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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 5 of 131
Found at i:1591247 original size:28 final size:30
Alignment explanation
Indices: 1591202--1591259 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1591192 TAATTTGATC
*
1591202 AAATCAAAATTTCATGTAT-GAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
*
1591231 AAATCAAAGTTT-ATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
1591260 TTAAACCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATACAATTGCACA
Found at i:1600668 original size:20 final size:20
Alignment explanation
Indices: 1600643--1600682 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1600633 ATGTGACGGT
1600643 TAAAAGCAAAGTGAGTGGAA
1 TAAAAGCAAAGTGAGTGGAA
**
1600663 TAAAAGCATTGTGAGTGGAA
1 TAAAAGCAAAGTGAGTGGAA
1600683 GAGTGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (20 bp):
TAAAAGCAAAGTGAGTGGAA
Found at i:1603034 original size:32 final size:32
Alignment explanation
Indices: 1602990--1603056 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
1602980 TTAAGGTGCT
* *
1602990 TTGATCAGCGGTGAGACTAAAAACAACGACGG
1 TTGATCAACGGTGAGACTAAAAACAACGACAG
1603022 TTGATCAACGGTGAGACTAAAAACAACGACAG
1 TTGATCAACGGTGAGACTAAAAACAACGACAG
1603054 TTG
1 TTG
1603057 TGAAATTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (32 bp):
TTGATCAACGGTGAGACTAAAAACAACGACAG
Found at i:1604859 original size:10 final size:10
Alignment explanation
Indices: 1604844--1604877 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1604834 TATTAATTTT
1604844 AAAAAAATTA
1 AAAAAAATTA
*
1604854 AAAAAAATCA
1 AAAAAAATTA
*
1604864 CAAAAAATTA
1 AAAAAAATTA
1604874 AAAA
1 AAAA
1604878 GATTGGAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:1613095 original size:3 final size:3
Alignment explanation
Indices: 1613081--1613114 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1613071 CAAATGAGTA
* *
1613081 AAT AAT AGT AAT AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1613115 CAAAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1614569 original size:44 final size:44
Alignment explanation
Indices: 1614501--1614697 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 44
1614491 GATGCGATCT
* * *
1614501 GCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* * ** *
1614545 GCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTT-TT-AATCC
* ** * *** **
1614589 GCTCCACTACTGCTT-AGGGAGATAAGA-CT-T-GATGCGATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* * *
1614629 GCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
1614673 GCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
1614698 GGACTGGTTT
Statistics
Matches: 111, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
40 12 0.11
41 11 0.10
42 6 0.05
43 17 0.15
44 65 0.59
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
Found at i:1614623 original size:128 final size:128
Alignment explanation
Indices: 1614485--1614743 Score: 455
Period size: 128 Copynumber: 2.0 Consensus size: 128
1614475 CGGGGAGACG
*
1614485 AGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCC
1 AGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCC
* * *
1614550 ACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATA
66 ACTGCAACTTCAGGGAGATAGGACTGGTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATA
* * *
1614613 AGACTTGATGCGATTTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCC
1 AGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCC
1614678 ACTGCAACTTCAGGGAGATAGGACTGGTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATA
66 ACTGCAACTTCAGGGAGATAGGACTGGTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATA
1614741 AGA
1 AGA
1614744 TCTACAATCT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 124 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (128 bp):
AGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCC
ACTGCAACTTCAGGGAGATAGGACTGGTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATA
Found at i:1614722 original size:44 final size:43
Alignment explanation
Indices: 1614498--1614724 Score: 131
Period size: 44 Copynumber: 5.3 Consensus size: 43
1614488 CTGGATGCGA
* * * * **
1614498 TCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTG-GTTTCTTTG
* * *
1614542 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTTTCTT-TG
* ** * * * **
1614586 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGATGCGAT-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTTTCTTTG
* * * * **
1614627 T-TGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTG-GTTTCTTTG
* *
1614670 TCCGCTCCACTGCAACTTCAGGGAGATAGGACTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTTTCTT-TG
*
1614714 TCTACTCCACT
1 TCTGCTCCACT
1614725 ACTGCTTAGG
Statistics
Matches: 132, Mismatches: 42, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
40 11 0.08
41 12 0.09
42 9 0.07
43 27 0.20
44 73 0.55
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTTTCTTTG
Found at i:1614755 original size:44 final size:43
Alignment explanation
Indices: 1614707--1614830 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 43
1614697 AGGACTGGTT
* *
1614707 TCTTCTGTCTACTCCACTACTGCTTAGGAAGATAAGATCTACAA
1 TCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGAT-TACAA
* * * * * ****
1614751 TCTTCAACCTACTCCACTACTACTCAGGGAGATAGGATTGGTT
1 TCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGATTACAA
* *
1614794 TCTTCTATCTGCTCCACTATTGCTTAGGGAGATAAGA
1 TCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGA
1614831 CTTAATGCGA
Statistics
Matches: 62, Mismatches: 18, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
43 31 0.50
44 31 0.50
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (43 bp):
TCTTCTATCTACTCCACTACTGCTTAGGGAGATAAGATTACAA
Found at i:1614794 original size:128 final size:127
Alignment explanation
Indices: 1614511--1614784 Score: 345
Period size: 128 Copynumber: 2.1 Consensus size: 127
1614501 GCTCTACTGC
* *
1614511 AACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTG
1 AACTTCAGAGAGATAAGA-CTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTG
* * ** * ** * * *
1614576 GTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATTTGCTCTACTGT
65 GTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATAAGACTCAATGCAACCTACTCCACTCT
1614639 AACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTG
1 AACTTCAGAGAGATAAGA-CTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTG
*
1614704 GTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTACTCCACT
65 GTTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATAAGA-CT-CAA--TGCAACCTACTCCACT
1614769 ACT
126 -CT
*
1614772 -AC-TCAGGGAGATA
1 AACTTCAGAGAGATA
1614785 GGATTGGTTT
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
128 101 0.80
129 2 0.02
130 1 0.01
131 10 0.08
132 12 0.09
133 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (127 bp):
AACTTCAGAGAGATAAGACTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTGG
TTTCTTCTGTCTACTCCACTACTGCTTAGGAAGATAAGACTCAATGCAACCTACTCCACTCT
Found at i:1615325 original size:24 final size:24
Alignment explanation
Indices: 1615293--1615350 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1615283 CGGTTTGACC
1615293 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
* *
1615317 CCACTGTAATCTTCAACGTTCAGT
1 CCACTGTAATCTTCAAAGTTCAAT
*
1615341 CCACTATAAT
1 CCACTGTAAT
1615351 TTTGGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:1616321 original size:15 final size:14
Alignment explanation
Indices: 1616291--1616333 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1616281 TTGGCCTCTC
1616291 ATTTTTCTTTACTTTT
1 ATTTTTCTTT--TTTT
*
1616307 CTTTTTCCTTTTTTT
1 ATTTTT-CTTTTTTT
1616322 ATTTTTCTTTTT
1 ATTTTTCTTTTT
1616334 CTTTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 5 0.21
17 4 0.17
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTTCTTTTTTT
Found at i:1616327 original size:21 final size:20
Alignment explanation
Indices: 1616293--1616340 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1616283 GGCCTCTCAT
1616293 TTTTCTTTACTTTTCTTTTTCC
1 TTTT-TTTACTTTTCTTTTT-C
*
1616315 TTTTTTTATTTTTCTTTTTC
1 TTTTTTTACTTTTCTTTTTC
1616335 TTTTTT
1 TTTTTT
1616341 ATGAAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTACTTTTCTTTTTC
Found at i:1619019 original size:118 final size:119
Alignment explanation
