATATCGCTGGCCTTGAATCAACATATTAGCTCCTTGTCTTTAAGACCAATGTCACTGGCCTTGAA
1 ATATAGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGAA
* *
1789937 TCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCACCATCTTTA
66 TAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTTA
**
1790002 AATCTG
131 AATCCA
* * *
1790008 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAA
1 ATATAGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGAA
* *
1790073 TAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGCCATCTTTA
66 TAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTTA
1790138 AGA-CCA
131 A-ATCCA
* * * *
1790144 ATGTAGTTGGCCTTGAATCAGCACATTAGCAC
1 ATATAGCTGGCCTTGAATCAACATATTAGCAC
1790176 AAGCCCAATA
Statistics
Matches: 152, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
136 151 0.99
137 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (136 bp):
ATATAGCTGGCCTTGAATCAACATATTAGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGAA
TAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCACCATCTTTA
AATCCA
Found at i:1790167 original size:88 final size:87
Alignment explanation
Indices: 1790008--1790263 Score: 386
Period size: 88 Copynumber: 2.9 Consensus size: 87
1789998 TTTAAATCTG
* ** *
1790008 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTGAA
*
1790073 TAAGCACATTGGCACAAGCCCA
66 TCAGCACATTGGCACAAGCCCA
* *
1790095 ATATCGCTGGCCTTGAATCAGCATATTGGCACCGCCATCTTTAAGACCAATGTAGTTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATCTTTAAGACCAATGTCGTTGGCCTTGA
*
1790160 ATCAGCACATTAGCACAAGCCCA
65 ATCAGCACATTGGCACAAGCCCA
* * * *
1790183 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACCGATGTCGTTGGCTTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATCTTTAAGACCAATGTCGTTGGCCTTGA
1790248 ATCAGCACATTGGCAC
65 ATCAGCACATTGGCAC
1790264 CTTAACCATC
Statistics
Matches: 152, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 32 0.21
88 120 0.79
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (87 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTGAA
TCAGCACATTGGCACAAGCCCA
Found at i:1790178 original size:224 final size:223
Alignment explanation
Indices: 1789784--1790315 Score: 742
Period size: 224 Copynumber: 2.4 Consensus size: 223
1789774 TCTAAGTCCA
* *
1789784 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTCAAGACCAATGTCACTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCTGGCCTTGA
* * * * * ***
1789849 ATCAGTACATTGGCATAAGTCCGATATCGCTGGCCTTGAATCAACATATTAGCTCCTTGTCTTTA
65 ATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTAGCACCCCATCTTTA
* * *
1789914 AGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCA
130 AGACCAATGTCACTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCGCTAGCCTTGAATCA
* *
1789979 ACATATTGGCACCACCATCTTTAAATCTG
195 ACATATTGGCACCACCATCTTTAAAACCG
* *
1790008 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGCCTTGAA
* * *
1790073 TAAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGCCATCTTTA
66 TCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTAGCACC-CCATCTTTA
*
1790138 AGACCAATGT-AGTTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCGCTAGCCTTGAATC
130 AGACCAATGTCA-CTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCGCTAGCCTTGAATC
* **
1790202 AGCATATTGGCACCTTCATCTTTAAAACCG
194 AACATATTGGCACCACCATCTTTAAAACCG
* * * *
1790232 ATGTCGTTGGCTTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTCGCTGGCCT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT----ATCTTTAAGACCAATGTCGCTGGCCT
1790297 TGAATCAGCACATTGGCAC
62 TGAATCAGCACATTGGCAC
1790316 CTTCATCTTT
Statistics
Matches: 271, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
223 77 0.28
224 151 0.56
228 43 0.16
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (223 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTAGCACCCCATCTTTAA
GACCAATGTCACTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCGCTAGCCTTGAATCAA
CATATTGGCACCACCATCTTTAAAACCG
Found at i:1790300 original size:52 final size:49
Alignment explanation
Indices: 1790180--1790459 Score: 251
Period size: 52 Copynumber: 5.6 Consensus size: 49
1790170 TAGCACAAGC
* * * *
1790180 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * *
1790229 CCGATGTCGTTGGCTTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGA
*
1790281 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * * * * ** *
1790330 CCGATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCTTTAAGA
* * * * *
1790382 CCAATGTCACTGGCCTT-ATCTCAGCACATTGGCA--TTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGA-ATCAGCACATTGGCACCTTCATCTTTAAGA
* * *
1790429 CTAATGTCGCTAGCCATGAATCAGCACATTG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTG
1790460 TCATTCTTCG
Statistics
Matches: 186, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
47 30 0.16
48 1 0.01
49 73 0.39
50 3 0.02
51 1 0.01
52 78 0.42
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
Found at i:1790355 original size:101 final size:101
Alignment explanation
Indices: 1790180--1790415 Score: 305
Period size: 101 Copynumber: 2.3 Consensus size: 101
1790170 TAGCACAAGC
* * * * *
1790180 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAACCGATGTCGTTGGCTT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCT
**
1790245 TGAATCAGCACATTGGCA-CCTTAACCATCTTTAAGA
66 TGAATCAGCACATTGGCATCCTTAA-CATCCCTAAGA
** *
1790281 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATTGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCT
* * *
1790346 TGAATCAGCATATTGGCATCTTTAACATCCCTAAGC
66 TGAATCAGCACATTGGCATCCTTAACATCCCTAAGA
* *
1790382 CCAATGTCACTGGCCTT-ATCTCAGCACATTGGCA
1 CCAATGTCGCTGGCCTTGA-ATCAGCACATTGGCA
1790416 TTCTTCTTCA
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
100 1 0.01
101 112 0.95
102 5 0.04
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (101 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAAACCGATATCGTTGGCCT
TGAATCAGCACATTGGCATCCTTAACATCCCTAAGA
Found at i:1791326 original size:13 final size:13
Alignment explanation
Indices: 1791308--1791335 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1791298 CATTATTCAA
1791308 TGTATCGATACAT
1 TGTATCGATACAT
1791321 TGTATCGATACAT
1 TGTATCGATACAT
1791334 TG
1 TG
1791336 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1791330 original size:33 final size:33
Alignment explanation
Indices: 1791288--1791353 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1791278 GCCAAGGAAA
1791288 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
1791321 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
1791354 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:1797033 original size:13 final size:13
