Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 66 of 349
Found at i:19289061 original size:40 final size:40
Alignment explanation
Indices: 19289017--19289093 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
19289007 TTGATAATGG
19289017 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
*
19289057 GTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAAT
19289094 GTTCCATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
Found at i:19290623 original size:26 final size:26
Alignment explanation
Indices: 19290594--19290646 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
19290584 TTTACAGTTT
19290594 TACCCATAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
19290620 TACCCCTAGGGTTAAATTGACCGAAA
1 TACCCATAGGGATAAATTGACCGAAA
19290646 T
1 T
19290647 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:19291137 original size:136 final size:136
Alignment explanation
Indices: 19290894--19291178 Score: 484
Period size: 136 Copynumber: 2.1 Consensus size: 136
19290884 GAGTAGTCTC
*
19290894 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
*
19290959 GTTATCTGAATAAGGGGCTAAGGCCCGGTTTATTGTAATCTGAAAAGGGCTCT-GCCC-GATACC
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAG-TACC
19291022 ACTGTTA
130 ACTGTTA
19291029 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
19291094 TGTTATCTGAATAAGGGGCTAATGCCCAGTTTATTGTAATCTGAAAATGGCTTTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
19291159 ACTGTTA
130 ACTGTTA
*
19291166 CCTAAATGGGCTT
1 CCCAAATGGGCTT
19291179 AGGCCCAATA
Statistics
Matches: 141, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
135 20 0.14
136 93 0.66
137 27 0.19
138 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:19292795 original size:21 final size:21
Alignment explanation
Indices: 19292769--19292808 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19292759 TCAAGAAAGT
19292769 GATGATGGTGATGATGACGAC
1 GATGATGGTGATGATGACGAC
19292790 GATGATGGTGATGATGACG
1 GATGATGGTGATGATGACG
19292809 GTGAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.40, T:0.25
Consensus pattern (21 bp):
GATGATGGTGATGATGACGAC
Found at i:19294934 original size:21 final size:21
Alignment explanation
Indices: 19294910--19294956 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
19294900 TAGTTAAAGA
19294910 AAGCTGCTAGTTAATAATTTC
1 AAGCTGCTAGTTAATAATTTC
*
19294931 AAGCTGCTAGTTGATAATTTC
1 AAGCTGCTAGTTAATAATTTC
19294952 AAGCT
1 AAGCT
19294957 CAGCTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (21 bp):
AAGCTGCTAGTTAATAATTTC
Found at i:19301654 original size:15 final size:15
Alignment explanation
Indices: 19301603--19301654 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
19301593 CCTAAAGTTA
19301603 TTAATTC-TAATTAT
1 TTAATTCTTAATTAT
* * *
19301617 TCTAATATTTTATTTAA
1 T-TAAT-TCTTAATTAT
19301634 TTAATTCTTAATTAT
1 TTAATTCTTAATTAT
19301649 TTAATT
1 TTAATT
19301655 ATATAATCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 17 0.59
16 5 0.17
17 6 0.21
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTCTTAATTAT
Found at i:19301667 original size:32 final size:31
Alignment explanation
Indices: 19301602--19301668 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
19301592 ACCTAAAGTT
* * *
19301602 ATTAATTCTAATTATTCTAATATTTTATTTA
1 ATTAATTCTAATTATTCTAATATATAATCTA
19301633 ATTAATTCTTAATTATT-TAATTATATAATCTA
1 ATTAATTC-TAATTATTCTAA-TATATAATCTA
19301665 ATTA
1 ATTA
19301669 TAGTTTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTAATTCTAATTATTCTAATATATAATCTA
Found at i:19302873 original size:40 final size:40
Alignment explanation
Indices: 19302813--19302897 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
19302803 GAATGTACAT
*
19302813 GATGCTGTGGTTAGTTGTTGACGGAAAAGAGTTAATTTGA
1 GATGTTGTGGTTAGTTGTTGACGGAAAAGAGTTAATTTGA
19302853 GATGTTGTGGTTAGTTGTTGACGGAAAAGAGTTAATTTGA
1 GATGTTGTGGTTAGTTGTTGACGGAAAAGAGTTAATTTGA
19302893 GATGT
1 GATGT
19302898 CCGAATGGCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (40 bp):
GATGTTGTGGTTAGTTGTTGACGGAAAAGAGTTAATTTGA
Found at i:19306533 original size:20 final size:20
Alignment explanation
Indices: 19306430--19306539 Score: 60
Period size: 20 Copynumber: 5.5 Consensus size: 20
19306420 CATATTCGTG
*
19306430 CCCCTATTTGTACTTTGGTA
1 CCCCTATTTGTACTTCGGTA
* * * * ** *
19306450 CCCTTGTTTGCACATATGTG
1 CCCCTATTTGTACTTCGGTA
* * *
19306470 CCCCTGTTTGTTCTTCGATA
1 CCCCTATTTGTACTTCGGTA
* * * *
19306490 CCTCTATTTGCACATAC-GTG
1 CCCCTATTTGTAC-TTCGGTA
19306510 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
*
19306530 CCCCTTTTTG
1 CCCCTATTTG
19306540 CACATAAGTG
Statistics
Matches: 61, Mismatches: 27, Indels: 4
0.66 0.29 0.04
Matches are distributed among these distances:
19 2 0.03
20 57 0.93
21 2 0.03
ACGTcount: A:0.14, C:0.29, G:0.15, T:0.42
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGGTA
Found at i:19306560 original size:40 final size:40
Alignment explanation
Indices: 19306427--19306561 Score: 155
Period size: 40 Copynumber: 3.4 Consensus size: 40
19306417 TTGCATATTC
* * *
19306427 GTGCCCCTATTTGTACTTTGGTA-CCCTTGTTTGCACATAT
1 GTGCCCCTGTTTGTACTTCGGTACCCCTT-TTTGCACATAA
* * * * *
19306467 GTGCCCCTGTTTGTTCTTCGATACCTCTATTTGCACATAC
1 GTGCCCCTGTTTGTACTTCGGTACCCCTTTTTGCACATAA
*
19306507 GTGCCCCTATTTGTACTTCGGTACCCCTTTTTGCACATAA
1 GTGCCCCTGTTTGTACTTCGGTACCCCTTTTTGCACATAA
**
19306547 GTGTTCCTGTTTGTA
1 GTGCCCCTGTTTGTA
19306562 TTATGACAGC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 75 0.96
41 3 0.04
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (40 bp):
GTGCCCCTGTTTGTACTTCGGTACCCCTTTTTGCACATAA
Found at i:19315971 original size:5 final size:5
Alignment explanation
Indices: 19315956--19316024 Score: 57
Period size: 5 Copynumber: 13.0 Consensus size: 5
19315946 ATTGGGGTAG
* * * *
19315956 GATAT AATAT GTTAT GATAT GAGATAT GATAT GATAT GATAC GATAT GTAATCT
1 GATAT GATAT GATAT GATAT --GATAT GATAT GATAT GATAT GATAT G--ATAT
*
19316010 GATAT GGTAT GATAT
1 GATAT GATAT GATAT
19316025 AAGATATACT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
5 41 0.82
7 9 0.18
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (5 bp):
GATAT
Found at i:19316012 original size:27 final size:27
Alignment explanation
Indices: 19315956--19316023 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
19315946 ATTGGGGTAG
* * *
19315956 GATATAATATGTTATGATATGAGATAT
1 GATATGATATGATACGATATGAGATAT
*
19315983 GATATGATATGATACGATATGTA-ATCT
1 GATATGATATGATACGATATG-AGATAT
*
19316010 GATATGGTATGATA
1 GATATGATATGATA
19316024 TAAGATATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (27 bp):
GATATGATATGATACGATATGAGATAT
Found at i:19316030 original size:17 final size:16
Alignment explanation
Indices: 19315956--19316031 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 16
19315946 ATTGGGGTAG
*
19315956 GATATA-ATATGTTAT
1 GATATAGATATGATAT
19315971 GATATGAGATATGATAT
1 GATAT-AGATATGATAT
*
19315988 GATAT-GATACGATAT
1 GATATAGATATGATAT
* *
19316003 G-TAATCTGATATGGTAT
1 GAT-AT-AGATATGATAT
19316020 GATATAAGATAT
1 GATAT-AGATAT
19316032 ACTCTGATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
14 1 0.02
15 17 0.35
16 1 0.02
17 29 0.59
18 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (16 bp):
GATATAGATATGATAT
Found at i:19319502 original size:32 final size:31
Alignment explanation
Indices: 19319421--19319513 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 31
19319411 TCGCAATTTA
19319421 GCAGAGCTCGCACAATATAGCACAGTTCAC-AATT
1 GCAGAGCTCG--CAATAT--CACAGTTCACAAATT
* *
19319455 -CATAGTTCGCAATATCACAGTTCACAAATCT
1 GCAGAGCTCGCAATATCACAGTTCACAAAT-T
* *
19319486 GCAGAGCTCGCAATATCATAATTCACAA
1 GCAGAGCTCGCAATATCACAGTTCACAA
19319514 TTCATAGTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
29 10 0.20
30 3 0.06
31 7 0.14
32 23 0.46
33 7 0.14
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.24
Consensus pattern (31 bp):
GCAGAGCTCGCAATATCACAGTTCACAAATT
Found at i:19319742 original size:52 final size:52
Alignment explanation
Indices: 19319648--19319931 Score: 224
Period size: 52 Copynumber: 5.4 Consensus size: 52
19319638 AATATAGCAA
* *
19319648 GGTTCACACATAAGCTAGGGTTCACACTTTTGGTTAGGTTCACACATTTA-GTAG
1 GGTTCACACATTAG-TA-GGTTCACACTTTAGG-TAGGTTCACACATTTAGGTAG
* *
19319702 GGTTAACACATTAGTAGGTTCACACTTTAGGTTGGATTCACACA-TTAGGTAG
1 GGTTCACACATTAGTAGGTTCACACTTTAGGTAGG-TTCACACATTTAGGTAG
* * *** * * *
19319754 GGTTCTCACATTGGTAGGGTTTGTACATTA-GTAGGGTTCGCAC-TTTAGGAAG
1 GGTTCACACATTAGTA-GGTTCACACTTTAGGTA-GGTTCACACATTTAGGTAG
* * * * * *
19319806 GGTTTACACATTAGTAGGGTCTGCACATT-GGTAAGGTTTACAC-TTTAGGAAG
1 GGTTCACACATTAGTAGGTTC-ACACTTTAGGT-AGGTTCACACATTTAGGTAG
*
19319858 GGTTCGCACATTAGTAAGGTTCACACTTTAGGTAGGGTTCACACA-TT-GGTAG
1 GGTTCACACATTAGT-AGGTTCACACTTTAGGTA-GGTTCACACATTTAGGTAG
* *
19319910 GGTTTACATATTAGTAGAGTTC
1 GGTTCACACATTAGTAG-GTTC
19319932 GCACAATGAC
Statistics
Matches: 185, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
51 11 0.06
52 130 0.70
53 32 0.17
54 12 0.06
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (52 bp):
GGTTCACACATTAGTAGGTTCACACTTTAGGTAGGTTCACACATTTAGGTAG
Found at i:19319743 original size:18 final size:17
Alignment explanation
Indices: 19319647--19319910 Score: 112
Period size: 18 Copynumber: 15.2 Consensus size: 17
19319637 AAATATAGCA
* * *
19319647 AGGTTCACACATAAGCT
1 AGGTTCACACTTTAGGT
*
19319664 AGGGTTCACACTTTTGGTT
1 A-GGTTCACACTTTAGG-T
19319683 AGGTTCACACATTTA-GT
1 AGGTTCACAC-TTTAGGT
* *
19319700 AGGGTTAACACATTA-GT
1 A-GGTTCACACTTTAGGT
19319717 AGGTTCACACTTTAGGT
1 AGGTTCACACTTTAGGT
* *
19319734 TGGATTCACACATTAGGT
1 AGG-TTCACACTTTAGGT
* *
19319752 AGGGTTCTCACATT-GGT
1 A-GGTTCACACTTTAGGT
*** *
19319769 AGGGTTTGTACATTA-GT
1 A-GGTTCACACTTTAGGT
* *
19319786 AGGGTTCGCACTTTAGGA
1 A-GGTTCACACTTTAGGT
* *
19319804 AGGGTTTACACATTA-GT
1 A-GGTTCACACTTTAGGT
* * *
19319821 AGGGTCTGCACATT-GGT
1 AGGTTC-ACACTTTAGGT
* *
19319838 AAGGTTTACACTTTAGGA
1 -AGGTTCACACTTTAGGT
* *
19319856 AGGGTTCGCACATTA-GT
1 A-GGTTCACACTTTAGGT
