Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 78 of 206
Found at i:22257275 original size:29 final size:28
Alignment explanation
Indices: 22257180--22257346 Score: 103
Period size: 29 Copynumber: 5.9 Consensus size: 28
22257170 TTCCTTTACG
*
22257180 GAGATT-GCCATAAAGGC-TTTCTTGTCTA
1 GAGATTAGCCACAAAGGCTTTTCTT-T-TA
* * * *
22257208 GAG-TTTGCCACAGAGGCTTTCCTTTGACA
1 GAGATTAGCCACAAAGGCTTTTCTTT--TA
*
22257237 GAGA-TCGCCACAAAGGCTTTTTCTTTTA
1 GAGATTAGCCACAAAGGC-TTTTCTTTTA
* * *
22257265 GAGATTAGCCACAAAAGC-TATCCTTTA
1 GAGATTAGCCACAAAGGCTTTTCTTTTA
* *
22257292 GCAGGTTCA-CCACAAAGGCTTTCCTTTCTA
1 G-AGATT-AGCCACAAAGGCTTTTCTTT-TA
* *
22257322 GAGTTTTGCCACAAAGGCTTTTCTT
1 GAGATTAGCCACAAAGGCTTTTCTT
22257347 CTTCTGGTAA
Statistics
Matches: 107, Mismatches: 21, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
27 10 0.09
28 31 0.29
29 56 0.52
30 10 0.09
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (28 bp):
GAGATTAGCCACAAAGGCTTTTCTTTTA
Found at i:22257290 original size:28 final size:28
Alignment explanation
Indices: 22257259--22257336 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
22257249 AAGGCTTTTT
22257259 CTTTTAGAGATTAGCCACAAAAGCTATC
1 CTTTTAGAGATTAGCCACAAAAGCTATC
* * *
22257287 C-TTTAGCAGGTTCA-CCACAAAGGCTTTC
1 CTTTTAG-AGATT-AGCCACAAAAGCTATC
* *
22257315 CTTTCTAGAGTTTTGCCACAAA
1 CTTT-TAGAGATTAGCCACAAA
22257337 GGCTTTTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.12
28 18 0.45
29 14 0.35
30 3 0.08
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (28 bp):
CTTTTAGAGATTAGCCACAAAAGCTATC
Found at i:22257573 original size:53 final size:53
Alignment explanation
Indices: 22257488--22257666 Score: 207
Period size: 53 Copynumber: 3.4 Consensus size: 53
22257478 CACTCACTAG
* * *
22257488 TTACGGTCTTACATGATATGGTATTAGTTCCATATGATGTCATAACCCGCCAA
1 TTACGGTCTTACACGATATGGTCTTAGTTCCATATGATGTCATAACCCACCAA
* * * * *
22257541 TTACAGTCTTACACGATATGATCTTTA-TTCCATATAATGCCATAACCCACCAG
1 TTACGGTCTTACACGATATGGTC-TTAGTTCCATATGATGTCATAACCCACCAA
* * * * * *
22257594 TTATGGTATTACATGATATGGTCATATTTCCATATGATGTCATAACCCACTAA
1 TTACGGTCTTACACGATATGGTCTTAGTTCCATATGATGTCATAACCCACCAA
*
22257647 TTACGATCTTACACGATATG
1 TTACGGTCTTACACGATATG
22257667 CTCCTTCAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
52 2 0.02
53 97 0.95
54 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (53 bp):
TTACGGTCTTACACGATATGGTCTTAGTTCCATATGATGTCATAACCCACCAA
Found at i:22262548 original size:43 final size:43
Alignment explanation
Indices: 22262486--22262746 Score: 204
Period size: 43 Copynumber: 6.1 Consensus size: 43
22262476 TTTTAGAAAT
* * * * *
22262486 AAACGCTGCTAAAGGTCATGACTTTTAGTGGCGCTTATCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * *
22262529 AAACGCCACCATAGATCATGATTTTTAGCAGCGGTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* *
22262572 AAACGCCGCTATAGGTCATGACTTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * *
22262615 AAATGCCGCTATAGATCATCAGTTTTAGCGACACTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * * * **
22262658 CAACGTCGCTATATAACA--AATCTTTAGCGACGCTTTTTCGTAC
1 AAACGCCGCTATAGATCATGACT-TTTAGCGGCGC-TTTTCCCAC
* * * ** *
22262701 AAACGCCACTATAGAACA-GACCTTTAAAGGCGCTTTTCACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
22262743 AAAC
1 AAAC
22262747 ACCGATAAAA
Statistics
Matches: 171, Mismatches: 44, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
41 2 0.01
42 21 0.12
43 147 0.86
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:22262593 original size:86 final size:86
Alignment explanation
Indices: 22262486--22262670 Score: 228
Period size: 86 Copynumber: 2.2 Consensus size: 86
22262476 TTTTAGAAAT
* * ** * *
22262486 AAACGCTGCTAAAGGTCATGACTTTTAGTGGCGCTTATCCCACAAACGCCACCATAGATCATGAT
1 AAACGCCGCTATAGGTCATGACTTTTAACGGCGCTTATCCCACAAACGCCACCATAGATCATCAG
**
22262551 TTTTAGC-AGCGGTTTTCCCAC
66 TTTTAGCGA-CACTTTTCCCAC
* * * *
22262572 AAACGCCGCTATAGGTCATGACTTTTAACGGCGCTTTTCCCACAAATGCCGCTATAGATCATCAG
1 AAACGCCGCTATAGGTCATGACTTTTAACGGCGCTTATCCCACAAACGCCACCATAGATCATCAG
22262637 TTTTAGCGACACTTTTCCCAC
66 TTTTAGCGACACTTTTCCCAC
* *
22262658 CAACGTCGCTATA
1 AAACGCCGCTATA
22262671 TAACAAATCT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 83 0.99
87 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTATAGGTCATGACTTTTAACGGCGCTTATCCCACAAACGCCACCATAGATCATCAG
TTTTAGCGACACTTTTCCCAC
Found at i:22263079 original size:43 final size:43
Alignment explanation
Indices: 22263013--22263103 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
22263003 ACATATGCAA
* * * * *
22263013 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAAATACAATACATTTACTAAATCAAGGAAATCTT
* *
22263056 GGTAATAAAAAATATAATACATTTACTAAATCAAGGATATCTT
1 GGTAATAAAAAATACAATACATTTACTAAATCAAGGAAATCTT
22263099 -GTAAT
1 GGTAAT
22263104 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAAATACAATACATTTACTAAATCAAGGAAATCTT
Found at i:22267232 original size:7 final size:7
Alignment explanation
Indices: 22267222--22267252 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
22267212 CTCTAACTCT
22267222 TAACCCC
1 TAACCCC
22267229 TAACCCC
1 TAACCCC
*
22267236 TAACTCC
1 TAACCCC
22267243 TAACCCC
1 TAACCCC
22267250 TAA
1 TAA
22267253 ACGTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (7 bp):
TAACCCC
Found at i:22269047 original size:41 final size:41
Alignment explanation
Indices: 22269002--22269132 Score: 174
Period size: 41 Copynumber: 3.2 Consensus size: 41
22268992 ATGTTTTTTT
*
22269002 GCGGCGCTTTTTCAAAAATGCAGCTAAAACCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCAGCTAAAACCCCGAGCATTA
*** * *
22269043 GCGGCGCTACATCAAAAACGCCGCTAAAACCTCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCAGCTAAAACCCCGAGCATTA
* *
22269084 GCGGCGCTTTTTAAAAAACACAGCTAAAACCCAC-AGCATTA
1 GCGGCGCTTTTTCAAAAACGCAGCTAAAACCC-CGAGCATTA
22269125 GCGGCGCT
1 GCGGCGCT
22269133 ACTCCAAAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 75 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCAGCTAAAACCCCGAGCATTA
Found at i:22269141 original size:82 final size:82
Alignment explanation
Indices: 22269002--22269152 Score: 225
Period size: 82 Copynumber: 1.8 Consensus size: 82
22268992 ATGTTTTTTT
* ** *
22269002 GCGGCGCTTTTTCAAAAATGCAGCTAAAACCCCGAGCATTAGCGGCGCTACATCAAAAACGCCGC
1 GCGGCGCTTTTTAAAAAACACAGCTAAAACCCCGAGCATTAGCGGCGCTACATCAAAAACGCCAC
22269067 TAAAACCTCGAGCATTA
66 TAAAACCTCGAGCATTA
*
22269084 GCGGCGCTTTTTAAAAAACACAGCTAAAACCCAC-AGCATTAGCGGCGCTAC-TCCAAAAATGCC
1 GCGGCGCTTTTTAAAAAACACAGCTAAAACCC-CGAGCATTAGCGGCGCTACAT-CAAAAACGCC
22269147 ACTAAA
64 ACTAAA
22269153 GCCCCCGATA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
81 1 0.02
82 60 0.97
83 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (82 bp):
GCGGCGCTTTTTAAAAAACACAGCTAAAACCCCGAGCATTAGCGGCGCTACATCAAAAACGCCAC
TAAAACCTCGAGCATTA
Found at i:22269152 original size:41 final size:40
Alignment explanation
Indices: 22269013--22269157 Score: 145
Period size: 41 Copynumber: 3.6 Consensus size: 40
22269003 CGGCGCTTTT
22269013 TCAAAAATG-CAGCTAAAACCCCGAGCATTAGCGGCGCTAC
1 TCAAAAATGCCAGCTAAAACCCC-AGCATTAGCGGCGCTAC
* * **
22269053 ATCAAAAACGCC-GCTAAAACCTCGAGCATTAGCGGCGCTTT
1 -TCAAAAATGCCAGCTAAAACC-CCAGCATTAGCGGCGCTAC
* *
22269094 TTAAAAA-ACACAGCTAAAACCCACAGCATTAGCGGCGCTAC
1 TCAAAAATGC-CAGCTAAAACCC-CAGCATTAGCGGCGCTAC
*
22269135 TCCAAAAATGCCA-CTAAAGCCCC
1 T-CAAAAATGCCAGCTAAAACCCC
22269158 CGATAGGTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
39 1 0.01
40 9 0.11
41 65 0.76
42 9 0.11
43 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.16
Consensus pattern (40 bp):
TCAAAAATGCCAGCTAAAACCCCAGCATTAGCGGCGCTAC
Found at i:22270047 original size:22 final size:22
Alignment explanation
Indices: 22270019--22270063 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22270009 TTCAAGGAAA
22270019 AATTTTGTATGGGTGATAGTAG
1 AATTTTGTATGGGTGATAGTAG
22270041 AATTTTGTATGGGTGATAGTAG
1 AATTTTGTATGGGTGATAGTAG
22270063 A
1 A
22270064 TAGGATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (22 bp):
AATTTTGTATGGGTGATAGTAG
Found at i:22272568 original size:45 final size:45
Alignment explanation
Indices: 22272471--22272692 Score: 209
Period size: 45 Copynumber: 5.0 Consensus size: 45
22272461 TAATAATCGT
* * * * **
22272471 TACACGATGG-ATCAGCATATAG-CACCACCCTTATAATCAATTA
1 TACACGGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGG
** * * ** *
22272514 TATTCGGTGGAATCAACACATAGAAACCACCTTTGTTTTCAATGAT
1 TACACGGTGGAATCAGCACATAGAAACCACCTTTATAATCAATG-G
* *
22272560 TTCA-GGTGGAGTCAGCACATAGAAACCACCTTTATAATCAATGG
1 TACACGGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGG
* *
22272604 TACACGGTGGAATCAGCATATAGCAACCACCTTTATAATCAATGG
1 TACACGGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGG
* * * *
22272649 TAC-CTAGAGGAATCAGCACATAGCAACCATCTTTATAATCAATG
1 TACAC-GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATG
22272693 ATACTTAGTA
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
43 7 0.05
44 14 0.10
45 123 0.85
46 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (45 bp):
TACACGGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGG
Found at i:22281058 original size:33 final size:33
Alignment explanation
Indices: 22281011--22281111 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
22281001 GTTAACTTGG
* * *
22281011 TATGGCATTATTTCATAATAGAGTTACTATGTA
1 TATGCCATTATTTCATAACAGAGTTACTATGCA
*
22281044 TATGCCATTATTTCATAACAGAGTTACTGTGCA
1 TATGCCATTATTTCATAACAGAGTTACTATGCA
*
22281077 TATGCCATTATTTCATAACAGAGTTACTGTGCA
1 TATGCCATTATTTCATAACAGAGTTACTATGCA
22281110 TA
1 TA
22281112 CTTTCGACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (33 bp):
TATGCCATTATTTCATAACAGAGTTACTATGCA
Found at i:22283600 original size:2 final size:2
Alignment explanation
Indices: 22283593--22283634 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22283583 TACATGTATT
22283593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22283635 ATTTATATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22284291 original size:23 final size:24
Alignment explanation
Indices: 22284247--22284293 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
22284237 TAATTTTCAA
*
22284247 TTTTTAAATAATTTTTATAATTTAT
1 TTTTTAAAT-ATTTTTAAAATTTAT
22284272 TTTTTAAAT-TTTTTAAAATTTA
1 TTTTTAAATATTTTTAAAATTTA
22284294 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTTAAATATTTTTAAAATTTAT
Found at i:22286738 original size:10 final size:10
Alignment explanation
Indices: 22286723--22286757 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
22286713 TATATCGAAA
22286723 AAATCAAATT
1 AAATCAAATT
22286733 AAATCAAATT
1 AAATCAAATT
22286743 AAATACAAAATT
1 AAAT-C-AAATT
22286755 AAA
1 AAA
22286758 ATTTTTCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.61
11 1 0.04
12 8 0.35
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATCAAATT
Found at i:22289747 original size:27 final size:27
Alignment explanation
Indices: 22289716--22289768 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
22289706 TCTCGAGTCG
22289716 TCTAGGATGAGTACTTCGACCGAGTAT
1 TCTAGGATGAGTACTTCGACCGAGTAT
*
22289743 TCTAGGATGAGTGCTTCGACCGAGTA
1 TCTAGGATGAGTACTTCGACCGAGTA
22289769 GTCTTCTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (27 bp):
TCTAGGATGAGTACTTCGACCGAGTAT
Found at i:22290078 original size:21 final size:21
Alignment explanation
Indices: 22290054--22290095 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22290044 AATCACTTTA
*
22290054 ATATTAAATTTAATCTAATAT
1 ATATTAAATTAAATCTAATAT
* *
22290075 ATATTAGATTAAATTTAATAT
1 ATATTAAATTAAATCTAATAT
22290096 TAAATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTAAATTAAATCTAATAT
Found at i:22294350 original size:13 final size:13
Alignment explanation
Indices: 22294332--22294357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22294322 CCAGATTAAA
22294332 TAATTAATTCAAT
1 TAATTAATTCAAT
22294345 TAATTAATTCAAT
1 TAATTAATTCAAT
22294358 AACTTACAAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTAATTCAAT
Found at i:22300000 original size:29 final size:29
Alignment explanation
Indices: 22299958--22300152 Score: 182
Period size: 29 Copynumber: 6.8 Consensus size: 29
22299948 CCACAAGGAA
*
22299958 TTTAACTGAGATAGCCATAAAGGCATCCT
1 TTTAACTGAGATAGCCACAAAGGCATCCT
*
22299987 TTTAACTGAGATAGCCACAAAGGTATCCT
1 TTTAACTGAGATAGCCACAAAGGCATCCT
* **
22300016 TTTAACTAATTTAGCCACAAAGGCATCCT
1 TTTAACTGAGATAGCCACAAAGGCATCCT
* * * * *
22300045 TTAAACCGAGATTGCCACAAAGGCTTAC-
1 TTTAACTGAGATAGCCACAAAGGCATCCT
* * * * *
22300073 TTTAACAGAGATTGCCATAAAGGC-TTCA
1 TTTAACTGAGATAGCCACAAAGGCATCCT
* **
22300101 TTTAA-TAGAGATCGCCACAAAGGTTTCC-
1 TTTAACT-GAGATAGCCACAAAGGCATCCT
*
22300129 TTTAACAGAGATAGCCACAAAGGC
1 TTTAACTGAGATAGCCACAAAGGC
22300153 TCACTTATAC
Statistics
Matches: 136, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
27 2 0.01
28 60 0.44
29 74 0.54
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (29 bp):
TTTAACTGAGATAGCCACAAAGGCATCCT
Found at i:22300094 original size:28 final size:28
Alignment explanation
Indices: 22300029--22300158 Score: 145
Period size: 28 Copynumber: 4.6 Consensus size: 28
22300019 AACTAATTTA
* * *
22300029 GCCACAAAGGCATCCTTTAAACCGAGATT
1 GCCACAAAGGCTTACTTT-AACAGAGATT
22300058 GCCACAAAGGCTTACTTTAACAGAGATT
1 GCCACAAAGGCTTACTTTAACAGAGATT
* * *
22300086 GCCATAAAGGCTT-CATTTAATAGAGATC
1 GCCACAAAGGCTTAC-TTTAACAGAGATT
* * *
22300114 GCCACAAAGGTTTCCTTTAACAGAGATA
1 GCCACAAAGGCTTACTTTAACAGAGATT
*
22300142 GCCACAAAGGCTCACTT
1 GCCACAAAGGCTTACTT
22300159 ATACAGAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 1 0.01
28 68 0.79
29 17 0.20
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (28 bp):
GCCACAAAGGCTTACTTTAACAGAGATT
Found at i:22307324 original size:22 final size:22
Alignment explanation
Indices: 22307270--22307326 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
22307260 ATCATTCGTG
**
22307270 AGCTCTCATGGCTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
22307292 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
22307314 AGCTCTCATGTTT
1 AGCTCTCATGTTT
22307327 GAACAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (22 bp):
AGCTCTCATGTTTAACGTACTA
Found at i:22311821 original size:25 final size:25
Alignment explanation
Indices: 22311783--22311835 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
22311773 TTTGTGAAGC
*
22311783 CTTTGTGGAGAACTCTCTT-TAAATT
1 CTTTGTGGAGAACTC-CTTGTAAAAT
22311808 CTTTGTGGCA-AACTCCTTGTAAAAT
1 CTTTGTGG-AGAACTCCTTGTAAAAT
22311833 CTT
1 CTT
22311836 CTTGGCGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 3 0.12
25 21 0.84
26 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (25 bp):
CTTTGTGGAGAACTCCTTGTAAAAT
Found at i:22319714 original size:23 final size:23
Alignment explanation
Indices: 22319686--22319732 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
22319676 ATAAAAGTTT
22319686 AAACATAAACATTTTCTAACCTA
1 AAACATAAACATTTTCTAACCTA
22319709 AAACATAAACATTTTCTAACCTA
1 AAACATAAACATTTTCTAACCTA
22319732 A
1 A
22319733 CATAATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (23 bp):
AAACATAAACATTTTCTAACCTA
Found at i:22319746 original size:23 final size:22
Alignment explanation
Indices: 22319685--22319737 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
22319675 TATAAAAGTT
22319685 TAAACATAAACATTTTCTAACC
1 TAAACATAAACATTTTCTAACC
22319707 TAAAACATAAACATTTTCTAACC
1 T-AAACATAAACATTTTCTAACC
22319730 T-AACATAA
1 TAAACATAA
22319738 TTTCATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.23
22 1 0.03
23 22 0.73
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAACATAAACATTTTCTAACC
Found at i:22320929 original size:6 final size:6
Alignment explanation
Indices: 22320882--22320926 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
22320872 TCATCCCCAA
* * *
22320882 AAATCA AAATCA AAATCC AAATCC AAATCC AAATCC AAACCC AAA
1 AAATCC AAATCC AAATCC AAATCC AAATCC AAATCC AAATCC AAA
22320927 CCCTAATCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (6 bp):
AAATCC
Found at i:22320934 original size:18 final size:18
Alignment explanation
Indices: 22320894--22320935 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22320884 ATCAAAATCA
* *
22320894 AAATCCAAATCCAAATCC
1 AAATCCAAACCCAAACCC
22320912 AAATCCAAACCCAAACCC
1 AAATCCAAACCCAAACCC
*
22320930 TAATCC
1 AAATCC
22320936 CACCTCCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (18 bp):
AAATCCAAACCCAAACCC
Found at i:22324912 original size:30 final size:30
Alignment explanation
Indices: 22324876--22324932 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
22324866 TGAGCAGGAA
22324876 TGATAAAGGGAAAGGGAAAATGGTTGATGC
1 TGATAAAGGGAAAGGGAAAATGGTTGATGC
*
22324906 TGATAAAGGGAAAGGGAAACTGGTTGA
1 TGATAAAGGGAAAGGGAAAATGGTTGA
22324933 CACCATACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.37, T:0.19
Consensus pattern (30 bp):
TGATAAAGGGAAAGGGAAAATGGTTGATGC
Found at i:22327760 original size:20 final size:20
Alignment explanation
Indices: 22327735--22327776 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
22327725 CCTACAATGT
22327735 AAAAGAAATTTTAACTTATC
1 AAAAGAAATTTTAACTTATC
22327755 AAAAGAAATTTTAACTTATC
1 AAAAGAAATTTTAACTTATC
22327775 AA
1 AA
22327777 GACACAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAGAAATTTTAACTTATC
Found at i:22329621 original size:42 final size:42
Alignment explanation
Indices: 22329556--22329759 Score: 243
Period size: 42 Copynumber: 4.9 Consensus size: 42
22329546 AAGGAGCACA
* * *
22329556 ATCACTTAAGCT--TGCATAGGGAGCTTCGGTGATACATAGCTT
1 ATCACTTAAGCTCATG--TAGGGAGCTTCGCTGATACACAACTT
* * *
22329598 GTCACTTAAGCTCAAGT-GAGGAGCTTTGCTGATACACAACTT
1 ATCACTTAAGCTCATGTAG-GGAGCTTCGCTGATACACAACTT
* * * ** *
22329640 ATCGCTTAAGCTCACGTAGGGAGTTTTTCTAATACACAACTT
1 ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTT
*
22329682 ATCACTTAAGCTCATGTGGGGAGCTTCGCTGATACACAACTT
1 ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTT
22329724 ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACA
1 ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACA
22329760 TAGCTTGTAA
Statistics
Matches: 138, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 135 0.98
43 1 0.01
44 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTT
Found at i:22329660 original size:84 final size:84
Alignment explanation
Indices: 22329556--22329767 Score: 280
Period size: 84 Copynumber: 2.5 Consensus size: 84
22329546 AAGGAGCACA
** * *
22329556 ATCACTTAAGCTTGCATAGGGAGCTTCGGTGATACATAGCTTGTCACTTAAGCTCAAGTGAGGAG
1 ATCACTTAAGCTCACGTAGGGAGCTTCGCTGATACATAGCTTGTCACTTAAGCTCAAGTGAGGAG
*
22329621 CTTTGCTGATACACAACTT
66 CTTCGCTGATACACAACTT
* * ** * * * * * *
22329640 ATCGCTTAAGCTCACGTAGGGAGTTTTTCTAATACACAACTTATCACTTAAGCTCATGTGGGGAG
1 ATCACTTAAGCTCACGTAGGGAGCTTCGCTGATACATAGCTTGTCACTTAAGCTCAAGTGAGGAG
22329705 CTTCGCTGATACACAACTT
66 CTTCGCTGATACACAACTT
*
22329724 ATCACTTAAGCTCATGTAGGGAGCTTCGCTGATACATAGCTTGT
1 ATCACTTAAGCTCACGTAGGGAGCTTCGCTGATACATAGCTTGT
22329768 AAAATCATTG
Statistics
Matches: 104, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 104 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
ATCACTTAAGCTCACGTAGGGAGCTTCGCTGATACATAGCTTGTCACTTAAGCTCAAGTGAGGAG
CTTCGCTGATACACAACTT
Found at i:22337712 original size:29 final size:28
Alignment explanation
Indices: 22337658--22337712 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
22337648 GGGGTTGGGA
* *
22337658 GGGAGGGAGTAAAGTTTGGGGAGAAAGT
1 GGGAAGGAGTAAAGTTTGAGGAGAAAGT
22337686 GGGAAGGAGTAAAAGTTTTGAGG-GAAA
1 GGGAAGGAGT-AAAG-TTTGAGGAGAAA
22337713 AGTAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 8 0.35
30 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.45, T:0.18
Consensus pattern (28 bp):
GGGAAGGAGTAAAGTTTGAGGAGAAAGT
Found at i:22337777 original size:9 final size:9
Alignment explanation
Indices: 22337763--22337799 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
22337753 TATAGTTTGA
22337763 TATTCGAAT
1 TATTCGAAT
22337772 TATTCGAAT
1 TATTCGAAT
*
22337781 TATTCGAGT
1 TATTCGAAT
22337790 TATTCGAAT
1 TATTCGAAT
22337799 T
1 T
22337800 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:22338572 original size:21 final size:20
Alignment explanation
Indices: 22338539--22338577 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22338529 GTTTTCTCAT
*
22338539 TCAATTGTATTTACAAGTTAG
1 TCAATTATATTTA-AAGTTAG
*
22338560 TCAATTATGTTTAAAGTT
1 TCAATTATATTTAAAGTT
22338578 GAGAACATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
TCAATTATATTTAAAGTTAG
Found at i:22341051 original size:25 final size:25
Alignment explanation
Indices: 22341023--22341075 Score: 92
Period size: 23 Copynumber: 2.2 Consensus size: 25
22341013 TTACTTGATG
22341023 TATTCTTTTATATAATATTTAAAAT
1 TATTCTTTTATATAATATTTAAAAT
22341048 TA-T-TTTTATATAATATTTAAAAT
1 TATTCTTTTATATAATATTTAAAAT
22341071 TATTC
1 TATTC
22341076 ATAATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 22 0.85
24 2 0.08
25 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTCTTTTATATAATATTTAAAAT
Found at i:22341055 original size:23 final size:23
Alignment explanation
Indices: 22341028--22341074 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
22341018 TGATGTATTC
22341028 TTTTATATAATATTTAAAATTAT
1 TTTTATATAATATTTAAAATTAT
22341051 TTTTATATAATATTTAAAATTAT
1 TTTTATATAATATTTAAAATTAT
22341074 T
1 T
22341075 CATAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATATAATATTTAAAATTAT
Found at i:22351491 original size:43 final size:43
Alignment explanation
Indices: 22351400--22351527 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
22351390 TCTTTTGCGG
** * *
22351400 CGTTTGTAAAAAAAACGTCGCTAAAAATCATGTTCCT-TAGCGG
1 CGTTTGTAAAAAAAGTGTCGCTAAAGATCATGTT-CTATAGCGA
* * *
22351443 TGTTTGTAATAAAAGTGTCGCTAAAGATCATGTTCTATAGTGA
1 CGTTTGTAAAAAAAGTGTCGCTAAAGATCATGTTCTATAGCGA
*** *
22351486 CGTTTGTAGGGAAAGTGCCGCTAAAGATCATGTTCTATAGCG
1 CGTTTGTAAAAAAAGTGTCGCTAAAGATCATGTTCTATAGCG
22351528 GCATTTTCCA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 2 0.03
43 69 0.97
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (43 bp):
CGTTTGTAAAAAAAGTGTCGCTAAAGATCATGTTCTATAGCGA
Found at i:22351997 original size:75 final size:74
Alignment explanation
Indices: 22351857--22352023 Score: 253
Period size: 75 Copynumber: 2.2 Consensus size: 74
22351847 ACTATAATTA
* * *
22351857 TTCCCTTATTAATAGAGAAGACAAGTGAAAAGTTAAAAAATAAATTATATTCTTTCCAAAAGAAT
1 TTCCCTTATTAATAGAAAAGACAAATGAAAAGTTAAAAAAGAAATTATATTCTTTCCAAAAGAAT
*
22351922 ATATGATTT
66 ATAAGATTT
* * *
22351931 TTCCCATATTAATAGAAAAGACAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAGAA
1 TTCCCTTATTAATAGAAAAGACAAATGAAAAGTTA-AAAAAGAAATTATATTCTTTCCAAAAGAA
22351996 TATAAGATTT
65 TATAAGATTT
*
22352006 TTCCCTTATTAATGGAAA
1 TTCCCTTATTAATAGAAA
22352024 GTTAGAAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 31 0.37
75 52 0.63
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (74 bp):
TTCCCTTATTAATAGAAAAGACAAATGAAAAGTTAAAAAAGAAATTATATTCTTTCCAAAAGAAT
ATAAGATTT
Found at i:22355201 original size:8 final size:8
Alignment explanation
Indices: 22355190--22355214 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22355180 ATATATACTA
22355190 AATAAAAT
1 AATAAAAT
22355198 AATAAAAT
1 AATAAAAT
22355206 AATAAAAT
1 AATAAAAT
22355214 A
1 A
22355215 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:22356106 original size:25 final size:25
Alignment explanation
Indices: 22356078--22356130 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
22356068 CTGAAGATCA
*
22356078 GTATGTTATCATGAGCTATAAAACG
1 GTATGCTATCATGAGCTATAAAACG
* * *
22356103 GTATGCTCTTATGAGCTATAAATCG
1 GTATGCTATCATGAGCTATAAAACG
22356128 GTA
1 GTA
22356131 GCCCTAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (25 bp):
GTATGCTATCATGAGCTATAAAACG
Found at i:22357775 original size:25 final size:25
Alignment explanation
Indices: 22357715--22357804 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
22357705 GTACATGTAT
* *
22357715 GCTCATAAGAGCTGTA-AACGGTAA
1 GCTCATAAGAGCTGAATAATGGTAA
* **
22357739 GCTCCTCCGAGCTGAATAATGGTAA
1 GCTCATAAGAGCTGAATAATGGTAA
* *
22357764 GCTCATATGAGCTGAGT-ATCGGTAA
1 GCTCATAAGAGCTGAATAAT-GGTAA
22357789 GCTCATAAGAGCTGAA
1 GCTCATAAGAGCTGAA
22357805 ATCAATAACC
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 14 0.26
25 39 0.74
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
GCTCATAAGAGCTGAATAATGGTAA
Found at i:22366198 original size:48 final size:48
Alignment explanation
Indices: 22366141--22366376 Score: 274
Period size: 48 Copynumber: 4.9 Consensus size: 48
22366131 CAGAATTCTT
* * * * * * *
22366141 GGTGGCCTGCACACAGTCTGTACCACCTTTGTGTAATAACATATTTTC
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
* * * * * *
22366189 GGTGGCCTGCACATATTCCGTGCCACCCTTGTATCTTAACAGATTATT
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
*
22366237 GGTGGCCTGCATACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
* * * **
22366285 AGTGGCCTACACACAGCCCATGCCACCCTTGTATCATAACAGAATATC
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
* * *
22366333 AGTGGCCTGCACACAGTCTGTGCCACTCTTGTGTCATAACAGAA
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAA
22366377 CATTGGTACG
Statistics
Matches: 158, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 158 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCATAACAGAATATC
Found at i:22369439 original size:42 final size:42
Alignment explanation
Indices: 22369359--22369440 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
22369349 CATTTTCTCT
* **
22369359 ATGCCATAGTCCAACTATGGTCTTACATATATTTACATATTG
1 ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
*
22369401 ATGCCATAG-CCTAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGTCC-AACTATGGTCTTACACA-TATGCACATAT
22369441 CACACCGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 2 0.06
42 30 0.88
43 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (42 bp):
ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
Found at i:22380773 original size:22 final size:22
Alignment explanation
Indices: 22380716--22380796 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
22380706 TTCTATATGG
* **
22380716 GAGCTTAGTACGTGAAACATGA
1 GAGCTTAGTACGTTAGCCATGA
22380738 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
22380760 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
* * *
22380782 GGGTTTAGTTCGTTA
1 GAGCTTAGTACGTTA
22380797 TATAGGTAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (22 bp):
GAGCTTAGTACGTTAGCCATGA
Found at i:22389993 original size:59 final size:61
Alignment explanation
Indices: 22389930--22390048 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
22389920 TTTGGTGATC
* * *
22389930 ATTTTGTAACATTTCATAGTTGAGT-GA-C-AAAAAAGAAATTTACTAATAATTGGGTGACG
1 ATTTTGTAACATTTCATAGCT-AATAGACCAAAAAAAAAAATTTACTAATAATTGGGTGACG
* *
22389989 ATTTTGTAACTTTTCATAGCTAATAGACCAAAAAAAAAAATTTACTAATAGTTGGGTGAC
1 ATTTTGTAACATTTCATAGCTAATAGACCAAAAAAAAAAATTTACTAATAATTGGGTGAC
22390049 TACTAGTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
58 2 0.04
59 21 0.40
60 1 0.02
61 28 0.54
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (61 bp):
ATTTTGTAACATTTCATAGCTAATAGACCAAAAAAAAAAATTTACTAATAATTGGGTGACG
Found at i:22390258 original size:20 final size:20
Alignment explanation
Indices: 22390212--22390258 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22390202 ATTTCTAATA