Alignment explanation
Indices: 1797015--1797039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1797005 ACAATGAACA
1797015 TGTATCGATACAT
1 TGTATCGATACAT
1797028 TGTATCGATACA
1 TGTATCGATACA
1797040 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1797989 original size:33 final size:33
Alignment explanation
Indices: 1797950--1798047 Score: 142
Period size: 33 Copynumber: 3.0 Consensus size: 33
1797940 TTAAGAGAAC
*
1797950 TAAAGTGCTCATCCGTGTGCTACGAGAGTGAAA
1 TAAAGTGCTCATCCATGTGCTACGAGAGTGAAA
* *
1797983 TGAAGTGCTCATCCATGTGCTACAAGAGTGAAA
1 TAAAGTGCTCATCCATGTGCTACGAGAGTGAAA
* * *
1798016 TAAAGTGCTCATTCATGTGCTGCGAAAGTGAA
1 TAAAGTGCTCATCCATGTGCTACGAGAGTGAA
1798048 GTGATTAACT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (33 bp):
TAAAGTGCTCATCCATGTGCTACGAGAGTGAAA
Found at i:1805746 original size:20 final size:19
Alignment explanation
Indices: 1805704--1805756 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1805694 GTTTGAGGCA
*
1805704 ATGTATCGATACAATTCTTC
1 ATGTATCGATAC-ATTCTCC
*
1805724 ATGTATCGATACATTGTGCC
1 ATGTATCGATACATTCT-CC
*
1805744 ATGTATCAATACA
1 ATGTATCGATACA
1805757 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACATTCTCC
Found at i:1805809 original size:20 final size:20
Alignment explanation
Indices: 1805784--1805821 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1805774 TACTGCTAGT
1805784 TTCATGTACCGATACATTTG
1 TTCATGTACCGATACATTTG
*
1805804 TTCATGTATCGATACATT
1 TTCATGTACCGATACATT
1805822 GCATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (20 bp):
TTCATGTACCGATACATTTG
Found at i:1811295 original size:152 final size:153
Alignment explanation
Indices: 1811125--1811443 Score: 342
Period size: 151 Copynumber: 2.1 Consensus size: 153
1811115 ATCTCAAAGA
* ** *
1811125 CGTTTTGGTAATTTTTCTAAAATAGA-TATTGATGTAGTTA-CTGGATGATTTTATGCCAAAAGT
1 CGTTTTAGTAATTTTTCTAAAATAGAGT-CCGATGTAGTCATC-GGAT-ATTTTATGCCAAAAGT
*
1811188 GTGCATTTAGGATAGGTTCATCCTTCTAATATTATTTTCGAGTCCTTTAAAGTTACT-AGATA-C
63 GTGCATTTAGGATAGGTTCAGCCTTCTAATATTATTTTCGAGTCCTTTAAAGTTACTGAGATATC
1811251 TCTCATGTCGAAAGTATACCCTAA-GG
128 T-TCATGTCGAAAGTATACCCTAAGGG
* * * *
1811277 CGTTTTAGTAATTTTTCTAGAATTGAGTCCGATGTAGTCATCGGATTTTTTATGCCAAAGGTGTG
1 CGTTTTAGTAATTTTTCTAAAATAGAGTCCGATGTAGTCATCGGATATTTTATGCCAAAAGTGTG
* * * * * ** * * * *
1811342 TATTTTGGATAGGTTTAGCCTTTTATTATTATTTTTTAGTCTTTTAAGGTTATTGAGATATCTTT
66 CATTTAGGATAGGTTCAGCCTTCTAATATTATTTTCGAGTCCTTTAAAGTTACTGAGATATCTTC
* * **
1811407 ATGTCTAAGGTATATTCTAAGGG
131 ATGTCGAAAGTATACCCTAAGGG
*
1811430 CATTTTAGTAATTT
1 CGTTTTAGTAATTT
1811444 GGCATTAAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
151 60 0.44
152 58 0.42
153 19 0.14
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.44
Consensus pattern (153 bp):
CGTTTTAGTAATTTTTCTAAAATAGAGTCCGATGTAGTCATCGGATATTTTATGCCAAAAGTGTG
CATTTAGGATAGGTTCAGCCTTCTAATATTATTTTCGAGTCCTTTAAAGTTACTGAGATATCTTC
ATGTCGAAAGTATACCCTAAGGG
Found at i:1812072 original size:13 final size:13
Alignment explanation
Indices: 1812054--1812079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1812044 TATACCAAGT
1812054 ATGTATCGATACA
1 ATGTATCGATACA
1812067 ATGTATCGATACA
1 ATGTATCGATACA
1812080 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1812218 original size:46 final size:46
Alignment explanation
Indices: 1812151--1812242 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1812141 TATCGATACA
1812151 TCAAAAATTGTATCGATACATTTACACGGGAAATCATTAAAACAAG
1 TCAAAAATTGTATCGATACATTTACACGGGAAATCATTAAAACAAG
1812197 TCAAAAATTGTATCGATACATTTACACGGGAAATCATTAAAACAAG
1 TCAAAAATTGTATCGATACATTTACACGGGAAATCATTAAAACAAG
1812243 CTCCAACAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (46 bp):
TCAAAAATTGTATCGATACATTTACACGGGAAATCATTAAAACAAG
Found at i:1814585 original size:13 final size:13
Alignment explanation
Indices: 1814567--1814625 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 13
1814557 TTTCAACAAT
1814567 TTGTATCGATACA
1 TTGTATCGATACA
1814580 TTGTATCGATACATAA
1 TTGTATCGATAC---A
1814596 GTGTTGTATCGATACA
1 ---TTGTATCGATACA
*
1814612 ATGTATCGATACA
1 TTGTATCGATACA
1814625 T
1 T
1814626 AAGTCTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 24 0.63
16 2 0.05
19 12 0.32
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1814604 original size:19 final size:18
Alignment explanation
Indices: 1814580--1814643 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
1814570 TATCGATACA
1814580 TTGTATCGATACATAAGT
1 TTGTATCGATACATAAGT
1814598 GTTGTATCGATAC--AA--
1 -TTGTATCGATACATAAGT
1814613 -TGTATCGATACATAAGT
1 TTGTATCGATACATAAGT
1814630 CTTGTATCGATACA
1 -TTGTATCGATACA
1814644 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACATAAGT
Found at i:1814608 original size:32 final size:32
Alignment explanation
Indices: 1814567--1814651 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
1814557 TTTCAACAAT
* *
1814567 TTGTATCGATACATTGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTC
1814599 TTGTATCGATACAATGTATCGATACATAAGTC
1 TTGTATCGATACAATGTATCGATACATAAGTC
1814631 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
1814652 CTACGAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTC
Found at i:1824159 original size:22 final size:21
Alignment explanation
Indices: 1824131--1824171 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1824121 AAAGAATTTC
*
1824131 TTGAAAATTTTAGGAAAAATAT
1 TTGAAAATTTT-GAAAAAATAT
1824153 TTGAAAATTTTGAAAAAAT
1 TTGAAAATTTTGAAAAAAT
1824172 CACTAGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
TTGAAAATTTTGAAAAAATAT
Found at i:1825705 original size:33 final size:31
Alignment explanation
Indices: 1825635--1825714 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
1825625 GATACTTTGA
* *
1825635 AGAATGTATCGATACATTTGGGTCAAAACCC
1 AGAATGTATCGATACAGTTGGGTAAAAACCC
* * *
1825666 AAAATGTATCGATATAGTTGGGTGAAAAAACCT
1 AGAATGTATCGATACAGTTGGGT--AAAAACCC
*
1825699 AGAATGTATTGATACA
1 AGAATGTATCGATACA
1825715 ATGAAAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 20 0.51
33 19 0.49
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (31 bp):
AGAATGTATCGATACAGTTGGGTAAAAACCC
Found at i:1825819 original size:20 final size:21
Alignment explanation
Indices: 1825796--1825846 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1825786 TTCAAACATA
*
1825796 TATCGATAGATTCAC-T-TGTG
1 TATCGATACATTCACATAT-TG
*
1825816 TATCAATACATTCACATATTG
1 TATCGATACATTCACATATTG
1825837 TATCGATACA
1 TATCGATACA
1825847 AATTGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.50
21 12 0.46
22 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (21 bp):