Indices: 1618799--1619036 Score: 460
Period size: 118 Copynumber: 2.0 Consensus size: 119
1618789 CGGGAGTACT
1618799 AGATCTGGGACCAAACTTAGATCCTTGGCGTCAACCCCGCAAGGGTAATCAGTGTGACAGCCCGA
1 AGATCTGGGACCAAACTTAGATCCTTGGCGTCAACCCCGCAAGGGTAATCAGTGTGACAGCCCGA
1618864 TTTCGACCTTAATCGGACATAGTGGTTTCGGGACCACAAATTTGAGTCAAAAAA
66 TTTCGACCTTAATCGGACATAGTGGTTTCGGGACCACAAATTTGAGTCAAAAAA
1618918 AGATCTGGGA-CAAACTTAGATCCTTGGCGTCAACCCCGCAAGGGTAATCAGTGTGACAGCCCGA
1 AGATCTGGGACCAAACTTAGATCCTTGGCGTCAACCCCGCAAGGGTAATCAGTGTGACAGCCCGA
*
1618982 TTTCGACCTTAATCGGACATAGTGGTTTCGGGGCCACAAATTTGAGTCAAAAAA
66 TTTCGACCTTAATCGGACATAGTGGTTTCGGGACCACAAATTTGAGTCAAAAAA
1619036 A
1 A
1619037 TATTTTAATA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
118 108 0.92
119 10 0.08
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (119 bp):
AGATCTGGGACCAAACTTAGATCCTTGGCGTCAACCCCGCAAGGGTAATCAGTGTGACAGCCCGA
TTTCGACCTTAATCGGACATAGTGGTTTCGGGACCACAAATTTGAGTCAAAAAA
Found at i:1620630 original size:41 final size:41
Alignment explanation
Indices: 1620573--1620740 Score: 282
Period size: 41 Copynumber: 4.1 Consensus size: 41
1620563 NNNNNNNCCG
* *
1620573 GTGATCTAAATCAGGTTATAAACCTAGCAGGCTAAGTGCTA
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCA
*
1620614 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCA
*
1620655 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCA
* *
1620696 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCA
1620737 GTGA
1 GTGA
1620741 ATCTATTAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 121 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (41 bp):
GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCA
Found at i:1622062 original size:12 final size:12
Alignment explanation
Indices: 1622021--1622054 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1622011 TCTAGTTGTT
*
1622021 CTTGCATCTGGG
1 CTTGCATTTGGG
1622033 CTTGCATTTGGG
1 CTTGCATTTGGG
1622045 CTTGCATTTG
1 CTTGCATTTG
1622055 TTCTTGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.29, T:0.41
Consensus pattern (12 bp):
CTTGCATTTGGG
Found at i:1623985 original size:33 final size:33
Alignment explanation
Indices: 1623943--1624009 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1623933 CCTCGACACG
1623943 CCCAAAATTGGTACCTAGTTGATTAATTAATGT
1 CCCAAAATTGGTACCTAGTTGATTAATTAATGT
1623976 CCCAAAATTGGTACCTAGTTGATTAATTAATGT
1 CCCAAAATTGGTACCTAGTTGATTAATTAATGT
1624009 C
1 C
1624010 TTAGTGTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (33 bp):
CCCAAAATTGGTACCTAGTTGATTAATTAATGT
Found at i:1624814 original size:21 final size:22
Alignment explanation
Indices: 1624790--1624832 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1624780 GTACATGTAT
1624790 ATGT-GTATATATATTATAAAA
1 ATGTAGTATATATATTATAAAA
1624811 ATGTAAGTATATATATTATAAA
1 ATGT-AGTATATATATTATAAA
1624833 GTATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
23 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (22 bp):
ATGTAGTATATATATTATAAAA
Found at i:1624946 original size:3 final size:3
Alignment explanation
Indices: 1624926--1624968 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
1624916 CAAATGAGTA
* * *
1624926 AAT AAT AGT AAT AGT AAT AAT AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1624969 CAAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1626832 original size:82 final size:83
Alignment explanation
Indices: 1626731--1626895 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
1626721 TTATCTTTAA
1626731 ATAAAAATATTATTAGGAAAATATTTATGCTTTTTAATAATTTATATAAATTTTTTTAAAAAAAA
1 ATAAAAATATTATTAGGAAAATATTTATGCTTTTTAATAATTTATATAAATTTTTTTAAAAAAAA
1626796 AACTACCCTTCTAAAAAT
66 AACTACCCTTCTAAAAAT
1626814 ATAAAAATA-TATTAGGAAAATATTTATGCTTTTTAATAATTTATATAAATTTTTTTAAAAAAAA
1 ATAAAAATATTATTAGGAAAATATTTATGCTTTTTAATAATTTATATAAATTTTTTTAAAAAAAA
1626878 AACTACCCTTCTAAAAAT
66 AACTACCCTTCTAAAAAT
1626896 TACATTTAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 73 0.89
83 9 0.11
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (83 bp):
ATAAAAATATTATTAGGAAAATATTTATGCTTTTTAATAATTTATATAAATTTTTTTAAAAAAAA
AACTACCCTTCTAAAAAT
Found at i:1628081 original size:128 final size:123
Alignment explanation
Indices: 1627735--1628065 Score: 371
Period size: 125 Copynumber: 2.6 Consensus size: 123
1627725 TTAATTTTTT
* * * * *
1627735 TTTAA-AAAAAAAAATACAAGTTAGTATAATGGTACATTTGCAATTTGACCCCTCCAAAAATTTA
1 TTTAATAAAAAAAATTATAAGTTAGTATAATGGTAAATTTTCAGTTTGA-CCCTCCAAAAATTTA
* *
1627799 TCATTCATC-TTTGGCCCTCTTAAAGCAATTTGCTTTGCCACTAATTTGCTTTGTAGCCTC
65 TGATTCATCTTTTAG--CTCTTAAAGCAATTTGCTTTGCCACTAATTTGCTTTGTAGCCTC
** * *
1627859 TTTAATAAAAAAAATTATAAGTTAGTATAATAATAAAATTTCAGTTTGACCCTTCAAAAAATTTA
1 TTTAATAAAAAAAATTATAAGTTAGTATAATGGTAAATTTTCAGTTTGACCC-TCCAAAAATTTA
* * *
1627924 TGATTCATC-TTTAGCCCCTTAAAGCAATTTGCTTTGCCCCTGATTTGCTTTGTAGCCTC
65 TGATTCATCTTTTAG-CTCTTAAAGCAATTTGCTTTGCCACTAATTTGCTTTGTAGCCTC
*****
1627983 TTTAATTTTTTTTTTAAATTATAAGTTAGTATAATGGTAAATTTTCAGTTTGATCCCTCCAAAAA
1 TTTAA----TAAAAAAAATTATAAGTTAGTATAATGGTAAATTTTCAGTTTGA-CCCTCCAAAAA
*
1628048 TTTATGATTAATCTTTTA
61 TTTATGATTCATCTTTTA
1628066 TGTTCTAAAA
Statistics
Matches: 175, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
124 55 0.31
125 58 0.33
128 55 0.31
129 7 0.04
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (123 bp):
TTTAATAAAAAAAATTATAAGTTAGTATAATGGTAAATTTTCAGTTTGACCCTCCAAAAATTTAT
GATTCATCTTTTAGCTCTTAAAGCAATTTGCTTTGCCACTAATTTGCTTTGTAGCCTC
Found at i:1632614 original size:13 final size:13
Alignment explanation
Indices: 1632564--1632615 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
1632554 AAAGATAAAT
1632564 ACAAATGTAAGAA
1 ACAAATGTAAGAA
* *
1632577 A-GAACGTAAGAA
1 ACAAATGTAAGAA
*
1632589 AGAAAT-TACAGAA
1 ACAAATGTA-AGAA
1632602 ACAAATGTAAGAA
1 ACAAATGTAAGAA
1632615 A
1 A
1632616 GAATGGCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 12 0.39
13 17 0.55
14 2 0.06
ACGTcount: A:0.62, C:0.08, G:0.17, T:0.13
Consensus pattern (13 bp):
ACAAATGTAAGAA
Found at i:1633424 original size:20 final size:20
Alignment explanation
Indices: 1633399--1633436 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1633389 ACTATTGGGA
1633399 ATATCAGAGAAAGAAAAAAT
1 ATATCAGAGAAAGAAAAAAT
1633419 ATATCAGAGAAAGAAAAA
1 ATATCAGAGAAAGAAAAA
1633437 TAAAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.13
Consensus pattern (20 bp):
ATATCAGAGAAAGAAAAAAT
Found at i:1635308 original size:22 final size:22
Alignment explanation
Indices: 1635283--1635331 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1635273 ATTATAATTT
1635283 TATATATATTTACGACTTGAAG
1 TATATATATTTACGACTTGAAG
1635305 TATATATATTTACGACTTGAAG
1 TATATATATTTACGACTTGAAG
1635327 TATAT
1 TATAT
1635332 TTGATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (22 bp):
TATATATATTTACGACTTGAAG
Found at i:1638516 original size:36 final size:36
Alignment explanation
Indices: 1638461--1638539 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
1638451 CTGGTTTTGG
* **
1638461 CCACATCTTTTTTGGTTTATTTTAGGTTGACATGAT
1 CCACATCTTTTTTGGTTTATTTTAGATCAACATGAT
* *
1638497 CCACTTCTTTTTTGTTTTATTTTAGATCAACATGAT
1 CCACATCTTTTTTGGTTTATTTTAGATCAACATGAT
1638533 CCACATC
1 CCACATC
1638540 ATTATGCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (36 bp):
CCACATCTTTTTTGGTTTATTTTAGATCAACATGAT
Found at i:1649891 original size:16 final size:17
Alignment explanation
Indices: 1649855--1649888 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1649845 TTTATTGAAG
1649855 TTGT-TATGTATTTGAT
1 TTGTGTATGTATTTGAT
*
1649871 TTGTGTATGTGTTTGAT
1 TTGTGTATGTATTTGAT
1649888 T
1 T
1649889 GTGGATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.62
Consensus pattern (17 bp):
TTGTGTATGTATTTGAT
Found at i:1650712 original size:35 final size:35
Alignment explanation
Indices: 1650673--1650802 Score: 172
Period size: 35 Copynumber: 3.7 Consensus size: 35
1650663 TTTTCAGTAA
*
1650673 GCATGCTTTACATGCAAATAAGAATCAGTGTAATG
1 GCATGCTTAACATGCAAATAAGAATCAGTGTAATG
* * *
1650708 GCATGCTTAACATGTAGATCAA-AATCAATGTAATG
1 GCATGCTTAACATGCAAAT-AAGAATCAGTGTAATG
* *
1650743 GCATGCTTAACATGCGAATCAGAATCAGTGTAATG
1 GCATGCTTAACATGCAAATAAGAATCAGTGTAATG
* *
1650778 GCATGCTTGACATGCAAATCAGAAT
1 GCATGCTTAACATGCAAATAAGAAT
1650803 ATCGACAGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.01
35 79 0.96