19319873 AAGGTTCACACTTTAGGT
1 -AGGTTCACACTTTAGGT
*
19319891 AGGGTTCACACATT-GGT
1 A-GGTTCACACTTTAGGT
19319908 AGG
1 AGG
19319911 GTTTACATAT
Statistics
Matches: 191, Mismatches: 39, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
16 16 0.08
17 74 0.39
18 94 0.49
19 7 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (17 bp):
AGGTTCACACTTTAGGT
Found at i:19319782 original size:35 final size:35
Alignment explanation
Indices: 19319684--19319936 Score: 221
Period size: 35 Copynumber: 7.3 Consensus size: 35
19319674 CTTTTGGTTA
* * *
19319684 GGTTCACACATTTAGTAGGGTTAACACATTA-GTA-
1 GGTTCGCACA-TTGGTAGGGTTTACACATTAGGTAG
* * * * *
19319718 GGTTCACACTTTAGGTTGGATTCACACATTAGGTAG
1 GGTTCGCACATT-GGTAGGGTTTACACATTAGGTAG
* **
19319754 GGTTCTCACATTGGTAGGGTTTGTACATTA-GTAG
1 GGTTCGCACATTGGTAGGGTTTACACATTAGGTAG
* *
19319788 GGTTCGCACTTTAGGAAGGGTTTACACATTA-GTAG
1 GGTTCGCACATT-GGTAGGGTTTACACATTAGGTAG
* * *
19319823 GG-TCTGCACATTGGTAAGGTTTACACTTTAGGAAG
1 GGTTC-GCACATTGGTAGGGTTTACACATTAGGTAG
* * * *
19319858 GGTTCGCACATTAGTAAGGTTCACACTTTAGGTAG
1 GGTTCGCACATTGGTAGGGTTTACACATTAGGTAG
* *
19319893 GGTTCACACATTGGTAGGGTTTACATATTA-GTAG
1 GGTTCGCACATTGGTAGGGTTTACACATTAGGTAG
*
19319927 AGTTCGCACA
1 GGTTCGCACA
19319937 ATGACATGAT
Statistics
Matches: 179, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
33 2 0.01
34 66 0.37
35 99 0.55
36 12 0.07
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (35 bp):
GGTTCGCACATTGGTAGGGTTTACACATTAGGTAG
Found at i:19319982 original size:16 final size:15
Alignment explanation
Indices: 19319963--19320015 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
19319953 CACACATCAT
19319963 ATAGAAGTCACACAAC
1 ATAG-AGTCACACAAC
**
19319979 ATAGCTTCACACATCAC
1 ATAGAGTCACACA--AC
19319996 ATAGCAGTCACACAAC
1 ATAG-AGTCACACAAC
19320012 ATAG
1 ATAG
19320016 GTTCGCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 6 0.20
18 7 0.23
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (15 bp):
ATAGAGTCACACAAC
Found at i:19319993 original size:33 final size:33
Alignment explanation
Indices: 19319951--19320029 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
19319941 CATGATAAGG
*
19319951 TTCACACATCATATAGAAGTCACACAACATAGC
1 TTCACACATCACATAGAAGTCACACAACATAGC
* *
19319984 TTCACACATCACATAGCAGTCACACAACATAGG
1 TTCACACATCACATAGAAGTCACACAACATAGC
*
19320017 TTCGCACATCACA
1 TTCACACATCACA
19320030 ATAGGGTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.20
Consensus pattern (33 bp):
TTCACACATCACATAGAAGTCACACAACATAGC
Found at i:19320008 original size:18 final size:18
Alignment explanation
Indices: 19319952--19320009 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
19319942 ATGATAAGGT
* *
19319952 TCACACATCATATAGAAG
1 TCACACATCACATAGCAG
*
19319970 TCACACA--ACATAGC-T
1 TCACACATCACATAGCAG
19319985 TCACACATCACATAGCAG
1 TCACACATCACATAGCAG
19320003 TCACACA
1 TCACACA
19320010 ACATAGGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 7 0.21
18 14 0.42
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.19
Consensus pattern (18 bp):
TCACACATCACATAGCAG
Found at i:19320059 original size:22 final size:22
Alignment explanation
Indices: 19320034--19320093 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
19320024 ATCACAATAG
*
19320034 GGTTCACATGAAATTATAACAA
1 GGTTCACATGACATTATAACAA
* * * *
19320056 GGTTTACATGACATTTTAGCAG
1 GGTTCACATGACATTATAACAA
19320078 GGTTCACATGACATTA
1 GGTTCACATGACATTA
19320094 CCTAGGCTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (22 bp):
GGTTCACATGACATTATAACAA
Found at i:19322740 original size:22 final size:22
Alignment explanation
Indices: 19322715--19322757 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19322705 TAGAGAATAC
* *
19322715 AAACGACAAATTTCATATTCGA
1 AAACCACAAATTCCATATTCGA
19322737 AAACCACAAATTCCATATTCG
1 AAACCACAAATTCCATATTCG
19322758 GCATCATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (22 bp):
AAACCACAAATTCCATATTCGA
Found at i:19326960 original size:16 final size:16
Alignment explanation
Indices: 19326939--19326969 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19326929 TTTCTAGTAT
19326939 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTG
19326955 TTTATTTACTAGCGT
1 TTTATTTACTAGCGT
19326970 ATTTGCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTATTTACTAGCGTG
Found at i:19336746 original size:23 final size:22
Alignment explanation
Indices: 19336716--19336760 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
19336706 TCACTTTGAT
* * *
19336716 TTATTTATTTATTTAGTTATTA
1 TTATTTATATACTTAATTATTA
19336738 TTATATTATATACTTAATTATTA
1 TTAT-TTATATACTTAATTATTA
19336761 AGTATTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTATATACTTAATTATTA
Found at i:19337534 original size:6 final size:6
Alignment explanation
Indices: 19337525--19337569 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
19337515 TTCTACTTTA
* * * *
19337525 TTTATT TTTATT TCTAGT TGTACT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
19337570 TTTGTTTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:19344158 original size:13 final size:13
Alignment explanation
Indices: 19344140--19344165 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19344130 AGCACGACTT
19344140 ACACGGGCGTGTC
1 ACACGGGCGTGTC
19344153 ACACGGGCGTGTC
1 ACACGGGCGTGTC
19344166 CCTGCCGAAC
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:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:19350201 original size:18 final size:19
Alignment explanation
Indices: 19350161--19350219 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
19350151 ACAAAGGCAC
19350161 AAAAAGAAA-ATAAATA-AA
1 AAAAAGAAAGATAAA-AGAA
*
19350179 TAAAAAAAAAGATAAAAGAA
1 -AAAAAGAAAGATAAAAGAA
* *
19350199 AAAAAGCAAGATAAAGGAA
1 AAAAAGAAAGATAAAAGAA
19350218 AA
1 AA
19350220 TAAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 27 0.79
20 7 0.21
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.08
Consensus pattern (19 bp):
AAAAAGAAAGATAAAAGAA
Found at i:19350287 original size:4 final size:4
Alignment explanation
Indices: 19350266--19350299 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
19350256 GGTAAAAACT
* *
19350266 AATA AATA AGTA AGTA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
19350300 GGACTCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19351803 original size:89 final size:89
Alignment explanation
Indices: 19351652--19351956 Score: 287
Period size: 89 Copynumber: 3.4 Consensus size: 89
19351642 TGCATATACC
* * * * ** * * * *
19351652 ACTTCAAGGAGATAAGATTCGTAGCTTCAATCTACTCCGCTGC-GACTTTAGGGAGATGAGATTA
1 ACTTCAAGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTACAG-CTTAAAGAAGATGAGATTA
* * *
19351716 GTGATTTTTAACTTGCTCCACTGTA
65 GTGATTTTTAACCTGCTACACTGCA
* *
19351741 ACTTCAAGGAGATAAGGTTTGTAGTTTTGATCTGCTCTACTACAGCTTAAAGAAGATGAGATTAG
1 ACTTCAAGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTACAGCTTAAAGAAGATGAGATTAG
19351806 TGATTTTTAACCTGCTACACTGCA
66 TGATTTTTAACCTGCTACACTGCA
* * * **
19351830 ACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTGCAGCTT-CAGAGAGACAAGATT-
1 ACTTCAAGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTACAGCTTAAAGA-AGATGAGATTA
* *
19351893 -TGATATTTTCAATCTACT-CTACTGCA
65 GTGAT-TTTT-AACCTGCTAC-ACTGCA
* * * *
19351919 ACTTCAGGGAGATAAGATTTGTAATCTTTAACCTGCTC
1 ACTTCAAGGAGATAAGGTTTGT-AGCTTTAATCTGCTC
19351957 CACTGCAACT
Statistics
Matches: 183, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.02
88 8 0.04
89 157 0.86
90 14 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (89 bp):
ACTTCAAGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTACAGCTTAAAGAAGATGAGATTAG
TGATTTTTAACCTGCTACACTGCA
Found at i:19351865 original size:44 final size:44
Alignment explanation
Indices: 19351652--19352683 Score: 610
Period size: 44 Copynumber: 22.8 Consensus size: 44
19351642 TGCATATACC
* * * * * *
19351652 ACTTCAAGGAGATAAGATTCGTAGCTTCAATCTACTCCGCTGCG
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * ** *
19351696 ACTTTAGGGAGATGAGATTAGTGATTTTTAA-CTTGCTCCACTGTA
1 ACTTCAGGGAGATAAGATTTGT-AGCTTTAATC-TGCTCCACTGCA
* * * * * *
19351741 ACTTCAAGGAGATAAGGTTTGTAGTTTTGATCTGCTCTACTACA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * * * ** * *
19351785 GCTTAAAGAAGATGAGATTAGTGATTTTTAACCTGCTACACTGCA
1 ACTTCAGGGAGATAAGATTTGT-AGCTTTAATCTGCTCCACTGCA
* *
19351830 ACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCTACTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * * *
19351874 GCTTCAGAGAGACAAGATTTGATA-TTTTCAATCTACTCTACTGCA
1 ACTTCAGGGAGATAAGATTTG-TAGCTTT-AATCTGCTCCACTGCA
* *
19351919 ACTTCAGGGAGATAAGATTTGTAATCTTTAACCTGCTCCACTGCA
1 ACTTCAGGGAGATAAGATTTGT-AGCTTTAATCTGCTCCACTGCA
* * * * * *
19351964 ACTTCAAGGAGATAAGGTTTGTGGCTTTTATCTACTCCACTGCG
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * *
19352008 ACTTCAGAGAGATAAGATTTGTAACTTTGATCTACTCCAGTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * *
19352052 ACTTCAGGGAGATAAGATTTGTAACTTTAACCTGCTCTACTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * *
19352096 ACTTCTGGGAGATAATATTTGTAATTTGTAGCTTTAATCTGTTCCACTACA
1 ACTTCAGGGAGAT-A-A---G--ATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * ** * * * * **
19352147 AATTTAAGGATATAAGATTCACTATCTTCAGTCTGTTCCACTATA
1 ACTTCAGGGAGATAAGATT-TGTAGCTTTAATCTGCTCCACTGCA
* * * * * * * *
19352192 ATTTTAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTCCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * *
19352236 ACTTCAGGGAGATAAGGTTTGTTATCTTCAGTCTGCTCCACTACA
1 ACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCCACTGCA
* ** * * *
19352281 ACTTCAGGGAGATAAGACTTAAAGTTTTAATCTACTCTACTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * * ** * *
19352325 ACTTCAGAGAGGTAATATTTTTTATCTTCGATCTACTCCACTGTA
1 ACTTCAGGGAGATAAGA-TTTGTAGCTTTAATCTGCTCCACTGCA
** * * * *
19352370 ACTTCAATGAGATAAGATCTATAACTTCAATCTGCTCCACTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * **
19352414 ACTTCAGGGAGATCCGATTTGTAATTTGTAGCCTTAATCTATTCCACTGCA