TATCGATACATTCACATATTG
Found at i:1829736 original size:45 final size:45
Alignment explanation
Indices: 1829685--1829781 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
1829675 TATCATTTTA
* * *
1829685 AGTGCATTTGCACTATTGAATGACTTTGCCATTTGCCTTGTTTCG
1 AGTGCATTTGCACTATTAAATGACATTGCCAATTGCCTTGTTTCG
1829730 AGTGCATTTGCACTATTAAATGACATTGCCAATTGCCTTGTTTCG
1 AGTGCATTTGCACTATTAAATGACATTGCCAATTGCCTTGTTTCG
1829775 AGTGCAT
1 AGTGCAT
1829782 CTACCTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (45 bp):
AGTGCATTTGCACTATTAAATGACATTGCCAATTGCCTTGTTTCG
Found at i:1830193 original size:73 final size:73
Alignment explanation
Indices: 1830107--1830254 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
1830097 TTGACACTTT
* *
1830107 TTATGATTTTTACACTTGCAATATGTAGCATTGCAATTGCTCATATAAAGTTCTTGTTTAGGTTT
1 TTATGATTTTTACACTTGCAATATGGAGCATTGCAACTGCTCATATAAAGTTCTTGTTTAGGTTT
1830172 TGGTTTCA
66 TGGTTTCA
1830180 TTATGATTTTTACACTTGCAATATGGAGCATTGCAACTGCTCATATAAAGTTCTTGTTTAGGTTT
1 TTATGATTTTTACACTTGCAATATGGAGCATTGCAACTGCTCATATAAAGTTCTTGTTTAGGTTT
1830245 TGGTTTCA
66 TGGTTTCA
1830253 TT
1 TT
1830255 GAAGCCATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (73 bp):
TTATGATTTTTACACTTGCAATATGGAGCATTGCAACTGCTCATATAAAGTTCTTGTTTAGGTTT
TGGTTTCA
Found at i:1831117 original size:133 final size:132
Alignment explanation
Indices: 1830839--1831298 Score: 462
Period size: 133 Copynumber: 3.5 Consensus size: 132
1830829 TTCAAACAAT
* * * * **
1830839 CCCTTTTCAAATTAGGTTTCGCCTTAATCACCCTTAGTTGACTTTATCAATTTTGCCTTAGTCAA
1 CCCTTTTTAACTTAGGTTTCACCATGCTCACCCTTAGTTGACTTTATCAATTTTGCCTTAGTCAA
** * ** *
1830904 CCTTTTTTTCGACTTAGG-TTCTACCCTGGTTACCCTTAGTTGACTTTATC-GATTTTACTCAGG
66 CCCCTTTTT-GACTTAGGTTTC-ACCCTGGTCACCCTTAGTTGACTTTATCAG-TTTTGTTCTGG
1830967 TCAAC
128 TCAAC
* * * * *
1830972 CCCTTTTCAACTTAGGTTTCACCATGCTTACTCTTACTTGACTTTATCAGTTTTGCCTTAGTCAA
1 CCCTTTTTAACTTAGGTTTCACCATGCTCACCCTTAGTTGACTTTATCAATTTTGCCTTAGTCAA
* * * *
1831037 CCCCTTTTTGACTTAGGTTTCACCCTAGCCACCTTTAGTTAACTTTATCAGTTTTGTTCTGGTCA
66 CCCCTTTTTGACTTAGGTTTCACCCTGGTCACCCTTAGTTGACTTTATCAGTTTTGTTCTGGTCA
1831102 AC
131 AC
* * * * * *
1831104 CCCTTTTTTAACTTAGATTTCACCATGGTCGCCCTTAGTTGACTTTTTTAATTTTACCTT-GTTC
1 CCC-TTTTTAACTTAGGTTTCACCATGCTCACCCTTAGTTGACTTTATCAATTTTGCCTTAG-TC
* * ** *
1831168 AACCCCTTTTTGACTTCGGTTTCGCTGTGGTCACCCTTAGTTGACTTTATTAGTTTTGCTT-TGG
64 AACCCCTTTTTGACTTAGGTTTCACCCTGGTCACCCTTAGTTGACTTTATCAGTTTTG-TTCTGG
*
1831232 TTAAC
128 TCAAC
* * * * * * *
1831237 CCCTTTTTGACTTAGGTTCCACCCTAG-TCACCCTTAGTTGATTTTATCGATTTCGCCCTAGT
1 CCCTTTTTAACTTAGGTTTCACCAT-GCTCACCCTTAGTTGACTTTATCAATTTTGCCTTAGT
1831299 TAGTCCCTTT
Statistics
Matches: 268, Mismatches: 52, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
132 91 0.34
133 175 0.65
134 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.43
Consensus pattern (132 bp):
CCCTTTTTAACTTAGGTTTCACCATGCTCACCCTTAGTTGACTTTATCAATTTTGCCTTAGTCAA
CCCCTTTTTGACTTAGGTTTCACCCTGGTCACCCTTAGTTGACTTTATCAGTTTTGTTCTGGTCA
AC
Found at i:1831267 original size:66 final size:66
Alignment explanation
Indices: 1830866--1831284 Score: 405
Period size: 66 Copynumber: 6.3 Consensus size: 66
1830856 TTCGCCTTAA
* * **
1830866 TCACCCTTAGTTGACTTTATCAATTTTGCCTTAGTCAACCTTTTTTTCGACTTAGG-TTCTACCC
1 TCACCCTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCCTTTTT-GACTTAGGTTTC-ACCC
1830930 TGG
64 TGG
* * * ** *
1830933 TTACCCTTAGTTGACTTTATC-GATTTT-ACTCAGGTCAACCCCTTTTCAACTTAGGTTTCACCA
1 TCACCCTTAGTTGACTTTATCAG-TTTTGCCT-TGGTCAACCCCTTTTTGACTTAGGTTTCACCC
*
1830996 TGC
64 TGG
* * * * *
1830999 TTACTCTTACTTGACTTTATCAGTTTTGCCTTAGTCAACCCCTTTTTGACTTAGGTTTCACCCTA
1 TCACCCTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCCTTTTTGACTTAGGTTTCACCCTG
1831064 G
66 G
* * * * * * *
1831065 CCACCTTTAGTTAACTTTATCAGTTTTG-TTCTGGTCAACCCCTTTTTTAACTTAGATTTCACCA
1 TCACCCTTAGTTGACTTTATCAGTTTTGCCT-TGGTCAACCCC-TTTTTGACTTAGGTTTCACCC
1831129 TGG
64 TGG
* * * * * * * * **
1831132 TCGCCCTTAGTTGACTTTTTTAATTTTACCTTGTTCAACCCCTTTTTGACTTCGGTTTCGCTGTG
1 TCACCCTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCCTTTTTGACTTAGGTTTCACCCTG
1831197 G
66 G
* * * * *
1831198 TCACCCTTAGTTGACTTTATTAGTTTTGCTTTGGTTAACCCCTTTTTGACTTAGGTTCCACCCTA
1 TCACCCTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCCTTTTTGACTTAGGTTTCACCCTG
1831263 G
66 G
*
1831264 TCACCCTTAGTTGATTTTATC
1 TCACCCTTAGTTGACTTTATC
1831285 GATTTCGCCC
Statistics
Matches: 280, Mismatches: 64, Indels: 17
0.78 0.18 0.05
Matches are distributed among these distances:
65 1 0.00
66 187 0.67
67 91 0.32
68 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44
Consensus pattern (66 bp):
TCACCCTTAGTTGACTTTATCAGTTTTGCCTTGGTCAACCCCTTTTTGACTTAGGTTTCACCCTG
G
Found at i:1839441 original size:13 final size:13
Alignment explanation
Indices: 1839425--1839455 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1839415 ATACAATGAG
1839425 CAATGTATCGATA
1 CAATGTATCGATA
1839438 CAATGTATCGATA
1 CAATGTATCGATA
1839451 CAATG
1 CAATG
1839456 AGCGATGTAT
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:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1839452 original size:33 final size:33
Alignment explanation
Indices: 1839406--1839473 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1839396 TACATTATAA
1839406 AATGTATCAATACAATGAGCAATGTATCGATAC
1 AATGTATCAATACAATGAGCAATGTATCGATAC
* * *
1839439 AATGTATCGATACAATGAGCGATGTATTGATAC
1 AATGTATCAATACAATGAGCAATGTATCGATAC
1839472 AA
1 AA
1839474 CACAAAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (33 bp):
AATGTATCAATACAATGAGCAATGTATCGATAC
Found at i:1839549 original size:13 final size:13
Alignment explanation
Indices: 1839531--1839556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1839521 ACAAAGATCG
1839531 ATGTATCGATACA
1 ATGTATCGATACA
1839544 ATGTATCGATACA
1 ATGTATCGATACA
1839557 TTAAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1840679 original size:34 final size:34
Alignment explanation
Indices: 1840641--1840723 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
1840631 CGACATCAAT
* *
1840641 ATATATTTACCACAATTCAACAATATATTAGCAA
1 ATATATATACCACAATTCAACAATATATCAGCAA
1840675 ATATATATACCACAATTCAACAATATATCAGCAA
1 ATATATATACCACAATTCAACAATATATCAGCAA
*
1840709 ATATATATGCCACAA
1 ATATATATACCACAA
1840724 ATTTATGTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (34 bp):
ATATATATACCACAATTCAACAATATATCAGCAA
Found at i:1842709 original size:20 final size:20
Alignment explanation
Indices: 1842684--1842737 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1842674 TAATATAGAC
1842684 AATGTATCGATACATTAGTA
1 AATGTATCGATACATTAGTA
* *
1842704 AATGTATCGATACATTATTC