* *
22390212 ATTTTTATATACATTTTTAT
1 ATTTTTTTATACATTTTCAT
22390232 ATTTTTTTATAC-TTTTCAGT
1 ATTTTTTTATACATTTTCA-T
22390252 ATTTTTT
1 ATTTTTT
22390259 CAGAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTTTATACATTTTCAT
Found at i:22391768 original size:3 final size:3
Alignment explanation
Indices: 22391750--22391805 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
22391740 TGTTTAATTA
* *
22391750 ATT ATT -TT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
22391798 ATT ATT AT
1 ATT ATT AT
22391806 CAGTTTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:22395769 original size:19 final size:19
Alignment explanation
Indices: 22395745--22395789 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
22395735 AATTTTCATC
22395745 TTTAATT-ATTTTTAAATA
1 TTTAATTGATTTTTAAATA
*
22395763 GTTTAATTGATTTTTAATTA
1 -TTTAATTGATTTTTAAATA
22395783 TTTAATT
1 TTTAATT
22395790 CTAAAAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTAATTGATTTTTAAATA
Found at i:22395898 original size:21 final size:19
Alignment explanation
Indices: 22395869--22395941 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
22395859 TGTTAATATG
* *
22395869 TTATGAAATATATGAAAAT
1 TTATAAAATATATAAAAAT
22395888 ATTATATAAATAATATAAAAAT
1 -TTATA-AAAT-ATATAAAAAT
* *
22395910 TTATAAAATTTATTTAAAAT
1 TTATAAAATATA-TAAAAAT
22395930 GTTATAAAATAT
1 -TTATAAAATAT
22395942 TATTTGAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 19 0.43
22 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TTATAAAATATATAAAAAT
Found at i:22395917 original size:9 final size:10
Alignment explanation
Indices: 22395849--22395944 Score: 63
Period size: 10 Copynumber: 9.3 Consensus size: 10
22395839 CTAGATAAAA
22395849 TATAAAATAT
1 TATAAAATAT
* * *
22395859 TGTTAATATGT
1 T-ATAAAATAT
*
22395870 TATGAAATA-
1 TATAAAATAT
22395879 TATGAAAATAT
1 TAT-AAAATAT
*
22395890 TATATAAATAA
1 TATA-AAATAT
22395901 TATAAAA-ATT
1 TATAAAATA-T
22395911 TATAAAAT-T
1 TATAAAATAT
*
22395920 TATTTAAAATGT
1 TA--TAAAATAT
22395932 TATAAAATAT
1 TATAAAATAT
22395942 TAT
1 TAT
22395945 TTGAAGTATT
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
9 7 0.11
10 31 0.47
11 25 0.38
12 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (10 bp):
TATAAAATAT
Found at i:22395980 original size:2 final size:2
Alignment explanation
Indices: 22395962--22395997 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
22395952 ATTAAAAAGT
* *
22395962 TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22395998 ACTAAAGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:22396429 original size:31 final size:31
Alignment explanation
Indices: 22396392--22396472 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
22396382 ATATAATCTC
22396392 TAAAAATCAATTAAGCCCTCT-TAAAATAAT
1 TAAAAATCAATTAAGCCCTCTGTAAAATAAT
* *
22396422 TAAAAAATCAATTGAGCTCT-TGTAAAATAAT
1 T-AAAAATCAATTAAGCCCTCTGTAAAATAAT
*
22396453 TAAAAATTAATTAAGCCCTC
1 TAAAAATCAATTAAGCCCTC
22396473 CATTTCAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 17 0.40
31 26 0.60
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (31 bp):
TAAAAATCAATTAAGCCCTCTGTAAAATAAT
Found at i:22398630 original size:40 final size:40
Alignment explanation
Indices: 22398579--22398734 Score: 217
Period size: 40 Copynumber: 3.9 Consensus size: 40
22398569 GAAAAGGTAG
*
22398579 ATATCCGAAATGGATATCAAATGAAAAGGTT-AAAACAGAT
1 ATATCTGAAATGGATATCAAATGAAAAGGTTGAAAA-AGAT
* * *
22398619 ATATTTGAAATGAATATCAAATGAAAAGGTTGAAAAGGAT
1 ATATCTGAAATGGATATCAAATGAAAAGGTTGAAAAAGAT
*
22398659 ATATCTGAAATGGATATCAAATGAAAAGGTTGAAAATGAT
1 ATATCTGAAATGGATATCAAATGAAAAGGTTGAAAAAGAT
* *
22398699 ATATCCGAAACT-GATATGAAATGAAAAGGTTGAAAA
1 ATATCTGAAA-TGGATATCAAATGAAAAGGTTGAAAA
22398735 GGTTGTTACC
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 100 0.95
41 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (40 bp):
ATATCTGAAATGGATATCAAATGAAAAGGTTGAAAAAGAT
Found at i:22398721 original size:80 final size:81
Alignment explanation
Indices: 22398567--22398737 Score: 249
Period size: 80 Copynumber: 2.1 Consensus size: 81
22398557 CTCCGAATTC
**
22398567 TTGAAAAGGTAGATATCCGAAATGGATATCAAATGAAAAGGTTAAAACAGATATATTTGAAATGA
1 TTGAAAAGGTAGATATCCGAAATGGATATCAAATGAAAAGGTTAAAACAGATATATCCGAAATGA
22398632 ATATCAAATGAAAAGG
66 ATATCAAATGAAAAGG
* * *
22398648 TTGAAAAGG-ATATATCTGAAATGGATATCAAATGAAAAGGTTGAAAA-TGATATATCCGAAACT
1 TTGAAAAGGTAGATATCCGAAATGGATATCAAATGAAAAGGTT-AAAACAGATATATCCGAAA-T
*
22398711 G-ATATGAAATGAAAAGG
64 GAATATCAAATGAAAAGG
22398728 TTGAAAAGGT
1 TTGAAAAGGT
22398738 TGTTACCCTA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
80 66 0.81
81 15 0.19
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (81 bp):
TTGAAAAGGTAGATATCCGAAATGGATATCAAATGAAAAGGTTAAAACAGATATATCCGAAATGA
ATATCAAATGAAAAGG
Found at i:22400898 original size:16 final size:16
Alignment explanation
Indices: 22400877--22400915 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
22400867 TTTTATTAAA
22400877 ATTAAAACTAATTGAT
1 ATTAAAACTAATTGAT
* *
22400893 ATTAAAAGTAATTGTT
1 ATTAAAACTAATTGAT
22400909 ATTAAAA
1 ATTAAAA
22400916 TTATATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTAAAACTAATTGAT
Found at i:22400898 original size:22 final size:23
Alignment explanation
Indices: 22400848--22400899 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
22400838 CCGTTTTTTA
* **
22400848 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTGAT
22400871 ATTAAAATTAAAACTA-ATTGAT
1 ATTAAAATTAAAACTATATTGAT
22400893 ATTAAAA
1 ATTAAAA
22400900 GTAATTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGAT
Found at i:22401043 original size:53 final size:52
Alignment explanation
Indices: 22400982--22401162 Score: 166
Period size: 53 Copynumber: 3.3 Consensus size: 52
22400972 TTTGTTAGTA
22400982 AAATTATTAATTGTTAATTGCATTAATTGTTAGTAAAATTATCAAATTATATC
1 AAATTATTAATTGTTAATTGCATTAATT-TTAGTAAAATTATCAAATTATATC
** ** * ** * *
22401035 AAATTATTAATTGTTACTACCAGTCAAAACATTTT-GTAAAATCTAACATTTTGTTAGTA
1 AAATTATTAATTGTTA--A-TTG-CATTA-ATTTTAGTAAAAT-TATCAAATT-ATA-TC
*
22401094 AAATTATTAATTGTTAATTGTATTAATTTTTAGTAAAATTATCAAATTATATC
1 AAATTATTAATTGTTAATTGCATTAA-TTTTAGTAAAATTATCAAATTATATC
*
22401147 AAATTATTAGTTGTTA
1 AAATTATTAATTGTTA
22401163 GTAAAATCTA
Statistics
Matches: 98, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
53 32 0.33
54 3 0.03
55 13 0.13
56 16 0.16
57 12 0.12
58 5 0.05
59 17 0.17
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (52 bp):
AAATTATTAATTGTTAATTGCATTAATTTTAGTAAAATTATCAAATTATATC
Found at i:22401065 original size:112 final size:112
Alignment explanation
Indices: 22400946--22401162 Score: 391
Period size: 112 Copynumber: 1.9 Consensus size: 112
22400936 TTTGTATCAA
22400946 TCAAAACATTTTGTAAAATC-AAGCATTTTGTTAGTAAAATTATTAATTGTTAATTGCATTAATT
1 TCAAAACATTTTGTAAAATCTAA-CATTTTGTTAGTAAAATTATTAATTGTTAATTGCATTAATT
22401010 GTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTACTACCAG
65 GTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTACTACCAG
* *
22401058 TCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTT
1 TCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGCATTAATTG
*
22401123 TTAGTAAAATTATCAAATTATATCAAATTATTAGTTGTTA
66 TTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTA
22401163 GTAAAATCTA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
112 99 0.98
113 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (112 bp):
TCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGCATTAATTG
TTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTACTACCAG
Found at i:22401109 original size:19 final size:19
Alignment explanation
Indices: 22401085--22401169 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
22401075 ATCTAACATT
22401085 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
22401104 TTG-T--T-AATTGTATTAA
1 TTGTTAGTAAAAT-TATTAA
* *
22401120 TTTTTAGTAAAATTATCAAA
1 TTGTTAGTAAAATTAT-TAA
* * *
22401140 TT-ATA-TCAAATTATTAG
1 TTGTTAGTAAAATTATTAA
22401157 TTGTTAGTAAAAT
1 TTGTTAGTAAAAT
22401170 CTAACATTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
15 3 0.06
16 9 0.19
17 4 0.08
18 11 0.23
19 14 0.29
20 7 0.15
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:22401155 original size:37 final size:38
Alignment explanation
Indices: 22401003--22401169 Score: 112
Period size: 37 Copynumber: 4.5 Consensus size: 38
22400993 TGTTAATTGC
22401003 ATTAATTGTTAGTAAAATTATCAAATTATATCAAAT-T
1 ATTAATTGTTAGTAAAATTATCAAATTATATCAAATCT
* * * * * * * *
22401040 ATTAATTGTTACTACCAGTCA-AAACATTTTGTAAAATCT
1 ATTAATTGTTAGTA-AAATTATCAA-ATTATATCAAATCT
** * * * * *
22401079 AACATTTTGTTAGTAAAATTAT-TAATTGT-T-AATTGT
1 ATTA-ATTGTTAGTAAAATTATCAAATTATATCAAATCT
*
22401115 ATTAATTTTTAGTAAAATTATCAAATTATATCAAAT-T
1 ATTAATTGTTAGTAAAATTATCAAATTATATCAAATCT
*
22401152 ATTAGTTGTTAGTAAAAT
1 ATTAATTGTTAGTAAAAT
22401170 CTAACATTTT
Statistics
Matches: 94, Mismatches: 28, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
35 15 0.16
36 11 0.12
37 34 0.36
38 19 0.20
39 7 0.07
40 8 0.09
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (38 bp):