1 ACTTCAGGGAGAT---A--AG--ATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * * * *
19352465 AATTTAGGGAAATAAGATTCGCTATCTTTAGTCTACTCCACTGCA
1 ACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCCACTGCA
* * *
19352510 ACTTCAGGGAGATGAGACTTGTAATTTATAGCTTTAATCTGTTCCACTACA
1 ACTTCAGGGAGAT-A-A---G--ATTTGTAGCTTTAATCTGCTCCACTGCA
* * * * * * *
19352561 ACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCATTGCA
1 ACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCCACTGCA
* * *
19352606 ACTTCAGGGAGATAAGACTTGTAACTTTAACCTGCTCCACTGCA
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
* * *
19352650 ACTTCAAGGAGATAAGGTTTATAGCTTTAATCTG
1 ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
19352684 TTCTAAGATT
Statistics
Matches: 750, Mismatches: 204, Indels: 68
0.73 0.20 0.07
Matches are distributed among these distances:
44 339 0.45
45 298 0.40
46 8 0.01
47 2 0.00
48 1 0.00
49 4 0.01
50 3 0.00
51 92 0.12
52 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (44 bp):
ACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCA
Found at i:19351997 original size:89 final size:87
Alignment explanation
Indices: 19351824--19352435 Score: 346
Period size: 89 Copynumber: 6.8 Consensus size: 87
19351814 AACCTGCTAC
* * * * *
19351824 ACTGCAACTTCAGGGAGATAAGGTTTGT-AGCTTTAATCTGCTCTACTGCAGCTTC-AGAGAGAC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAG-GAGAT
*
19351887 AAGATTTGATATTTTCAATCTACTCT
65 AAGATTTG-TCTTTT--ATCTACTCT
*
19351913 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAACCTGCTCCACTGCAACTTCAAGGAGATA
1 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATA
* *
19351978 AGGTTTGTGGCTTTTATCTACTCC
66 AGATTTGT--CTTTTATCTACTCT
* * * * * *
19352002 ACTGCGACTTCAGAGAGATAAGATTTGTAA-CTTTGATCTACTCCAGTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATA
* * *
19352066 AGATTTGTAACTTTAACCTGCTCT
66 AGATTTGT--CTTTTATCTACTCT
* * * * * *
19352090 ACTGCAACTTCTGGGAGATAATATTTGTAATTTGTAGCTTTAATCTGTTCCACTACAAATTTAAG
1 ACTGCAACTTCAGGGAGATAAGATTTGTAA----T--CTTTAATCTGCTCCACTGCAACTTCAAG
* * * ** *
19352155 GATATAAGATTCACTATC-TTCAGTCTGTTCC
60 GAGATAAGATT---TGTCTTTTA-TCTACTCT
** * * * * * * * *
19352186 ACTATAATTTTAGGGAGATAAGACTTGTAA-CTTCAACCTACTCCACTCCAACTTCAGGGAGATA
1 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATA
* * *
19352250 AGGTTTGT-TATCTTCAGTCTGCTCC
66 AGATTTGTCT-T-TT-A-TCTACTCT
* * * * * *
19352275 ACTACAACTTCAGGGAGATAAGACTT-AAAGT-TTTAATCTACTCTACTGCAACTTC-AGAGAGG
1 ACTGCAACTTCAGGGAGATAAGATTTGTAA-TCTTTAATCTGCTCCACTGCAACTTCAAG-GAGA
* * *
19352337 TAATATTT-TTTATCTTCGATCTACTCC
64 TAAGATTTGTCT-T-TT--ATCTACTCT
* ** * * * * *
19352364 ACTGTAACTTCAATGAGATAAGATCTATAA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATA
*
19352428 CGATTTGT
66 AGATTTGT
19352436 AATTTGTAGC
Statistics
Matches: 405, Mismatches: 90, Indels: 55
0.74 0.16 0.10
Matches are distributed among these distances:
86 2 0.00
87 1 0.00
88 77 0.19
89 216 0.53
90 39 0.10
91 6 0.01
95 33 0.08
96 29 0.07
98 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (87 bp):
ACTGCAACTTCAGGGAGATAAGATTTGTAATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATA
AGATTTGTCTTTTATCTACTCT
Found at i:19352518 original size:96 final size:96
Alignment explanation
Indices: 19352394--19352634 Score: 329
Period size: 96 Copynumber: 2.5 Consensus size: 96
19352384 AGATCTATAA
* * * * *
19352394 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATCCGATTTGTAATTTGTAGCCTTAATCTATTCC
1 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATCAGACTTGTAATTTATAGCCTTAATCTATTCC
* *
19352459 ACTGCAAATTTAGGGAAATAAGATTCGCTAT
66 ACTACAAATTCAGGGAAATAAGATTCGCTAT
* * * *
19352490 CTTTAGTCTACTCCACTGCAACTTCAGGGAGATGAGACTTGTAATTTATAGCTTTAATCTGTTCC
1 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATCAGACTTGTAATTTATAGCCTTAATCTATTCC
*
19352555 ACTACAACTTCAGGGAAATAAGATTCGCTAT
66 ACTACAAATTCAGGGAAATAAGATTCGCTAT
** * *
19352586 CTTCAGTCTGTTCCATTGCAACTTCAGGGAGATAAGACTTGTAACTTTA
1 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATCAGACTTGTAA-TTTA
19352635 ACCTGCTCCA
Statistics
Matches: 127, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
96 123 0.97
97 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (96 bp):
CTTCAGTCTACTCCACTGCAACTTCAGGGAGATCAGACTTGTAATTTATAGCCTTAATCTATTCC
ACTACAAATTCAGGGAAATAAGATTCGCTAT
Found at i:19352634 original size:140 final size:137
Alignment explanation
Indices: 19351811--19352665 Score: 550
Period size: 140 Copynumber: 6.3 Consensus size: 137
19351801 ATTAGTGATT
* * * * *
19351811 TTTAACCTGCTACACTGCAACTTCAGGGAGATAAG---G--TTTGTAGCTTTAATCTGCTCTACT
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGATTGTATTTATAGCTTCAATCTGCTCCACT
* * * * * * * *
19351871 GCAGCTTCAGAGAGACAAGATTTGATATTTTCAATCTACTCTACTGCAACTTCAGGGAGATAAGA
66 ACAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGA
*
19351936 TTTGTAATC
130 CTTGTAA-C
* * * * ** *
19351945 TTTAACCTGCTCCACTGCAACTTCAAGGAGATAAG---G--TTTGTGGCTTTTATCTACTCCACT
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGATTGTATTTATAGCTTCAATCTGCTCCACT
* * * * * ** * * *
19352005 GCGACTTCAGAGAGATAAGATTTGTAACTTTGATCTACTCCAGTGCAACTTCAGGGAGATAAGAT
66 ACAACTTCAGGGAGATAAGATTCGTATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGAC
19352070 TTGTAAC
131 TTGTAAC
* * * * * * *
19352077 TTTAACCTGCTCTACTGCAACTTCTGGGAGATAATATTTGTAATTTGTAGCTTTAATCTGTTCCA
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGA-TTGT-ATTTATAGCTTCAATCTGCTCCA
* * * * * * * ** * *
19352142 CTACAAATTTAAGGATATAAGATTCACTATCTTCAGTCTGTTCCACTATAATTTTAGGGAGATAA
64 CTACAACTTCAGGGAGATAAGATTC-GTATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAA
19352207 GACTTGTAAC
128 GACTTGTAAC
* * * * *
19352217 TTCAACCTACTCCACTCCAACTTCAGGGAGATAAGGTT-T-GTTAT--CTTCAGTCTGCTCCACT
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGATTGTATTTATAGCTTCAATCTGCTCCACT
* * * * *
19352278 ACAACTTCAGGGAGATAAGACTTAAAGT-T-TT-AATCTACTCTACTGCAACTTCAGAGAGGTAA
66 ACAACTTCAGGGAGATAAGA-TT--CGTATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAA
* * * *
19352340 TATTTTTTATC
128 GA-CTTGTAAC
** * * ** *
19352351 TTCGATCTACTCCACTGTAACTTCAATGAGATAAGA-TCTA--TA-A-CTTCAATCTGCTCCACT
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGATTGTATTTATAGCTTCAATCTGCTCCACT
* ** * * * * *
19352411 GCAACTTCAGGGAGATCCGATTTGTAATTTGTAGCCTTAATCTATTCCACTGCAAATTTAGGGAA
66 ACAACTTCAGGGAGATAAGATTCGT-ATCT-T---C--AATCTATTCCACTGCAACTTCAGGGAG
*
19352476 ATAAGA-TTCGCTATC
124 ATAAGACTT-G-TAAC
** * * *
19352491 TTTAGTCTACTCCACTGCAACTTCAGGGAGATGAGACTTGTAATTTATAGCTTTAATCTGTTCCA
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGA-TTGT-ATTTATAGCTTCAATCTGCTCCA
* * * *
19352556 CTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCATTGCAACTTCAGGGAGATAA
64 CTACAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAA
19352621 GACTTGTAAC
128 GACTTGTAAC
* *
19352631 TTTAACCTGCTCCACTGCAACTTCAAGGAGATAAG
1 TTTAACCTACTCCACTGCAACTTCAGGGAGATAAG
19352666 GTTTATAGCT
Statistics
Matches: 560, Mismatches: 125, Indels: 66
0.75 0.17 0.09
Matches are distributed among these distances:
130 2 0.00
132 35 0.06
133 100 0.18
134 143 0.26
135 3 0.01
136 5 0.01
138 3 0.01
139 37 0.07
140 156 0.28
141 28 0.05
142 4 0.01
143 2 0.00
145 2 0.00
146 2 0.00
147 37 0.07
148 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (137 bp):
TTTAACCTACTCCACTGCAACTTCAGGGAGATAAGATTGTATTTATAGCTTCAATCTGCTCCACT
ACAACTTCAGGGAGATAAGATTCGTATCTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGAC
TTGTAAC
Found at i:19352767 original size:44 final size:44
Alignment explanation
Indices: 19352713--19352825 Score: 111
Period size: 44 Copynumber: 2.6 Consensus size: 44
19352703 CGATCTACTT
*
19352713 CACTGTAACTTCAGGAAGATAAGATCTATAACTTCAACCTGCTC
1 CACTGCAACTTCAGGAAGATAAGATCTATAACTTCAACCTGCTC
** * * ** * *
19352757 CACTGCAACTTCAAAAAGATAAGGTTTATGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGAAGATAAGATCTATAACTTCAACCTGCTC
* *
19352801 CATTACAACTTCAAGG-AGATAAGAT
1 CACTGCAACTTC-AGGAAGATAAGAT
19352826 TTGCTACGAT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (44 bp):
CACTGCAACTTCAGGAAGATAAGATCTATAACTTCAACCTGCTC
Found at i:19359359 original size:23 final size:23
Alignment explanation
Indices: 19359333--19359377 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19359323 TGGGTATGTG
*
19359333 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
19359356 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
19359378 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:19361194 original size:26 final size:24
Alignment explanation
Indices: 19361165--19361213 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19361155 TTATTATAAT
19361165 GAATTAACATTGGCACTATGTGTGCG
1 GAATTAA-A-TGGCACTATGTGTGCG
* *
19361191 GAATTAAATGTCACTTTGTGTGC
1 GAATTAAATGGCACTATGTGTGC
19361214 AGATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (24 bp):
GAATTAAATGGCACTATGTGTGCG
Found at i:19361290 original size:94 final size:94
Alignment explanation
Indices: 19361138--19361377 Score: 444
Period size: 94 Copynumber: 2.6 Consensus size: 94
19361128 TATGTTAATT
* *
19361138 GAAGTAAGTTAATTGCCTTATTATAATGAATTAACATTGGCACTATGTGTGCGGAATTAAATGTC
1 GAAGTAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGAAATTAAATGTC
19361203 ACTTTGTGTGCAGATTTTATATGCTATTC
66 ACTTTGTGTGCAGATTTTATATGCTATTC
*
19361232 GAAGTAAGTTAATTGCCTTATTATAATGAGTTAGCATTGGCACTATGTGTGCGAAATTAAATGTC
1 GAAGTAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGAAATTAAATGTC
19361297 ACTTTGTGTGCAGATTTTATATGCTATTC
66 ACTTTGTGTGCAGATTTTATATGCTATTC
*
19361326 GAAGTAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATATGTGC
1 GAAGTAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC
19361378 AGATTTGAAT
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 141 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (94 bp):
GAAGTAAGTTAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGAAATTAAATGTC
ACTTTGTGTGCAGATTTTATATGCTATTC