36 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (35 bp):
GCATGCTTAACATGCAAATAAGAATCAGTGTAATG
Found at i:1652468 original size:27 final size:27
Alignment explanation
Indices: 1652437--1652490 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1652427 TTTTACAAGA
*
1652437 TTACAAACTCATTTATATTATTTACTG
1 TTACAAACTCATTTAGATTATTTACTG
1652464 TTACAAACTCATTTAGATTATTTACTG
1 TTACAAACTCATTTAGATTATTTACTG
1652491 AAGTAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (27 bp):
TTACAAACTCATTTAGATTATTTACTG
Found at i:1652751 original size:179 final size:179
Alignment explanation
Indices: 1652451--1652808 Score: 671
Period size: 179 Copynumber: 2.0 Consensus size: 179
1652441 AAACTCATTT
*
1652451 ATATTATTTACTGTTACAAACTCATTTAGATTATTTACTGAAGTAAGTTATCTTTCTGGCAATGT
1 ATATTATTTACTGTTACAAACTCATTTAGATTATTTACTGAAGTAAGTTATCTTTCTCGCAATGT
* *
1652516 AAACGTTCTTATAATGCCACTTATCATCAATTTGAACTTAAACAATCAATGAACTAATATTTGTT
66 AAACGTTCTTATAATGCCACTTATCATCAATTTGAACTTAAACAACCAATGAACTAATATTTGCT
1652581 TGTCACAATTTTGCTATGCATGCAAAACATGAAAGAGAAAAACACAAAA
131 TGTCACAATTTTGCTATGCATGCAAAACATGAAAGAGAAAAACACAAAA
1652630 ATATTATTTACTGTTACAAACTCATTTAGATTATTTACTGAAGTAAGTTATCTTTCTCGCAATGT
1 ATATTATTTACTGTTACAAACTCATTTAGATTATTTACTGAAGTAAGTTATCTTTCTCGCAATGT
* *
1652695 AAACGTTCTTATAGTGTCACTTATCATCAATTTGAACTTAAACAACCAATGAACTAATATTTGCT
66 AAACGTTCTTATAATGCCACTTATCATCAATTTGAACTTAAACAACCAATGAACTAATATTTGCT
1652760 TGTCACAATTTTGCTATGCATGCAAAACATGAAAGAGAAAAACACAAAA
131 TGTCACAATTTTGCTATGCATGCAAAACATGAAAGAGAAAAACACAAAA
1652809 GACATAATAG
Statistics
Matches: 174, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 174 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (179 bp):
ATATTATTTACTGTTACAAACTCATTTAGATTATTTACTGAAGTAAGTTATCTTTCTCGCAATGT
AAACGTTCTTATAATGCCACTTATCATCAATTTGAACTTAAACAACCAATGAACTAATATTTGCT
TGTCACAATTTTGCTATGCATGCAAAACATGAAAGAGAAAAACACAAAA
Found at i:1654982 original size:3 final size:3
Alignment explanation
Indices: 1654976--1655002 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1654966 ATTTATAATA
1654976 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1655003 CATGAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1658816 original size:31 final size:31
Alignment explanation
Indices: 1658781--1658842 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1658771 TCCATAAGCG
1658781 GGATTAAGATTTTGCCACGTGTTTTAAAATT
1 GGATTAAGATTTTGCCACGTGTTTTAAAATT
1658812 GGATTAAGATTTTGCCACGTGTTTTAAAATT
1 GGATTAAGATTTTGCCACGTGTTTTAAAATT
1658843 TTTAAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (31 bp):
GGATTAAGATTTTGCCACGTGTTTTAAAATT
Found at i:1662758 original size:26 final size:24
Alignment explanation
Indices: 1662715--1662768 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 24
1662705 CCATGATCGA
1662715 TATTTCCTTGTAATTTGTCTTAAT
1 TATTTCCTTGTAATTTGTCTTAAT
*
1662739 TATTTCCATTGTAAATTTGTGTTAAT
1 TATTTCC-TTGT-AATTTGTCTTAAT
1662765 TATT
1 TATT
1662769 GTTAATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 4 0.15
26 16 0.59
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.57
Consensus pattern (24 bp):
TATTTCCTTGTAATTTGTCTTAAT
Found at i:1662991 original size:31 final size:31
Alignment explanation
Indices: 1662948--1663026 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1662938 TTAATATACT
1662948 ATTTGGTACCTAATTTTAGCTTGAATGTTCA
1 ATTTGGTACCTAATTTTAGCTTGAATGTTCA
* * * *
1662979 ATTTCGTACCTAAATTTGGCTTTAATGTTCA
1 ATTTGGTACCTAATTTTAGCTTGAATGTTCA
* *
1663010 CTTTGGTACTTAATTTT
1 ATTTGGTACCTAATTTT
1663027 TTTTCAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTTGGTACCTAATTTTAGCTTGAATGTTCA
Found at i:1663237 original size:18 final size:17
Alignment explanation
Indices: 1663191--1663237 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1663181 CAACAGACAC
1663191 ATTTTATAATTTTATAAT
1 ATTTT-TAATTTTATAAT
*
1663209 ATTTTTTATTTTAATAAT
1 ATTTTTAATTTT-ATAAT
1663227 -TTATTTAATTT
1 ATT-TTTAATTT
1663238 GAACCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTAATTTTATAAT
Found at i:1663456 original size:43 final size:43
Alignment explanation
Indices: 1663395--1663479 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
1663385 AGATGGCAAA
*
1663395 TGCAGCAGCCACATTCTTCTGGCCGCCGGTGAAGGGACTTCAG
1 TGCAGCAGCCACATTCTTCTGGCCGCCGATGAAGGGACTTCAG
1663438 TGCAGCAGCCACATTCTTCTGGCCGCCGATGAAGGGACTTCA
1 TGCAGCAGCCACATTCTTCTGGCCGCCGATGAAGGGACTTCA
1663480 CCCTGACCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (43 bp):
TGCAGCAGCCACATTCTTCTGGCCGCCGATGAAGGGACTTCAG
Found at i:1669840 original size:5 final size:5
Alignment explanation
Indices: 1669830--1669889 Score: 120
Period size: 5 Copynumber: 12.0 Consensus size: 5
1669820 AAATCACTAT
1669830 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1669880 TAATA TAATA
1 TAATA TAATA
1669890 AACTGCAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1672193 original size:25 final size:25
Alignment explanation
Indices: 1672114--1672204 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
1672104 ACATTTGCCG
***
1672114 TCAATTCATCCTTTTGCATTTTATGG
1 TCAATTCATCC-TTTGCATTTTACCA
** *
1672140 TCAATTTGTCCTTTGCA-TATACCA
1 TCAATTCATCCTTTGCATTTTACCA
*
1672164 TCAATTCATCCTTTGCATTTTACCT
1 TCAATTCATCCTTTGCATTTTACCA
*
1672189 TCAATTCATCATTTGC
1 TCAATTCATCCTTTGC
1672205 CACAGAACGA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 18 0.34
25 26 0.49
26 9 0.17
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (25 bp):
TCAATTCATCCTTTGCATTTTACCA
Found at i:1674470 original size:6 final size:6
Alignment explanation
Indices: 1674454--1674483 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1674444 TAAGTTTCCA
*
1674454 AAAATG GAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
1674484 GAAACTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:1674471 original size:12 final size:12
Alignment explanation
Indices: 1674454--1674487 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1674444 TAAGTTTCCA
1674454 AAAATGGAAATG
1 AAAATGGAAATG
*
1674466 AAAATGAAAATG
1 AAAATGGAAATG
1674478 AAAATGGAAA
1 AAAATGGAAA
1674488 CTTGCAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:1674662 original size:25 final size:25
Alignment explanation
Indices: 1674628--1674701 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
1674618 ACGAATTTTC
1674628 TCAAAATTTTAC-AGGAGTAAAATCA
1 TCAAAATTTTACAAGG-GTAAAATCA
**
1674653 TCAAAATTTTATCAAGGGTAAAATTG
1 TCAAAATTTTA-CAAGGGTAAAATCA
*
1674679 TCAAAATTTTACTAGGGTAAAAT
1 TCAAAATTTTACAAGGGTAAAAT
1674702 AAAGATGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 22 0.50
26 19 0.43
27 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTACAAGGGTAAAATCA
Found at i:1677779 original size:25 final size:25
Alignment explanation
Indices: 1677729--1677823 Score: 88
Period size: 24 Copynumber: 3.9 Consensus size: 25
1677719 CCCTCTCTCA
* **
1677729 AGCCATATAACAGGAAGCTCCGAAG
1 AGCCATATAACGGGAAGCTCATAAG
*
1677754 AGCCAT-TAACGGGAAGCTTATCAAG
1 AGCCATATAACGGGAAGCTCAT-AAG
**
1677779 A-CTGTATAACGGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATAAG
* *
1677803 AGCCATA-ATCGAGAAGCTCAT
1 AGCCATATAACGGGAAGCTCAT
1677824 GCGAGCCAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
24 29 0.52
25 27 0.48
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATAAG
Found at i:1678412 original size:21 final size:21
Alignment explanation
Indices: 1678388--1678428 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1678378 AGTAAATTTA
*
1678388 GCTCAATTTAATACAATTCAT
1 GCTCAATTCAATACAATTCAT
*
1678409 GCTCAATTCAATCCAATTCA
1 GCTCAATTCAATACAATTCA
1678429 CATCTTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (21 bp):
GCTCAATTCAATACAATTCAT
Found at i:1686266 original size:23 final size:23
Alignment explanation
Indices: 1686235--1686285 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1686225 ACCTACTTTC
* * *
1686235 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
1686258 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
1686281 TTACA
1 TTACA
1686286 CAATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:1687787 original size:105 final size:101
Alignment explanation
Indices: 1687609--1687808 Score: 283
Period size: 105 Copynumber: 1.9 Consensus size: 101
1687599 AATTGACGGA
* * *
1687609 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGAAATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTGGGCTATGAAATTCTAA
1687674 TGACAAGACCATAACTGGGTTATGGCACTATGAACG
66 TGACAAGACCATAACTGGGTTATGGCACTATGAACG
* * **
1687710 TAAGACCCTGGTTGGACCATGGCAGTATATATACATGTATAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGGCA--ATATATAAATG--TAAGACCATAGCTGGGCTATGAAATT
* *
1687775 CTGATGATAAGACCATAACTGGGTTATGGCACTA
62 CTAATGACAAGACCATAACTGGGTTATGGCACTA
1687809 CAAATGTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 23 0.27
103 8 0.09
105 55 0.64
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTGGGCTATGAAATTCTAA
TGACAAGACCATAACTGGGTTATGGCACTATGAACG
Found at i:1687836 original size:105 final size:105
Alignment explanation
Indices: 1687644--1687838 Score: 257
Period size: 105 Copynumber: 1.9 Consensus size: 105
1687634 TGTTTAAATG
* **
1687644 TAAGACCATAGCTGGGCTATGAAATTTTAATGACAAGACCATAACTGGGTTATGGCACTATGAAC
1 TAAGACCATAGCTGGGCTATGAAATTCTAATGACAAGACCATAACTGGGTTATGGCACTACAAAC
* * **
1687709 GTAAGACCCTGGTTGGACCATGGCAGTATATATACATGTA
66 GTAAAACCATGGAAGGACCATGGCAGTATATATACATGTA
** * * *
1687749 TAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAAT
1 TAAGACCATAGCTGGGCTATGAAATTCTAATGACAAGACCATAACTGGGTTATGGCACTACAAAC
*
1687814 GTAAAACCATGGCAAGG-TCATGGCA
66 GTAAAACCATGG-AAGGACCATGGCA
1687839 ATACATGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 74 0.97
106 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (105 bp):
TAAGACCATAGCTGGGCTATGAAATTCTAATGACAAGACCATAACTGGGTTATGGCACTACAAAC
GTAAAACCATGGAAGGACCATGGCAGTATATATACATGTA
Found at i:1690604 original size:13 final size:13
Alignment explanation
Indices: 1690586--1690611 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1690576 TATTATTAAT
1690586 ATTATTTTGTGTG
1 ATTATTTTGTGTG
1690599 ATTATTTTGTGTG
1 ATTATTTTGTGTG
1690612 CATTTGATTG
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:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
ATTATTTTGTGTG
Found at i:1691834 original size:43 final size:43
Alignment explanation
Indices: 1691773--1691886 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
1691763 TATATGTTAT
* *
1691773 CGTGTAAGACCATGTCTGGGACGTTGGCACCGACT-TGTGTTTA
1 CGTGTAAGACCCTGTCTGGGACGTTGGCACCGA-TATGTGATTA
* * *
1691816 CGTGTAAGACCCTATCTGGGACAG-TAGCATCGATATGTGATTA
1 CGTGTAAGACCCTGTCTGGGAC-GTTGGCACCGATATGTGATTA
* * *
1691859 CATGTAAGACCCCGTCTGGAACGTTGGC
1 CGTGTAAGACCCTGTCTGGGACGTTGGC
1691887 TTTGTAAGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.03
43 55 0.95
44 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (43 bp):
CGTGTAAGACCCTGTCTGGGACGTTGGCACCGATATGTGATTA
Found at i:1693892 original size:27 final size:27
Alignment explanation
Indices: 1693862--1694082 Score: 237
Period size: 27 Copynumber: 8.2 Consensus size: 27
1693852 CCCTAAAATA
* * *
1693862 GGTATAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
1693889 GGTAAAATGATCATAATACCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
1693916 GGTAAAATAACCGTAATGCCTCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1693943 GGTAAAATGA-CGATAATACCCCTATAA
1 GGTAAAATGACCG-TAATGCCCCTATAG
* * *
1693970 GGTAAAATGACCATAATACCCCCATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * * *
1693997 GATAGAATGACCATAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1694024 GGTAAAACGATCGTAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
1694051 GGTAAAATGACCGTAATGCCCCTAAAG
1 GGTAAAATGACCGTAATGCCCCTATAG
1694078 GGTAA
1 GGTAA
1694083 GTGACTATTT
Statistics
Matches: 160, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 2 0.01
27 157 0.98
28 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTATAG
Found at i:1694014 original size:81 final size:81
Alignment explanation
Indices: 1693862--1694072 Score: 280
Period size: 81 Copynumber: 2.6 Consensus size: 81
1693852 CCCTAAAATA
* * * * *
1693862 GGTATAATGATCGTAATGCCCCTGTAGGGTAAAATGATCATAATACCCCTATAGGGTAAAATAAC
1 GGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCATAATACCCCCATAGGATAAAATAAC
* *
1693927 CGTAATGCCTCTGTAG
66 CATAATGCCCCTGTAG
* * * *
1693943 GGTAAAATGA-CGATAATACCCCTATAAGGTAAAATGACCATAATACCCCCATAGGATAGAATGA
1 GGTAAAATGATCG-TAATGCCCCTATAGGGTAAAATGACCATAATACCCCCATAGGATAAAATAA
1694007 CCATAATGCCCCTGTAG
65 CCATAATGCCCCTGTAG
* * *
1694024 GGTAAAACGATCGTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCC
1 GGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCATAATACCCC
1694073 TAAAGGGTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 2 0.02
81 108 0.96
82 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (81 bp):
GGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCATAATACCCCCATAGGATAAAATAAC
CATAATGCCCCTGTAG
Found at i:1694134 original size:24 final size:24
Alignment explanation
Indices: 1694104--1694166 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1694094 GCCCCTCGAG
*
1694104 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCCGTGA
* *
1694128 TGTAAATGACTGGTTTGTCTGTGA
1 TGTAAATGACTGATTTGTCCGTGA
* **
1694152 TTTGTATGACTGATT
1 TGTAAATGACTGATT
1694167 CTAAGCATGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCCGTGA
Found at i:1694377 original size:32 final size:32
Alignment explanation
Indices: 1694336--1694508 Score: 206
Period size: 32 Copynumber: 5.4 Consensus size: 32
1694326 TTGTTGCGAT
*
1694336 GTTACTGATGGCTTTGTGCCGATCATATTACC
1 GTTACTGATGGCTTTGTGCCAATCATATTACC
*
1694368 GTTACTGATGACTTTGTGCCAATCATATTACC
1 GTTACTGATGGCTTTGTGCCAATCATATTACC
* *
1694400 GTTACTGATGGTTTTGTGCCGATCATATTACC
1 GTTACTGATGGCTTTGTGCCAATCATATTACC
* *
1694432 GTTACTGATGG-TTGTGTGCCAATCATATCACT
1 GTTACTGATGGCTT-TGTGCCAATCATATTACC
** *** *
1694464 ACTACTGATGGCTTTACCCCAATCATATTACT
1 GTTACTGATGGCTTTGTGCCAATCATATTACC
*
1694496 G-TACTTATGGCTT
1 GTTACTGATGGCTT
1694509 GTAGCCATTC
Statistics
Matches: 123, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
31 13 0.11
32 108 0.88
33 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (32 bp):
GTTACTGATGGCTTTGTGCCAATCATATTACC
Found at i:1694525 original size:22 final size:22
Alignment explanation
Indices: 1694500--1694551 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1694490 ATTACTGTAC
*
1694500 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
* **
1694522 TTATAGCTTATAGTTATTCTGT
1 TTATGGCTTATAGCCATTCTGT
*
1694544 TTACGGCT
1 TTATGGCT
1694552 CTTAACCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.48
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:1696034 original size:2 final size:2
Alignment explanation
Indices: 1696027--1696056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1696017 CTACTGCCTG
1696027 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
1696057 GAAATATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1697097 original size:25 final size:25
Alignment explanation
Indices: 1697069--1697118 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1697059 TTGTAGCGTA
1697069 AGATAAAAAGTAAGTTAAATACACT
1 AGATAAAAAGTAAGTTAAATACACT
1697094 AGATAAAAAGTAAGTTAAATACACT
1 AGATAAAAAGTAAGTTAAATACACT
1697119 GCACTTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (25 bp):
AGATAAAAAGTAAGTTAAATACACT
Found at i:1698596 original size:16 final size:17
Alignment explanation
Indices: 1698575--1698606 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1698565 TGGATTGGAT
1698575 CCCTTTCAGC-TTTTTC
1 CCCTTTCAGCATTTTTC
1698591 CCCTTTCAGCATTTTT
1 CCCTTTCAGCATTTTT
1698607 GCCGATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.50
Consensus pattern (17 bp):
CCCTTTCAGCATTTTTC
Found at i:1699762 original size:21 final size:21
Alignment explanation
Indices: 1699720--1699762 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1699710 ACAACAATGG
* *
1699720 CAATGAGATTAATTATTGTAA
1 CAATGAGATTAATTACTATAA
1699741 CAATGAGATTAGA-TACTATAA
1 CAATGAGATTA-ATTACTATAA
1699762 C
1 C
1699763 GTAAGACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (21 bp):
CAATGAGATTAATTACTATAA
Found at i:1701611 original size:39 final size:39
Alignment explanation
Indices: 1701568--1701647 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
1701558 GGGGTTTTAA
1701568 TTAGAAAGAGATTTCGATTAATCAACCTAGAGTCAGTTG
1 TTAGAAAGAGATTTCGATTAATCAACCTAGAGTCAGTTG
1701607 TTAGAAAGAGATTTCGATTAATCAACCTAGAGTCAGTTG
1 TTAGAAAGAGATTTCGATTAATCAACCTAGAGTCAGTTG
1701646 TT
1 TT
1701648 CTTACTCTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (39 bp):
TTAGAAAGAGATTTCGATTAATCAACCTAGAGTCAGTTG