ATTAATTGTTAGTAAAATTATCAAATTATATCAAATCT
Found at i:22401260 original size:21 final size:20
Alignment explanation
Indices: 22401236--22401281 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
22401226 AAACTAAAAG
*
22401236 TTTAAAACTAAACAAGTATAT-
1 TTTAAAAATAAA-AA-TATATA
22401257 TTTAAAAATAAAAATATATA
1 TTTAAAAATAAAAATATATA
22401277 TTTAA
1 TTTAA
22401282 TATATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTAAAAATAAAAATATATA
Found at i:22410089 original size:17 final size:17
Alignment explanation
Indices: 22410067--22410102 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
22410057 TAATTTGACC
22410067 ATTAAAAATATTAAGTT
1 ATTAAAAATATTAAGTT
22410084 ATTAAAAATATTAAGTT
1 ATTAAAAATATTAAGTT
22410101 AT
1 AT
22410103 AATAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTAAAAATATTAAGTT
Found at i:22410474 original size:16 final size:16
Alignment explanation
Indices: 22410433--22410477 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
22410423 AATTCCATAA
22410433 AGTACTTAA-TTTTTC
1 AGTACTTAATTTTTTC
*
22410448 AATACTT-ATTTTTTC
1 AGTACTTAATTTTTTC
22410463 AGTACTTAATTTTTT
1 AGTACTTAATTTTTT
22410478 TTTTTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.69
16 7 0.27
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (16 bp):
AGTACTTAATTTTTTC
Found at i:22416079 original size:24 final size:22
Alignment explanation
Indices: 22416026--22416081 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 22
22416016 TGATGGATCA
22416026 AAAGGGGAAGAGAAAAGAAAAG
1 AAAGGGGAAGAGAAAAGAAAAG
22416048 AAAGGGGGAAGAGAAAAGAAGAAG
1 AAA-GGGGAAGAGAAAAGAA-AAG
*
22416072 ATGAGGGGAA
1 A-AAGGGGAA
22416082 ATTGCCAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 3 0.10
23 16 0.53
24 10 0.33
25 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (22 bp):
AAAGGGGAAGAGAAAAGAAAAG
Found at i:22429943 original size:25 final size:25
Alignment explanation
Indices: 22429900--22429990 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
22429890 AGAGAGTTCG
* *
22429900 CCACAAAGGCCTTAC-AAAGTATTCA
1 CCACAAAGG-CTTTCTAAAGAATTCA
* **
22429925 CCACAAAGGATTTCTAAAGAATTTG
1 CCACAAAGGCTTTCTAAAGAATTCA
22429950 CC-CTAAAGGCTTTC-AAGAGAATTCA
1 CCAC-AAAGGCTTTCTAA-AGAATTCA
22429975 CCACAAAGGCTTTCTA
1 CCACAAAGGCTTTCTA
22429991 GGTAATTCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
24 6 0.11
25 45 0.85
26 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (25 bp):
CCACAAAGGCTTTCTAAAGAATTCA
Found at i:22429997 original size:25 final size:24
Alignment explanation
Indices: 22429920--22429998 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
22429910 CTTACAAAGT
* *
22429920 ATTCACCACAAAGGATTTCTAAAGA
1 ATTCACCACAAAGGCTTTCT-AGGA
** *
22429945 ATTTGCC-CTAAAGGCTTTCAAGAGA
1 ATTCACCAC-AAAGGCTTTCTAG-GA
22429970 ATTCACCACAAAGGCTTTCTAGGTA
1 ATTCACCACAAAGGCTTTCTAGG-A
22429995 ATTC
1 ATTC
22429999 GTGTTTACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 3 0.07
25 38 0.90
26 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (24 bp):
ATTCACCACAAAGGCTTTCTAGGA
Found at i:22435849 original size:18 final size:18
Alignment explanation
Indices: 22435828--22435862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22435818 AAGGCAAAGA
*
22435828 TAAAAATGAAAATAAAAC
1 TAAAAATAAAAATAAAAC
*
22435846 TAAAACTAAAAATAAAA
1 TAAAAATAAAAATAAAA
22435863 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAATAAAAC
Found at i:22439356 original size:41 final size:41
Alignment explanation
Indices: 22439295--22439446 Score: 171
Period size: 41 Copynumber: 3.7 Consensus size: 41
22439285 TGAAAATAAG
* * *
22439295 ATGTTTCAGACTTTACGTCTAGGAGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
* *
22439336 ATGTTTCAGAATTTATGTCTAGCAGGATTGATGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
* **
22439377 TTACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAA
* * * * *
22439418 ATGTATCGGGCTTTGTGCCTAGCAGGCTT
1 ATGTTTCAGACTTTATGTCTAGCAGGCTT
22439447 TATGTTGGTG
Statistics
Matches: 92, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.02
41 87 0.95
42 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (41 bp):
ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
Found at i:22440923 original size:29 final size:29
Alignment explanation
Indices: 22440818--22441113 Score: 247
Period size: 28 Copynumber: 10.5 Consensus size: 29
22440808 GATTTCCACG
* *
22440818 AGGC-TTCCTTTATCA-AAGTTTGCCACAA
1 AGGCTTTCCTTT-TCAGAGGTTCGCCACAA
22440846 AGGCTTT-CTTTAT-AGAGGTTCGCCACAA
1 AGGCTTTCCTTT-TCAGAGGTTCGCCACAA
* * *
22440874 AGGATTT-CTTTAT-ACAGGTTCGCCATAA
1 AGGCTTTCCTTT-TCAGAGGTTCGCCACAA
*
22440902 AGGCTTTCCTTTTCAGAGGTTCCCCACAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
* ** *
22440931 AGGCTTTCC-TTTAAGGAGGTTTTCGACAA
1 AGGCTTTCCTTTTCA-GAGGTTCGCCACAA
* *
22440960 AGGTTTTCC-TTCCAGAGGTTCGCCACAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
* * *
22440988 AGGCTTTCC-TTTCAGA-TTTTGCCATAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
* *
22441015 AGGCTTTCCTTTGCAGAGGTTTGCCACAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
* * * *
22441044 AGGCTTTCATTTGCAGTGGTTTGCCACAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
* * *
22441073 AGTCTTTCC-TTTCAAAGGTTCGCCAAAA
1 AGGCTTTCCTTTTCAGAGGTTCGCCACAA
*
22441101 AGG-TTTCCATTTC
1 AGGCTTTCCTTTTC
22441114 TTGGCGCATT
Statistics
Matches: 223, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.10
28 108 0.48
29 92 0.41
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (29 bp):
AGGCTTTCCTTTTCAGAGGTTCGCCACAA
Found at i:22441035 original size:113 final size:111
Alignment explanation
Indices: 22440835--22441113 Score: 310
Period size: 113 Copynumber: 2.5 Consensus size: 111
22440825 CTTTATCAAA
* * ** *
22440835 GTTTGCCACAAAGGCTTTCTTTATAGAGGTTCGCCACAAAGGATTTCTTTATACAGGTTCGCCAT
1 GTTTGCCACAAAGTCTTTCCTTCCAGAGGTTCGCCACAAAGG-TTTCCTT-T-CAGGTTCGCCAT
* *
22440900 AAAGGCTTTCCTTTTCAGAGGTTCCCCACAAAGGCTTTCCTTT-AAGGAG
63 AAAGGCTTTCCTTTGCAGAGGTTCCCCACAAAGGCTTTCATTTGAA-GAG
* * * *
22440949 GTTTTCGACAAAGGT-TTTCCTTCCAGAGGTTCGCCACAAAGGCTTTCCTTTCAGATTTTGCCAT
1 GTTTGCCACAAA-GTCTTTCCTTCCAGAGGTTCGCCACAAAGG-TTTCCTTTCAG-GTTCGCCAT
** * *
22441013 AAAGGCTTTCCTTTGCAGAGGTTTGCCACAAAGGCTTTCATTTGCAGTG
63 AAAGGCTTTCCTTTGCAGAGGTTCCCCACAAAGGCTTTCATTTGAAGAG
* * *
22441062 GTTTGCCACAAAGTCTTTCCTTTCAAAGGTTCGCCAAAAAGGTTTCCATTTC
1 GTTTGCCACAAAGTCTTTCCTTCCAGAGGTTCGCCACAAAGGTTTCC-TTTC
22441114 TTGGCGCATT
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
112 10 0.07
113 87 0.63
114 41 0.29
115 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (111 bp):
GTTTGCCACAAAGTCTTTCCTTCCAGAGGTTCGCCACAAAGGTTTCCTTTCAGGTTCGCCATAAA
GGCTTTCCTTTGCAGAGGTTCCCCACAAAGGCTTTCATTTGAAGAG
Found at i:22441588 original size:21 final size:21
Alignment explanation
Indices: 22441563--22441604 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22441553 CTTAACATAT
22441563 ATCTCAAACATTCACTTATAG
1 ATCTCAAACATTCACTTATAG
22441584 ATCTCAAACATTCACTTATAG
1 ATCTCAAACATTCACTTATAG
22441605 TCATACTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (21 bp):
ATCTCAAACATTCACTTATAG
Found at i:22443285 original size:24 final size:24
Alignment explanation
Indices: 22443253--22443305 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
22443243 GTCCTCATCT
*
22443253 TCTTCATCTTCAACTCGA-CCCTCG
1 TCTTCATCTTCAACTCCACCCCT-G
*
22443277 TCTTCATCTTCATCTCCACCCCTG
1 TCTTCATCTTCAACTCCACCCCTG
22443301 TCTTC
1 TCTTC
22443306 GTTTTTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.13, C:0.43, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTTCATCTTCAACTCCACCCCTG
Found at i:22443578 original size:12 final size:12
Alignment explanation
Indices: 22443561--22443603 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
22443551 GGTACATGTT
22443561 TCAACATAT-ACG
1 TCAACAT-TGACG
22443573 TCAACATTGACG
1 TCAACATTGACG
22443585 TCAACATTGACG
1 TCAACATTGACG
22443597 TCAACAT
1 TCAACAT
22443604 CGAGGCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 1 0.03
12 29 0.97
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (12 bp):
TCAACATTGACG
Found at i:22451596 original size:25 final size:24
Alignment explanation
Indices: 22451515--22451631 Score: 105
Period size: 25 Copynumber: 4.8 Consensus size: 24
22451505 TACTGTAATA
*
22451515 GCCTTTGTGGCATATTTTGTATGAT
1 GCCTTTGTGGCATATTCTGTATG-T
* * ** *
22451540 GTCTTTATGGCATCCTCTG-AT-A
1 GCCTTTGTGGCATATTCTGTATGT
22451562 GCCTTTGTGGCATATTCTGTATGCT
1 GCCTTTGTGGCATATTCTGTATG-T
*
22451587 GCCTTTGTGGCGTATTCTGTATGTT
1 GCCTTTGTGGCATATTCTGTATG-T
*
22451612 TCCTTTGTGG-AGTATTCTGT
1 GCCTTTGTGGCA-TATTCTGT
22451632 CTAGCCCTTA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
22 15 0.21
23 2 0.03
24 2 0.03
25 54 0.74
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (24 bp):
GCCTTTGTGGCATATTCTGTATGT
Found at i:22457922 original size:89 final size:89
Alignment explanation
Indices: 22457771--22457946 Score: 316
Period size: 89 Copynumber: 2.0 Consensus size: 89
22457761 AAAACAAAAT
* *
22457771 AAAATATTGGGTCTACTTGCAGTAAGATCAAGCAATGAGCCAATCATTGGCCTATATAAATTTGT