Found at i:19361444 original size:24 final size:24
Alignment explanation
Indices: 19361412--19361475 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
19361402 GAAAATTTTA
* *
19361412 GGCACTATGTGTGCG-GTTTAGTAT
1 GGCACTATGTGTGCGAGCTTAAT-T
19361436 GGCACTATGTGTGCGAGCTTAATT
1 GGCACTATGTGTGCGAGCTTAATT
*
19361460 AGCACTATGTGTGCGA
1 GGCACTATGTGTGCGA
19361476 ATTCGGGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (24 bp):
GGCACTATGTGTGCGAGCTTAATT
Found at i:19375344 original size:53 final size:53
Alignment explanation
Indices: 19375218--19375325 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
19375208 AAATAAAATA
19375218 ACAATGATGATAATAAAAAATGTACCAATAAAAACATGTGTAAAATCCAATTT
1 ACAATGATGATAATAAAAAATGTACCAATAAAAACATGTGTAAAATCCAATTT
* * *
19375271 ACAATGATGATAATAAAAAATGTACCGATAAAAGCATGTGTACAATCCAATTT
1 ACAATGATGATAATAAAAAATGTACCAATAAAAACATGTGTAAAATCCAATTT
19375324 AC
1 AC
19375326 GAGTATGTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (53 bp):
ACAATGATGATAATAAAAAATGTACCAATAAAAACATGTGTAAAATCCAATTT
Found at i:19375355 original size:15 final size:15
Alignment explanation
Indices: 19375335--19375364 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19375325 CGAGTATGTG
19375335 TAAAAAAAATAAAAA
1 TAAAAAAAATAAAAA
*
19375350 TAAAAATAATAAAAA
1 TAAAAAAAATAAAAA
19375365 CAAATATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:19375460 original size:19 final size:20
Alignment explanation
Indices: 19375436--19375488 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
19375426 CAAAGGCACA
19375436 AAAAGAAAATAAAA-AAGAT
1 AAAAGAAAATAAAACAAGAT
*
19375455 AAAAGAAAA-AAAAGCACGAT
1 AAAAGAAAATAAAA-CAAGAT
*
19375475 AAAGGAAAATAAAA
1 AAAAGAAAATAAAA
19375489 TAAAAAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 12 0.41
21 4 0.14
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAGAAAATAAAACAAGAT
Found at i:19375544 original size:4 final size:4
Alignment explanation
Indices: 19375519--19375560 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
19375509 TAAAAAATGG
*
19375519 TAAA -AAA T-AA TAAA TAAG TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
19375561 GGACTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:19381995 original size:16 final size:18
Alignment explanation
Indices: 19381959--19381995 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19381949 TAGTGTTTTG
*
19381959 TATTTTGTTATAGTTATT
1 TATTTTGTTATAGTAATT
19381977 TATTTTGTTA-A-TAATT
1 TATTTTGTTATAGTAATT
19381993 TAT
1 TAT
19381996 GGGATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
TATTTTGTTATAGTAATT
Found at i:19382185 original size:104 final size:106
Alignment explanation
Indices: 19382023--19382430 Score: 537
Period size: 106 Copynumber: 3.9 Consensus size: 106
19382013 TGATAGTGTT
* * * *
19382023 TAGTGTTTTAG-GGTATTAGTGTATTGTGGTTTTTTTAATAATATATTTTTAAAAAATAATTTTA
1 TAGTG-TTTAGTGGTATTAGTGTATTAT-GATTTTTTAGTAATATATTTTAAAAAAATAATTTTA
19382087 TAGCTATTTTATTAGTAATTTATGATTAGGTTACATAAATTGC
64 TAGCTATTTTATTAGTAATTTATGATTAGGTTACATAAATTGC
* *
19382130 TAGTGTTTAGTGGT-TTAGTGTATTATGA-TTTTTAGTAATGTATTTAAAAAAAATAATTTTATA
1 TAGTGTTTAGTGGTATTAGTGTATTATGATTTTTTAGTAATATATTTTAAAAAAATAATTTTATA
* * *
19382193 GTTATTTTGTTAGTTATTTATGATTAGGTTACATAAATTGC
66 GCTATTTTATTAGTAATTTATGATTAGGTTACATAAATTGC
*
19382234 TA--G-TTAGT-GTATTAGTGTATTGTGATTTTTTTAGTAATAATATATTTTAAAAAAATAATTT
1 TAGTGTTTAGTGGTATTAGTGTATTATGA-TTTTTTAG---TAATATATTTTAAAAAAATAATTT
* *
19382295 TATAGCTATTTTATTAGTAATTTATGATTAGGTTATATAAATTGT
62 TATAGCTATTTTATTAGTAATTTATGATTAGGTTACATAAATTGC
* *
19382340 TAGTGTTTAGTGGT-TTAGTGTATTATGATTTTTTAGTAATGTA-TTTAAAAAAATAATTTTTTA
1 TAGTGTTTAGTGGTATTAGTGTATTATGATTTTTTAGTAATATATTTTAAAAAAATAATTTTATA
* *
19382403 GTTATTTTGTGTTAGTAATTTATGATTA
66 GCTA-TTT-TATTAGTAATTTATGATTA
19382431 TAAATTTTAG
Statistics
Matches: 266, Mismatches: 22, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
100 2 0.01
101 18 0.07
102 1 0.00
103 7 0.03
104 93 0.35
105 10 0.04
106 98 0.37
107 8 0.03
108 9 0.03
109 18 0.07
110 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.51
Consensus pattern (106 bp):
TAGTGTTTAGTGGTATTAGTGTATTATGATTTTTTAGTAATATATTTTAAAAAAATAATTTTATA
GCTATTTTATTAGTAATTTATGATTAGGTTACATAAATTGC
Found at i:19382359 original size:210 final size:209
Alignment explanation
Indices: 19382030--19382430 Score: 682
Period size: 210 Copynumber: 1.9 Consensus size: 209
19382020 GTTTAGTGTT
*
19382030 TTAGGGTATTAGTGTATTGTGGTTTTTTTAATAATATATTTTTAAAAAATAATTTTATAGCTATT
1 TTAGGGTATTAGTGTATTGTGGTTTTTTTAATAATATATTTTAAAAAAATAATTTTATAGCTATT
19382095 TTATTAGTAATTTATGATTAGGTTACATAAATTGCTAGTGTTTAGTGGTTTAGTGTATTATGA-T
66 TTATTAGTAATTTATGATTAGGTTACATAAATTGCTAGTGTTTAGTGGTTTAGTGTATTATGATT
*
19382159 TTTTAGTAATGTATTTAAAAAAAATAATTTTATAGTTA-TTT-TGTTAGTTATTTATGATTAGGT
131 TTTTAGTAATGTATTT-AAAAAAATAATTTTATAGTTATTTTGTGTTAGTAATTTATGATTAGGT
19382222 TACATAAATTGCTAG
195 TACATAAATTGCTAG
* *
19382237 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATAATATATTTTAAAAAAATAATTTTATAGCT
1 TTAGGGTATTAGTGTATTGTG-GTTTTTT--TAATAATATATTTTAAAAAAATAATTTTATAGCT
* *
19382302 ATTTTATTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTATG
63 ATTTTATTAGTAATTTATGATTAGGTTACATAAATTGCTAGTGTTTAGTGGTTTAGTGTATTATG
*
19382367 ATTTTTTAGTAATGTATTTAAAAAAATAATTTTTTAGTTATTTTGTGTTAGTAATTTATGATTA
128 ATTTTTTAGTAATGTATTTAAAAAAATAATTTTATAGTTATTTTGTGTTAGTAATTTATGATTA
19382431 TAAATTTTAG
Statistics
Matches: 181, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
207 20 0.11
208 6 0.03
210 117 0.65
211 20 0.11
212 18 0.10
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.51
Consensus pattern (209 bp):
TTAGGGTATTAGTGTATTGTGGTTTTTTTAATAATATATTTTAAAAAAATAATTTTATAGCTATT
TTATTAGTAATTTATGATTAGGTTACATAAATTGCTAGTGTTTAGTGGTTTAGTGTATTATGATT
TTTTAGTAATGTATTTAAAAAAATAATTTTATAGTTATTTTGTGTTAGTAATTTATGATTAGGTT
ACATAAATTGCTAG
Found at i:19382487 original size:104 final size:102
Alignment explanation
Indices: 19382038--19382472 Score: 405
Period size: 104 Copynumber: 4.2 Consensus size: 102
19382028 TTTTAGGGTA
* * * *
19382038 TTAGTGTATTGTGGTTTTTTTAATAA-TATATTTTTAAAAAATAATTTTATAGCTATTTTATTAG
1 TTAGTGTATTGTGATTTTTTTAGTAATTGTA-TTTAAAAAAATAATTTTATAGCTATTTTATTAG
* * *
19382102 TAATTTATGATTAGGTTACATAAATTGCTAGTGTTTAGTGGT
65 TAATTTATG--TA-G-TATATAAATTGTTAGTGTTTAGTAGT
* * *
19382144 TTAGTGTATTATGA--TTTTTAGTAA-TGTATTTAAAAAAAATAATTTTATAGTTATTTTGTTAG
1 TTAGTGTATTGTGATTTTTTTAGTAATTGTATTT-AAAAAAATAATTTTATAGCTATTTTATTAG
* * *
19382206 TTATTTATGATTAGGTTACATAAATTGCTA--G-TTAGT-GT
65 TAATTTATG--TA-G-TATATAAATTGTTAGTGTTTAGTAGT
*
19382244 ATTAGTGTATTGTGATTTTTTTAGTAATAATATATTTTAAAAAAATAATTTTATAGCTATTTTAT
1 -TTAGTGTATTGTGATTTTTTTAGTAAT--TGTA-TTTAAAAAAATAATTTTATAGCTATTTTAT
*
19382309 TAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGT
62 TAGTAATTTATG--TA-G-TATATAAATTGTTAGTGTTTAGTAGT
* * * *
19382354 TTAGTGTATTATGA-TTTTTTAGTAA-TGTATTTAAAAAAATAATTTTTTAGTTATTTTGTGTTA
1 TTAGTGTATTGTGATTTTTTTAGTAATTGTATTTAAAAAAATAATTTTATAGCTA-TTT-TATTA
19382417 GTAATTTATG-A-T-TATAAATT-TTAGTGTTTA-TAGT
64 GTAATTTATGTAGTATATAAATTGTTAGTGTTTAGTAGT
*
19382451 TTAGTGTTTTGTGATTTTTTTA
1 TTAGTGTATTGTGATTTTTTTA
19382473 ATGTAATTTC
Statistics
Matches: 291, Mismatches: 23, Indels: 38
0.83 0.07 0.11
Matches are distributed among these distances:
97 15 0.05
98 17 0.06
99 8 0.03
100 3 0.01
101 18 0.06
102 1 0.00
103 14 0.05
104 90 0.31
105 6 0.02
106 84 0.29
107 3 0.01
108 12 0.04
109 18 0.06
110 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.52
Consensus pattern (102 bp):
TTAGTGTATTGTGATTTTTTTAGTAATTGTATTTAAAAAAATAATTTTATAGCTATTTTATTAGT
AATTTATGTAGTATATAAATTGTTAGTGTTTAGTAGT
Found at i:19385162 original size:19 final size:19
Alignment explanation
Indices: 19385140--19385179 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19385130 AGAGAATGAG
19385140 TATTAAAAACAATCAATTT
1 TATTAAAAACAATCAATTT
*
19385159 TATTAAAAACAATTAATTT
1 TATTAAAAACAATCAATTT
19385178 TA
1 TA
19385180 AAATACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
TATTAAAAACAATCAATTT
Found at i:19388232 original size:24 final size:24
Alignment explanation
Indices: 19388187--19388232 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19388177 ACTTCTGTTC
* * *
19388187 TGCTAAATTTTGTGTTTTTTGCAA
1 TGCTAAATTTTCTGTATGTTGCAA
19388211 TGCTAAATTTTCTGTATGTTGC
1 TGCTAAATTTTCTGTATGTTGC
19388233 TCATCTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TGCTAAATTTTCTGTATGTTGCAA
Found at i:19388967 original size:11 final size:11
Alignment explanation
Indices: 19388918--19388974 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
19388908 TAAATTAATC
19388918 AAAATTTTT-A
1 AAAATTTTTAA
19388928 AAAATTTTGTAA
1 AAAATTTT-TAA
*
19388940 ATAAA-TATTAA
1 A-AAATTTTTAA
19388951 ATAAATTTTTAA
1 A-AAATTTTTAA
19388963 AAAATTTATTAA
1 AAAATTT-TTAA
19388975 TATTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 8 0.20
11 15 0.38
12 14 0.35
13 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AAAATTTTTAA
Found at i:19403203 original size:37 final size:40
Alignment explanation
Indices: 19403107--19403246 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 40
19403097 AACATACTAG
* * * *
19403107 TTTGGCACCCAGTGCCTTATCAGATAATTCGAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAATCAAAGTAATAA
* ** *
19403147 TTTGACACCCAGTATCTCATCGGCTAAATCAAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAATCAAAGTAATAA
* * * *
19403185 -TTGGCACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAA
1 TTTGGCACCCAGTGCCTCATCGGATAAAT-CAAAGTAATAA
* * * *
19403225 ATTGACACCCAATGTCTCATCG
1 TTTGGCACCCAGTGCCTCATCG
19403247 ACTCGAAGTC
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 22 0.29
38 7 0.09
39 1 0.01
40 29 0.38
41 18 0.23
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAATCAAAGTAATAA
Found at i:19403234 original size:41 final size:40
Alignment explanation
Indices: 19403112--19403247 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 40
19403102 ACTAGTTTGG
* * *