Found at i:1701851 original size:14 final size:14
Alignment explanation
Indices: 1701828--1701858 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1701818 TGTCGCGTTC
*
1701828 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
1701842 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
1701856 TTA
1 TTA
1701859 AAACAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:1703606 original size:23 final size:25
Alignment explanation
Indices: 1703554--1703626 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
1703544 AATAATATTA
*
1703554 TTTTAATAGTTTAATATT-AAAGT-
1 TTTTAATACTTTAATATTAAAAGTG
*
1703577 TAATTTAATAC-TT-ATATTAATAGTG
1 T--TTTAATACTTTAATATTAAAAGTG
*
1703602 TTTTATTACTTTAATATTAAAAGTG
1 TTTTAATACTTTAATATTAAAAGTG
1703627 ATTATCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
23 13 0.32
24 8 0.20
25 19 0.47
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTTAATACTTTAATATTAAAAGTG
Found at i:1711354 original size:12 final size:12
Alignment explanation
Indices: 1711337--1711361 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1711327 CCCAAAATAT
1711337 AAAATATAAAAC
1 AAAATATAAAAC
1711349 AAAATATAAAAC
1 AAAATATAAAAC
1711361 A
1 A
1711362 TCTGAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATATAAAAC
Found at i:1717226 original size:18 final size:18
Alignment explanation
Indices: 1717203--1717239 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1717193 TTGGAGAAAG
1717203 ATAATTAATTTGCCCCGA
1 ATAATTAATTTGCCCCGA
1717221 ATAATTAATTTGCCCCGA
1 ATAATTAATTTGCCCCGA
1717239 A
1 A
1717240 GTGAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (18 bp):
ATAATTAATTTGCCCCGA
Found at i:1718211 original size:3 final size:3
Alignment explanation
Indices: 1718146--1718194 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1718136 GGAGAGTGAC
1718146 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1718194 T
1 T
1718195 TAAGCTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1726315 original size:11 final size:11
Alignment explanation
Indices: 1726296--1726345 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
1726286 TAAACTAGCC
*
1726296 ATTAATATACA
1 ATTAATATATA
*
1726307 ATTATTATATA
1 ATTAATATATA
1726318 ATATATATATATA
1 AT-TA-ATATATA
1726331 ATTAATATAATA
1 ATTAATAT-ATA
1726343 ATT
1 ATT
1726346 TTATAACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 15 0.45
12 10 0.30
13 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTAATATATA
Found at i:1731595 original size:191 final size:192
Alignment explanation
Indices: 1731374--1731756 Score: 759
Period size: 191 Copynumber: 2.0 Consensus size: 192
1731364 ATATTAAAAC
1731374 AATATAATATAAAATATGTATTTAAAAAATTAAAAAAATAATATGGGTGGATCTAAAATGGATTT
1 AATATAATATAAAATATGTATTTAAAAAATTAAAAAAATAATATGGGTGGATCTAAAATGGATTT
1731439 AGATTAATTTTTTACAAATATGAACGGATTTGGGTAAATTTTTAAACCCGTATCTCGGCGAGGGC
66 AGATTAATTTTTTACAAATATGAACGGATTTGGGTAAATTTTTAAACCCGTATCTCGGCGAGGGC
1731504 TGAGTTTGGACAAGCGTAAAATATGTTAATATCAGATTTAGGCCCGACCCGACCTATGAACA
131 TGAGTTTGGACAAGCGTAAAATATGTTAATATCAGATTTAGGCCCGACCCGACCTATGAACA
1731566 AATATAATAT-AAATATGTATTTAAAAAATTAAAAAAATAATATGGGTGGATCTAAAATGGATTT
1 AATATAATATAAAATATGTATTTAAAAAATTAAAAAAATAATATGGGTGGATCTAAAATGGATTT
1731630 AGATTAATTTTTTACAAATATGAACGGATTTGGGTAAATTTTTAAACCCGTATCTCGGCGAGGGC
66 AGATTAATTTTTTACAAATATGAACGGATTTGGGTAAATTTTTAAACCCGTATCTCGGCGAGGGC
1731695 TGAGTTTGGACAAGCGTAAAATATGTTAATATCAGATTTAGGCCCGACCCGACCTATGAACA
131 TGAGTTTGGACAAGCGTAAAATATGTTAATATCAGATTTAGGCCCGACCCGACCTATGAACA
1731757 CCTCCATTGC
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
191 181 0.95
192 10 0.05
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (192 bp):
AATATAATATAAAATATGTATTTAAAAAATTAAAAAAATAATATGGGTGGATCTAAAATGGATTT
AGATTAATTTTTTACAAATATGAACGGATTTGGGTAAATTTTTAAACCCGTATCTCGGCGAGGGC
TGAGTTTGGACAAGCGTAAAATATGTTAATATCAGATTTAGGCCCGACCCGACCTATGAACA
Found at i:1733408 original size:20 final size:23
Alignment explanation
Indices: 1733363--1733413 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1733353 GTTTTATGTG
1733363 TATTTTAATGTTTACATATATTAAT
1 TATTTT-AT-TTTACATATATTAAT
1733388 T-TTTTATTTTACAT-T-TTAAT
1 TATTTTATTTTACATATATTAAT
1733408 TATTTT
1 TATTTT
1733414 GTCTTAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.24
21 5 0.20
22 7 0.28
23 2 0.08
24 4 0.16
25 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTTTATTTTACATATATTAAT
Found at i:1734490 original size:13 final size:13
Alignment explanation
Indices: 1734472--1734515 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1734462 TTTAAATAAA
1734472 CAGTTAATAGAAT
1 CAGTTAATAGAAT
*
1734485 CAGTTAGTCA-AAT
1 CAGTTAAT-AGAAT
*
1734498 CGGTTAATAGAAT
1 CAGTTAATAGAAT
1734511 CAGTT
1 CAGTT
1734516 TCTAACACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (13 bp):
CAGTTAATAGAAT
Found at i:1736059 original size:50 final size:50
Alignment explanation
Indices: 1736012--1736107 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
1736002 CCAAGCCATT
*
1736012 TATCGGGAAGCTCA-AGAGAGCCAAATATCGGGAAGCTCGTGAGAGCCAAA
1 TATCGGGAAGCTCATA-AGAGCCAAATAACGGGAAGCTCGTGAGAGCCAAA
* * *
1736062 TATCTGGATGCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGC
1 TATCGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCGTGAGAGC
1736108 TGTGGTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (50 bp):
TATCGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCGTGAGAGCCAAA
Found at i:1736108 original size:25 final size:25
Alignment explanation
Indices: 1736012--1736107 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
1736002 CCAAGCCATT
*
1736012 TATCGGGAAGCTCAAGAGAGCCAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
*
1736037 TATCGGGAAGCTCGTGAGAGCCAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
* * * *
1736062 TATCTGGATGCTCATAAGAGCTAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
* *
1736087 TAACGGGAAGCTCGTGAGAGC
1 TATCGGGAAGCTCATGAGAGC
1736108 TGTGGTGTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (25 bp):
TATCGGGAAGCTCATGAGAGCCAAA
Found at i:1736284 original size:22 final size:23
Alignment explanation
Indices: 1736254--1736300 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1736244 AACTACACAT
*
1736254 TTCACACACATA-ACAATATTCAA
1 TTCACACACATACA-AATATACAA
1736277 TTCA-ACACATACAAATATACAA
1 TTCACACACATACAAATATACAA
1736299 TT
1 TT
1736301 TAGTTATACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (23 bp):
TTCACACACATACAAATATACAA
Found at i:1749131 original size:25 final size:25
Alignment explanation
Indices: 1749103--1749157 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1749093 AAATTCAAAA
**
1749103 TAAATAAAACTGGTTCGATTTTTAG
1 TAAATAAAACTGGTTAAATTTTTAG
**
1749128 TAAATAAATTTGGTTAAATTTTTAG
1 TAAATAAAACTGGTTAAATTTTTAG
1749153 TAAAT
1 TAAAT
1749158 TACAAGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.44
Consensus pattern (25 bp):
TAAATAAAACTGGTTAAATTTTTAG
Found at i:1749554 original size:10 final size:10
Alignment explanation
Indices: 1749531--1749564 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1749521 TTCTAATTTT
1749531 TTTTTTAAGA
1 TTTTTTAAGA
1749541 -TTTTTAAGA
1 TTTTTTAAGA
*
1749550 TTTTTTAAAA
1 TTTTTTAAGA
1749560 TTTTT
1 TTTTT
1749565 GTAGGAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (10 bp):
TTTTTTAAGA
Found at i:1751976 original size:20 final size:20
Alignment explanation
Indices: 1751930--1751977 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1751920 AATTTACATT
1751930 TTATAAAATTCTTTTAAAAA
1 TTATAAAATTCTTTTAAAAA
*
1751950 TTTTAAAATT-TTTTAAAAA
1 TTATAAAATTCTTTTAAAAA
1751969 TATATAAAA
1 T-TATAAAA
1751978 AGTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAAAATTCTTTTAAAAA
Found at i:1753598 original size:11 final size:11
Alignment explanation
Indices: 1753543--1753598 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
1753533 TATTCTCTTG
1753543 TTATTTT-TTA
1 TTATTTTATTA
* *
1753553 TTGTTTTATTG
1 TTATTTTATTA
* *
1753564 TCATTTCATTA
1 TTATTTTATTA
* *
1753575 TTATATTACTA
1 TTATTTTATTA
1753586 TTATTTTATTA
1 TTATTTTATTA
1753597 TT
1 TT
1753599 TTTGTTTAGA
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
10 6 0.18
11 27 0.82
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:1756856 original size:7 final size:7
Alignment explanation
Indices: 1756844--1756876 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1756834 CTTCCAAACA
