Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_pilon, whole genome shotgun sequence
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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1628734 original size:36 final size:36
Alignment explanation
Indices: 1628687--1629051 Score: 314
Period size: 36 Copynumber: 10.4 Consensus size: 36
1628677 ATTGAAAACA
* *
1628687 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1628723 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1628760 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* * * *
1628797 TTTCTCTTGAAACATAA-------AC-ATTGAAAACA-
1 TTTCCCTTGAAACA-AATTTTGTCTCTCTTG-AGACAG
* * **
1628826 TTTCCCTTTAAATAAATTTCATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
1628862 TATCCCTTGAAACAAATTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
1628898 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
1628927 TTTTATTTGAAACAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
1628963 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
1629000 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1629036 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
1629052 ATCTTTGAAT
Statistics
Matches: 270, Mismatches: 37, Indels: 44
0.77 0.11 0.13
Matches are distributed among these distances:
28 4 0.01
29 32 0.12
30 7 0.03
31 1 0.00
34 1 0.00
35 6 0.02
36 115 0.43
37 104 0.39
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1628753 original size:22 final size:22
Alignment explanation
Indices: 1628725--1628791 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 22
1628715 TGAGATAGTT
1628725 TCCCTTGAAACAAAATTTTGTC
1 TCCCTTGAAACAAAATTTTGTC
* *
1628747 TCCCTTGAGAC---A----GTT
1 TCCCTTGAAACAAAATTTTGTC
1628762 TCCCTTGAAACAAAATTTTGTC
1 TCCCTTGAAACAAAATTTTGTC
1628784 TCCCTTGA
1 TCCCTTGA
1628792 GACAGTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
15 12 0.35
18 1 0.03
19 1 0.03
22 20 0.59
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (22 bp):
TCCCTTGAAACAAAATTTTGTC
Found at i:1628754 original size:37 final size:37
Alignment explanation
Indices: 1628687--1628810 Score: 205
Period size: 37 Copynumber: 3.4 Consensus size: 37
1628677 ATTGAAAACA
* * *
1628687 TTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1628723 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1628760 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
1628797 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1628811 TAAACATTGA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 13 0.16
37 70 0.84
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1628851 original size:139 final size:138
Alignment explanation
Indices: 1628600--1628918 Score: 503
Period size: 139 Copynumber: 2.3 Consensus size: 138
1628590 TAAAAAGAAG
* *
1628600 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAATTTCTCT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAATTTCTCT
* ** * *
1628665 TGAAACATAAACATTGAAAACATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCT
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTATCCCT
1628730 TGAAACAAA
131 TGAAAC-AA
* * *
1628739 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAATTTCTCT
* *
1628804 TGAAACATAAACATTGAAAACATTTCCCTTTAAATAAATTTCATCTCTCTTGAGACAGTATCCCT
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTATCCCT
1628869 TGAAACAA
131 TGAAACAA
* *
1628877 ATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATT
1628919 TGAATATGTT
Statistics
Matches: 164, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
138 40 0.24
139 124 0.76
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (138 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAATTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTATCCCT
TGAAACAA
Found at i:1628989 original size:138 final size:138
Alignment explanation
Indices: 1628847--1629105 Score: 383
Period size: 138 Copynumber: 1.9 Consensus size: 138
1628837 ATAAATTTCA
*
1628847 TCTCTCTTGAGACAGTATCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTATCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * ** * *
1628912 AATTATTTGAATATGTTTTATTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAACT
66 AAATATTTGAATATATTTCACATAAAACAAATTTTATCTCCCTTGAGACAATTTCTTTTGGAACT
1628977 AAGTTTTG
131 AAGTTTTG
* * *
1628985 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTATCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * *
1629050 AAATCTTTGAATTTATTTCCCATAAAACAAATTTTGTCTCCCTTGAGACAATTTCT
66 AAATATTTGAATATATTTCACATAAAACAAATTTTATCTCCCTTGAGACAATTTCT
1629106 CTTGAAACAC
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 106 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (138 bp):
TCTCTCTTGAGACAGTATCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACA
AAATATTTGAATATATTTCACATAAAACAAATTTTATCTCCCTTGAGACAATTTCTTTTGGAACT
AAGTTTTG
Found at i:1629016 original size:102 final size:101
Alignment explanation
Indices: 1628729--1629017 Score: 348
Period size: 101 Copynumber: 2.8 Consensus size: 101
1628719 ATAGTTTCCC
* *
1628729 TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGA
1 TTGAAAC-AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGA
** *
1628794 CAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
64 CAGTTTCTCTTGAAACA-AATTATTGAAAACATTTCCAT
* * * * *
1628833 TT-AAATAAATTTCATCTCTCTTGAGACAGTATCCCTTGAAACAAATTTTATCTCTCTTGAGACA
1 TTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * ** *
1628897 GTTTCCCTTGAAACAAATTATTTGAATATGTTT-TAT
66 GTTTCTCTTGAAACAAATTA-TTGAAAACATTTCCAT
** * *
1628933 TTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGAC
1628998 AGTTTCTCTTGAAACAAATT
65 AGTTTCTCTTGAAACAAATT
1629018 TCGTCTCTCT
Statistics
Matches: 157, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
100 6 0.04
101 76 0.48
102 70 0.45
103 3 0.02
104 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (101 bp):
TTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
GTTTCTCTTGAAACAAATTATTGAAAACATTTCCAT
Found at i:1629113 original size:65 final size:67
Alignment explanation
Indices: 1629009--1629166 Score: 221
Period size: 65 Copynumber: 2.4 Consensus size: 67
1628999 GTTTCTCTTG
* * * **
1629009 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAA-TCTTTGAATTTATTTCCCA
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAACTCTTCAAATTTATTTCCCA
1629072 TA
66 TA
* *
1629074 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAACTCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAACTCTTCAAATTTATTTCCCA
1629139 TA
66 TA
*
1629141 AAACAAAATTTTGTTTCCCTTGAGAC
1 AAAC-AAATTTTGTCTCCCTTGAGAC
1629167 CGTTTTCATG
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
65 37 0.45
66 3 0.04
67 22 0.27
68 20 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAACTCTTCAAATTTATTTCCCA
TA
Found at i:1629179 original size:67 final size:66
Alignment explanation
Indices: 1629009--1629187 Score: 209
Period size: 65 Copynumber: 2.7 Consensus size: 66
1628999 GTTTCTCTTG
* * * * * **
1629009 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATTTATTTCCCAT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAATCTTCAAATTTATTTCCCAT
1629073 A
66 A
* *
1629074 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAACTCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAA-TCTTCAAATTTATTTCCCA
1629139 TA
65 TA
* **
1629141 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAACAAAT
1 AAAC-AAATTTTGTCTCCCTTGAGACAATTTCTCATGAAAC-ACAAAT
1629188 ATCTTTGAGA
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
65 37 0.37
66 3 0.03
67 31 0.31
68 28 0.28
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (66 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAATCTTCAAATTTATTTCCCAT
A
Found at i:1630097 original size:110 final size:110
Alignment explanation
Indices: 1629899--1630149 Score: 325
Period size: 110 Copynumber: 2.3 Consensus size: 110
1629889 GTTTTCCAGT
* * *
1629899 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACATAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
1629964 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1630009 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * * *
1630074 CAGCGAAGGGGCGGCTGGCTGTCAACAAACAAC-TTCCAG-TTC-
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1630116 --CAGAGCCAATTTCAATTTCAC-GACGGAGGATATT
1 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATT
1630150 AGACTCGGAA
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
104 1 0.01
105 28 0.23
108 3 0.02
109 5 0.04
110 87 0.70
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1631546 original size:14 final size:14
Alignment explanation
Indices: 1631527--1631566 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1631517 TATTCCTTTT
1631527 TTATTTATATTATA
1 TTATTTATATTATA
*
1631541 TTATTTTTATTATA
1 TTATTTATATTATA
1631555 TATATCTTATAT
1 T-TAT-TTATAT
1631567 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:1631632 original size:17 final size:18
Alignment explanation
Indices: 1631615--1631681 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1631605 ACTATGTATA
1631615 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
*
1631633 TATATTTAATAAGTT-TTTATA-
1 TATATTT--T---TTCTTAATAT
1631654 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
1631672 TATATTTTTT
1 TATATTTTTT
1631682 GTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.05
17 5 0.12
18 17 0.43
19 1 0.03
20 1 0.03
21 7 0.17
22 5 0.12
23 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:1631690 original size:18 final size:18
Alignment explanation
Indices: 1631645--1631695 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1631635 TATTTAATAA
1631645 GTTTTTATATATATTTTTT
1 GTTTTTAT-TATATTTTTT
* **
1631664 CTTAATATTATATTTTTT
1 GTTTTTATTATATTTTTT
1631682 GTTTTTATT-TATTT
1 GTTTTTATTATATTT
1631696 ATATATATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (18 bp):
GTTTTTATTATATTTTTT
Found at i:1631736 original size:18 final size:18
Alignment explanation
Indices: 1631713--1631748 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1631703 TATATATATG
1631713 ATTTTTTTACT-TTATTTT
1 ATTTTTTT-CTATTATTTT
1631731 ATTTTTTTCTATTATTTT
1 ATTTTTTTCTATTATTTT
1631749 TTTCTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTTTTCTATTATTTT
Found at i:1631745 original size:13 final size:13
Alignment explanation
Indices: 1631729--1631753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1631719 TTACTTTATT
1631729 TTATTTTTTTCTA
1 TTATTTTTTTCTA
1631742 TTATTTTTTTCT
1 TTATTTTTTTCT
1631754 TAATATCATG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:1631835 original size:36 final size:34
Alignment explanation
Indices: 1631767--1631835 Score: 84
Period size: 36 Copynumber: 2.0 Consensus size: 34
1631757 TATCATGTAT
* * *
1631767 ATATTTATTTTTTATTTGTTTTACTTAGTATTAC
1 ATATTTATTTTTTATTTATTTTACTAAATATTAC
*
1631801 ATATTTATTATTTTTATTTATTTTAGTAAATATTA
1 ATATTTA-T-TTTTTATTTATTTTACTAAATATTA
1631836 TTTTATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 7 0.24
35 1 0.03
36 21 0.72
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (34 bp):
ATATTTATTTTTTATTTATTTTACTAAATATTAC
Found at i:1631885 original size:18 final size:18
Alignment explanation
Indices: 1631862--1631898 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1631852 TATTTTTATT
1631862 CCTTTTTAATTTCTTTTA
1 CCTTTTTAATTTCTTTTA
*
1631880 CCTTTTTTATTTCTTTTA
1 CCTTTTTAATTTCTTTTA
1631898 C
1 C
1631899 TCCATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.68
Consensus pattern (18 bp):
CCTTTTTAATTTCTTTTA
Found at i:1631964 original size:19 final size:17
Alignment explanation
Indices: 1631942--1631976 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1631932 TTTTTTAACA
1631942 TTTTATTCATATTTTTTAT
1 TTTTATT-AT-TTTTTTAT
1631961 TTTTATTATTTTTTTA
1 TTTTATTATTTTTTTA
1631977 CGTGTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTATTTTTTTAT
Found at i:1632021 original size:27 final size:27
Alignment explanation
Indices: 1631955--1632021 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
1631945 TATTCATATT
*
1631955 TTTTATTT-TTATTATTTTTTTACGTG
1 TTTTATTTATTATTCTTTTTTTACGTG
* *
1631981 TTTT-GTTATT-TTCTATTTTTT-CTTG
1 TTTTATTTATTATTCT-TTTTTTACGTG
1632006 TTTTATTTATTATTCT
1 TTTTATTTATTATTCT
1632022 CATGTTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
25 12 0.36
26 17 0.52
27 4 0.12
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTTATTTATTATTCTTTTTTTACGTG
Found at i:1633091 original size:8 final size:8
Alignment explanation
Indices: 1633080--1633106 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1633070 TCTTTTTATT
1633080 TTTTTTTA
1 TTTTTTTA
1633088 TTTTTTTA
1 TTTTTTTA
1633096 TTTTTTTA
1 TTTTTTTA
1633104 TTT
1 TTT
1633107 ATTGCTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1634619 original size:17 final size:18
Alignment explanation
Indices: 1634597--1634635 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1634587 ATATATTATT
1634597 TATTATTTACT-TTATAA
1 TATTATTTACTATTATAA
*
1634614 TATTATTTATTATTATAA
1 TATTATTTACTATTATAA
1634632 -ATTA
1 TATTA
1634636 AATTTATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTTACTATTATAA
Found at i:1635640 original size:2 final size:2
Alignment explanation
Indices: 1635633--1635676 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1635623 TGTAATGCCC
1635633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1635675 AT
1 AT
1635677 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1635681 original size:2 final size:2
Alignment explanation
Indices: 1635676--1635712 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1635666 TATATATATA
*
1635676 TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1635713 ATAAAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1639354 original size:96 final size:96
Alignment explanation
Indices: 1639178--1639373 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
1639168 ATTCTTTTAA
* * ** *
1639178 AGGTGTAAAGGCCAAGATGTTGACTCAAGAGATAGATACATTCATACCAAGAACGAAAAGACCCT
1 AGGTGCAAAGGCCAAGATGTTGACTCAACAGATAGATACAGCCATACCAAGAACGAAAAGACCAT
* *
1639243 TCACAGAGACGTGAAGACCACTTCGCATTAG
66 TCACAAAGACATGAAGACCACTTCGCATTAG
* * * * * * *
1639274 AGGTGCAAAGGCCAATATGTTGATTCAACAGATAGATATAGCCATACCAAGGATGAGAAGATCAT
1 AGGTGCAAAGGCCAAGATGTTGACTCAACAGATAGATACAGCCATACCAAGAACGAAAAGACCAT