19403112 CACCCAGTGCCTTATC-AGA-TAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGA-ATTAA-TCGAAGTAGTAAATTGA
** ** * *
19403152 CACCCAGTATCTCATCGGCTAAATC-AA--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATTAATCGAAGTAGTAAATTGA
19403189 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAAT-CGAAGTAGTAAATTGA
* *
19403230 CACCCAATGTCTCATCGA
1 CACCCAGTGCCTCATCGA
19403248 CTCGAAGTCG
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
37 26 0.36
38 1 0.01
39 4 0.05
40 15 0.21
41 27 0.37
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATTAATCGAAGTAGTAAATTGA
Found at i:19411970 original size:43 final size:45
Alignment explanation
Indices: 19411908--19412002 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 45
19411898 CTGCTTTTGG
** *
19411908 AGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCTACCTCAGAA
1 AGATAAGATCTTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAA
*
19411953 AGATAAGA-C-TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAG
1 AGATAAGATCTTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAA
19411996 AGATAAG
1 AGATAAG
19412003 GCCAGTGGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 37 0.80
44 1 0.02
45 8 0.17
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (45 bp):
AGATAAGATCTTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAA
Found at i:19413660 original size:21 final size:20
Alignment explanation
Indices: 19413636--19413678 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
19413626 TCATTCATTT
* *
19413636 AACAAATCCATAACATGATCA
1 AACAAACCCAAAACATG-TCA
*
19413657 AACACACCCAAAACATGTCA
1 AACAAACCCAAAACATGTCA
19413677 AA
1 AA
19413679 ACAATCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.53, C:0.28, G:0.05, T:0.14
Consensus pattern (20 bp):
AACAAACCCAAAACATGTCA
Found at i:19414382 original size:40 final size:40
Alignment explanation
Indices: 19414323--19414399 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
19414313 AACACACCAG
* **
19414323 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
19414363 TTTGACACCTAGTGTCTCATCGGCTAAACCGAAGTAA
1 TTTGACACCCAGTGCCTCATCGGATAAACCGAAGTAA
19414400 ATTAACATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:19414539 original size:21 final size:21
Alignment explanation
Indices: 19414515--19414554 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19414505 CATGCCATCT
19414515 ATATCCGACTCAACCCGATTA
1 ATATCCGACTCAACCCGATTA
19414536 ATATCCGACTCAACCCGAT
1 ATATCCGACTCAACCCGAT
19414555 ACAGTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.23
Consensus pattern (21 bp):
ATATCCGACTCAACCCGATTA
Found at i:19426341 original size:25 final size:25
Alignment explanation
Indices: 19426313--19426363 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19426303 TTCCTTATAA
**
19426313 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
19426338 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
19426363 A
1 A
19426364 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:19426362 original size:12 final size:12
Alignment explanation
Indices: 19426316--19426363 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
19426306 CTTATAAACT
19426316 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
19426328 TTCTATTAGGACT
1 TTAAATTAGGA-A
19426341 TTAAATTAGGAA
1 TTAAATTAGGAA
*
19426353 TTAGATTAGGA
1 TTAAATTAGGA
19426364 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:19442251 original size:21 final size:21
Alignment explanation
Indices: 19442227--19442270 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19442217 GTAACATTAA
19442227 ACTAAAGATTAAAGAGTGATT
1 ACTAAAGATTAAAGAGTGATT
19442248 ACTAAAGATTAAAGAGTGATT
1 ACTAAAGATTAAAGAGTGATT
19442269 AC
1 AC
19442271 AACTACTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (21 bp):
ACTAAAGATTAAAGAGTGATT
Found at i:19447609 original size:34 final size:34
Alignment explanation
Indices: 19447569--19447645 Score: 145
Period size: 34 Copynumber: 2.2 Consensus size: 34
19447559 CAAACATACG
19447569 AAGTAATAATTAAATAATGCATGATATACAAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAAA
19447603 AAGTAATAATTAAATAATGCATGATATACAAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAAA
19447637 AGAGTAATA
1 A-AGTAATA
19447646 CAATATCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 35 0.83
35 7 0.17
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.26
Consensus pattern (34 bp):
AAGTAATAATTAAATAATGCATGATATACAAAAA
Found at i:19447990 original size:19 final size:19
Alignment explanation
Indices: 19447931--19447994 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
19447921 AAAAGAATTT
* *
19447931 ATAAAATAACACATAATAT
1 ATAAAATAATACATAATAA
**
19447950 A-AAAAT-AT-CATTTTAA
1 ATAAAATAATACATAATAA
19447966 AGTAAAATAATACATAATAA
1 A-TAAAATAATACATAATAA
19447986 AT-AAATAAT
1 ATAAAATAAT
19447995 TAATAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 17 0.49
19 4 0.11
20 7 0.20
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAATAATACATAATAA
Found at i:19450300 original size:16 final size:15
Alignment explanation
Indices: 19450279--19450313 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
19450269 TCATAAACTG
19450279 AAATAAAAAATATAAA
1 AAATAAAAAATA-AAA
19450295 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
19450310 AAAT
1 AAAT
19450314 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:19450981 original size:35 final size:35
Alignment explanation
Indices: 19450935--19451004 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
19450925 TCTCTCGGCC
19450935 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
1 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
19450970 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
1 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
19451005 CCTAGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (35 bp):
TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
Found at i:19455230 original size:16 final size:16
Alignment explanation
Indices: 19455191--19455264 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
19455181 AATTTCCCAT
*
19455191 TTTCTTTCTTT-TCTCC
1 TTTCTTTCTTTCTCT-A
19455207 TTTCTTTCTTTC-CTA
1 TTTCTTTCTTTCTCTA
*
19455222 TTTCGTTTCATTCTCTA
1 TTTC-TTTCTTTCTCTA
*
19455239 TTTCTTTCTTTATCT-
1 TTTCTTTCTTTCTCTA
*
19455254 TTTGTTTCTTT
1 TTTCTTTCTTT
19455265 ATTTTATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
15 14 0.28
16 29 0.58
17 7 0.14
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCTTTCTTTCTCTA
Found at i:19455324 original size:15 final size:15
Alignment explanation
Indices: 19455288--19455317 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19455278 TATGTTTAAT
19455288 TAATATAATATATTA
1 TAATATAATATATTA
19455303 TAATATAATAATATT
1 TAATATAAT-ATATT
19455318 TTATATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATAATATATTA
Found at i:19457463 original size:64 final size:64
Alignment explanation
Indices: 19457257--19457573 Score: 284
Period size: 64 Copynumber: 4.9 Consensus size: 64
19457247 CATATTTTTG
* * * *
19457257 GCTCTCTTGTAC-ACATGGTGA-ACACTTAGTACCACCCATGTGACCTAGCCAC-TTTATCTCGT
1 GCTCTCTTGT-CTACATGGT-ATACACATAGTATCACCCATGTGACCTAGCTACATATATCTCGT
19457319 A
64 A
* * * * * * * * ** *
19457320 GCTCTCTTGTTTACATGGTGTCCTTCACTTGGAACCACACATGAAACCTAGCTACATTTATCTCG
1 GCTCTCTTGTCTACAT-G-GT-ATACACATAGTATCACCCATGTGACCTAGCTACATATATCTCG
19457385 TA
63 TA
*
19457387 GCTCTCTTGTCTACATGGTATACACATAGTATCACCCATGTGACCTAGCTACATATATCCCGTA
1 GCTCTCTTGTCTACATGGTATACACATAGTATCACCCATGTGACCTAGCTACATATATCTCGTA
* * * *
19457451 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGATCTAGCTACCTCATAATGTCTC
1 GCTCTCTTGTCTACATGGTATACACATAGTATCACCCATGTGACCTAGCTA---CAT-ATATCTC
19457516 GTA
62 GTA
** * *
19457519 GCTCTCTTGTAC-ACATGGTATACATC-CCGTATTACACATGTGACCTAGCTACATA
1 GCTCTCTTGT-CTACATGGTATACA-CATAGTATCACCCATGTGACCTAGCTACATA
19457574 CCATCTGTAT
Statistics
Matches: 209, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
63 14 0.07
64 84 0.40
65 7 0.03
66 25 0.12
67 29 0.14
68 48 0.23
69 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTATACACATAGTATCACCCATGTGACCTAGCTACATATATCTCGTA
Found at i:19457537 original size:132 final size:128
Alignment explanation
Indices: 19457257--19457573 Score: 327
Period size: 132 Copynumber: 2.4 Consensus size: 128
19457247 CATATTTTTG
* * * *
19457257 GCTCTCTTGTACACATGGTGA-ACACTTAGTACCACCCATGTGACCTAGCCAC-TTTATCTCGTA
1 GCTCTCTTGTACACATGGT-ATACAC-TAGTATCACCCATGTGACCTAGCTACATATATCCCGTA
* * * * *
19457320 GCTCTCTTGTTTACATGGTGTCCTTCACTTGGAACCACACATGAAACCTAGCTACATTTATCTCG
64 GCTCTCTTGTCTACATGGTG--CTACACATAGAACCACACATGAAACCTAGCTACATATATCTCG
19457385 TA
127 TA
19457387 GCTCTCTTGT-CTACATGGTATACACATAGTATCACCCATGTGACCTAGCTACATATATCCCGTA
1 GCTCTCTTGTAC-ACATGGTATACAC-TAGTATCACCCATGTGACCTAGCTACATATATCCCGTA
* * * ** * *
19457451 GCTCTCTTGTCTACATGGTG-TACACATAGTATCACCCATGCGATCTAGCTACCTCATAATGTCT
64 GCTCTCTTGTCTACATGGTGCTACACATAGAACCACACATGAAACCTAGCTA---CAT-ATATCT
19457515 CGTA
125 CGTA
** * *
19457519 GCTCTCTTGTACACATGGTATACATCCCGTATTACACATGTGACCTAGCTACATA
1 GCTCTCTTGTACACATGGTATACA-CTAGTATCACCCATGTGACCTAGCTACATA
19457574 CCATCTGTAT
Statistics
Matches: 157, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
128 22 0.14
129 2 0.01
130 45 0.29
131 31 0.20
132 55 0.35
133 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (128 bp):
GCTCTCTTGTACACATGGTATACACTAGTATCACCCATGTGACCTAGCTACATATATCCCGTAGC
TCTCTTGTCTACATGGTGCTACACATAGAACCACACATGAAACCTAGCTACATATATCTCGTA
Found at i:19471932 original size:44 final size:43
Alignment explanation
Indices: 19471862--19472019 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 43
19471852 ATGTGTTATT
* ** * *
19471862 GTGTAAGACCACGTCTAAGACGTTGGCACCGACT-TCTATTTCAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGA-TATCTATTT-AC
19471906 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATCTGATTT-C
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATCT-ATTTAC
* * * * * *