1 AAAATATAGGGTCTACTTGCAGTAAGATAAAGCAATGAGCCAATCATTGGCCTATATAAATTTGT
22457836 ATCAACACATTTACCTTCTTAAAC
66 ATCAACACATTTACCTTCTTAAAC
* *
22457860 AAAATATAGGTTCTACTTGCAGTAAGATAAAGCAATGAGCCAATCATTGGCCTATGTAAATTTGT
1 AAAATATAGGGTCTACTTGCAGTAAGATAAAGCAATGAGCCAATCATTGGCCTATATAAATTTGT
22457925 ATCAACACATTTACCTTCTTAA
66 ATCAACACATTTACCTTCTTAA
22457947 TATTTGTCAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (89 bp):
AAAATATAGGGTCTACTTGCAGTAAGATAAAGCAATGAGCCAATCATTGGCCTATATAAATTTGT
ATCAACACATTTACCTTCTTAAAC
Found at i:22460985 original size:21 final size:22
Alignment explanation
Indices: 22460934--22460985 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
22460924 TCATTTTTTC
22460934 TCAAAATCATTTATAATTACTT
1 TCAAAATCATTTATAATTACTT
* * *
22460956 GC-AAGTCATTTAT-CTTACTT
1 TCAAAATCATTTATAATTACTT
*
22460976 TCAAATTCAT
1 TCAAAATCAT
22460986 GATTAGCCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 7 0.29
21 16 0.67
22 1 0.04
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (22 bp):
TCAAAATCATTTATAATTACTT
Found at i:22461818 original size:20 final size:20
Alignment explanation
Indices: 22461793--22461834 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
22461783 TAAGATTTCT
22461793 ACACAAATCTTAATACTCTA
1 ACACAAATCTTAATACTCTA
22461813 ACACAAATCTTAATACTCTA
1 ACACAAATCTTAATACTCTA
22461833 AC
1 AC
22461835 CCTCTCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (20 bp):
ACACAAATCTTAATACTCTA
Found at i:22466243 original size:44 final size:45
Alignment explanation
Indices: 22466146--22466263 Score: 122
Period size: 44 Copynumber: 2.7 Consensus size: 45
22466136 AGCCATGTTG
* *
22466146 TTTAGCGGCGCTTTTTATCACAAACGCCGCT-AAATAACATGACC
1 TTTAGCAGCGCTTTTTATCACAAACGCCACTAAAATAACATGACC
* * **
22466190 TTTAACAGCGCTTTTTATCACAAACGCCCCTAAAAGT-ACAT-TTC
1 TTTAGCAGCGCTTTTTATCACAAACGCCACTAAAA-TAACATGACC
*
22466234 TTTAGCAGCG--TTTTA-CAAAAACGCCACTAA
1 TTTAGCAGCGCTTTTTATCACAAACGCCACTAA
22466264 CTTTGGCAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 13 0.20
42 5 0.08
44 38 0.59
45 7 0.11
46 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (45 bp):
TTTAGCAGCGCTTTTTATCACAAACGCCACTAAAATAACATGACC
Found at i:22466614 original size:21 final size:21
Alignment explanation
Indices: 22466529--22466617 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
22466519 TGCTATGCTT
22466529 TGCTTCCCTCGCTGCTGCCTC
1 TGCTTCCCTCGCTGCTGCCTC
* *
22466550 TACTTCCCTCACTGCTGCCTC
1 TGCTTCCCTCGCTGCTGCCTC
* * *
22466571 TTCTTCTCC-CGCTACTGCTTC
1 TGCTTC-CCTCGCTGCTGCCTC
* *
22466592 TGCTTCCTTCGCTGTTGCCTC
1 TGCTTCCCTCGCTGCTGCCTC
22466613 TGCTT
1 TGCTT
22466618 TAAGCTGTAG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
20 1 0.02
21 52 0.95
22 2 0.04
ACGTcount: A:0.03, C:0.43, G:0.15, T:0.39
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCTGCCTC
Found at i:22472103 original size:9 final size:9
Alignment explanation
Indices: 22472089--22472320 Score: 142
Period size: 9 Copynumber: 26.0 Consensus size: 9
22472079 TAGGTATAAT
22472089 TAAGTTATG
1 TAAGTTATG
22472098 TAAGTTATG
1 TAAGTTATG
* * *
22472107 ATATGATATA
1 -TAAGTTATG
*
22472117 T-ATTTATG
1 TAAGTTATG
22472125 T-A-TTATG
1 TAAGTTATG
22472132 TAAGTTATG
1 TAAGTTATG
22472141 TAAGTTATG
1 TAAGTTATG
*
22472150 TGAGTTATG
1 TAAGTTATG
22472159 TAAGTTATG
1 TAAGTTATG
* * *
22472168 ATATGATATA
1 -TAAGTTATG
*
22472178 T-ATTTATG
1 TAAGTTATG
*
22472186 T-A-TTACG
1 TAAGTTATG
*
22472193 TAAGTTCTG
1 TAAGTTATG
* *
22472202 TGAGCTATG
1 TAAGTTATG
*
22472211 TAAGTTATT
1 TAAGTTATG
*
22472220 TATTA-TATATT
1 TA--AGT-TATG
22472231 TAAGTTAT-
1 TAAGTTATG
22472239 TAAGTTATG
1 TAAGTTATG
22472248 TAAGTTATG
1 TAAGTTATG
*
22472257 TGAGTTATG
1 TAAGTTATG
* *
22472266 ATATGATATATA
1 -TAAG-T-TATG
22472278 TAAGTTAT-
1 TAAGTTATG
22472286 TAAGTTATG
1 TAAGTTATG
*
22472295 TATG-TATG
1 TAAGTTATG
*
22472303 TGAGTTATG
1 TAAGTTATG
22472312 TAAGTTATG
1 TAAGTTATG
22472321 ATCTGACATA
Statistics
Matches: 173, Mismatches: 34, Indels: 32
0.72 0.14 0.13
Matches are distributed among these distances:
7 11 0.06
8 34 0.20
9 97 0.56
10 17 0.10
11 11 0.06
12 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:22472131 original size:34 final size:34
Alignment explanation
Indices: 22472093--22472198 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 34
22472083 TATAATTAAG
22472093 TTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGATATGATATATATTTATGTA
* * *
22472127 TTATGTAAGTTATG-TAAG-T-TAT-GTGA-G--
1 TTATGTAAGTTATGATATGATATATATTTATGTA
22472154 TTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGATATGATATATATTTATGTA
*
22472188 TTACGTAAGTT
1 TTATGTAAGTT
22472199 CTGTGAGCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
27 14 0.24
28 3 0.05
29 2 0.03
30 5 0.09
31 5 0.09
32 2 0.03
33 3 0.05
34 24 0.41
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:22472186 original size:61 final size:61
Alignment explanation
Indices: 22472089--22472218 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 61
22472079 TAGGTATAAT
* *
22472089 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTACGTAAGTTATGTAAGCTATG
* * *
22472150 TGAGTTATGTAAGTTATGATATGATATATATTTATGTATTACGTAAGTTCTGTGAGCTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTACGTAAGTTATGTAAGCTATG
22472211 TAAGTTAT
1 TAAGTTAT
22472219 TTATTATATA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (61 bp):
TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTACGTAAGTTATGTAAGCTATG
Found at i:22472320 original size:55 final size:55
Alignment explanation
Indices: 22472230--22472347 Score: 157
Period size: 55 Copynumber: 2.1 Consensus size: 55
22472220 TATTATATAT
* *
22472230 TTAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATATATAAGTTA
1 TTAAGTTATTAAGTTATGTAAGTTATGTAAGTTATGATATGACATATATAAGTTA
* * * *
22472285 TTAAGTTATGTATG-TATGTGAGTTATGTAAGTTATGATCTGACATATATAATTTA
1 TTAAGTTAT-TAAGTTATGTAAGTTATGTAAGTTATGATATGACATATATAAGTTA
*
22472340 ATAAGTTA
1 TTAAGTTA
22472348 AGATCCAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 52 0.95
56 3 0.05
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.45
Consensus pattern (55 bp):
TTAAGTTATTAAGTTATGTAAGTTATGTAAGTTATGATATGACATATATAAGTTA
Found at i:22473544 original size:8 final size:8
Alignment explanation
Indices: 22473531--22473571 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
22473521 TGAAAATACG
22473531 TATATAGA
1 TATATAGA
22473539 TATATAGA
1 TATATAGA
22473547 TATAT--A
1 TATATAGA
* *
22473553 TAGATATA
1 TATATAGA
22473561 TATATAGA
1 TATATAGA
22473569 TAT
1 TAT
22473572 GTAAACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
6 5 0.18
8 23 0.82
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (8 bp):
TATATAGA
Found at i:22473561 original size:12 final size:12
Alignment explanation
Indices: 22473538--22473571 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
22473528 ACGTATATAG
22473538 ATATATAG--AT
1 ATATATAGATAT
22473548 ATATATAGATAT
1 ATATATAGATAT
22473560 ATATATAGATAT
1 ATATATAGATAT
22473572 GTAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
12 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (12 bp):
ATATATAGATAT
Found at i:22473571 original size:10 final size:10
Alignment explanation
Indices: 22473538--22473564 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22473528 ACGTATATAG
22473538 ATATATAGAT
1 ATATATAGAT
22473548 ATATATAGAT
1 ATATATAGAT
22473558 ATATATA
1 ATATATA
22473565 TAGATATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
ATATATAGAT
Found at i:22473605 original size:20 final size:20
Alignment explanation
Indices: 22473568--22473605 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22473558 ATATATATAG
*
22473568 ATATGTAAACAAATTATAAA
1 ATATGTAAACAAAATATAAA
22473588 ATATGTATAA-AAAATATA
1 ATATGTA-AACAAAATATA
22473606 TGAGTACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
ATATGTAAACAAAATATAAA
Found at i:22473869 original size:50 final size:53
Alignment explanation
Indices: 22473797--22473899 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 53
22473787 ATAAACGAAT
* *
22473797 AATAATAATAAATAGATAAATAAGAGTAATAATA-ATAATAATAATAGTAAAAA
1 AATAATAAAAAATAGATAAATAACAGTAATAA-ACATAATAATAATAGTAAAAA
* *
22473850 AATAA-AAAAAATAG-T-AATAACAGTATTAAACATAATAATAGTAGTAAAAA
1 AATAATAAAAAATAGATAAATAACAGTAATAAACATAATAATAATAGTAAAAA
22473900 TAACGATAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
49 1 0.02
50 30 0.67
51 1 0.02
52 8 0.18
53 5 0.11
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (53 bp):
AATAATAAAAAATAGATAAATAACAGTAATAAACATAATAATAATAGTAAAAA
Found at i:22473887 original size:18 final size:18
Alignment explanation
Indices: 22473864--22473902 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22473854 AAAAAAATAG
* *
22473864 TAATAACAGTATTAAACA
1 TAATAACAGTAGTAAAAA
*
22473882 TAATAATAGTAGTAAAAA
1 TAATAACAGTAGTAAAAA
22473900 TAA
1 TAA
22473903 CGATAACATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (18 bp):
TAATAACAGTAGTAAAAA
Found at i:22473889 original size:3 final size:3
Alignment explanation
Indices: 22473794--22473869 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