* * * *
1639339 TCATAAAGATATGAAGACCACTTTGCATTGG
66 TCACAAAGACATGAAGACCACTTCGCATTAG
1639370 AGGT
1 AGGT
1639374 AAGAATGAAG
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (96 bp):
AGGTGCAAAGGCCAAGATGTTGACTCAACAGATAGATACAGCCATACCAAGAACGAAAAGACCAT
TCACAAAGACATGAAGACCACTTCGCATTAG
Found at i:1643702 original size:19 final size:19
Alignment explanation
Indices: 1643678--1643719 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1643668 AATTCCACAA
1643678 AGGAGATCTGGTGCTCAAG
1 AGGAGATCTGGTGCTCAAG
1643697 AGGAGATCTGGTGCTCAAG
1 AGGAGATCTGGTGCTCAAG
1643716 AGGA
1 AGGA
1643720 TATTGCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.38, T:0.19
Consensus pattern (19 bp):
AGGAGATCTGGTGCTCAAG
Found at i:1644029 original size:193 final size:193
Alignment explanation
Indices: 1643700--1644056 Score: 669
Period size: 193 Copynumber: 1.8 Consensus size: 193
1643690 GCTCAAGAGG
*
1643700 AGATCTGGTGCTCAAGAGGATATTGCCCATTCAAAAGGGATTTCCGAGGGAAATGGATGCCCAAG
1 AGATCTGGTGCTCAAGAGGATATTGCCCATTCAAAAGGGATTTCCGAGGAAAATGGATGCCCAAG
* *
1643765 TGGGAGGGACCCTATGTTGTCAAGAAAACCTTTTCTGGGGGAGCTCTAGTCTTAACCGAGATGGA
66 TGGGAGAGACCCTATGTTGTCAAGAAAACCTTTTCTGGGGAAGCTCTAGTCTTAACCGAGATGGA
*
1643830 TGGTTCAGAATTATCCTATCCAGTGAATTCTGACAAAGTTTGCCTTCGAGAATTCCACGAAGA
131 TGGTTCAGAATTACCCTATCCAGTGAATTCTGACAAAGTTTGCCTTCGAGAATTCCACGAAGA
*
1643893 AGATCTGGTGCTCAAGAGGATATTGCCCATTTAAAAGGGATTTCCGAGGAAAATGGATGCCCAAG
1 AGATCTGGTGCTCAAGAGGATATTGCCCATTCAAAAGGGATTTCCGAGGAAAATGGATGCCCAAG
1643958 TGGGAGAGACCCTATGTTGTCAAGAAAACCTTTTCTGGGGAAGCTCTAGTCTTAACCGAGATGGA
66 TGGGAGAGACCCTATGTTGTCAAGAAAACCTTTTCTGGGGAAGCTCTAGTCTTAACCGAGATGGA
1644023 TGGTTCAGAATTACCCTATCCAGTGAATTCTGAC
131 TGGTTCAGAATTACCCTATCCAGTGAATTCTGAC
1644057 GCAGTTAAGA
Statistics
Matches: 159, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 159 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (193 bp):
AGATCTGGTGCTCAAGAGGATATTGCCCATTCAAAAGGGATTTCCGAGGAAAATGGATGCCCAAG
TGGGAGAGACCCTATGTTGTCAAGAAAACCTTTTCTGGGGAAGCTCTAGTCTTAACCGAGATGGA
TGGTTCAGAATTACCCTATCCAGTGAATTCTGACAAAGTTTGCCTTCGAGAATTCCACGAAGA
Found at i:1644170 original size:16 final size:15
Alignment explanation
Indices: 1644090--1644169 Score: 69
Period size: 16 Copynumber: 5.5 Consensus size: 15
1644080 AAGAAGAAAT
*
1644090 AAATGAAAACAAGAGA
1 AAATGAAAAAAAGA-A
* *
1644106 GAAT-AAAAAATGAA
1 AAATGAAAAAAAGAA
1644120 AAATGAAAAAAA-AA
1 AAATGAAAAAAAGAA
*
1644134 AAA--AAAAAAAAAA
1 AAATGAAAAAAAGAA
*
1644147 AAAAGAAGAAAAAGAA
1 AAATGAA-AAAAAGAA
1644163 AAATGAA
1 AAATGAA
1644170 GGAAAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
12 7 0.13
13 5 0.10
14 9 0.17
15 15 0.29
16 16 0.31
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.06
Consensus pattern (15 bp):
AAATGAAAAAAAGAA
Found at i:1644174 original size:17 final size:16
Alignment explanation
Indices: 1644124--1644179 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1644114 AATGAAAAAT
1644124 GAAAAAAAAAAAA-AA
1 GAAAAAAAAAAAAGAA
1644139 -AAAAAAAAAAAAGAA
1 GAAAAAAAAAAAAGAA
* *
1644154 GAAAAAGAAAAATGAA
1 GAAAAAAAAAAAAGAA
1644170 GGAAAAAAAA
1 -GAAAAAAAA
1644180 GAGGGTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.34
15 2 0.06
16 13 0.37
17 8 0.23
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (16 bp):
GAAAAAAAAAAAAGAA
Found at i:1644175 original size:16 final size:15
Alignment explanation
Indices: 1644124--1644179 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1644114 AATGAAAAAT
*
1644124 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAGAA
*
1644139 AAAAAAAAAAAAGAA
1 GAAAAAAAAAAAGAA
*
1644154 GAAAAAGAAAAATGAA
1 GAAAAA-AAAAAAGAA
1644170 GGAAAAAAAA
1 -GAAAAAAAA
1644180 GAGGGTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 18 0.51
16 11 0.31
17 6 0.17
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAAAAGAA
Found at i:1644178 original size:20 final size:20
Alignment explanation
Indices: 1644125--1644181 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1644115 ATGAAAAATG
1644125 AAAAAAAA-AAAAAAAA-AA
1 AAAAAAAAGAAAAAAAAGAA
*
1644143 AAAAAAAAGAAGAAAAAGAA
1 AAAAAAAAGAAAAAAAAGAA
** *
1644163 AAATGAAGGAAAAAAAAGA
1 AAAAAAAAGAAAAAAAAGA
1644182 GGGTTCAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 17 0.53
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAGAA
Found at i:1644179 original size:1 final size:1
Alignment explanation
Indices: 1644125--1644165 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
1644115 ATGAAAAATG
* * *
1644125 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1644166 TGAAGGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1645527 original size:55 final size:55
Alignment explanation
Indices: 1645428--1646407 Score: 1010
Period size: 55 Copynumber: 18.0 Consensus size: 55
1645418 TAGTGAAGTA
*** *
1645428 AAAGAAGGGAGCGAACCCGTAAAAAGAAGA-TATTCGAGTTCTATACTCCCTAAAG
1 AAAG-AGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * *
1645483 AAAGAGGGAGCGAACCCGTTTGCAGAATATTGTTTGAGTTCTATACTCCCTAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * *
1645538 AAAGAAGGAGCAAACCCG--T-AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAA
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * * * * * *
1645589 AAATAGGGTG-TAGACACATTTGCAGAAGATTGTTTGAGTTTTATACTCCCTAAAG
1 AAAGAGGGAGCGA-ACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * *
1645644 AAAGAGGGAGTGAACTCG--T-AAGAAGATT-TTTGAGTTCTATACTCCCTGAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
** * * *
1645695 AAAGAGAAAGCGAACCCCTTTGTAA-AAGATTGTTCGAGTTCTATACTCCCTGAAT
1 AAAGAGGGAGCGAACCCGTTTG-AAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* **
1645750 AAAGAGGGAGCAAACTTGTTT-ACAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
1 AAAGAGGGAGCGAACCCGTTTGA-AGAAGATTGTTCGAGTTCTATACTCCCTAAAG
** *
1645805 AAAGAGGGAGCGAACCCGTAAGAAGAATATTGTTCGAGTTCTATACTCCCTAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * *
1645860 AAAGAGGGACCGAACCCG--T-AAGAAGA-TGTTCGAGTTCTATACTCCTTGAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * ** *
1645911 AAAGAGAGAGCGAACCCGTTTGTAA-AAGATTGTTCAAGTTCTATACTTTCTGAAG
1 AAAGAGGGAGCGAACCCGTTTG-AAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* *
1645966 AAAGAGGGAGCGAACCTGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* ** * *
1646021 AAAGAGAGAGCGAACCCGTAAGAAGAAGA-TATTCGAGTTCTATACTCCCCAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* *
1646075 AAAGAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATATTCCCTAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * ** * *
1646130 AAAGAAGGAGCGAACCCATAAGAAGAAGATTGTTCGAGTTCTATACTTCCTGAATG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * **
1646186 AAAGAGGGAGCGAACCCGTTTGTAGAAGATTATTCGAGTTCTATACTTTCTGAAAG
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * * * * * * *
1646242 AAAAAGGAAGCGAACCCGTTTGTAGAAGATTATTCAAGATATATACTCCCTGAAAA
1 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * **
1646298 AAAGAGGGAACAAACATGTTTGTAA-AAGATTGTTCGAGTTCTATACTCCCTGAAAG
1 AAAGAGGGAGCGAACCCGTTTG-AAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * *** * *