19471948 GTGTAAGACCCTCTCTGGGACAGTGGCATCGATGTTTAATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATCTATTTAC
* * *
19471991 ATGTAAGACCATATCTGGGACGTTGGCAT
1 GTGTAAGACCATGTCTGGGACATTGGCAT
19472020 TGTATATGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 33 0.35
43 31 0.33
44 30 0.32
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGATATCTATTTAC
Found at i:19471965 original size:42 final size:42
Alignment explanation
Indices: 19471904--19472024 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 42
19471894 CTTCTATTTC
* *
19471904 ACGTGTAAGACCATGTCTGGGACATTGGCATCGTATCTGATT
1 ACGTGTAAGACCATATCTGGGACATTGGCATCGTATCTAATT
* * * * * *
19471946 TCGTGTAAGACCCTCTCTGGGACAGTGGCATCGATGTTTAATT
1 ACGTGTAAGACCATATCTGGGACATTGGCATCG-TATCTAATT
* * *
19471989 ACATGTAAGACCATATCTGGGACGTTGGCATTGTAT
1 ACGTGTAAGACCATATCTGGGACATTGGCATCGTAT
19472025 ATGCTTTCTG
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 31 0.49
43 32 0.51
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (42 bp):
ACGTGTAAGACCATATCTGGGACATTGGCATCGTATCTAATT
Found at i:19478510 original size:21 final size:22
Alignment explanation
Indices: 19478481--19478527 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
19478471 CAGAAGGAGT
*
19478481 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19478503 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19478524 GAGT
1 GAGT
19478528 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:19486351 original size:2 final size:2
Alignment explanation
Indices: 19486338--19486393 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
19486328 CTAACGAATA
*
19486338 TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19486380 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
19486394 AGAGAGAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19490710 original size:3 final size:3
Alignment explanation
Indices: 19490702--19490729 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19490692 GCTAGTTAAC
19490702 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
19490730 AGAGGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19490909 original size:3 final size:3
Alignment explanation
Indices: 19490901--19490925 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19490891 AGAATTTTTC
19490901 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
19490926 GCATAGCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:19493187 original size:3 final size:3
Alignment explanation
Indices: 19493179--19493203 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19493169 AAATGTATAT
19493179 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
19493204 AGAAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19493704 original size:7 final size:7
Alignment explanation
Indices: 19493692--19493731 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
19493682 TAAAAATTTA
*
19493692 AATATTT
1 AATATTC
19493699 AATATTC
1 AATATTC
19493706 AATATTC
1 AATATTC
19493713 AATATTC
1 AATATTC
19493720 AATATTC
1 AATATTC
19493727 AATAT
1 AATAT
19493732 GAAATTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (7 bp):
AATATTC
Found at i:19497536 original size:22 final size:22
Alignment explanation
Indices: 19497505--19497546 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19497495 CTTTATTCCT
* *
19497505 AATTTCTATATATTAATAAAGG
1 AATTTATATAGATTAATAAAGG
19497527 AATTTATATAGATTAATAAA
1 AATTTATATAGATTAATAAA
19497547 TTAGCATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTTATATAGATTAATAAAGG
Found at i:19504456 original size:28 final size:29
Alignment explanation
Indices: 19504424--19504492 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
19504414 AAGTAATTAA
* *
19504424 TATTAATTATTTAAA-ATTTAATTAAAAT
1 TATTAATTATTTAAATATTTAAATAAAAC
*
19504452 TATT-A-TATTTTAAATATTTAAATATAAC
1 TATTAATTA-TTTAAATATTTAAATAAAAC
*
19504480 CATTAATTATTTA
1 TATTAATTATTTA
19504493 TAAAAGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.06
27 7 0.21
28 17 0.52
29 5 0.15
30 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTAATTATTTAAATATTTAAATAAAAC
Found at i:19521060 original size:176 final size:176
Alignment explanation
Indices: 19520757--19521246 Score: 746
Period size: 176 Copynumber: 2.8 Consensus size: 176
19520747 TTTCTTCTTG
* *
19520757 AAGTTGCAGGAAGCAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGAAGATCG
1 AAGTTGCAGGAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCG
* *
19520822 AGGATGGCGAGCCTTATCTCCATGTATCGGTTATGGAGTAGATTTTAGCCACTAACCTTATCTCT
66 AGGATGGCGAGCCTTATCTCTATGTATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCT
*
19520887 TTGAAGTTGCAGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTA
131 TTGAAGTTGCAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTA
* *
19520933 AAGTTACAAGAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCG
1 AAGTTGCAGGAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCG
*
19520998 AGGATGGCGAGCCTTATCTCTATGCATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCT
66 AGGATGGCGAGCCTTATCTCTATGTATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCT
*
19521063 TTGAAGTTGCAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTG
131 TTGAAGTTGCAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTA
* * *
19521109 AAGTTGCAGGAAGCAGACTGAAAACTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCG
1 AAGTTGCAGGAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCG
* * ** * * ** * ** * *
19521174 AAGACGGCGAATCTTATCTGTATGTATTGGCAATGGAGCAGATTTAAGTTACTAGCCTTATCTCC
66 AGGATGGCGAGCCTTATCTCTATGTATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCT
*
19521239 CTGAAGTT
131 TTGAAGTT
19521247 TCAGTGGAGC
Statistics
Matches: 285, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 285 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (176 bp):
AAGTTGCAGGAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCG
AGGATGGCGAGCCTTATCTCTATGTATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCT
TTGAAGTTGCAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTA
Found at i:19522788 original size:21 final size:22
Alignment explanation
Indices: 19522739--19522798 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
19522729 TTCTCGTATT
* * *
19522739 ATTTTATGTAAATATTTTCTTAA
1 ATTTTATATATATATATT-TTAA
19522762 ATTTTATATATATATATTTTAA
1 ATTTTATATATATATATTTTAA
*
19522784 A-TTTATTTATATATA
1 ATTTTATATATATATA
19522799 ATTTGGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 15 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTATATATATATATTTTAA
Found at i:19526109 original size:21 final size:21
Alignment explanation
Indices: 19526060--19526110 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
19526050 TTAAAATTTA
*
19526060 AAATA-TAAATGTTAAATTCT
1 AAATATTAAATCTTAAATTCT
* *
19526080 AACTCTTAAATCTTAAATAT-T
1 AAATATTAAATCTTAAAT-TCT
19526101 AAATATTAAA
1 AAATATTAAA
19526111 GTTTAATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATTAAATCTTAAATTCT
Found at i:19526461 original size:12 final size:12
Alignment explanation
Indices: 19526446--19526472 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19526436 ATACATTTAA
19526446 AAATATTAAAAC
1 AAATATTAAAAC
19526458 AAATATTAAAAC
1 AAATATTAAAAC
19526470 AAA
1 AAA
19526473 AAACAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:19527048 original size:22 final size:21
Alignment explanation
Indices: 19527005--19527049 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
19526995 TAATATTATT
* *
19527005 ATATTAATTTATAATTTTAAA
1 ATATTAATTTATAATATCAAA
19527026 ATATTAATATTATAATATCAAA
1 ATATTAAT-TTATAATATCAAA
19527048 AT
1 AT
19527050 TCTTCAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTAATTTATAATATCAAA
Found at i:19527622 original size:23 final size:26
Alignment explanation
Indices: 19527569--19527629 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 26
19527559 TGCAGAAACT
*
19527569 TATGACATATTTTAACTTGATATAGAA
1 TATGA-ATATTTCAACTTGATATAGAA
19527596 TATGAATATTTCAA-TT-ATATA-AA
1 TATGAATATTTCAACTTGATATAGAA
*
19527619 TATGAGTATTT
1 TATGAATATTT
19527630 GTTTAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 12 0.38
24 5 0.16
25 2 0.06
26 8 0.25
27 5 0.16
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (26 bp):
TATGAATATTTCAACTTGATATAGAA
Found at i:19527764 original size:22 final size:23
Alignment explanation
Indices: 19527725--19527773 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
19527715 TATTAAGTTT
*
19527725 ATATATGATATTAATTATTACAAA
1 ATATATAATATT-ATTATTACAAA
*
19527749 ATATATAATATT-TTATTATAAA
1 ATATATAATATTATTATTACAAA
19527771 ATA
1 ATA
19527774 AATTTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATATAATATTATTATTACAAA
Found at i:19535506 original size:8 final size:8
Alignment explanation
Indices: 19535485--19535514 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
19535475 AATTTCTAGG
19535485 AAAAAATT
1 AAAAAATT
19535493 ATAAAAATT
1 A-AAAAATT
19535502 AAAAAATT
1 AAAAAATT
19535510 AAAAA
1 AAAAA
19535515 TATGTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:19536326 original size:24 final size:23
Alignment explanation
Indices: 19536299--19536357 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
19536289 TTATATAATT
*
19536299 ATTTTATATTCATATTATACTTTAA
1 ATTTTATATTCAT-TCATA-TTTAA
* *
19536324 TTTTTTTATTCATTCATATTTAAA
1 ATTTTATATTCATTCATATTT-AA
19536348 ATTTTATATT
1 ATTTTATATT
19536358 TATAAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.11
24 14 0.50
25 11 0.39
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATATTCATTCATATTTAA
Found at i:19536773 original size:27 final size:27
Alignment explanation
Indices: 19536743--19536825 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
19536733 CCCACCCATA
19536743 TTATTTTTTATTATATTTAAAATTTTT
1 TTATTTTTTATTATATTTAAAATTTTT
19536770 TTATTTTATT-TTAATATTTAATAATTTTAT
1 TTATTTT-TTATT-ATATTTAA-AATTTT-T
** *
19536800 ACATTTTTTATT-TATTAAAAATTTTT
1 TTATTTTTTATTATATTTAAAATTTTT