1756844 CAAAAGC
1 CAAAAGC
1756851 CAAAAGC
1 CAAAAGC
*
1756858 CAAAATC
1 CAAAAGC
1756865 CAAAAGC
1 CAAAAGC
1756872 CAAAA
1 CAAAA
1756877 ACACCTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.27, G:0.09, T:0.03
Consensus pattern (7 bp):
CAAAAGC
Found at i:1763739 original size:20 final size:20
Alignment explanation
Indices: 1763710--1763749 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1763700 TTCACCTCAT
1763710 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
*
1763730 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
1763750 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:1770274 original size:2 final size:2
Alignment explanation
Indices: 1770267--1770294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1770257 ACGTAGTGTT
1770267 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1770295 CTGTGTCTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1780678 original size:22 final size:23
Alignment explanation
Indices: 1780625--1780680 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1780615 CCCGTTTTGC
* * *
1780625 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
1780648 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
1780670 ATTAAAATTAA
1 ATTAAAATTAA
1780681 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:1780693 original size:16 final size:16
Alignment explanation
Indices: 1780656--1780695 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1780646 TTAATAAAAT
* *
1780656 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1780672 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1780688 TAAAATTA
1 TAAAATTA
1780696 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1780780 original size:9 final size:9
Alignment explanation
Indices: 1780768--1780804 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
1780758 TTTATCAAAT
1780768 TATTAATTG
1 TATTAATTG
1780777 TATTAATTG
1 TATTAATTG
1780786 --TTAATTG
1 TATTAATTG
1780793 TATTAATTG
1 TATTAATTG
1780802 TAT
1 TAT
1780805 GGAACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
9 19 0.73
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1780801 original size:16 final size:16
Alignment explanation
Indices: 1780765--1780802 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1780755 AAATTTATCA
*
1780765 AATTATTAATTGTATT
1 AATTGTTAATTGTATT
1780781 AATTGTTAATTGTATT
1 AATTGTTAATTGTATT
1780797 AATTGT
1 AATTGT
1780803 ATGGAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (16 bp):
AATTGTTAATTGTATT
Found at i:1781515 original size:2 final size:2
Alignment explanation
Indices: 1781508--1781541 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1781498 ATGGAAGGGA
1781508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1781542 TTCAAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1782298 original size:202 final size:201
Alignment explanation
Indices: 1781953--1782358 Score: 751
Period size: 202 Copynumber: 2.0 Consensus size: 201
1781943 TTAATTCAAA
*
1781953 CTGTTTCTAAGAAAAAGTAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
1 CTGTTTCTAAGAAAAAGGAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
1782018 ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
66 ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
*
1782083 AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAATAGTG
131 AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAGTG
1782148 GGTAAT
196 GGTAAT
1782154 CTGTTTCTAAGAAAAAGGAAGAATTGTATTAAATATCCTCCATT-AGCATGAATCACTACTGACT
1 CTGTTTCTAAGAAAAAGGAAGAATTGTATT-AATATCCTCCATTGA-CATGAATCACTACTGACT
1782218 CTACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAAC
64 CTACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAAC
* *
1782283 AAAACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCGAATCATCTTGAGAGGTAAAAGAG
129 AAAACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAG
1782348 TGGGTAAT
194 TGGGTAAT
1782356 CTG
1 CTG
1782359 CAGAAAGTGG
Statistics
Matches: 199, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
201 30 0.15
202 169 0.85
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (201 bp):
CTGTTTCTAAGAAAAAGGAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAGTG
GGTAAT
Found at i:1784780 original size:22 final size:22
Alignment explanation
Indices: 1784735--1784780 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1784725 ATAAATTGAG
* *
1784735 AATAACATTAAAACAAGAAGAA
1 AATAACATTAAAACAACAAAAA
* *
1784757 AATAGCATTGAAACAACAAAAA
1 AATAACATTAAAACAACAAAAA
1784779 AA
1 AA
1784781 ACAACAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (22 bp):
AATAACATTAAAACAACAAAAA
Found at i:1787540 original size:28 final size:29
Alignment explanation
Indices: 1787481--1787541 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1787471 AAAATTGCAG
* *
1787481 AAAAAATTGTAAAATTTATTAAACATTAT
1 AAAAAATTGTAAAATTTATTAAAAATCAT
*
1787510 AAAAAATTG-AACAA-TTATTAAAAATCGT
1 AAAAAATTGTAA-AATTTATTAAAAATCAT
1787538 AAAA
1 AAAA
1787542 TTATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAAATTGTAAAATTTATTAAAAATCAT
Found at i:1787600 original size:18 final size:18
Alignment explanation
Indices: 1787505--1787603 Score: 68
Period size: 18 Copynumber: 5.7 Consensus size: 18
1787495 TTTATTAAAC
1787505 ATTATAAAAAATTGAACA
1 ATTATAAAAAATTGAACA
* *
1787523 ATTATTAAAAATCGTAA-A
1 ATTATAAAAAATTG-AACA
*
1787541 ATTATAATAAA---AA-A
1 ATTATAAAAAATTGAACA
* * *
1787555 ACTGTAAAAATATTAAAC-
1 ATTATAAAAA-ATTGAACA
1787573 ATT-TAGAAAAATTGAACA
1 ATTATA-AAAAATTGAACA
1787591 ATTATAAAAAATT
1 ATTATAAAAAATT
1787604 TAAAAAGTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
17 8 0.13
18 40 0.63
19 4 0.06
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
ATTATAAAAAATTGAACA
Found at i:1787636 original size:18 final size:18
Alignment explanation
Indices: 1787596--1787636 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1787586 GAACAATTAT
* *
1787596 AAAAAATTTAAAAAGTAG
1 AAAAAATTTAAAAACTAA
*
1787614 TAAAAATTTAAAAACTAA
1 AAAAAATTTAAAAACTAA
1787632 AAAAA
1 AAAAA
1787637 TATATGTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAAATTTAAAAACTAA
Found at i:1787675 original size:29 final size:29
Alignment explanation
Indices: 1787616--1787677 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1787606 AAAAGTAGTA
**
1787616 AAAATTTAAAAACTAAAAAAATATATGTT
1 AAAATTTAAAAACTAAAAAAATATAAATT
* *
1787645 AAAATTTGAAAATTATAAAAAAT-TAAATT
1 AAAATTTAAAAACTA-AAAAAATATAAATT
1787674 AAAA
1 AAAA
1787678 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATTTAAAAACTAAAAAAATATAAATT
Found at i:1811433 original size:28 final size:29
Alignment explanation
Indices: 1811383--1811437 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1811373 TTAAAAGTTA
*
1811383 AAAATTTAATTTTTTTTGAATTTTTATTG
1 AAAATATAATTTTTTTTGAATTTTTATTG
1811412 AAAATATAATTTTTTTT-AATTTTTAT
1 AAAATATAATTTTTTTTGAATTTTTAT
1811438 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
AAAATATAATTTTTTTTGAATTTTTATTG
Found at i:1817529 original size:37 final size:37
Alignment explanation
Indices: 1817479--1817553 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1817469 CCAAGTTGAA
1817479 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
1 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
*
1817516 TACTTATTCCAAATTGTTTAGGAAAAGGATTCTTTTT
1 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
1817553 T
1 T
1817554 GTTAAGTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (37 bp):
TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
Found at i:1818726 original size:15 final size:17
Alignment explanation
Indices: 1818696--1818727 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1818686 ATGTCGCCAA
1818696 TTTTGTACTGTGTTTGT
1 TTTTGTACTGTGTTTGT
1818713 TTTTG-ACT-TGTTTGT
1 TTTTGTACTGTGTTTGT
1818728 GATCCTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (17 bp):
TTTTGTACTGTGTTTGT
Found at i:1823223 original size:7 final size:6
Alignment explanation
Indices: 1823184--1823221 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1823174 CTTTTTTCCC
*
1823184 AAAA-A AAAA-A AAAAGA AAAAGG AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1823222 AGGGAACTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1824013 original size:183 final size:183
Alignment explanation
Indices: 1823701--1824438 Score: 1196