1646354 CAAGAGGGAGTGAACCCGTCCCCAA-AAGATTCTTCGAGTTCTATGCTCCCTAAA
1 AAAGAGGGAGCGAACCCGT-TTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAA
1646408 ACAATAGGGA
Statistics
Matches: 769, Mismatches: 131, Indels: 50
0.81 0.14 0.05
Matches are distributed among these distances:
50 1 0.00
51 106 0.14
52 19 0.02
53 6 0.01
54 86 0.11
55 368 0.48
56 182 0.24
57 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (55 bp):
AAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
Found at i:1645613 original size:106 final size:106
Alignment explanation
Indices: 1645428--1646407 Score: 807
Period size: 106 Copynumber: 9.0 Consensus size: 106
1645418 TAGTGAAGTA
* *
1645428 AAAGAAGGGAGCGAACCCGTAAAAAGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAG
1 AAAG-AGGGAGCGAACCCGT---AAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAG
* * *
1645493 CGAACCCGTTTGCAGAATATTGTTTGAGTTCTATACTCCCTAAAG
62 AGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * *
1645538 AAAGAAGGAGCAAACCCGTAAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAATAGGGTGTAG-
1 AAAGAGGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAG-AGA
* * * *
1645602 ACACATTTGCAGAAGATTGTTTGAGTTTTATACTCCCTAAAG
65 ACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * * * * ** *
1645644 AAAGAGGGAGTGAACTCGTAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAAGAGAAAGCGAA
1 AAAGAGGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAGAGAA
* * * * *
1645709 CCCCTTTGTAAAAGATTGTTCGAGTTCTATACTCCCTGAAT
66 CCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* ** *
1645750 AAAGAGGGAGCAAACTTGTTTACAGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAG
1 AAAGAGGGAGCGAACCCG--TA-AGAAGA-TGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAG
* ** * *
1645815 CGAACCCGTAAGAAGAATATTGTTCGAGTTCTATACTCCCTAAAG
62 AGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * * * *
1645860 AAAGAGGGACCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCTTGAAGAAAGAGAGAGCGAA
1 AAAGAGGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAGAGAA
* * * ** *
1645925 CCCGTTTGTAAAAGATTGTTCAAGTTCTATACTTTCTGAAG
66 CCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * *
1645966 AAAGAGGGAGCGAACCTGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGAGAG
1 AAAGAGGGAGCGAACCCG--T-AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAG
* ** * * *
1646031 CGAACCCGTAAGAAGAAGA-TATTCGAGTTCTATACTCCCCAAAG
62 AGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
* * * *
1646075 AAAGAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATATTCCCTAAAGAAAGAAGGAG
1 AAAGAGGGAGCGAACCCG--T-AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAG
* * ** * * *
1646140 CGAACCCATAAGAAGAAGATTGTTCGAGTTCTATACTTCCTGAATG
62 AGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * ** *
1646186 AAAGAGGGAGCGAACCCGTTTGTAGAAGATTATTCGAGTTCTATACTTTCTGAAAGAAAA-AGGA
1 AAAGAGGGAGCGAACCCG--T-AAGAAGA-TGTTCGAGTTCTATACTCCCT-AAA-AAAAGAGGG
* * * * * * *
1646250 AGCGAACCCGTTTGTAGAAGATTATTCAAGATATATACTCCCTGAAAA
60 AGAGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCT-AAAG
* * ** **
1646298 AAAGAGGGAACAAACATGTTTGTAA-AAGATTGTTCGAGTTCTATACTCCCTGAAAGCAAGAGGG
1 AAAGAGGGAGCGAAC----CCGTAAGAAGA-TGTTCGAGTTCTATACTCCCT-AAAAAAAGAGGG
* *** * * *
1646362 AGTGAACCCGTCCCCAAAAGATTCTTCGAGTTCTATGCTCCCTAAA
60 AGAGAACCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAA
1646408 ACAATAGGGA
Statistics
Matches: 722, Mismatches: 129, Indels: 37
0.81 0.15 0.04
Matches are distributed among these distances:
105 1 0.00
106 258 0.36
107 7 0.01
108 5 0.01
109 123 0.17
110 151 0.21
111 54 0.07
112 117 0.16
113 4 0.01
114 1 0.00
116 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (106 bp):
AAAGAGGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCCTAAAAAAAGAGGGAGAGAA
CCCGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAG
Found at i:1645737 original size:161 final size:160
Alignment explanation
Indices: 1645452--1646370 Score: 847
Period size: 161 Copynumber: 5.6 Consensus size: 160
1645442 ACCCGTAAAA
* * *
1645452 AGAAGA-TATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAGAATATTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG--TGAAGAAGATTGT
*
1645516 TTGAGTTCTATACTCCCTAAAGAAAGA-AGGAGC-AAACCC-GTAAGAAGATGTTCGAGTTCTAT
64 TTGAGTTCTATACTCCCTAAAGAAAGAGA-GAGCGAACCCCTGTAAGAAGATGTTCGAGTTCTAT
* * * *
1645578 ACTCCCTAAAAAAATAGGGTGTAGACACATTTGC
128 ACTCCCTAAAAAAAGAGGGAG-AGACCCGTTTGC
* * * *
1645612 AGAAGATTGTTTGAGTTTTATACTCCCTAAAGAAAGAGGGAGTGAACTCGT-AAGAAGATT-TTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGAAGAAGATTGTTT
* *
1645675 GAGTTCTATACTCCCTGAAGAAAGAGAAAGCGAACCCCTTTGTAA-AAGATTGTTCGAGTTCTAT
66 GAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCC--TGTAAGAAGA-TGTTCGAGTTCTAT
* * * ** *
1645739 ACTCCCTGAATAAAGAGGGAGCAAACTTGTTTAC
128 ACTCCCTAAAAAAAGAGGGAG-AGACCCGTTTGC
*
1645773 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAATATTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGT--GAAGAAGATTGT
* * *
1645838 TCGAGTTCTATACTCCCTAAAGAAAGAGGGACCGAA-CCC-GTAAGAAGATGTTCGAGTTCTATA
64 TTGAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCCTGTAAGAAGATGTTCGAGTTCTATA
* * * * * *
1645901 CTCCTTGAAGAAAGAGAGAGCGAACCCGTTTGT
129 CTCCCTAAAAAAAGAGGGAGAG-ACCCGTTTGC
* * ** * * *
1645934 AAAAGATTGTTCAAGTTCTATACTTTCTGAAGAAAGAGGGAGCGAACCTGTTTGCAGAAGATTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG--TGAAGAAGATTGT
* * *
1645999 TCGAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCGTAAG-AAGAAGATATTCGAGTTCTA
64 TTGAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCCT--GTAAGAAGATGTTCGAGTTCTA
* * *
1646063 TACTCCCCAAAGAAAGAGGGAGCGAACCCGTTTGC
127 TACTCCCTAAAAAAAGAGGGAGAG-ACCCGTTTGC
* * *
1646098 AGAAGATTGTTCGAGTTCTATATTCCCTAAAGAAAGAAGGAGCGAACCCATAAGAAGAAGATTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGT--GAAGAAGATTGT
* * * * * *
1646163 TCGAGTTCTATACTTCCTGAATGAAAGAGGGAGCGAACCCGTTTGT-AGAAGATTATTCGAGTTC
64 TTGAGTTCTATACTCCCT-AAAGAAAGAGAGAGCGAACCC--CTGTAAGAAGA-TGTTCGAGTTC
** * * *
1646227 TATACTTTCTGAAAGAAAA-AGGAAGCGAACCCGTTTGT
125 TATACTCCCT-AAA-AAAAGAGGGAGAG-ACCCGTTTGC
* * * * * * * **
1646265 AGAAGATTATTCAAGATATATACTCCCTGAAAAAAAGAGGGAACAAACATGTTTGTAA-AAGATT
1 AGAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCG--TG-AAGAAGATT
* * * *
1646329 GTTCGAGTTCTATACTCCCTGAAAGCAAGAGGGAGTGAACCC
62 GTTTGAGTTCTATACTCCCT-AAAGAAAGAGAGAGCGAACCC
1646371 GTCCCCAAAA
Statistics
Matches: 635, Mismatches: 92, Indels: 56
0.81 0.12 0.07
Matches are distributed among these distances:
157 30 0.05
158 13 0.02
159 1 0.00
160 10 0.02
161 257 0.40
162 7 0.01
163 1 0.00
164 129 0.20
165 59 0.09
166 18 0.03
167 44 0.07
168 63 0.10
169 2 0.00
170 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (160 bp):
AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGAAGAAGATTGTTT
GAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCCTGTAAGAAGATGTTCGAGTTCTATACT
CCCTAAAAAAAGAGGGAGAGACCCGTTTGC
Found at i:1646752 original size:2 final size:2
Alignment explanation
Indices: 1646745--1646781 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1646735 TAATGCCCAT