22473784 TTAATAAACG
* *
22473794 AAT AAT AAT AAT AAAT AGAT AAAT AAG AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
22473842 AGT AA- AAA AAT AAA AAA AAT AGT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22473870 CAGTATTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
2 2 0.03
3 48 0.83
4 7 0.12
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:22474572 original size:23 final size:23
Alignment explanation
Indices: 22474542--22474588 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
22474532 CTTTTAAGCC
22474542 CCTAAACCCAAATCTGAACTCAA
1 CCTAAACCCAAATCTGAACTCAA
*
22474565 CCTAAACCCGAATCTGAACTCAA
1 CCTAAACCCAAATCTGAACTCAA
22474588 C
1 C
22474589 ACTCCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.36, G:0.06, T:0.17
Consensus pattern (23 bp):
CCTAAACCCAAATCTGAACTCAA
Found at i:22475259 original size:9 final size:9
Alignment explanation
Indices: 22475221--22475333 Score: 77
Period size: 9 Copynumber: 12.4 Consensus size: 9
22475211 TGTACATAAA
22475221 TTATGTAAG
1 TTATGTAAG
*
22475230 TTATGATATGG
1 TTATG-TA-AG
22475241 TTAT-TAAG
1 TTATGTAAG
22475249 TTATGTAAG
1 TTATGTAAG
*
22475258 TTATGTGAG
1 TTATGTAAG
*
22475267 TTATGTAAA
1 TTATGTAAG
* *
22475276 TTATATAAT
1 TTATGTAAG
*
22475285 TTATGTAAA
1 TTATGTAAG
* *
22475294 TTTTGATATG
1 TTATG-TAAG
* * *
22475304 ATATAT-AT
1 TTATGTAAG
22475312 TTATGTAAG
1 TTATGTAAG
*
22475321 TTATGTAAA
1 TTATGTAAG
22475330 TTAT
1 TTAT
22475334 ATATTAATTT
Statistics
Matches: 78, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
8 9 0.12
9 58 0.74
10 6 0.08
11 5 0.06
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:22475673 original size:20 final size:20
Alignment explanation
Indices: 22475650--22475687 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22475640 ATAGTATTAA
* *
22475650 TAATATTAAAATAACTAATT
1 TAATAATAAAAAAACTAATT
22475670 TAATAATAAAAAAACTAA
1 TAATAATAAAAAAACTAA
22475688 AATAACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAATAAAAAAACTAATT
Found at i:22475811 original size:15 final size:16
Alignment explanation
Indices: 22475793--22475824 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22475783 AATGTAAACA
22475793 AATTTGAAAAT-AATG
1 AATTTGAAAATGAATG
22475808 AATTTGAAAATGAATG
1 AATTTGAAAATGAATG
22475824 A
1 A
22475825 TAAGGGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
AATTTGAAAATGAATG
Found at i:22475870 original size:23 final size:23
Alignment explanation
Indices: 22475844--22475888 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
22475834 AAAAATTTTG
* *
22475844 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
22475867 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
22475889 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:22476118 original size:19 final size:19
Alignment explanation
Indices: 22476094--22476185 Score: 166
Period size: 19 Copynumber: 4.8 Consensus size: 19
22476084 AATCATATCT
22476094 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
22476113 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
22476132 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
22476151 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
22476170 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
22476186 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:22476143 original size:38 final size:38
Alignment explanation
Indices: 22476071--22476185 Score: 185
Period size: 38 Copynumber: 2.9 Consensus size: 38
22476061 AAATTAAATC
*
22476071 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
22476113 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
22476151 TCTAAGATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
22476186 CTTGAAGATT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 54 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:22476532 original size:28 final size:29
Alignment explanation
Indices: 22476436--22476547 Score: 110
Period size: 28 Copynumber: 4.1 Consensus size: 29
22476426 AATCAAATAT
* * **
22476436 AAAATCGATAATTTAAT-AAATTAAATAA
1 AAAATCGATAATTTATTCACATTAAATCG
* **
22476464 AAAATTGATAATTTATTCACAAAAAATC-
1 AAAATCGATAATTTATTCACATTAAATCG
22476492 -AAA-C-ATAATTTATTCA-ATTAAATCG
1 AAAATCGATAATTTATTCACATTAAATCG
*
22476517 AAAATCGATAATTTATTCACATTAAACCG
1 AAAATCGATAATTTATTCACATTAAATCG
22476546 AA
1 AA
22476548 TAAACTAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
24 6 0.09
25 12 0.18
26 3 0.04
27 4 0.06
28 27 0.40
29 16 0.24
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATCGATAATTTATTCACATTAAATCG
Found at i:22476556 original size:28 final size:27
Alignment explanation
Indices: 22476492--22476556 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
22476482 ACAAAAAATC
*
22476492 AAACATAATTTATTCAATTAAATCGAA
1 AAACATAATTTATTCAATTAAACCGAA
*
22476519 AATCGATAATTTATTCACATTAAACCGAA
1 AAAC-ATAATTTATTCA-ATTAAACCGAA
22476548 TAAAC-TAAT
1 -AAACATAAT
22476557 CAAACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (27 bp):
AAACATAATTTATTCAATTAAACCGAA
Found at i:22477941 original size:31 final size:32
Alignment explanation
Indices: 22477906--22477968 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
22477896 AACCTAATCA
*
22477906 AGGGAAGAA-AAACTAAAAGGCAGAAAATAAT
1 AGGGAAGAATAAACCAAAAGGCAGAAAATAAT
* *
22477937 AGGGAAGAATTGAACCAAAAGGCATAAAATAA
1 AGGGAAGAA-TAAACCAAAAGGCAGAAAATAA
22477969 GGGGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 9 0.33
33 18 0.67
ACGTcount: A:0.59, C:0.08, G:0.22, T:0.11
Consensus pattern (32 bp):
AGGGAAGAATAAACCAAAAGGCAGAAAATAAT
Found at i:22478553 original size:21 final size:21
Alignment explanation
Indices: 22478509--22478555 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
22478499 TGATTGACAT
* *
22478509 ATTTTTATATTTTTATATTTA
1 ATTTTTATATTTTCATATTCA
22478530 ATTTTTATATATTTCATA-TCA
1 ATTTTTATAT-TTTCATATTCA
22478551 ATTTT
1 ATTTT
22478556 AAATCATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTTATATTTTCATATTCA
Found at i:22478747 original size:8 final size:7
Alignment explanation
Indices: 22478714--22478894 Score: 84
Period size: 7 Copynumber: 25.4 Consensus size: 7
22478704 AAAACCTTAG
22478714 ACCCTAA
1 ACCCTAA
22478721 ACCCT-A
1 ACCCTAA
*
22478727 TCCCTTAA
1 ACCC-TAA
22478735 ACCCTAA
1 ACCCTAA
22478742 AGCCCT-A
1 A-CCCTAA
*
22478749 TCCCTAA
1 ACCCTAA
*
22478756 ACCCTTA
1 ACCCTAA
22478763 ACACCTAA
1 AC-CCTAA
*
22478771 ACCTTAA
1 ACCCTAA
*
22478778 ACCC-CA
1 ACCCTAA
22478784 ACCCTTAA
1 ACCC-TAA
* *
22478792 ATCATAA
1 ACCCTAA
*
22478799 CCCCTAA
1 ACCCTAA
22478806 ACCCCTAA
1 A-CCCTAA
* *
22478814 ACCATAT
1 ACCCTAA
**
22478821 ACAATAA
1 ACCCTAA
*
22478828 ACACTAA
1 ACCCTAA
*
22478835 ACCTTAA
1 ACCCTAA
**
22478842 ACTATAA
1 ACCCTAA
22478849 ACCCTAA
1 ACCCTAA
22478856 ACCCCT-A
1 A-CCCTAA
*
22478863 ACTCTTAA
1 AC-CCTAA
*
22478871 CCCCT-A
1 ACCCTAA
22478877 ACGCCTAA
1 AC-CCTAA
*
22478885 ACCTTAA
1 ACCCTAA
22478892 ACC
1 ACC
22478895 TTAACCCTTA
Statistics
Matches: 129, Mismatches: 32, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
6 16 0.12
7 80 0.62
8 33 0.26
ACGTcount: A:0.40, C:0.39, G:0.01, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:22479021 original size:135 final size:135
Alignment explanation
Indices: 22478839--22479134 Score: 371
Period size: 135 Copynumber: 2.2 Consensus size: 135
22478829 CACTAAACCT
* *
22478839 TAAACTATAAACCCTAAACCCCTAACTCTTAACCCCTAACGCCTAAACCTTAAAC-CTTAACCCT
1 TAAACTATAAACCCTAAACCCCTAACACTTAACCCCTAACACCTAAACCTTAAACAC-TAACCCT
* * * ** *
22478903 TAAATCGTAAACCACAAACCATAATCCTTAAAACTTTAACAC-ATTTCCCCTAAACCTTGAATCA
65 TAAACCATAAACCACAAACCATAATCCATAAAACCCTAAC-CTATATCCCCTAAACCTTGAATCA
22478967 TAAAACA
129 TAAAACA
** * *
22478974 TAAACTATAAATGCTAAACCCCTAACACTTAACCTCTAACACGTAAACCTTAAACACTAACCCTT
1 TAAACTATAAACCCTAAACCCCTAACACTTAACCCCTAACACCTAAACCTTAAACACTAACCCTT
* * * * * *
22479039 AAACCATAACCCATAACCCATAATCCATAAACCCCTAACCTATATCCCTTAAACCTTGTATCATA
66 AAACCATAAACCACAAACCATAATCCATAAAACCCTAACCTATATCCCCTAAACCTTGAATCATA
*
22479104 GAACA
131 AAACA
* *
22479109 TAAATTATAAACCCTAAACTCCTAAC
1 TAAACTATAAACCCTAAACCCCTAAC
22479135 CATTAAACCC
Statistics
Matches: 136, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
134 1 0.01
135 134 0.99
136 1 0.01
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.24
Consensus pattern (135 bp):
TAAACTATAAACCCTAAACCCCTAACACTTAACCCCTAACACCTAAACCTTAAACACTAACCCTT
AAACCATAAACCACAAACCATAATCCATAAAACCCTAACCTATATCCCCTAAACCTTGAATCATA
AAACA
Found at i:22479025 original size:21 final size:21
Alignment explanation
Indices: 22479001--22479049 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
22478991 ACCCCTAACA
*
22479001 CTTAACCTCTAACACGTAAAC
1 CTTAACCACTAACACGTAAAC
* * *
22479022 CTTAAACACTAACCCTTAAAC
1 CTTAACCACTAACACGTAAAC
*
22479043 CATAACC
1 CTTAACC
22479050 CATAACCCAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.22
Consensus pattern (21 bp):
CTTAACCACTAACACGTAAAC
Found at i:22479054 original size:7 final size:7
Alignment explanation
Indices: 22479031--22479078 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