1 AATGTATCGATACATTAGTA
*
1842724 ATTGTATCGATACA
1 AATGTATCGATACA
1842738 ATTTGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTAGTA
Found at i:1842812 original size:49 final size:47
Alignment explanation
Indices: 1842705--1842813 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 47
1842695 ACATTAGTAA
*
1842705 ATGTATCGATACATTATTCATTGTATCGATACAATTTGAAAAACCTAG
1 ATGTATCGATACA-TATTCATTATATCGATACAATTTGAAAAACCTAG
* *
1842753 ATATATCGATACA-AGTTGCATTATATCGATAC-ATTCTGGAAAAATCTAG
1 ATGTATCGATACATA-TT-CATTATATCGATACAATT-T-GAAAAACCTAG
1842802 ATGTATCGATAC
1 ATGTATCGATAC
1842814 TTTGATCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 1 0.02
47 5 0.09
48 26 0.49
49 21 0.40
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (47 bp):
ATGTATCGATACATATTCATTATATCGATACAATTTGAAAAACCTAG
Found at i:1846777 original size:36 final size:36
Alignment explanation
Indices: 1846731--1846800 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
1846721 AAATGAGAAA
**
1846731 ATAATAATAATGATATAACCCCTAAAAATAAAAATAG
1 ATAATAATAATGATAT-ACCAATAAAAATAAAAATAG
*
1846768 ATAA-AATAATGATATACCAATAAATATAAAAAT
1 ATAATAATAATGATATACCAATAAAAATAAAAAT
1846801 GAGAGCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 15 0.50
36 11 0.37
37 4 0.13
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (36 bp):
ATAATAATAATGATATACCAATAAAAATAAAAATAG
Found at i:1846903 original size:17 final size:16
Alignment explanation
Indices: 1846877--1846923 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1846867 GAAAATCCAC
1846877 TTTC-TTTTCTTTTTT
1 TTTCTTTTTCTTTTTT
1846892 TTTCATTTTTCTTTCTTT
1 TTTC-TTTTTCTTT-TTT
*
1846910 TTTCTTTTTATTTT
1 TTTCTTTTTCTTTT
1846924 CCTTCTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 1 0.04
17 16 0.57
18 7 0.25
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTT
Found at i:1846923 original size:22 final size:22
Alignment explanation
Indices: 1846877--1846941 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
1846867 GAAAATCCAC
1846877 TTTCTTT-TCTTTTTTTTTCATT
1 TTTCTTTCT-TTTTTTTTTCATT
*
1846899 TTTCTTTCTTTTTTCTTTTTA-T
1 TTTCTTTCTTTTTT-TTTTCATT
*
1846921 TTTCCTTCTTTAGTTTTTTTC
1 TTTCTTTCTTT--TTTTTTTC
1846942 TACTAAGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 23 0.64
23 10 0.28
24 3 0.08
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTCTTTCTTTTTTTTTTCATT
Found at i:1846924 original size:18 final size:18
Alignment explanation
Indices: 1846881--1846918 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1846871 ATCCACTTTC
1846881 TTTTCTTT-TTTTTTCAT
1 TTTTCTTTCTTTTTTCAT
1846898 TTTTCTTTCTTTTTTC-T
1 TTTTCTTTCTTTTTTCAT
1846915 TTTT
1 TTTT
1846919 ATTTTCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTCTTTTTTCAT
Found at i:1848744 original size:19 final size:19
Alignment explanation
Indices: 1848696--1848736 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1848686 TTTTACAAAT
*
1848696 ATAT-AAAAAATTAATATA
1 ATATGAAAAAATTAATACA
1848714 ATATGAAAAAATTAATACA
1 ATATGAAAAAATTAATACA
1848733 ATAT
1 ATAT
1848737 TCATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATGAAAAAATTAATACA
Found at i:1850062 original size:2 final size:2
Alignment explanation
Indices: 1850055--1850089 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1850045 GATATTTTAG
1850055 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1850090 GTGTTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1851117 original size:5 final size:5
Alignment explanation
Indices: 1851107--1851133 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1851097 CTGTTTGCAA
1851107 AAAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AA
1851134 GCACAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:1851661 original size:3 final size:3
Alignment explanation
Indices: 1851616--1851644 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1851606 TCAAACTTAC
1851616 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1851645 AACTCCTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:1851687 original size:15 final size:15
Alignment explanation
Indices: 1851669--1851727 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
1851659 ATCGTCGTCG
1851669 TCATCAACAAACTCA
1 TCATCAACAAACTCA
*
1851684 TCATCAACGAACTCA
1 TCATCAACAAACTCA
**
1851699 TCATCAA-ACTCTTCA
1 TCATCAACAAAC-TCA
*
1851714 TCATCACCAAACTC
1 TCATCAACAAACTC
1851728 CATATTATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
14 1 0.03
15 32 0.91
16 2 0.06
ACGTcount: A:0.39, C:0.36, G:0.02, T:0.24
Consensus pattern (15 bp):
TCATCAACAAACTCA
Found at i:1851714 original size:12 final size:12
Alignment explanation
Indices: 1851669--1851716 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1851659 ATCGTCGTCG
*
1851669 TCATCAACAAAC
1 TCATCATCAAAC
1851681 TCATCATCAACGAAC
1 TCATCATC-A--AAC
1851696 TCATCATCAAAC
1 TCATCATCAAAC
*
1851708 TCTTCATCA
1 TCATCATCA
1851717 TCACCAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 1 0.03
15 11 0.35
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.25
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:1852693 original size:15 final size:15
Alignment explanation
Indices: 1852673--1852713 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1852663 TATTTTATTA
1852673 ATATTTTTAGTTTTT
1 ATATTTTTAGTTTTT
*
1852688 ATA-TTTAAGTTTTT
1 ATATTTTTAGTTTTT
1852702 -TATTTTTA-TTTT
1 ATATTTTTAGTTTT
1852714 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 14 0.61
15 3 0.13
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (15 bp):
ATATTTTTAGTTTTT
Found at i:1854382 original size:25 final size:24
Alignment explanation
Indices: 1854354--1854401 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1854344 CTTGTTAATG
* *
1854354 ATAAGATAATTTTATCTTTTAAAAA
1 ATAAGA-AAATTTATATTTTAAAAA
*
1854379 ATAATAAAATTTATATTTTAAAA
1 ATAAGAAAATTTATATTTTAAAA
1854402 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAGAAAATTTATATTTTAAAAA
Found at i:1854479 original size:29 final size:29
Alignment explanation
Indices: 1854446--1854505 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1854436 AATCTTGATA
*
1854446 AATATGATATTATC-TATTAACCAAATCTT
1 AATATGATATTACCGT-TTAACCAAATCTT
*
1854475 AATATTATATTACCGTTTAACCAAATCTT
1 AATATGATATTACCGTTTAACCAAATCTT
1854504 AA
1 AA
1854506 CATGCCCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (29 bp):
AATATGATATTACCGTTTAACCAAATCTT
Found at i:1855140 original size:19 final size:20
Alignment explanation
Indices: 1855116--1855156 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1855106 TTAACTTTCG
*
1855116 ATATTTGAAAATAATTT-TT
1 ATATTTCAAAATAATTTATT
*