1646745 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1646782 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1651879 original size:17 final size:18
Alignment explanation
Indices: 1651842--1651879 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1651832 TAGGCCTGAC
1651842 GGTATCGATACTAGGACTAT
1 GGTATCGATACT--GACTAT
1651862 GGTATCGATACT-ACTAT
1 GGTATCGATACTGACTAT
1651879 G
1 G
1651880 TAAAGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
20 12 0.67
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (18 bp):
GGTATCGATACTGACTAT
Found at i:1652204 original size:140 final size:141
Alignment explanation
Indices: 1651952--1652234 Score: 559
Period size: 140 Copynumber: 2.0 Consensus size: 141
1651942 AGTTGGTAGT
1651952 ATCGATACTACCTAGTGAGTATCGATACTTGCCTTACCTTTGGTATTGGTACCATATGAACAATA
1 ATCGATACTACCTAGTGAGTATCGATACTTGCCTTACCTTTGGTATTGGTACCATATGAACAATA
1652017 TCGGTAATGTTCATGAGGTATCGATACTGTAAGAACAATACCGGTAATGCTTGTCCAG-AAAATA
66 TCGGTAATGTTCATGAGGTATCGATACTGTAAGAACAATACCGGTAATGCTTGTCCAGAAAAATA
1652081 TTTTGTGCTCA
131 TTTTGTGCTCA
1652092 ATCGATACTACCTAGTGAGTATCGATACTTGCCTTACCTTTGGTATTGGTACCATATGAACAATA
1 ATCGATACTACCTAGTGAGTATCGATACTTGCCTTACCTTTGGTATTGGTACCATATGAACAATA
1652157 TCGGTAATGTTCATGAGGTATCGATACTGTAAGAACAATACCGGTAATGCTTGTCCAGAAAAATA
66 TCGGTAATGTTCATGAGGTATCGATACTGTAAGAACAATACCGGTAATGCTTGTCCAGAAAAATA
1652222 TTTTGTGCTCA
131 TTTTGTGCTCA
1652233 AT
1 AT
1652235 TCCAAGTTAA
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 123 0.87
141 19 0.13
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (141 bp):
ATCGATACTACCTAGTGAGTATCGATACTTGCCTTACCTTTGGTATTGGTACCATATGAACAATA
TCGGTAATGTTCATGAGGTATCGATACTGTAAGAACAATACCGGTAATGCTTGTCCAGAAAAATA
TTTTGTGCTCA
Found at i:1653681 original size:10 final size:10
Alignment explanation
Indices: 1653639--1653690 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
1653629 GTTGGAAACT
1653639 GGTTTTGACC
1 GGTTTTGACC
*
1653649 GG-TTTAACC
1 GGTTTTGACC
1653658 GGTTTTGAACC
1 GGTTTTG-ACC
1653669 GGTTTTGACC
1 GGTTTTGACC
1653679 GG-TTTGACC
1 GGTTTTGACC
1653688 GGT
1 GGT
1653691 CACGACCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:1653728 original size:18 final size:18
Alignment explanation
Indices: 1653705--1653752 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1653695 ACCGTTTACC
1653705 GTTTACCCGACCCGACCA
1 GTTTACCCGACCCGACCA
*
1653723 GTTTACCCGACCCGACCC
1 GTTTACCCGACCCGACCA
1653741 GTTTACCCGACC
1 GTTTACCCGACC
1653753 GTTGACCCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.46, G:0.17, T:0.19
Consensus pattern (18 bp):
GTTTACCCGACCCGACCA
Found at i:1653748 original size:13 final size:13
Alignment explanation
Indices: 1653731--1653772 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1653721 CAGTTTACCC
1653731 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1653744 TACCCGA-CCGTT
1 GACCCGACCCGTT
1653756 GACCCGACCCGTT
1 GACCCGACCCGTT
1653769 GACC
1 GACC
1653773 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1653848 original size:29 final size:29
Alignment explanation
Indices: 1653787--1653853 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1653777 ACCGTTGACC
* * *** *
1653787 GGTGCTATTCTGGGAATTAATTTGGTTTT
1 GGTGCTATTCTGAGAATTAATTCGAAATG
1653816 GGTGCTATTCTGAGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATTAATTCGAAATG
1653845 GGTGCTATT
1 GGTGCTATT
1653854 TTAGTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCGAAATG
Found at i:1653862 original size:29 final size:28
Alignment explanation
Indices: 1653816--1653870 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1653806 ATTTGGTTTT
1653816 GGTGCTATTCTGAGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATT-ATTCGAAATG
* *
1653845 GGTGCTATT-TTAGTAATTTTTCGAAA
1 GGTGCTATTCTGAG-AATTATTCGAAA
1653871 AAATAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (28 bp):
GGTGCTATTCTGAGAATTATTCGAAATG
Found at i:1660880 original size:20 final size:22
Alignment explanation
Indices: 1660855--1660900 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1660845 GTTGGAAACT
1660855 GGTTTTTG-ACCGG-TTTAACC
1 GGTTTTTGAACCGGTTTTAACC
*
1660875 GG-TTTTGAACCGGTTTTGACC
1 GGTTTTTGAACCGGTTTTAACC
1660896 GGTTT
1 GGTTT
1660901 GACCGGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 8 0.36
22 2 0.09
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.41
Consensus pattern (22 bp):
GGTTTTTGAACCGGTTTTAACC
Found at i:1660885 original size:11 final size:10
Alignment explanation
Indices: 1660858--1660907 Score: 68
Period size: 9 Copynumber: 5.1 Consensus size: 10
1660848 GGAAACTGGT
1660858 TTTTGACCGG
1 TTTTGACCGG
*
1660868 -TTTAACCGG
1 TTTTGACCGG
1660877 TTTTGAACCGG
1 TTTTG-ACCGG
1660888 TTTTGACCGG
1 TTTTGACCGG
1660898 -TTTGACCGG
1 TTTTGACCGG
1660907 T
1 T
1660908 CACGACCCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 17 0.49
10 8 0.23
11 10 0.29
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.38
Consensus pattern (10 bp):
TTTTGACCGG
Found at i:1660965 original size:17 final size:18
Alignment explanation
Indices: 1660923--1660969 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1660913 CCCGTTTACC
1660923 GTTTACCCGACCCGACCA
1 GTTTACCCGACCCGACCA
*
1660941 GTTTACCCGACCCGACCC
1 GTTTACCCGACCCGACCA
1660959 G-TTACCCGACC
1 GTTTACCCGACC
1660970 GTTGACCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.19, C:0.47, G:0.17, T:0.17
Consensus pattern (18 bp):
GTTTACCCGACCCGACCA
Found at i:1660967 original size:12 final size:13
Alignment explanation
Indices: 1660949--1660989 Score: 68
Period size: 12 Copynumber: 3.3 Consensus size: 13
1660939 CAGTTTACCC
1660949 GACCCGACCCGTT
1 GACCCGACCCGTT
1660962 -ACCCGA-CCGTT
1 GACCCGACCCGTT
1660973 GACCCGACCCGTT
1 GACCCGACCCGTT
1660986 GACC
1 GACC
1660990 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.19
12 12 0.46
13 9 0.35
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1660981 original size:24 final size:26
Alignment explanation
Indices: 1660949--1661003 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
1660939 CAGTTTACCC
1660949 GACCCGACCCGTT-ACC-CGACCGTT
1 GACCCGACCCGTTGACCGCGACCGTT
*
1660973 GACCCGACCCGTTGACCGTTGACCGTT
1 GACCCGACCCGTTGACCG-CGACCGTT
1661000 GACC
1 GACC
1661004 GGTGCTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.48
25 3 0.11
27 11 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (26 bp):
GACCCGACCCGTTGACCGCGACCGTT
Found at i:1661063 original size:27 final size:28
Alignment explanation
Indices: 1661004--1661068 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1660994 ACCGTTGACC
*** *
1661004 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCT-GGAATTAATTCGAAATG
1661033 GGTGCTATTCT-GAATTAATTCGAAATG
1 GGTGCTATTCTGGAATTAATTCGAAATG
1661060 GGTGCTATT
1 GGTGCTATT
1661069 TTAGTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 21 0.66
29 11 0.34
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (28 bp):
GGTGCTATTCTGGAATTAATTCGAAATG
Found at i:1664837 original size:21 final size:21
Alignment explanation
Indices: 1664813--1664865 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1664803 AGTACAAAGG
1664813 GTATCGATACTCCTACAGAGA
1 GTATCGATACTCCTACAGAGA