19536826 ATATAGTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 15 0.31
28 16 0.33
29 8 0.17
30 8 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATTTTTTATTATATTTAAAATTTTT
Found at i:19536789 original size:28 final size:28
Alignment explanation
Indices: 19536743--19536825 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 28
19536733 CCCACCCATA
19536743 TTATTTTTTATTATATTTAA-AATTTTT
1 TTATTTTTTATTATATTTAATAATTTTT
19536770 TTATTTTATT-TTAATATTTAATAATTTTAT
1 TTATTTT-TTATT-ATATTTAATAATTTT-T
** *
19536800 ACATTTTTTATT-TA-TTAAAAATTTTT
1 TTATTTTTTATTATATTTAATAATTTTT
19536826 ATATAGTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 19 0.40
28 12 0.25
29 8 0.17
30 8 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (28 bp):
TTATTTTTTATTATATTTAATAATTTTT
Found at i:19538206 original size:39 final size:39
Alignment explanation
Indices: 19538152--19538228 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
19538142 GTTTGCAACC
19538152 CTAAACCCACATGCCTTATTATTTACTTTAATCCTTACA
1 CTAAACCCACATGCCTTATTATTTACTTTAATCCTTACA
19538191 CTAAACCCACATGCCTTATTATTTACTTTAATCCTTAC
1 CTAAACCCACATGCCTTATTATTTACTTTAATCCTTAC
19538229 TGCCAGCTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.39
Consensus pattern (39 bp):
CTAAACCCACATGCCTTATTATTTACTTTAATCCTTACA
Found at i:19543172 original size:76 final size:76
Alignment explanation
Indices: 19543039--19543186 Score: 185
Period size: 76 Copynumber: 1.9 Consensus size: 76
19543029 AACAAAGAGA
* * * * *
19543039 TTGAACCAATTGTATTAGAAACTACACGAAATAGATAAAAATTGAAATTTGGAACAAAAATCAGT
1 TTGAACCAATTGTATTAGAAACTACACGAAAAAGATAAAAATCGAAACTAGGAACAAAAATCAAT
19543104 AGTTGAAGGGG
66 AGTTGAAGGGG
* *
19543115 TTGAACCAATTGTATTA-AAAGCTGCTCGAAACAAG-TAAAAATCGAAAACTAGG-ACAAAAATC
1 TTGAACCAATTGTATTAGAAA-CTACACGAAA-AAGATAAAAATCG-AAACTAGGAACAAAAATC
19543177 AATAGTTGAA
63 AATAGTTGAA
19543187 CAGGTTGTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
75 3 0.05
76 51 0.82
77 8 0.13
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (76 bp):
TTGAACCAATTGTATTAGAAACTACACGAAAAAGATAAAAATCGAAACTAGGAACAAAAATCAAT
AGTTGAAGGGG
Found at i:19549360 original size:16 final size:16
Alignment explanation
Indices: 19549339--19549377 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
19549329 TTTGGTTTGC
19549339 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
**
19549355 TGTAATTTAATAGAGT
1 TGTAATGGAATAGAGT
19549371 TGTAATG
1 TGTAATG
19549378 AGTAATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:19549517 original size:30 final size:31
Alignment explanation
Indices: 19549483--19549540 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
19549473 AAAAATTGAA
19549483 ATGATTAGAATA-CCTTAAAAGAATCTATCT
1 ATGATTAGAATACCCTTAAAAGAATCTATCT
**
19549513 ATGATTAGAATACCCTTAGCAGAATCTA
1 ATGATTAGAATACCCTTAAAAGAATCTA
19549541 CATAAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (31 bp):
ATGATTAGAATACCCTTAAAAGAATCTATCT
Found at i:19549608 original size:13 final size:13
Alignment explanation
Indices: 19549590--19549614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19549580 TTAATCATAT
19549590 TTTAATATAATTA
1 TTTAATATAATTA
19549603 TTTAATATAATT
1 TTTAATATAATT
19549615 TAATAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATATAATTA
Found at i:19562590 original size:46 final size:46
Alignment explanation
Indices: 19562523--19562657 Score: 182
Period size: 46 Copynumber: 2.9 Consensus size: 46
19562513 GTGTGCTCTC
*
19562523 TGATATGAAATGTATAAGATCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
19562569 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
* * * * * * *
19562615 TGACA-GAAAATGAGTAAGACCATAGTTGGAAGACACTATGGCA
1 TGATATG-AAATGAATAAGATCATGGTTGAAAGATACCATGGCA
19562658 TCATATCAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
Found at i:19567213 original size:23 final size:21
Alignment explanation
Indices: 19567162--19567215 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
19567152 TATTAAATAA
*
19567162 TAATTTAATTTAATTTTTATT
1 TAATTAAATTTAATTTTTATT
19567183 TAATATTAAATTTAAATTTTTTATT
1 T-A-ATTAAATTT-AA-TTTTTATT
19567208 TAATTAAA
1 TAATTAAA
19567216 AATGAAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 14 0.50
24 3 0.11
25 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTAAATTTAATTTTTATT
Found at i:19567218 original size:25 final size:23
Alignment explanation
Indices: 19567168--19567216 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
19567158 ATAATAATTT
*
19567168 AATTTAATTTTTATTTAATATTA
1 AATTTAATTTTTATTTAATATAA
19567191 AATTTAAATTTTTTATTTAAT-TAA
1 AATTT-AA-TTTTTATTTAATATAA
19567215 AA
1 AA
19567217 ATGAAAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTAATTTTTATTTAATATAA
Found at i:19568204 original size:18 final size:18
Alignment explanation
Indices: 19568163--19568206 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19568153 TAAAAACAGA
*
19568163 AGTTAAGTTGACAAAAAT
1 AGTTAAGTTAACAAAAAT
*
19568181 AATTAAGTTAACAAAAA-
1 AGTTAAGTTAACAAAAAT
19568198 ATGTTAAGT
1 A-GTTAAGT
19568207 GACCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (18 bp):
AGTTAAGTTAACAAAAAT
Found at i:19568402 original size:59 final size:61
Alignment explanation
Indices: 19568336--19568496 Score: 159
Period size: 57 Copynumber: 2.7 Consensus size: 61
19568326 TTATTATAAC
* * * * *
19568336 ATTTGGTACTTAAACTTGACATTTTTTTTTCTAATTTTGTGCATAAAATTTTTT-GTCC-A
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAAATTTTTTGGGCCTA
* * * *
19568395 ATTTGGTACTTTAACTTGACA--CTTTTTCCTAATATGGTACCTAAACTTTTTTGGGGCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAAATTTTTT-GGGCCTA
* * * * *
19568455 ATTTGGTACTTGAACTTGGCATTTTTTTCCCTAGTTTGGTAC
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTAC
19568497 CTAAGCTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
57 24 0.29
59 23 0.28
60 20 0.24
62 15 0.18
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (61 bp):
ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAAATTTTTTGGGCCTA
Found at i:19568465 original size:60 final size:63
Alignment explanation
Indices: 19568394--19568509 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 63
19568384 TTTTTTGTCC
*
19568394 AATTTGGTACTTTAACTTGACA-CTTTTT-CCTAATATGGTACCTAAACT-TTTTTGGGGCCT
1 AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTTGGGGCCT
* * * * *
19568454 AATTTGGTACTTGAACTTGGCATTTTTTTCCCTAGTTTGGTACCTAAGCTATTTTT
1 AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTT
19568510 TAGGTTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 20 0.43
61 5 0.11
62 17 0.36
63 5 0.11
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (63 bp):
AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTTGGGGCCT
Found at i:19568985 original size:60 final size:61
Alignment explanation
Indices: 19568908--19569023 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 61
19568898 ATCGAACAAA
* * * *
19568908 AAAAGAAGATTAGATACCAAATTAGGAAAAAGAGTTAAGTTTAGGTATCAAATTAGACACT
1 AAAAGAAGATTAAATACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAGACACT
* ** **
19568969 AAAA-AAGATTAAATACCAACTTTTAAAAAATTGTCAAGTTTAGGTACCAAATTAG
1 AAAAGAAGATTAAATACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAG
19569024 GAAGTGTCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 42 0.91
61 4 0.09
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (61 bp):
AAAAGAAGATTAAATACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAGACACT
Found at i:19569063 original size:31 final size:31
Alignment explanation
Indices: 19568994--19569079 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 31
19568984 CCAACTTTTA
*
19568994 AAAAATTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
*
19569025 ---AAGTGTCAAGTTTAGGTACTAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
**
19569053 AAAAAGTGTCAAGTTTATATACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
19569080 GTTATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 26 0.55
31 21 0.45
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
Found at i:19569469 original size:19 final size:17
Alignment explanation
Indices: 19569445--19569479 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
19569435 ATTGTTAGGA
19569445 TATTGTATAACTTTTATTT
1 TATTGT-TAA-TTTTATTT
19569464 TATTGTTAATTTTATT
1 TATTGTTAATTTTATT
19569480 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTATTT
Found at i:19573723 original size:30 final size:30
Alignment explanation
Indices: 19573672--19573728 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
19573662 GAAAATTTGA
19573672 AATTTAGTTCCTATATTTTTAT-TTTTAGG
1 AATTTAGTTCCTATATTTTTATATTTTAGG
* *
19573701 AATTTAGTTTCTCTACTTTTTATATTTT
1 AATTTAGTTCCTATA-TTTTTATATTTT
19573729 TAAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.54
30 7 0.29
31 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (30 bp):
AATTTAGTTCCTATATTTTTATATTTTAGG
Found at i:19576265 original size:7 final size:7
Alignment explanation
Indices: 19576253--19576278 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19576243 TAGTCGTTTT
19576253 GTATTTA
1 GTATTTA
19576260 GTATTTA
1 GTATTTA
19576267 GTATTTA
1 GTATTTA
19576274 GTATT
1 GTATT
19576279 ATGTATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:19576284 original size:14 final size:13
Alignment explanation
Indices: 19576250--19576284 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
19576240 AAATAGTCGT
19576250 TTTGTATTTAGTA
1 TTTGTATTTAGTA
19576263 TTTAGTATTTAGTA
1 TTT-GTATTTAGTA
19576277 TTATGTAT
1 TT-TGTAT
19576285 ATCAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTGTATTTAGTA
Found at i:19577189 original size:21 final size:21
Alignment explanation
Indices: 19577140--19577191 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
19577130 CACCCACAAC
*
19577140 CGAAGCAATCACAACCCCCGT
1 CGAAGCAACCACAACCCCCGT
*
19577161 CG-AGCAACCACAACCTCCGT
1 CGAAGCAACCACAACCCCCGT
19577181 CGAAGCAACCA
1 CGAAGCAACCA
19577192 ATGAGGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.35, C:0.42, G:0.15, T:0.08