Period size: 183 Copynumber: 4.0 Consensus size: 183
1823691 CTGTCATACC
* * * **
1823701 CTCAGTTGTAGCTGGTTTCAGAGTCAATTCTACACTCGGACTCAGTCTAGGCC-CTTTTGTCTTG
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTC-TTCATCTTG
* *
1823765 TGTCTTGCTATATCTTGGGAAGTGCTG-TGGTTGGTTGGTATGTGCTCCTTGGT-GATGCTGGGG
65 TATCTTGCTATATCTTGGGAAGTGCTGTTGG-TGGTTGGTATGTGCTCCTT-GTCGATGCCGGGG
*
1823828 GTTGTAGTTGCAGTGATTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
128 GTTGTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
1823884 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
1823949 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
* * *
1824014 GTAGTTGCCGTGGTTTGACCTAGTTCATGGTTCTGGACATCTGCCAAATGATA
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
*
1824067 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCAAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
* * *
1824132 ATCTTGCTATATCTAGGGAAGTACTGTTGGTGGTTGGTGTGTGCTCCTTGTCGATGCCGGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
*
1824197 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATAATA
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
1824250 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
* *
1824315 ATCTTGCAATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCAGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
* * * * * *
1824380 GTAGTTGCAGTGGTTTGGCCTAGTTCATGGCTT-AAGACCTCTGCCGAATGATC
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGG-TTCAGGACATCTGCCAAATGATA
1824433 CTCAGT
1 CTCAGT
1824439 CTCAGAAGGC
Statistics
Matches: 519, Mismatches: 32, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
182 2 0.00
183 511 0.98
184 6 0.01
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (183 bp):
CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
Found at i:1840723 original size:37 final size:37
Alignment explanation
Indices: 1840673--1840745 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
1840663 CATTGTTGTA
1840673 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
1 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
1840710 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTT
1 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTT
1840746 CTTAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (37 bp):
CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
Found at i:1841523 original size:22 final size:22
Alignment explanation
Indices: 1841498--1841547 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1841488 GTCCAGGTTG
* *
1841498 GGTGTCCTGACATCATATGGCT
1 GGTGTCCTAACATCACATGGCT
*
1841520 GGTGTCGTAACATCACATGGCT
1 GGTGTCCTAACATCACATGGCT
1841542 GGTGTC
1 GGTGTC
1841548 ATCACATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (22 bp):
GGTGTCCTAACATCACATGGCT
Found at i:1841554 original size:22 final size:22
Alignment explanation
Indices: 1841498--1841554 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1841488 GTCCAGGTTG
* * *
1841498 GGTGTCCTGACATCATATGGCT
1 GGTGTCATAACATCACATGGCT
*
1841520 GGTGTCGTAACATCACATGGCT
1 GGTGTCATAACATCACATGGCT
*
1841542 GGTGTCATCACAT
1 GGTGTCATAACAT
1841555 TGATGTCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (22 bp):
GGTGTCATAACATCACATGGCT
Found at i:1846525 original size:28 final size:27
Alignment explanation
Indices: 1846493--1846551 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1846483 TGAAGGAGAT
1846493 AAGACAAAGGATTTAATGGCTGAGCTAG
1 AAGACAAAGGATTTAATGGCT-AGCTAG
* * * *
1846521 AAGACTAAGTATTTCATGGCTAGCTTG
1 AAGACAAAGGATTTAATGGCTAGCTAG
1846548 AAGA
1 AAGA
1846552 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
AAGACAAAGGATTTAATGGCTAGCTAG
Found at i:1847862 original size:22 final size:22
Alignment explanation
Indices: 1847837--1847893 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1847827 CGTCCAGGTT
1847837 TGGTGTCATGACACCACATGGC
1 TGGTGTCATGACACCACATGGC
** * *
1847859 TGGTGTCGCGACATCACTTGGC
1 TGGTGTCATGACACCACATGGC
*
1847881 TGGTGTGATGACA
1 TGGTGTCATGACA
1847894 TTGATTGTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (22 bp):
TGGTGTCATGACACCACATGGC
Found at i:1852864 original size:22 final size:23
Alignment explanation
Indices: 1852838--1852884 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1852828 TTGTTTCCTT
*
1852838 TTGCTTCTCGATTCTTGTT-CTG
1 TTGCTTCTCAATTCTTGTTGCTG
* *
1852860 TTGCTTGTCAATTTTTGTTGCTG
1 TTGCTTCTCAATTCTTGTTGCTG
1852883 TT
1 TT
1852885 TTTAGAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.06, C:0.17, G:0.19, T:0.57
Consensus pattern (23 bp):
TTGCTTCTCAATTCTTGTTGCTG
Found at i:1857842 original size:50 final size:50
Alignment explanation
Indices: 1857777--1857959 Score: 188
Period size: 50 Copynumber: 3.6 Consensus size: 50
1857767 TTCGATATAT
* * * * *
1857777 GTAGTAGCATTCACATTGTACTACACACGTGATCAAACTTTTCGGTTCAC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTCGGTACAC
* * * *
1857827 GTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCAGTACGC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATC-AAACTATTCGGTACAC
* * * * ***
1857878 ATAGTAGCCTGCACATAGTACTACACATGCGACCTTTC-ATTCAGGTACAC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTC-GGTACAC
*
1857928 GTAGTAGCCTACACATAGTACTACACACGTGA
1 GTAGTAGCCTGCACATAGTACTACACACGTGA
1857960 CTATCACTTT
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 3 0.03
50 65 0.60
51 40 0.37
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTCGGTACAC
Found at i:1868564 original size:57 final size:57
Alignment explanation
Indices: 1868459--1868567 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
1868449 TGGTATCCAT
*
1868459 CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTGCTTGGAACTAAAA
1 CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTACTTGGAACTAAAA
* * * *
1868516 CACCGGTACATAGTACCTGGAACTTTAATCGTT-G-ACAACTAGTACTTGGAAC
1 CACCGATACATAGTACATGGAACTGTAATCATTAGCAC-A-TAGTACTTGGAAC
1868568 GCCCTAATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 2 0.04
57 41 0.91
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (57 bp):
CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTACTTGGAACTAAAA
Found at i:1870438 original size:67 final size:67
Alignment explanation
Indices: 1870330--1870555 Score: 296
Period size: 67 Copynumber: 3.4 Consensus size: 67
1870320 GAGGTTTAAG
* * *
1870330 GTGTAAGACCATATCTCGACTAT-AGCAACCA-ATAGAGTCCGCCAAGACATTAAATATGGGGTT
1 GTGTAAGACCATAGCTCGACTATGA-CAA-CATGTGGAGTCCGCCAAGACATTAAATATGGGGTT
1870393 ACAT
64 ACAT
*
1870397 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGATATT-AATCATGGGGTTA
1 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAAT-ATGGGGTTA
1870461 CAT
65 CAT
* * * * *
1870464 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCCGTCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAATATGGGGTTAC
1870529 AT
66 AT
* * *
1870531 GGGTAATACCATAGCTCAACTATGA
1 GTGTAAGACCATAGCTCGACTATGA
1870556 TAATAGATAA
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
66 5 0.04
67 132 0.94
68 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (67 bp):
GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAATATGGGGTTAC
AT
Found at i:1873196 original size:4 final size:4
Alignment explanation
Indices: 1873187--1873218 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1873177 ACGAGGAAAA
1873187 ATTT ATTT ATTT ATTT ATTT ATTT ATTAT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATT
1873219 CTTATGGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1876001 original size:42 final size:42
Alignment explanation
Indices: 1875946--1876048 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
1875936 AACCTGTAAG
* * **
1875946 GGTTGAACGGAAGCTCATCGGAGCTGAACGAAAACCCATAAA
1 GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
* * * *
1875988 GGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACCCATTAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
*
1876030 GGTTAAACAGAAACTCATA
1 GGTTAAACAGAAGCTCATA
1876049 TGAGTTAACA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
Found at i:1880853 original size:57 final size:57
Alignment explanation
Indices: 1880689--1880838 Score: 266
Period size: 57 Copynumber: 2.6 Consensus size: 57
1880679 GGGTGATCCT
**
1880689 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCAAACGGGTG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