1664834 GTATCGATACTCCTACAGAGA
1 GTATCGATACTCCTACAGAGA
*
1664855 GTATCGGTACT
1 GTATCGATACT
1664866 ACCTTTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (21 bp):
GTATCGATACTCCTACAGAGA
Found at i:1667516 original size:6 final size:6
Alignment explanation
Indices: 1667497--1667593 Score: 76
Period size: 6 Copynumber: 15.8 Consensus size: 6
1667487 TATTTTCACT
* *
1667497 CTCTCC CTCCCC CTCTCC CTCCCCC TCTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CT-CTCC -CTCTCC CTCTCC CTCTCC CTCTCC
* *
1667547 C-CTTCC CTCCCTCC CT-T-C CTTTCC CTCTCTC C-CTCC CTCTCA CTCTC
1 CTC-TCC CT--CTCC CTCTCC CTCTCC CTCTC-C CTCTCC CTCTCC CTCTC
1667594 TCCCCCTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.04
5 5 0.07
6 51 0.68
7 8 0.11
8 7 0.09
9 1 0.01
ACGTcount: A:0.01, C:0.66, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:1667531 original size:26 final size:27
Alignment explanation
Indices: 1667495--1667602 Score: 109
Period size: 26 Copynumber: 4.1 Consensus size: 27
1667485 TCTATTTTCA
1667495 CTCTCTCCCTCCC-CCTCTCCCTCCCC
1 CTCTCTCCCTCCCTCCTCTCCCTCCCC
* *
1667521 CTCTCTCCCTCTC-CCTCTCCCTCTCC
1 CTCTCTCCCTCCCTCCTCTCCCTCCCC
* **
1667547 C-CT-TCCCTCCCTCC-CTTCCTTTCC
1 CTCTCTCCCTCCCTCCTCTCCCTCCCC
* *
1667571 CTCTCTCCCTCCCTCTCACTCTCTCCCC
1 CTCTCTCCCTCCCTC-CTCTCCCTCCCC
1667599 CTCT
1 CTCT
1667603 TTCTCCCACT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.24
25 6 0.09
26 35 0.51
27 1 0.01
28 10 0.15
ACGTcount: A:0.01, C:0.66, G:0.00, T:0.33
Consensus pattern (27 bp):
CTCTCTCCCTCCCTCCTCTCCCTCCCC
Found at i:1667532 original size:20 final size:19
Alignment explanation
Indices: 1667501--1667557 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
1667491 TTCACTCTCT
1667501 CCCTC-CCCCTCTCCCTCC
1 CCCTCTCCCCTCTCCCTCC
*
1667519 CCCTCTCTCCCTCTCCCTCT
1 CCCTCTC-CCCTCTCCCTCC
1667539 CCCTCTCCCCT-TCCCTCC
1 CCCTCTCCCCTCTCCCTCC
1667557 C
1 C
1667558 TCCCTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 18 0.51
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (19 bp):
CCCTCTCCCCTCTCCCTCC
Found at i:1667594 original size:18 final size:18
Alignment explanation
Indices: 1667495--1667597 Score: 84
Period size: 18 Copynumber: 5.5 Consensus size: 18
1667485 TCTATTTTCA
1667495 CTCTCTCCCTCCCCCTCTCC
1 CTCTCTCCCT--CCCTCTCC
* *
1667515 CTCCCCCTCTCTCCCTCTCC
1 CT--CTCTCCCTCCCTCTCC
1667535 CTCTC-CCTCTCCC-CTTCC
1 CTCTCTCC-CTCCCTC-TCC
* * *
1667553 CTCCCTCCCTTCCTTTCC
1 CTCTCTCCCTCCCTCTCC
*
1667571 CTCTCTCCCTCCCTCTCA
1 CTCTCTCCCTCCCTCTCC
1667589 CTCTCTCCC
1 CTCTCTCCC
1667598 CCTCTTTCTC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.03
18 44 0.67
19 2 0.03
20 12 0.18
22 6 0.09
ACGTcount: A:0.01, C:0.66, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCTCTCCCTCCCTCTCC
Found at i:1667637 original size:22 final size:22
Alignment explanation
Indices: 1667599--1667648 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1667589 CTCTCTCCCC
* *
1667599 CTCTTTCTCCCACTCTCTCTAT
1 CTCTCTCTCCCACTCTCACTAT
*
1667621 CTCTCTCTCCC-CTTCTCACTCT
1 CTCTCTCTCCCAC-TCTCACTAT
1667643 CTCTCT
1 CTCTCT
1667649 ATTATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (22 bp):
CTCTCTCTCCCACTCTCACTAT
Found at i:1667656 original size:2 final size:2
Alignment explanation
Indices: 1667651--1667697 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1667641 CTCTCTCTAT
1667651 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
1667693 TA TA T
1 TA TA T
1667698 TAAATTTGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1675389 original size:63 final size:61
Alignment explanation
Indices: 1675238--1675398 Score: 178
Period size: 62 Copynumber: 2.6 Consensus size: 61
1675228 ATCCCTAGAC
** * * ** **
1675238 GGGTGCATCGATGCACTATCTATGCATCGGTGCATAAATCTTATTCGATGTTTGTATTTAG
1 GGGTGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTAG
* * *
1675299 GGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCA-TTT-AG
* *
1675363 GGGTGCATCGATGCACTCCCTGTGCATCGATACACA
1 GGGTGCATCGATGCACTCCCTATGCATCGATGCACA
1675399 CTGAACAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
61 3 0.04
62 43 0.52
63 32 0.39
64 4 0.05
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (61 bp):
GGGTGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTAG
Found at i:1689294 original size:15 final size:15
Alignment explanation
Indices: 1689276--1689352 Score: 66
Period size: 15 Copynumber: 4.7 Consensus size: 15
1689266 AAAAAGGAAC
1689276 AAATAAAAAGATGAA
1 AAATAAAAAGATGAA
1689291 AAATGAAAAA-ATGAA
1 AAAT-AAAAAGATGAA
* *
1689306 AAAGAAAAAAAATGAA
1 AAA-TAAAAAGATGAA
1689322 AAATGAAAAAAAGAAATGAA
1 AAAT---AAAAAG--ATGAA
1689342 AAATAAAAAGA
1 AAATAAAAAGA
1689353 AAAATGAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
15 18 0.35
16 13 0.25
17 6 0.12
18 5 0.10
20 9 0.18
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
AAATAAAAAGATGAA
Found at i:1689298 original size:7 final size:7
Alignment explanation
Indices: 1689266--1689359 Score: 72
Period size: 7 Copynumber: 13.1 Consensus size: 7
1689256 TTGAAGAAAA
*
1689266 AAAAAGG
1 AAAAATG
*
1689273 AACAAATA
1 AA-AAATG
1689281 AAAAGATG
1 AAAA-ATG
1689289 AAAAATG
1 AAAAATG
1689296 AAAAAATG
1 -AAAAATG
1689304 AAAAA-G
1 AAAAATG
1689310 AAAAAAAATG
1 ---AAAAATG
1689320 AAAAATG
1 AAAAATG
1689327 AAAAA--
1 AAAAATG
1689332 AAGAAATG
1 AA-AAATG
1689340 AAAAAT-
1 AAAAATG
1689346 AAAAA-G
1 AAAAATG
1689352 AAAAATG
1 AAAAATG
1689359 A
1 A
1689360 GGGTTTGAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
5 2 0.03
6 14 0.19
7 30 0.42
8 20 0.28
9 5 0.07
10 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:1689301 original size:31 final size:31
Alignment explanation
Indices: 1689265--1689359 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 31
1689255 CTTGAAGAAA
* *
1689265 AAAAAAGGAACAAA-TAAAAAGATGAAAAATG
1 AAAAAAGGAA-AAAGAAAAAAAATGAAAAATG
*
1689296 AAAAAATGAAAAAGAAAAAAAATGAAAAATG
1 AAAAAAGGAAAAAGAAAAAAAATGAAAAATG
*
1689327 AAAAAAAGAAATGAA-AAATAAAAA-GAAAAATG
1 AAAAAAGGAAA--AAGAAA-AAAAATGAAAAATG
1689359 A
1 A
1689360 GGGTTTGAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.05
31 34 0.61
32 12 0.21
33 7 0.12
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.09
Consensus pattern (31 bp):
AAAAAAGGAAAAAGAAAAAAAATGAAAAATG
Found at i:1689332 original size:16 final size:16
Alignment explanation
Indices: 1689264--1689337 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
1689254 GCTTGAAGAA
*
1689264 AAAAAAAGGAACAAAT-
1 AAAAAAATGAA-AAATG
*
1689280 AAAAAGATGAAAAATG
1 AAAAAAATGAAAAATG
1689296 -AAAAAATGAAAAA-G
1 AAAAAAATGAAAAATG
1689310 AAAAAAAATGAAAAATG
1 -AAAAAAATGAAAAATG
1689327 AAAAAAA-GAAA
1 AAAAAAATGAAA
1689338 TGAAAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
14 1 0.02
15 20 0.39
16 29 0.57
17 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:1689332 original size:24 final size:23
Alignment explanation
Indices: 1689263--1689356 Score: 99
Period size: 23 Copynumber: 4.2 Consensus size: 23
1689253 TGCTTGAAGA
*
1689263 AAAAAAAAGGAACAAAT-AAAAAG
1 AAAAAAAATGAA-AAATGAAAAAG
**
1689286 ATGAAAAATGAAAAAATGAAAAAG
1 AAAAAAAATG-AAAAATGAAAAAG
1689310 AAAAAAAATGAAAAATG--AAA-