1855135 ATATTTCAAAATTATTTATT
1 ATATTTCAAAATAATTTATT
1855155 AT
1 AT
1855157 TGTTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATATTTCAAAATAATTTATT
Found at i:1859106 original size:13 final size:13
Alignment explanation
Indices: 1859088--1859114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1859078 TACAAAACTT
1859088 ATGTATCGATACA
1 ATGTATCGATACA
1859101 ATGTATCGATACA
1 ATGTATCGATACA
1859114 A
1 A
1859115 ATTGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1862229 original size:20 final size:20
Alignment explanation
Indices: 1862204--1862279 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
1862194 TTTTTACCCA
1862204 AATGTATTGATACATTTTTC
1 AATGTATTGATACATTTTTC
** * *
1862224 AATGTATCAATACATTTATG
1 AATGTATTGATACATTTTTC
1862244 AATGTATCT-ATACATTTTTC
1 AATGTAT-TGATACATTTTTC
1862264 AATGTATTGATACATT
1 AATGTATTGATACATT
1862280 CAGTCTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (20 bp):
AATGTATTGATACATTTTTC
Found at i:1862250 original size:40 final size:40
Alignment explanation
Indices: 1862204--1862279 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1862194 TTTTTACCCA
1862204 AATGTAT-TGATACATTTTTCAATGTATCAATACATTTATG
1 AATGTATCT-ATACATTTTTCAATGTATCAATACATTTATG
**
1862244 AATGTATCTATACATTTTTCAATGTATTGATACATT
1 AATGTATCTATACATTTTTCAATGTATCAATACATT
1862280 CAGTCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (40 bp):
AATGTATCTATACATTTTTCAATGTATCAATACATTTATG
Found at i:1865697 original size:26 final size:29
Alignment explanation
Indices: 1865660--1865724 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 29
1865650 ATTTTAATAA
* *
1865660 TAATATTTAATAC-TAAAATATTA-TATT
1 TAATATTAAATACTTAAAATAATACTATT
*
1865687 A-ATATTAAATACTTAAAATAATACTATT
1 TAATATTAAATACTTAAAATAATACTATT
*
1865715 TATTATTAAA
1 TAATATTAAA
1865725 AATTAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 10 0.33
27 9 0.30
28 4 0.13
29 7 0.23
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATTAAATACTTAAAATAATACTATT
Found at i:1865834 original size:20 final size:23
Alignment explanation
Indices: 1865784--1865840 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
1865774 ATGTTATTTC
1865784 TATTAATATTTATACTATTAAAA
1 TATTAATATTTATACTATTAAAA
1865807 TATTAATATTT-TA-TA-TAAAA
1 TATTAATATTTATACTATTAAAA
1865827 -ATTAAATATTTATA
1 TATT-AATATTTATA
1865841 AATTATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 4 0.12
22 2 0.06
23 11 0.34
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAATATTTATACTATTAAAA
Found at i:1865858 original size:16 final size:16
Alignment explanation
Indices: 1865820--1865860 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1865810 TAATATTTTA
*
1865820 TATAAAAATTAAATAT
1 TATATAAATTAAATAT
1865836 T-TATAAATTATAAT-T
1 TATATAAATTA-AATAT
1865851 TATATAAATT
1 TATATAAATT
1865861 TATTATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATAAATTAAATAT
Found at i:1865966 original size:18 final size:18
Alignment explanation
Indices: 1865943--1865999 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
1865933 TTACAATTTA
1865943 TTATTAAAATAATAATAT
1 TTATTAAAATAATAATAT
1865961 TTATT---A-AATAATAT
1 TTATTAAAATAATAATAT
1865975 TTATTAAAATAATAA-AT
1 TTATTAAAATAATAATAT
1865992 TATATTAA
1 T-TATTAA
1866000 TTATATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 13 0.38
15 1 0.03
17 4 0.12
18 16 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTAAAATAATAATAT
Found at i:1865970 original size:14 final size:15
Alignment explanation
Indices: 1865953--1865988 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
1865943 TTATTAAAAT
1865953 AATAATATTTATT-A
1 AATAATATTTATTAA
1865967 AATAATATTTATTAA
1 AATAATATTTATTAA
1865982 AATAATA
1 AATAATA
1865989 AATTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAATATTTATTAA
Found at i:1867612 original size:15 final size:14
Alignment explanation
Indices: 1867588--1867649 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
1867578 ATTTATAAGT
1867588 AAATATAAATTTTA
1 AAATATAAATTTTA
1867602 AAATAATAAATATTTA
1 AAAT-ATAAAT-TTTA
* *
1867618 AGATCTAAAATTTT-
1 AAATAT-AAATTTTA
1867632 AAATATTAAATTTATA
1 AAATA-TAAATTT-TA
1867648 AA
1 AA
1867650 TAAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 13 0.34
15 12 0.32
16 13 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATATAAATTTTA
Found at i:1867649 original size:23 final size:22
Alignment explanation
Indices: 1867582--1867657 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 22
1867572 ATATATATTT
1867582 ATAAGTAAATA-TAAATTTTAAA
1 ATAA-TAAATATTAAATTTTAAA
*
1867604 ATAATAAATATTTAAGA-TCTAAA
1 ATAATAAATA-TTAA-ATTTTAAA
**
1867627 ATTTTAAATATTAAA-TTTATAA
1 ATAATAAATATTAAATTTTA-AA
1867649 ATAAATAAA
1 AT-AATAAA
1867658 AAATATATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
21 10 0.23
22 12 0.28
23 20 0.47
24 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (22 bp):
ATAATAAATATTAAATTTTAAA
Found at i:1867650 original size:15 final size:14
Alignment explanation
Indices: 1867587--1867651 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 14
1867577 TATTTATAAG
1867587 TAAATA-TAAATTT
1 TAAATATTAAATTT
*
1867600 TAAAATAATAAATATT
1 T-AAATATTAAAT-TT
* *
1867616 TAAGATCTAAAATTT
1 TAA-ATATTAAATTT
1867631 TAAATATTAAATTT
1 TAAATATTAAATTT
1867645 ATAAATA
1 -TAAATA
1867652 AATAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 1 0.02
14 14 0.33
15 18 0.43
16 9 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
TAAATATTAAATTT
Found at i:1868124 original size:15 final size:16
Alignment explanation
Indices: 1868085--1868134 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
1868075 ATCAGATTCG
1868085 GATATAAATATGAATATTA
1 GATATAAATAT--AT-TTA
1868104 GATATAAATATATTTA
1 GATATAAATATATTTA
*
1868120 G-TATAAATATTTTTA
1 GATATAAATATATTTA
1868135 AATTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 13 0.43
16 4 0.13
17 2 0.07
19 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
GATATAAATATATTTA
Found at i:1868160 original size:18 final size:18
Alignment explanation
Indices: 1868123--1868171 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1868113 ATATTTAGTA
*
1868123 TAAATATTTTTAAATTTT
1 TAAATATTTTTAAATATT
* *
1868141 TAAATTTTTTTATATATT
1 TAAATATTTTTAAATATT
*
1868159 TATCATATTTTTA
1 TA-AATATTTTTA
1868172 TACCTATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TAAATATTTTTAAATATT
Found at i:1869052 original size:15 final size:17
Alignment explanation
Indices: 1869032--1869066 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1869022 AATACTAAAA
1869032 TTTTAA-TTTTA-AATT
1 TTTTAATTTTTATAATT
1869047 TTTTAATTTTTATAATT
1 TTTTAATTTTTATAATT