1880746 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
*
1880803 ATCTTGATATAGCCCTCCTGAAGAATATGTG-GAAAA
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAA
1880839 TGGATTTAGC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
56 5 0.06
57 85 0.94
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (57 bp):
ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
Found at i:1884595 original size:2 final size:2
Alignment explanation
Indices: 1884588--1884613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1884578 AAAATAGGTG
1884588 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
1884614 ATTCTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1884645 original size:4 final size:4
Alignment explanation
Indices: 1884636--1884662 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1884626 CAATAATGAA
1884636 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1884663 ATTATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1884843 original size:47 final size:47
Alignment explanation
Indices: 1884757--1884849 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
1884747 TATGTATGTG
*
1884757 TATATTTTAAGACTATAAAATATATAAAAAGAATATATGTATGTATA
1 TATATTTTAAGACTATAAAATATATAAAAAGAATATATGTACGTATA
* *
1884804 TATAGTTTTAAG-TTATAAAATATATATAAAA-AATGTATGTACGTAT
1 TATA-TTTTAAGACTATAAAATATATA-AAAAGAATATATGTACGTAT
1884850 GAATTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (47 bp):
TATATTTTAAGACTATAAAATATATAAAAAGAATATATGTACGTATA
Found at i:1884959 original size:3 final size:3
Alignment explanation
Indices: 1884947--1885044 Score: 78
Period size: 3 Copynumber: 33.3 Consensus size: 3
1884937 TGAAGAAACT
* * * *
1884947 TAA T-A TAA TAA TACA TAA TAA -AT TTA TAA TAC TGA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
1884991 TAA TAA TAA TTT TAA -AA CAA -AA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1885037 TACA TAA T
1 TA-A TAA T
1885045 GAGCTTAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
2 7 0.09
3 62 0.83
4 6 0.08
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1884993 original size:18 final size:16
Alignment explanation
Indices: 1884947--1885101 Score: 92
Period size: 15 Copynumber: 9.8 Consensus size: 16
1884937 TGAAGAAACT
1884947 TAAT-ATAATAATACA
1 TAATAATAATAATACA
*
1884962 TAATAAATTTATAATAC-
1 TAAT-AA-TAATAATACA
*
1884979 TGATAATAATAATA-A
1 TAATAATAATAATACA
** *
1884994 TAATAATTTTAAAACA
1 TAATAATAATAATACA
*
1885010 AAATAATAATAATA-A
1 TAATAATAATAATACA
*
1885025 CAATAATAATAATACA
1 TAATAATAATAATACA
* *
1885041 TAATGAGCTTA-AATAC-
1 TAAT-A-ATAATAATACA
*
1885057 TAATATATAATAATAACT
1 TAATA-ATAATAAT-ACA
*
1885075 TAA-AATAATAGTACA
1 TAATAATAATAATACA
*
1885090 TATTAA-AATAAT
1 TAATAATAATAAT
1885102 GTATACATAT
Statistics
Matches: 106, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
15 47 0.44
16 33 0.31
17 13 0.12
18 13 0.12
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.34
Consensus pattern (16 bp):
TAATAATAATAATACA
Found at i:1885060 original size:26 final size:24
Alignment explanation
Indices: 1884984--1885091 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 24
1884974 AATACTGATA
*
1884984 ATAATAATA-ATAATAATTTTAAA-
1 ATAATAATACATAATAA-CTTAAAT
* *
1885007 ACAA-AATA-ATAATAA-TAACAAT
1 ATAATAATACATAATAACTTA-AAT
*
1885029 AATAATAATACATAATGAGCTTAAAT
1 -ATAATAATACATAAT-AACTTAAAT
1885055 ACTAATATATA-ATAATAACTTAAA-
1 A-TAATA-ATACATAATAACTTAAAT
*
1885079 ATAATAGTACATA
1 ATAATAATACATA
1885092 TTAAAATAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 13 0.19
23 14 0.21
24 5 0.07
25 13 0.19
26 14 0.21
27 5 0.07
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (24 bp):
ATAATAATACATAATAACTTAAAT
Found at i:1885121 original size:20 final size:19
Alignment explanation
Indices: 1885074--1885122 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1885064 TAATAATAAC
1885074 TTAAAATAA--TAGTACATA
1 TTAAAATAATGTA-TACATA
1885092 TTAAAATAATGTATACATA
1 TTAAAATAATGTATACATA
*
1885111 TATATAATAATG
1 T-TAAAATAATG
1885123 AATAAGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 7 0.26
20 11 0.41
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (19 bp):
TTAAAATAATGTATACATA
Found at i:1887184 original size:10 final size:10
Alignment explanation
Indices: 1887168--1887201 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1887158 TAAAAAATAC
1887168 ATAAATATTT
1 ATAAATATTT
* *
1887178 TTAAATATAT
1 ATAAATATTT
1887188 ATAAATATTT
1 ATAAATATTT
1887198 ATAA
1 ATAA
1887202 TTAGGATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAAATATTT
Found at i:1889630 original size:14 final size:14
Alignment explanation
Indices: 1889611--1889639 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1889601 CTACTATTTC
1889611 ACTATTATGTTATT
1 ACTATTATGTTATT
1889625 ACTATTATGTTATT
1 ACTATTATGTTATT
1889639 A
1 A
1889640 TTGTTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (14 bp):
ACTATTATGTTATT
Found at i:1895246 original size:135 final size:138
Alignment explanation
Indices: 1895009--1895283 Score: 504
Period size: 135 Copynumber: 2.0 Consensus size: 138
1894999 AATTATAAAT
1895009 TAAAGAAAGCTAAAAGGACTAAATAGGCAATTATACTTTTTTTCTAATTTGAGGCGGCATAACAA
1 TAAAGAAAGCTAAAAGGACTAAATAGGCAATTATACTTTTTTTCTAATTTGAGGCGGCATAACAA
1895074 AAGAAATATCTGAGATTTTTTTTATATATATTATATATTATGCTATTCAATTAATAAGTGAGTTG
66 AAGAAATATCTGAGATTTTTTTTATATATATTATATATTATGCTATTCAATTAATAAGTGAGTTG
1895139 TTATATTA
131 TTATATTA
*
1895147 TAAAGAAAGCT-AAAGGACTAAATAGGCAATTAT-GTTTTTTT-TAATTTGAGGCGGCATAACAA
1 TAAAGAAAGCTAAAAGGACTAAATAGGCAATTATACTTTTTTTCTAATTTGAGGCGGCATAACAA
1895209 AAGAAATATCTGAGATTTTTTTTATATATAATT-TATATTATGCTATTCAATTAATAAGTGAGTT
66 AAGAAATATCTGAGATTTTTTTTATATAT-ATTATATATTATGCTATTCAATTAATAAGTGAGTT
1895273 GTTATATTA
130 GTTATATTA
1895282 TA
1 TA
1895284 TTATTATATA
Statistics
Matches: 135, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
135 92 0.68
136 10 0.07
137 22 0.16
138 11 0.08
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (138 bp):
TAAAGAAAGCTAAAAGGACTAAATAGGCAATTATACTTTTTTTCTAATTTGAGGCGGCATAACAA
AAGAAATATCTGAGATTTTTTTTATATATATTATATATTATGCTATTCAATTAATAAGTGAGTTG
TTATATTA
Found at i:1895363 original size:11 final size:11
Alignment explanation
Indices: 1895347--1895372 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1895337 AAATTGAAAC
1895347 GAAACAGGGGA
1 GAAACAGGGGA
1895358 GAAACAGGGGA
1 GAAACAGGGGA
1895369 GAAA
1 GAAA
1895373 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:1904786 original size:41 final size:41
Alignment explanation
Indices: 1904725--1904806 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1904715 TGTCTAGTTA
*
1904725 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTCATTTG
1 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
*
1904766 TTGGGATGAAAATAGGTTTTTAATTAAATAAATTTAATTTG
1 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
1904807 GACTACCACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (41 bp):
TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
Found at i:1909340 original size:3 final size:3
Alignment explanation
Indices: 1909332--1909362 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1909322 GCTCTGTGAG
1909332 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1909363 GTCTGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1910140 original size:2 final size:2
Alignment explanation
Indices: 1910133--1910169 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1910123 ATTTAGTCCT
1910133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1910170 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1910207 original size:23 final size:24
Alignment explanation
Indices: 1910178--1910225 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1910168 ATTTTTTAAA
*
1910178 AAATGAGTGTGACTC-TCTATTTT
1 AAATGAGAGTGACTCTTCTATTTT
*
1910201 AAATGAGAGTTACTCTTTCTATTTT
1 AAATGAGAGTGACTC-TTCTATTTT
1910226 CAATATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (24 bp):
AAATGAGAGTGACTCTTCTATTTT
Found at i:1910980 original size:9 final size:9
Alignment explanation
Indices: 1910960--1910995 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
1910950 TTTTTAAAAA
1910960 TAAAAATGAT
1 TAAAAAT-AT
1910970 TAAAAATAT
1 TAAAAATAT
1910979 TAAAAATAT
1 TAAAAATAT
1910988 ATAAAAAT
1 -TAAAAAT
1910996 TTTAGTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Done.