1 AAAAAAAATGAAAAATGAAAAAG
*
1689330 AAAAGAAATGAAAAAT-AAAAAG
1 AAAAAAAATGAAAAATGAAAAAG
1689352 AAAAA
1 AAAAA
1689357 TGAGGGTTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
20 15 0.25
21 6 0.10
22 4 0.07
23 18 0.31
24 16 0.27
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.09
Consensus pattern (23 bp):
AAAAAAAATGAAAAATGAAAAAG
Found at i:1690802 original size:105 final size:105
Alignment explanation
Indices: 1690582--1690836 Score: 332
Period size: 105 Copynumber: 2.4 Consensus size: 105
1690572 CTCGCTTGAG
*
1690582 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC--TGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * *
1690647 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * * *
1690689 GAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
1690754 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
**
1690794 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATC
1690837 CACGAGAAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
104 5 0.04
105 112 0.88
107 11 0.09
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:1691019 original size:3 final size:3
Alignment explanation
Indices: 1691004--1691107 Score: 183
Period size: 3 Copynumber: 34.7 Consensus size: 3
1690994 AGTTAAAAAA
*
1691004 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1691051 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1691097 TAT TAT TAT TA
1 TAT TAT TAT TA
1691108 AGTGTGTTTA
Statistics
Matches: 97, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 1 0.01
3 93 0.96
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1701432 original size:19 final size:19
Alignment explanation
Indices: 1701408--1701455 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1701398 ATTTTAATGG
1701408 GTGCATCGATGCACTCCCT
1 GTGCATCGATGCACTCCCT
1701427 GTGCATCGATGCACTCCCT
1 GTGCATCGATGCACTCCCT
1701446 GTGCATCGAT
1 GTGCATCGAT
1701456 ACACACTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCACTCCCT
Found at i:1701432 original size:63 final size:61
Alignment explanation
Indices: 1701281--1701440 Score: 185
Period size: 62 Copynumber: 2.6 Consensus size: 61
1701271 ATCCCTAGAC
** * * ** **
1701281 GGGTGCATCGATGCACTATCTATGCATCGGTGCATAAATCTTATTCGATGTTTGTATTTAG
1 GGGTGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTAG
* * *
1701342 GGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCA-TTT-AG
*
1701406 GGGTGCATCGATGCACTCCCTGTGCATCGATGCAC
1 GGGTGCATCGATGCACTCCCTATGCATCGATGCAC
1701441 TCCCTGTGCA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
61 3 0.04
62 43 0.52
63 33 0.40
64 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (61 bp):
GGGTGCATCGATGCACTCCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTAG
Found at i:1703625 original size:17 final size:17
Alignment explanation
Indices: 1703603--1703665 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
1703593 TAAAAAATTT
1703603 GATATCATTGTTAGAGA
1 GATATCATTGTTAGAGA
* *
1703620 GATATCATT-TTAAAAAA
1 GATATCATTGTT-AGAGA
1703637 TTTGATATCATTGTTAGAGA
1 ---GATATCATTGTTAGAGA
1703657 GATATCATT
1 GATATCATT
1703666 TGCTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
20 12 0.32
21 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (17 bp):
GATATCATTGTTAGAGA
Found at i:1703638 original size:37 final size:37
Alignment explanation
Indices: 1703591--1703666 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1703581 ATCTTATGCA
1703591 TTTAAAAAATTTGATATCATTGTTAGAGAGATATCAT
1 TTTAAAAAATTTGATATCATTGTTAGAGAGATATCAT
1703628 TTTAAAAAATTTGATATCATTGTTAGAGAGATATCAT
1 TTTAAAAAATTTGATATCATTGTTAGAGAGATATCAT
1703665 TT
1 TT
1703667 GCTTTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTAAAAAATTTGATATCATTGTTAGAGAGATATCAT
Found at i:1705457 original size:20 final size:20
Alignment explanation
Indices: 1705432--1705598 Score: 135
Period size: 20 Copynumber: 8.3 Consensus size: 20
1705422 CTTGAAATTG
*
1705432 GGTTGGAACCTGAAATTTTA
1 GGTTGGAACCTGAATTTTTA
1705452 GGTTGGAAACCTGAATTTTTA
1 GGTTGG-AACCTGAATTTTTA
* * *
1705473 TGTTGGAACTTGATTTTTTA
1 GGTTGGAACCTGAATTTTTA
* * *
1705493 GATTGGAATCTTAA-TTTTA
1 GGTTGGAACCTGAATTTTTA
* **
1705512 AGTTAAAAACCT-AATTTTTA
1 GGTT-GGAACCTGAATTTTTA
*
1705532 GGTTAGAACCTGAATTTTTA
1 GGTTGGAACCTGAATTTTTA
*
1705552 GGTTGGGAAACCTG-AGTTTTA
1 GGTT-GG-AACCTGAATTTTTA
* *
1705573 AGTTGGAAACCTG-ATTATTA
1 GGTTGG-AACCTGAATTTTTA
1705593 GGTTGG
1 GGTTGG
1705599 GGACTAGATT
Statistics
Matches: 118, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.13
20 69 0.58
21 28 0.24
22 6 0.05
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (20 bp):
GGTTGGAACCTGAATTTTTA
Found at i:1705492 original size:41 final size:40
Alignment explanation
Indices: 1705432--1705617 Score: 139
Period size: 41 Copynumber: 4.6 Consensus size: 40
1705422 CTTGAAATTG
*
1705432 GGTT-GGAACCTGAAATTTTAGGTTGGAAACCTGAATTTTTA
1 GGTTGGGAACCTG-ATTTTTAGGTTGG-AACCTGAATTTTTA
* * * * *
1705473 TGTT-GGAACTTGATTTTTTAGATTGGAATCTTAA-TTTTA
1 GGTTGGGAACCTGA-TTTTTAGGTTGGAACCTGAATTTTTA
* *** * *
1705512 AGTTAAAAACCTAATTTTTAGGTTAGAACCTGAATTTTTA
1 GGTTGGGAACCTGATTTTTAGGTTGGAACCTGAATTTTTA
* * *
1705552 GGTTGGGAAACCTGAGTTTTAAGTTGGAAACCTG-ATTATTA
1 GGTTGGG-AACCTGATTTTTAGGTTGG-AACCTGAATTTTTA
*
1705593 GGTTGGGGA-CTAGATTTTTAGGTTG
1 GGTTGGGAACCT-GATTTTTAGGTTG
1705618 AAAGCTAGAT
Statistics
Matches: 112, Mismatches: 27, Indels: 13
0.74 0.18 0.09
Matches are distributed among these distances:
39 26 0.23
40 32 0.29
41 48 0.43
42 6 0.05
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.40
Consensus pattern (40 bp):
GGTTGGGAACCTGATTTTTAGGTTGGAACCTGAATTTTTA
Found at i:1707147 original size:2 final size:2
Alignment explanation
Indices: 1707140--1707195 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1707130 TAATATTTGG
1707140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1707182 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1707196 TAAATTTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1707408 original size:2 final size:2
Alignment explanation
Indices: 1707401--1707425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1707391 TAATTTAAAC
1707401 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1707426 TAAGACTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1711549 original size:18 final size:17
Alignment explanation
Indices: 1711518--1711551 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1711508 ATCATGTCAA
1711518 TTAATAACCCAATTAAG
1 TTAATAACCCAATTAAG
*
1711535 TTAATTAACCTAATTAA
1 TTAA-TAACCCAATTAA
1711552 ACTAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAATAACCCAATTAAG
Found at i:1711557 original size:18 final size:18
Alignment explanation
Indices: 1711522--1711560 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1711512 TGTCAATTAA
**
1711522 TAACCCAATTAAGTTAAT
1 TAACCCAATTAAACTAAT
*
1711540 TAACCTAATTAAACTAAT
1 TAACCCAATTAAACTAAT
1711558 TAA
1 TAA
1711561 TAAAATAATT
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:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (18 bp):
TAACCCAATTAAACTAAT
Found at i:1718029 original size:33 final size:34
Alignment explanation