1869064 TTT
1 TTT
1869067 GAGTTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTATAATT
Found at i:1869915 original size:58 final size:58
Alignment explanation
Indices: 1869804--1870071 Score: 145
Period size: 58 Copynumber: 4.6 Consensus size: 58
1869794 CATTTTAGTT
* ** * * * * * *
1869804 ATTTTTCATGA-CTTAGAGAC-TTCTATGTCATTTTACAAATCTTGTTGTTATTTAGGTC
1 ATTTTTCATGATC-TAGAGACTTTC-ATGTAATTTTATGAATGTTGATATCATTTAGATA
* *
1869862 ATTTTTCATGATCTAGAGA-TTTAGATTTAATTTTATGAATGTTGATATCATTTAGATA
1 ATTTTTCATGATCTAGAGACTTT-CATGTAATTTTATGAATGTTGATATCATTTAGATA
* ** * * * * * *
1869920 ACTTTTCGCGATCTAGGGACTTTCATGTAATTTTATGAATTTTGATGTTATTTAGCTT
1 ATTTTTCATGATCTAGAGACTTTCATGTAATTTTATGAATGTTGATATCATTTAGATA
* *** * * * * *
1869978 ATTTTCCATGA-CTTA-AGGACTTGGTTGTAAATTTATAAATTTTGATGTCATTT-GAGTC
1 ATTTTTCATGATC-TAGA-GACTTTCATGTAATTTTATGAATGTTGATATCATTTAGA-TA
* *
1870036 ATTTTTTATGGTCTAG-GAACTTTCATGTAATTTTAT
1 ATTTTTCATGATCTAGAG-ACTTTCATGTAATTTTAT
1870072 ACATCTTAGA
Statistics
Matches: 158, Mismatches: 42, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
57 3 0.02
58 150 0.95
59 5 0.03
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.48
Consensus pattern (58 bp):
ATTTTTCATGATCTAGAGACTTTCATGTAATTTTATGAATGTTGATATCATTTAGATA
Found at i:1871736 original size:24 final size:24
Alignment explanation
Indices: 1871701--1871747 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1871691 GATACATTAC
*
1871701 TGTTCATAACTGTTCATGTATCAA
1 TGTTCATAACTGTTAATGTATCAA
*
1871725 TGTTCATCACTGTTAATGTATCA
1 TGTTCATAACTGTTAATGTATCA
1871748 CTATTCAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (24 bp):
TGTTCATAACTGTTAATGTATCAA
Found at i:1871754 original size:24 final size:24
Alignment explanation
Indices: 1871703--1871754 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1871693 TACATTACTG
* *
1871703 TTCATAACTGTTCATGTATCAATG
1 TTCATAACTGTTAATGTATCAATA
* *
1871727 TTCATCACTGTTAATGTATCACTA
1 TTCATAACTGTTAATGTATCAATA
1871751 TTCA
1 TTCA
1871755 GTATCAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (24 bp):
TTCATAACTGTTAATGTATCAATA
Found at i:1871869 original size:20 final size:21
Alignment explanation
Indices: 1871823--1871869 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1871813 AATTTCAAGT
1871823 GCATGTATCGATACATTATGA
1 GCATGTATCGATACATTATGA
1871844 --ATTGTATCGATACATTA-GA
1 GCA-TGTATCGATACATTATGA
1871863 GCATGTA
1 GCATGTA
1871870 AACGCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (21 bp):
GCATGTATCGATACATTATGA
Found at i:1877498 original size:20 final size:21
Alignment explanation
Indices: 1877475--1877516 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1877465 TAATCATATT
1877475 TAAAATATT-ATATATTTATA
1 TAAAATATTAATATATTTATA
*
1877495 T-AAATTTTAATATATTTATA
1 TAAAATATTAATATATTTATA
1877515 TA
1 TA
1877517 TTCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAAATATTAATATATTTATA
Found at i:1878019 original size:16 final size:16
Alignment explanation
Indices: 1877952--1878028 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
1877942 AAGTTAAAAG
* * *
1877952 TTTAAGTTATTTGGAG
1 TTTAAATTATTTTGAA
* *
1877968 TTTGAATTGTTTTGAA
1 TTTAAATTATTTTGAA
* *
1877984 TTTAAGTTATATCATG--
1 TTTAAATTAT-T-TTGAA
1878000 TTTAAATTATTTTGAA
1 TTTAAATTATTTTGAA
*
1878016 TTTAAAATATTTT
1 TTTAAATTATTTT
1878029 AAGTCTGAAC
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 39 0.87
17 1 0.02
18 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTGAA
Found at i:1879401 original size:13 final size:13
Alignment explanation
Indices: 1879383--1879408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1879373 CAATTTTTTG
1879383 TGTATCGATACAT
1 TGTATCGATACAT
1879396 TGTATCGATACAT
1 TGTATCGATACAT
1879409 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1880135 original size:21 final size:21
Alignment explanation
Indices: 1880094--1880137 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1880084 TTCTCCTTTA
* *
1880094 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1880115 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1880136 TC
1 TC
1880138 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1881964 original size:13 final size:13
Alignment explanation
Indices: 1881946--1881971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1881936 ATAATCACCC
1881946 TGTATCGATACAA
1 TGTATCGATACAA
1881959 TGTATCGATACAA
1 TGTATCGATACAA
1881972 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1882186 original size:8 final size:8
Alignment explanation
Indices: 1882173--1882204 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
1882163 CATCATTCAA
1882173 CACAAAAT
1 CACAAAAT
1882181 CACAAAAT
1 CACAAAAT
1882189 CACAAAAT
1 CACAAAAT
1882197 CACAAAAT
1 CACAAAAT
1882205 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
CACAAAAT
Found at i:1884078 original size:15 final size:15
Alignment explanation
Indices: 1884058--1884088 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1884048 ATTTCGTTTG
*
1884058 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1884073 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1884088 G
1 G
1884089 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1885921 original size:21 final size:21
Alignment explanation
Indices: 1885892--1885936 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1885882 AAGTTTTCAT
*
1885892 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1885912 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1885934 TTT
1 TTT
1885937 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1888170 original size:13 final size:13
Alignment explanation
Indices: 1888152--1888177 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1888142 CAATTTTTTG
1888152 TGTATCGATACAT
1 TGTATCGATACAT
1888165 TGTATCGATACAT
1 TGTATCGATACAT
1888178 ACTTGCTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1902012 original size:46 final size:48
Alignment explanation
Indices: 1901899--1902016 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
1901889 TAACTTGTTG
* * * * *
1901899 CTTTTGCACAAACAAAGATACAAATTCTTCTCACAAAATAACTTGTAA
1 CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATAA
* * *
1901947 CTTTTGCACAGATCAAGTTACAAACTCTCCTCAC-AAA-AAGTTATATA
1 CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATA-A
1901994 -TTTTGCACAAATAAAGTTACAAA
1 CTTTTGCACAAATAAAGTTACAAA
1902017 TCCTTTAACA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 27 0.46
47 4 0.07
48 28 0.47
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (48 bp):
CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATAA
Found at i:1902044 original size:46 final size:46