22479021 CCTTAAACAC
*
22479031 TAACCCT
1 TAACCCA
*
22479038 TAAACCA
1 TAACCCA
22479045 TAACCCA
1 TAACCCA
22479052 TAACCCA
1 TAACCCA
*
22479059 TAATCCA
1 TAACCCA
*
22479066 TAAACCCC
1 T-AACCCA
22479074 TAACC
1 TAACC
22479079 TATATCCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
TAACCCA
Found at i:22479055 original size:21 final size:22
Alignment explanation
Indices: 22479017--22479078 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
22479007 CTCTAACACG
* * *
22479017 TAAACCTTAAACAC-TAACCCT
1 TAAACCATAAACCCATAACCCA
22479038 TAAACCAT-AACCCATAACCCA
1 TAAACCATAAACCCATAACCCA
* *
22479059 TAATCCATAAACCCCTAACC
1 TAAACCATAAACCCATAACC
22479079 TATATCCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 4 0.12
21 20 0.59
22 10 0.29
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCATAAACCCATAACCCA
Found at i:22485284 original size:18 final size:18
Alignment explanation
Indices: 22485253--22485287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22485243 ACTTAGTCGG
* *
22485253 TTTCTTCTTTCCCTTAGC
1 TTTCTGCTTCCCCTTAGC
22485271 TTTCTGCTTCCCCTTAG
1 TTTCTGCTTCCCCTTAG
22485288 AAGACAAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.34, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTCTGCTTCCCCTTAGC
Found at i:22488054 original size:68 final size:71
Alignment explanation
Indices: 22487922--22488059 Score: 201
Period size: 68 Copynumber: 2.0 Consensus size: 71
22487912 TGATTAAACT
* *
22487922 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTTAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATATCTATCTA-AAGATAAACATTAAATTTAATTTAAT
22487987 ATTAAGA
65 ATTAAGA
* **
22487994 TAATCACTTTAATATTGAATTAATAAAATA-CTAT-T-AAGATAAGTATTAAATTTAATTTAATA
1 TAATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTTAATTTAATA
22488056 TTAA
66 TTAA
22488060 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 29 0.48
70 1 0.02
71 3 0.05
72 28 0.46
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (71 bp):
TAATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTTAATTTAATA
TTAAGA
Found at i:22501994 original size:31 final size:32
Alignment explanation
Indices: 22501926--22501985 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
22501916 AATTTAGAAT
*
22501926 TTTTTTATATTTTTTATATTTTAAAAAGTTCA
1 TTTTTTATATTTTTTATAATTTAAAAAGTTCA
*
22501958 TTTTTTAT-TTTTTTA-AATTTAAAGAGTT
1 TTTTTTATATTTTTTATAATTTAAAAAGTT
22501986 TTTATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.42
31 7 0.27
32 8 0.31
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTTTTATATTTTTTATAATTTAAAAAGTTCA
Found at i:22502846 original size:33 final size:32
Alignment explanation
Indices: 22502809--22502875 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
22502799 TGCTAATTAG
22502809 GGTTTA-GGTTTT-TTTAAAATTTTTAAATGTTTA
1 GGTTTAGGGTTTTATTT--AATTTTTAAA-GTTTA
*
22502842 GGTTTAGGGTTTTATTTAATTTTTAGAGTTTA
1 GGTTTAGGGTTTTATTTAATTTTTAAAGTTTA
22502874 GG
1 GG
22502876 GGTTCTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 7 0.23
33 15 0.48
34 6 0.19
35 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (32 bp):
GGTTTAGGGTTTTATTTAATTTTTAAAGTTTA
Found at i:22502932 original size:29 final size:28
Alignment explanation
Indices: 22502877--22502953 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
22502867 GAGTTTAGGG
* *
22502877 GTTCTAAAAACATAATTTGTATAGGATGA
1 GTTCTAAAAAAATAATTT-TAAAGGATGA
*
22502906 GTTCTAAAAAAATAATTTTAAAGGGATGG
1 GTTCTAAAAAAATAATTTTAAA-GGATGA
* *
22502935 GTTCTGAAGAAATAATTTT
1 GTTCTAAAAAAATAATTTT
22502954 GACGAGATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 3 0.07
29 39 0.93
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (28 bp):
GTTCTAAAAAAATAATTTTAAAGGATGA
Found at i:22502962 original size:29 final size:29
Alignment explanation
Indices: 22502875--22502963 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 29
22502865 TAGAGTTTAG
* *
22502875 GGGTTCTAAAAACATAATTTGTATAG-GAT
1 GGGTTCTAAAAAAATAATTT-TAAAGAGAT
* *
22502904 GAGTTCTAAAAAAATAATTTTAAAGGGAT
1 GGGTTCTAAAAAAATAATTTTAAAGAGAT
* * * *
22502933 GGGTTCTGAAGAAATAATTTTGACGAGAT
1 GGGTTCTAAAAAAATAATTTTAAAGAGAT
22502962 GG
1 GG
22502964 ATTGATTTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 4 0.08
29 46 0.92
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (29 bp):
GGGTTCTAAAAAAATAATTTTAAAGAGAT
Found at i:22506837 original size:10 final size:9
Alignment explanation
Indices: 22506805--22506830 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22506795 TATGAAATAA
22506805 AAAAAATTT
1 AAAAAATTT
22506814 AAAAAATTT
1 AAAAAATTT
22506823 AAAAAATT
1 AAAAAATT
22506831 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:22512528 original size:157 final size:157
Alignment explanation
Indices: 22512239--22512711 Score: 768
Period size: 157 Copynumber: 3.0 Consensus size: 157
22512229 TAATATGCCA
* * *
22512239 TCCTTTTTTGGCTTCTAGTTATTGTACTCGTACTAGACTGAGGAAAAGAAATGCACAACCTCAAA
1 TCCTTTTTTGGCTTCTAGTTCTTGTACTCGTACCAGACTGA--AAAA-AAATGCACAACCCCAAA
* * * * * * * *
22512304 TTAGATTTAAATATTTTGAAACTTGACACTAAAAAAGTGTTTATGATATACATATGATCCAGTTG
63 TTAGATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTATGATCCAATTG
22512369 TGTTAGGTTGATTGCATGATCTTCTGTTGT
128 TGTTAGGTTGATTGCATGATCTTCTGTTGT
*
22512399 TCCTTTTTTGGCTTCTAGTTCTTGTACTCGTACCAGACTGAAAAAAAATGCATAACCCCAAATTA
1 TCCTTTTTTGGCTTCTAGTTCTTGTACTCGTACCAGACTGAAAAAAAATGCACAACCCCAAATTA
*
22512464 GATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTGTGATCCAATTGTGT
66 GATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTATGATCCAATTGTGT
*
22512529 TAGGTTGATTGCATGATCTTCTGTTTT
131 TAGGTTGATTGCATGATCTTCTGTTGT
* *
22512556 TTCTTTTTTGGCTTCTAGTTCTTGTACTCGTACGAGACTG-AAAAAAATGCACAACCCCAAATTA
1 TCCTTTTTTGGCTTCTAGTTCTTGTACTCGTACCAGACTGAAAAAAAATGCACAACCCCAAATTA
22512620 GATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTATGATCCAATTGTGT
66 GATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTATGATCCAATTGTGT
22512685 TAGGTTGATTGCATGATCTTCTGTTGT
131 TAGGTTGATTGCATGATCTTCTGTTGT
22512712 GACCTTTACC
Statistics
Matches: 294, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
156 113 0.38
157 138 0.47
158 4 0.01
160 39 0.13
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (157 bp):
TCCTTTTTTGGCTTCTAGTTCTTGTACTCGTACCAGACTGAAAAAAAATGCACAACCCCAAATTA
GATTTAAATATTTTGAAACTTAATAGTGAAAAAGTGTTTACGGTATACCTATGATCCAATTGTGT
TAGGTTGATTGCATGATCTTCTGTTGT
Found at i:22513955 original size:20 final size:20
Alignment explanation
Indices: 22513921--22513959 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
22513911 AGACAAATAA
22513921 AATATCAAAATAATATAAAC
1 AATATCAAAATAATATAAAC
22513941 AATA-CAAAATGAATATAAA
1 AATATCAAAAT-AATATAAA
22513960 GTTAATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
AATATCAAAATAATATAAAC
Found at i:22514448 original size:30 final size:30
Alignment explanation
Indices: 22514378--22514455 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
22514368 CTCAATATTA
* * *
22514378 AAAACCCT-AACCTAAAATCCCCAAATTCG
1 AAAACCCTAAACCTAAAATCCACAAACTCC
* * *
22514407 ACAACCTTAAACCTAAAATTCACAAACTCC
1 AAAACCCTAAACCTAAAATCCACAAACTCC
22514437 AAAACCCTAAACC-AAAATC
1 AAAACCCTAAACCTAAAATC
22514456 GAAATAACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (30 bp):
AAAACCCTAAACCTAAAATCCACAAACTCC
Found at i:22526148 original size:26 final size:24
Alignment explanation
Indices: 22526092--22526149 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
22526082 TATTGTATTT
*
22526092 AACTTTTTTTATATTTTAATTTTG
1 AACTATTTTTATATTTTAATTTTG
** *
22526116 ATGTATTTTTATTTTTATAATTTTTG
1 AACTATTTTTATATTT-TAA-TTTTG
22526142 AACTATTT
1 AACTATTT
22526150 GTTGACACGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 11 0.42
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (24 bp):
AACTATTTTTATATTTTAATTTTG
Found at i:22526335 original size:15 final size:17
Alignment explanation
Indices: 22526317--22526357 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
22526307 AATAATAATC
22526317 AAAATA-AT-AAAAAAT
1 AAAATATATCAAAAAAT
22526332 AAAA-ATATCAAAAAAT
1 AAAATATATCAAAAAAT
22526348 AAAAT-TATCA
1 AAAATATATCA
22526358 TTATACTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 6 0.26
16 16 0.70
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATATATCAAAAAAT
Found at i:22526338 original size:16 final size:16
Alignment explanation
Indices: 22526325--22526357 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22526315 TCAAAATAAT
22526325 AAAAAATAAAAATATC
1 AAAAAATAAAAATATC
*
22526341 AAAAAATAAAATTATC
1 AAAAAATAAAAATATC
22526357 A
1 A
22526358 TTATACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAAATATC
Found at i:22528294 original size:21 final size:21
Alignment explanation
Indices: 22528270--22528313 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
22528260 AGTGCCACAT
*
22528270 GTCAAACCAAAATTATCATGG
1 GTCAAACCAAAATTACCATGG
** *
22528291 GTCAAGTCGAAATTACCATGG
1 GTCAAACCAAAATTACCATGG
22528312 GT
1 GT
22528314 AAAAAGGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (21 bp):
GTCAAACCAAAATTACCATGG
Done.