Consensus pattern (21 bp):
CGAAGCAACCACAACCCCCGT
Found at i:19579363 original size:13 final size:13
Alignment explanation
Indices: 19579345--19579371 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19579335 ATTTTATGTT
19579345 TTATTATATTATA
1 TTATTATATTATA
19579358 TTATTATATTATA
1 TTATTATATTATA
19579371 T
1 T
19579372 ACTTAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:19583114 original size:125 final size:126
Alignment explanation
Indices: 19582889--19583266 Score: 454
Period size: 126 Copynumber: 3.0 Consensus size: 126
19582879 GGCCAATCAT
* * * * * *
19582889 GAACTACTGTAGAAAAA-AAGCGTCTATGTGGGAGCTTTTTTCAAAAATTTTGGTGACATTGCAT
1 GAACTACTGTAGAAAAAGAA-CGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCAT
* * * * *
19582953 CCTGCTTGAAGCATTTTTCACACTATTTGTTCAGAAACATCTTCTTAAAAATA-TTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * *
19583014 GAACTACTATAGAAAAAGAACGTCCACGTGGGAGCCTTTTTCTATAATTTTGCTAACAGTGTATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
* * *
19583079 CTGCTTGAAGCGTTTTTGACACTATTTATTTAGAAACGTCTTCTCAAAATTATTTTTTCAC
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * *** * * * *
19583140 GAACTACTGTAGAAAAAGAGCGTCCACATAAAAGATTTTTTCTGTAATTTTGTTGATAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
* * * *
19583205 TTGCTTGAAACGTTTTTGACATTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
19583266 G
1 G
19583267 GTACAAAATA
Statistics
Matches: 213, Mismatches: 38, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
125 97 0.46
126 116 0.54
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:19583397 original size:30 final size:29
Alignment explanation
Indices: 19583352--19583448 Score: 86
Period size: 34 Copynumber: 3.1 Consensus size: 29
19583342 ATTTAACCCT
* *
19583352 AAACCCTACACCCTAATTTAATTTATTTA
1 AAACCATAAACCCTAATTTAATTTATTTA
* *
19583381 AAACCCTAGAATCCTAATTTACTTAATTTATTTA
1 AAACCATA-AACCCTAA--T--TTAATTTATTTA
* *
19583415 GAAATCATAAACCCTAATTTAACTTATTTA
1 -AAACCATAAACCCTAATTTAATTTATTTA
19583445 AAAC
1 AAAC
19583449 ACTAATTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
29 11 0.20
30 17 0.31
32 2 0.04
34 19 0.35
35 6 0.11
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (29 bp):
AAACCATAAACCCTAATTTAATTTATTTA
Found at i:19583407 original size:34 final size:35
Alignment explanation
Indices: 19583369--19583444 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
19583359 ACACCCTAAT
* *
19583369 TTAATTTATTTA-AAACCCTAGAATCCTAATTT-AC
1 TTAATTTATTTAGAAACCATA-AACCCTAATTTAAC
*
19583403 TTAATTTATTTAGAAATCATAAACCCTAATTTAAC
1 TTAATTTATTTAGAAACCATAAACCCTAATTTAAC
19583438 TT-ATTTA
1 TTAATTTA
19583445 AAACACTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 27 0.73
35 10 0.27
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.43
Consensus pattern (35 bp):
TTAATTTATTTAGAAACCATAAACCCTAATTTAAC
Found at i:19583579 original size:34 final size:34
Alignment explanation
Indices: 19583511--19583580 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
19583501 TAGAACCCTA
*
19583511 ACTTAATTTATTTAAAACCTTAAAAACCCCAATTT
1 ACTTAATTTATTTAAAACCCT-AAAACCCCAATTT
*
19583546 ACTTAATTTATTTAACAACCCT-AAACCCTAATTT
1 ACTTAATTTATTTAA-AACCCTAAAACCCCAATTT
19583580 A
1 A
19583581 AATAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 12 0.38
35 15 0.47
36 5 0.16
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.37
Consensus pattern (34 bp):
ACTTAATTTATTTAAAACCCTAAAACCCCAATTT
Found at i:19583587 original size:34 final size:34
Alignment explanation
Indices: 19583514--19583596 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
19583504 AACCCTAACT
* **
19583514 TAATTTATTTAAAACCTTAAAAACCCCAATTTACT
1 TAATTTATTTAAAACCCT-AAAACCCCAATTTAAA
*
19583549 TAATTTATTTAACAACCCT-AAACCCTAATTTAAA
1 TAATTTATTTAA-AACCCTAAAACCCCAATTTAAA
19583583 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
19583597 TAATACTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 4 0.10
34 21 0.50
35 12 0.29
36 5 0.12
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.39
Consensus pattern (34 bp):
TAATTTATTTAAAACCCTAAAACCCCAATTTAAA
Found at i:19588945 original size:28 final size:27
Alignment explanation
Indices: 19588913--19589012 Score: 95
Period size: 28 Copynumber: 3.8 Consensus size: 27
19588903 AAATTTGTTA
*
19588913 TTTTATTTTCAATTTATTTATATTCATT
1 TTTTATTTTCAATTTATATATATTC-TT
19588941 TTTTATTTTC-ATTT-TATATATTCTT
1 TTTTATTTTCAATTTATATATATTCTT
* *
19588966 TATTTTTATTTCAATTT-TATATA---TA
1 T-TTTAT-TTTCAATTTATATATATTCTT
*
19588991 TTTTATTTTCAATATATATATA
1 TTTTATTTTCAATTTATATATA
19589013 CATTAATTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.13
24 10 0.16
25 5 0.08
26 12 0.19
27 8 0.13
28 20 0.32
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTATTTTCAATTTATATATATTCTT
Found at i:19588994 original size:22 final size:22
Alignment explanation
Indices: 19588969--19589012 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19588959 TATTCTTTAT
*
19588969 TTTTA-TTTCAATTTTATATATA
1 TTTTATTTTCAA-TATATATATA
19588991 TTTTATTTTCAATATATATATA
1 TTTTATTTTCAATATATATATA
19589013 CATTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATTTTCAATATATATATA
Found at i:19589021 original size:28 final size:27
Alignment explanation
Indices: 19588910--19589022 Score: 85
Period size: 26 Copynumber: 4.3 Consensus size: 27
19588900 ACTAAATTTG
* *
19588910 TTATTTTATTTTCAATTTATTTATATTCA
1 TTATTTTATTTTCAA--TATATATATACA
* * * *
19588939 TT-TTTTATTTTCATTTTATATATTCT
1 TTATTTTATTTTCAATATATATATACA
*
19588965 TTATTTT-TATTTCAAT-T-T-TATATA
1 TTATTTTAT-TTTCAATATATATATACA
19588989 -TATTTTATTTTCAATATATATATACA
1 TTATTTTATTTTCAATATATATATACA
19589015 TTAATTTT
1 TT-ATTTT
19589023 TTTGAAGTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
23 13 0.19
24 5 0.07
25 2 0.03
26 18 0.27
27 11 0.16
28 16 0.24
29 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTTATTTTCAATATATATATACA
Found at i:19589171 original size:55 final size:55
Alignment explanation
Indices: 19589110--19589219 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
19589100 AAAAAATAGG
19589110 AATGTTTAAGATGAACCCACGTGTCAGCTCAATGCATGTCCACATCAACAAAATC
1 AATGTTTAAGATGAACCCACGTGTCAGCTCAATGCATGTCCACATCAACAAAATC
19589165 AATGTTTAAGATGAACCCACGTGTCAGCTCAATGCATGTCCACATCAACAAAATC
1 AATGTTTAAGATGAACCCACGTGTCAGCTCAATGCATGTCCACATCAACAAAATC
19589220 TTGAAAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (55 bp):
AATGTTTAAGATGAACCCACGTGTCAGCTCAATGCATGTCCACATCAACAAAATC
Found at i:19591069 original size:43 final size:43
Alignment explanation
Indices: 19591008--19591095 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
19590998 TAAAATAGAC
* *
19591008 TAAAATTAGAGTTCTAATATGATTATAATATTGCTAGAATAAT
1 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
19591051 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
1 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
19591094 TA
1 TA
19591096 GAGTTTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (43 bp):
TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
Found at i:19591075 original size:23 final size:22
Alignment explanation
Indices: 19591008--19591080 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
19590998 TAAAATAGAC
19591008 TAAAATTAGAGTTCTAATATGAT
1 TAAAA-TAGAGTTCTAATATGAT
* *
19591031 TATAAT--A-TTGCTAGA-ATAAT
1 TAAAATAGAGTT-CTA-ATATGAT
19591051 TAAAACTAGAGTTCTAATATGAT
1 TAAAA-TAGAGTTCTAATATGAT
*
19591074 TATAATA
1 TAAAATA
19591081 TTCCTAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 15
0.66 0.09 0.26
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 2 0.05
22 4 0.11
23 16 0.42
24 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (22 bp):
TAAAATAGAGTTCTAATATGAT
Found at i:19601478 original size:25 final size:25
Alignment explanation
Indices: 19601450--19601593 Score: 75
Period size: 25 Copynumber: 5.8 Consensus size: 25
19601440 AGCATGTAAC
* * * *
19601450 GGGAAGCTCTTCCGAGCTATATAAT
1 GGGAAGCTCGTACGAGCCAAATAAT
*
19601475 GGGAAGCTCGTACGAGCCAAATATT
1 GGGAAGCTCGTACGAGCCAAATAAT
*
19601500 GGGAAGCTCAAG-A-GAGCC-ATTAATT
1 GGGAAGCTC--GTACGAGCCAAATAA-T
* *
19601525 GGGAAGCTCATGA-GAGCCAAA-CAT
1 GGGAAGCTCGT-ACGAGCCAAATAAT
* * * *
19601549 CGGAATGCTCATAAGAGCTAAATAAT
1 GGGAA-GCTCGTACGAGCCAAATAAT
*
19601575 AGGAAGCTCGTGA-GAGCCA
1 GGGAAGCTCGT-ACGAGCCA
19601594 TTGTGTGTCT
Statistics
Matches: 93, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
24 9 0.10
25 74 0.80
26 9 0.10
27 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
GGGAAGCTCGTACGAGCCAAATAAT
Found at i:19601559 original size:50 final size:50
Alignment explanation
Indices: 19601463--19601593 Score: 135
Period size: 50 Copynumber: 2.6 Consensus size: 50
19601453 AAGCTCTTCC
* * *
19601463 GAGCTATATAATGGGAAGCTCGT-ACGAGCCAAATATTGGGAAGCTCA-AGA
1 GAGCTAAATAATGGGAAGCTCGTGA-GAGCCAAACATTCGGAAGCTCATA-A
* * *
19601513 GAGC-CATTAATTGGGAAGCTCATGAGAGCCAAACA-TCGGAATGCTCATAA
1 GAGCTAAATAA-TGGGAAGCTCGTGAGAGCCAAACATTCGGAA-GCTCATAA
*
19601563 GAGCTAAATAATAGGAAGCTCGTGAGAGCCA
1 GAGCTAAATAATGGGAAGCTCGTGAGAGCCA
19601594 TTGTGTGTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
49 8 0.12
50 52 0.79
51 6 0.09
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (50 bp):
GAGCTAAATAATGGGAAGCTCGTGAGAGCCAAACATTCGGAAGCTCATAA
Found at i:19603618 original size:63 final size:63
Alignment explanation
Indices: 19603519--19603642 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
19603509 CTGATAACTA
* * * *
19603519 TTATTATATGAGAATTTGATTAACGACAGATATTTCTCCCAATTGCCTTCGAACTCTAAAATG
1 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTGCCTTCAAACTCTAAAATG
*
19603582 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCTAATTGCCTTCAAACTCTAAAA
1 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTGCCTTCAAACTCTAAAA
19603643 CACAACACCG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (63 bp):
TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTGCCTTCAAACTCTAAAATG
Done.