Alignment explanation
Indices: 1901889--1902062 Score: 129
Period size: 46 Copynumber: 3.7 Consensus size: 46
1901879 AACACTAATT
* * * * *
1901889 TAACTTGTTGCTTTTGCACAAACAAAGATACAAATTCTTCTCACAAAA
1 TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTT-TCAC-AAA
* * * * *
1901937 TAACTTGTAACTTTTGCACAGATCAAGTTACAAA-CTCTCCTCACAAA
1 TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATC-CT-TTCACAAA
* ** *
1901984 -AAGTTA-TATATTTTGCACAAATAAAGTTACAAATCCTTTAACAAA
1 TAA-CTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTTTCACAAA
* *
1902029 TAACTAGTAGCTTTTGTATGAAATAAAGTTACAA
1 TAACTAGTAGCTTTTGCA-CAAATAAAGTTACAA
1902063 TTTTTTTATA
Statistics
Matches: 98, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
45 8 0.08
46 37 0.38
47 19 0.19
48 34 0.35
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (46 bp):
TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTTTCACAAA
Found at i:1905877 original size:15 final size:15
Alignment explanation
Indices: 1905857--1905886 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1905847 GTAAGAAATA
1905857 CACTTAATCACTTTT
1 CACTTAATCACTTTT
1905872 CACTTAATCACTTTT
1 CACTTAATCACTTTT
1905887 AAAATGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CACTTAATCACTTTT
Found at i:1907050 original size:20 final size:19
Alignment explanation
Indices: 1907027--1907072 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1907017 ATTTGTATGG
*
1907027 ATACATGTCATAATGTATCA
1 ATACATG-CACAATGTATCA
*
1907047 ATACAATGCACAATGTATCG
1 ATAC-ATGCACAATGTATCA
1907067 ATACAT
1 ATACAT
1907073 TATGTGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
ATACATGCACAATGTATCA
Found at i:1907158 original size:20 final size:20
Alignment explanation
Indices: 1907133--1907203 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
1907123 AACCTTCATT
1907133 TGTATCGATACACATGAAAA
1 TGTATCGATACACATGAAAA
1907153 TGTATCGATACA-AT-ACACAA
1 TGTATCGATACACATGA-A-AA
* * *
1907173 TATATCGATACATC-CGTAAA
1 TGTATCGATACA-CATGAAAA
1907193 TGTATCGATAC
1 TGTATCGATAC
1907204 TCTAAGTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 37 0.88
21 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACATGAAAA
Found at i:1907183 original size:113 final size:112
Alignment explanation
Indices: 1906976--1907185 Score: 285
Period size: 113 Copynumber: 1.9 Consensus size: 112
1906966 AAATGTACCG
* * * * ** *
1906976 ATACATCTGTTGGCAGTAGCTAAAGAAGTGCTAAAACCCTCATTTGTATGGATACATGTCATAAT
1 ATACATCTGTTGGCAATAGCTAAAGAAATACTAAAACCCTCATTTGTATCGATACACATCAAAAT
* *
1907041 GTATCAATACAATGCACAATGTATCGATACATTATGTGAATGCATCA
66 GTATCAATACAATACACAATATATCGATACATTATGTGAATGCATCA
* * * *
1907088 ATACATCTGATTGGCAATAGCTAAAGAAATATTGAAACCTTCATTTGTATCGATACACATGAAAA
1 ATACATCTG-TTGGCAATAGCTAAAGAAATACTAAAACCCTCATTTGTATCGATACACATCAAAA
*
1907153 TGTATCGATACAATACACAATATATCGATACAT
65 TGTATCAATACAATACACAATATATCGATACAT
1907186 CCGTAAATGT
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
112 9 0.11
113 74 0.89
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (112 bp):
ATACATCTGTTGGCAATAGCTAAAGAAATACTAAAACCCTCATTTGTATCGATACACATCAAAAT
GTATCAATACAATACACAATATATCGATACATTATGTGAATGCATCA
Found at i:1912384 original size:19 final size:19
Alignment explanation
Indices: 1912360--1912422 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1912350 AAATAGTAAC
1912360 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
1912379 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
1912392 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
1912411 TGTATCGATACA
1 TGTATCGATACA
1912423 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1912397 original size:13 final size:13
Alignment explanation
Indices: 1912379--1912403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1912369 ACATAAGTGT
1912379 TGTATCGATACAA
1 TGTATCGATACAA
1912392 TGTATCGATACA
1 TGTATCGATACA
1912404 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1912401 original size:32 final size:32
Alignment explanation
Indices: 1912360--1912430 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
1912350 AAATAGTAAC
1912360 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1912392 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1912424 TGTATCG
1 TGTATCG
1912431 CTACGAAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1918605 original size:15 final size:15
Alignment explanation
Indices: 1918585--1918614 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1918575 ATAATGCTTA
1918585 CATTATTCTATTTTG
1 CATTATTCTATTTTG
1918600 CATTATTCTATTTTG
1 CATTATTCTATTTTG
1918615 ACATAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
CATTATTCTATTTTG
Found at i:1920155 original size:13 final size:13
Alignment explanation
Indices: 1920139--1920163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1920129 CAATTTATCA
1920139 TGTATCGATACAT
1 TGTATCGATACAT
1920152 TGTATCGATACA
1 TGTATCGATACA
1920164 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1920161 original size:33 final size:33
Alignment explanation
Indices: 1920119--1920183 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1920109 TTTGAAGCAA
* *
1920119 TGTATCGATACAATTTATCATGTATCGATACAT
1 TGTATCGATACAATGTACCATGTATCGATACAT
*
1920152 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
1920184 AACAGTGGTA
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:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:1920257 original size:19 final size:19
Alignment explanation
Indices: 1920213--1920284 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
1920203 CTACCAGTTT
**
1920213 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1920233 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1920252 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1920271 CATGTATCGATACA
1 CATGTATCGATACA
1920285 TCATATTGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 35 0.70
20 15 0.30
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1922645 original size:22 final size:21
Alignment explanation
Indices: 1922610--1922659 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1922600 TTTGTTGATG
*
1922610 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1922630 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1922651 AATTTGAAG
1 ATTTTGAAG
1922660 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1922656 original size:21 final size:22
Alignment explanation
Indices: 1922617--1922659 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1922607 ATGATTTTGA
* *
1922617 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1922639 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1922660 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1927249 original size:3 final size:3
Alignment explanation
Indices: 1927243--1927273 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1927233 TCCGAGTCAC
*
1927243 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1927274 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:1928841 original size:20 final size:20
Alignment explanation
Indices: 1928791--1928843 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1928781 TTCCGTAGCT
*
1928791 ATGTATCAATACAATTCATA
1 ATGTATCGATACAATTCATA
1928811 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
1928831 ATGTATTGATACA
1 ATGTATCGATACA
1928844 TGCATTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1928970 original size:20 final size:20
Alignment explanation
Indices: 1928945--1929002 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
1928935 CTGCCAGTTT
*
1928945 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
1928965 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
1928984 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
1929003 TCGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:1929004 original size:13 final size:13
Alignment explanation
Indices: 1928986--1929010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1928976 ACAATGAACA
1928986 TGTATCGATACAT
1 TGTATCGATACAT
1928999 TGTATCGATACA
1 TGTATCGATACA
1929011 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1929027 original size:33 final size:32
Alignment explanation
Indices: 1928967--1929031 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1928957 CAATTGTCCA
*
1928967 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
1928999 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGTATCGATACAT
1929032 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:1931366 original size:19 final size:18
Alignment explanation
Indices: 1931342--1931380 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1931332 GCATGAATCA
*
1931342 AAAATAATAATAAATATAG
1 AAAATAAAAATAAATA-AG
1931361 AAAATAAAAATAAATAAG
1 AAAATAAAAATAAATAAG
1931379 AA
1 AA
1931381 TTTCCAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATAAATAAG
Found at i:1937679 original size:391 final size:391
Alignment explanation
Indices: 1936952--1937680 Score: 910
Period size: 391 Copynumber: 1.9 Consensus size: 391
1936942 ACATGATCGG
* * *
1936952 ATGCCCATTGAAACCGATATTTTGAGTTACGAAACTCGAAATATCAATCCCGTGATCTACGTAAT
1 ATGCCCATTGAAACCGATATCTTGAGTTACGAAACTCGAAACATCAATCCCATGATCTACGTAAT
* * * * * *
1937017 TTAGATATTCACTGGTTGGGTTTGAGAGTTGGTTACACACAAAGAAGTATGAACCTCCTTGCGAC
66 TCAAAGATTCACTGGTTGGGTCTGAGAGTTGGTTACACACAAAGAAGTACGAACCTCCTCGCGAC
*** * ** *
1937082 GTCTGAAATCGGTACCTTACTAGCTATATTTTGACTTTACATTAGTTTAATTGGTTTCGACTTGA
131 GTCTGAAATCAACACCTTACTAGCAATATTTTGACTCAACATTAGTTTAATTAGTTTCGACTTGA
* *
1937147 TATTATTTCAATATGATCCCCTCGAATGCATGAATTTTGTATAAAAACAAATCCAAGTTTGATAA
196 TATTATTTCAATATAATCCCCTCGAATGCATGAATTTTATATAAAAACAAATCCAAGTTTGATAA
*
1937212 AAATTTTAATCTCATATGCGCCCCAGAGAGATGAGAAACATAGAAACATAAAAAGACCTTTGGAT
261 AAATTTTAATCTCATATGCGCCCCAGAGAGATGAGAAACATAGAAACATAAAAAGACCTCTGGAT
*
1937277 TTTACTTTGAAAAATAGATATTTCATGTCAAGCACTAGAGAGATACTGATGCGGAACATTGCCTT
326 TTCACTTTGAAAAATAGATATTTCATGTCAAGCACTAGAGAGATACTGATGCGGAACATTGCCTT
1937342 C
391 C
* * * * ** *
1937343 ATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCGAGACATTGATCCCATGGTCTACGTAAT
1 ATGCCCATTGAAACCGATATCTTGAGTTACGAAACTCGAAACATCAATCCCATGATCTACGTAAT
** * **
1937408 TCAAAGATTCGTTGGTTGGGTCTGGGAGTTGGTTATGCACAAA-AAGGTACGAACCTCCTCGCGA
66 TCAAAGATTCACTGGTTGGGTCTGAGAGTTGGTTACACACAAAGAA-GTACGAACCTCCTCGCGA
* * * * * * *
1937472 CGTCTTAAATCAACACTTTGCTAG-AATATTTTGACTCAATATTGGTTT-CTTCAGTTTTGA-TT
130 CGTCTGAAATCAACACCTTACTAGCAATATTTTGACTCAACATTAGTTTAATT-AGTTTCGACTT
* * ** * * *
1937534 TATCATTATTTCGATATAATCCCCTTTAATGCATGAATTTTATATAAAAATAAATTCAGGTCTTG
194 GAT-ATTATTTCAATATAATCCCCTCGAATGCATGAATTTTATATAAAAACAAATCCAAGT-TTG
* * * * *
1937599 ATAAAAATTTTAATCTCATATGCGTCTCAGAGAGATGGGAAACATA-AAGATATAAAATGACCTC
257 ATAAAAATTTTAATCTCATATGCGCCCCAGAGAGATGAGAAACATAGAA-ACATAAAAAGACCTC
*
1937663 TGGATTTCATTTTGAAAA
321 TGGATTTCACTTTGAAAA
1937681 CTGGGTATTA
Statistics
Matches: 281, Mismatches: 52, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
389 6 0.02
390 78 0.28
391 197 0.70
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (391 bp):
ATGCCCATTGAAACCGATATCTTGAGTTACGAAACTCGAAACATCAATCCCATGATCTACGTAAT
TCAAAGATTCACTGGTTGGGTCTGAGAGTTGGTTACACACAAAGAAGTACGAACCTCCTCGCGAC
GTCTGAAATCAACACCTTACTAGCAATATTTTGACTCAACATTAGTTTAATTAGTTTCGACTTGA
TATTATTTCAATATAATCCCCTCGAATGCATGAATTTTATATAAAAACAAATCCAAGTTTGATAA
AAATTTTAATCTCATATGCGCCCCAGAGAGATGAGAAACATAGAAACATAAAAAGACCTCTGGAT
TTCACTTTGAAAAATAGATATTTCATGTCAAGCACTAGAGAGATACTGATGCGGAACATTGCCTT
C
Found at i:1939192 original size:13 final size:13
Alignment explanation
Indices: 1939174--1939199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1939164 TACAGCAAGT
1939174 ATGTATCGATACA
1 ATGTATCGATACA
1939187 ATGTATCGATACA
1 ATGTATCGATACA
1939200 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1941446 original size:21 final size:21
Alignment explanation
Indices: 1941413--1941457 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1941403 TTGCAAGTTG
*
1941413 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1941435 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1941455 AAA
1 AAA
1941458 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1943281 original size:15 final size:15
Alignment explanation
Indices: 1943261--1943291 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1943251 TAAAAATGTC
*
1943261 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1943276 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1943291 C
1 C
1943292 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1945542 original size:21 final size:21
Alignment explanation
Indices: 1945518--1945564 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1945508 AAATCTTTTG
1945518 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1945539 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1945559 CAAAAT
1 CAAAAT
1945565 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1945561 original size:20 final size:19
Alignment explanation
Indices: 1945520--1945562 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1945510 ATCTTTTGCA
1945520 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1945540 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1945560 AAA
1 AAA
1945563 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Done.