Indices: 1717991--1718061 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1717981 AACCTTACAC
*
1717991 TCCCTAG-TTTTTC-CGGGCTAAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCT-AAACTAGAACCTT
*
1718024 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
1718058 TCCC
1 TCCC
1718062 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 7 0.21
34 21 0.62
35 6 0.18
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:1718340 original size:21 final size:21
Alignment explanation
Indices: 1718316--1718358 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1718306 CCCAGAATAG
*
1718316 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1718337 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1718358 A
1 A
1718359 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1718420 original size:21 final size:21
Alignment explanation
Indices: 1718394--1718436 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1718384 CTGTTGAACA
1718394 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1718415 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1718436 G
1 G
1718437 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:1718524 original size:19 final size:20
Alignment explanation
Indices: 1718497--1718535 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1718487 GGTATGTACC
*
1718497 GGGGTATCTGTA-CCCTGGG
1 GGGGAATCTGTACCCCTGGG
1718516 GGGGAATCTGTACCCCTGGG
1 GGGGAATCTGTACCCCTGGG
1718536 CAATCTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (20 bp):
GGGGAATCTGTACCCCTGGG
Found at i:1721519 original size:34 final size:32
Alignment explanation
Indices: 1721466--1721535 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1721456 ACCTTACAAC
*
1721466 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1721498 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1721532 TCCC
1 TCCC
1721536 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1721775 original size:20 final size:22
Alignment explanation
Indices: 1721750--1721789 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1721740 AGTCGTATAT
1721750 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1721770 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1721790 TATGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1721841 original size:21 final size:21
Alignment explanation
Indices: 1721817--1721859 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1721807 CCCAGAATAG
*
1721817 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1721838 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1721859 A
1 A
1721860 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1721984 original size:15 final size:15
Alignment explanation
Indices: 1721964--1721993 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1721954 TACCCCTTGG
1721964 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1721979 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1721994 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1722000 original size:35 final size:36
Alignment explanation
Indices: 1721944--1722014 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1721934 TTTAGACAGG
* *
1721944 GGGGAATCGGTA-CCCCTTGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
1721979 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
1722015 CCTGGGCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.14, C:0.27, G:0.37, T:0.23
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:1722003 original size:21 final size:21
Alignment explanation
Indices: 1721979--1722020 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1721969 ATCTGTACCC
*
1721979 GGGGTATCTGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
1722000 GGGGAATCTGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
1722021 CAATCTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:1726265 original size:15 final size:15
Alignment explanation
Indices: 1726245--1726278 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1726235 ATGCAACTTT
1726245 TTGATATTAAAGTAA
1 TTGATATTAAAGTAA
1726260 TTGATATTAAAGTAA
1 TTGATATTAAAGTAA
1726275 TTGA
1 TTGA
1726279 GTTTCTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (15 bp):
TTGATATTAAAGTAA
Found at i:1735670 original size:13 final size:13
Alignment explanation
Indices: 1735652--1735692 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1735642 AAAATTAATG
1735652 AAAATAAATGAAT
1 AAAATAAATGAAT
*
1735665 AAAATAAATAAAT
1 AAAATAAATGAAT
*
1735678 -AAAT-ATTGAAT
1 AAAATAAATGAAT
1735689 AAAA
1 AAAA
1735693 AATAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.21
12 7 0.29
13 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (13 bp):
AAAATAAATGAAT
Found at i:1735679 original size:21 final size:21
Alignment explanation
Indices: 1735653--1735716 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 21
1735643 AAATTAATGA
1735653 AAATAAATGAATAAAATAAAT
1 AAATAAATGAATAAAATAAAT
1735674 AAATAAATATTGAAT-AAA-AAAT
1 AAAT-AA-A-TGAATAAAATAAAT
1735696 -AAT-AATGAA-AAAATAAAT
1 AAATAAATGAATAAAATAAAT
1735714 AAA
1 AAA
1735717 GATAATATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
19 3 0.08
21 7 0.19
22 6 0.16
23 4 0.11
24 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAAATGAATAAAATAAAT
Found at i:1743747 original size:13 final size:13
Alignment explanation
Indices: 1743729--1743761 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1743719 AGCATTGTGA
*
1743729 AAAGAAAATAATG
1 AAAGAAAATAAAG
1743742 AAAGAAAATAAAG
1 AAAGAAAATAAAG
1743755 AAAGAAA
1 AAAGAAA
1743762 GATGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:1751288 original size:15 final size:15
Alignment explanation
Indices: 1751268--1751300 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1751258 ACCGTCCCCC
1751268 TACTGCCCTGTCTCA
1 TACTGCCCTGTCTCA
1751283 TACTGCCCTGTCTCA
1 TACTGCCCTGTCTCA
1751298 TAC
1 TAC
1751301 AGTCATACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.39, G:0.12, T:0.33
Consensus pattern (15 bp):
TACTGCCCTGTCTCA
Found at i:1759636 original size:18 final size:18
Alignment explanation
Indices: 1759613--1759681 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
1759603 GGGGCACAGG
1759613 GGAGAAGAAAGAAA-AACA
1 GGAGAAGAAAGAAAGAA-A
*
1759631 GGAGAATAAAGAAAGAAA
1 GGAGAAGAAAGAAAGAAA
1759649 GGAAGAAG-AAGAAAGAAA
1 GG-AGAAGAAAGAAAGAAA
*
1759667 --AGAAGAAAGGAAGAA
1 GGAGAAGAAAGAAAGAA
1759682 GAAAAAATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
15 5 0.11
16 8 0.18
18 26 0.58
19 6 0.13
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.01
Consensus pattern (18 bp):
GGAGAAGAAAGAAAGAAA
Found at i:1759672 original size:26 final size:26
Alignment explanation
Indices: 1759638--1759729 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 26
1759628 ACAGGAGAAT
1759638 AAAGAAAGAAAGGAAGAAGAAGAAAGA
1 AAAG-AAGAAAGGAAGAAGAAGAAAGA
* *
1759665 AAAGAAGAAAGGAAGAAGAAAAAATAGG
1 AAAGAAGAAAGGAAGAAG-AAGAA-AGA
1759693 AAAGAAGAAGAGGAAAGATA-AAGAAAGA
1 AAAGAAGAA-AGG-AAGA-AGAAGAAAGA
1759721 ATAAGAAGA
1 A-AAGAAGA
1759730 TAAGAAAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
26 14 0.25
27 8 0.15
28 14 0.25
29 14 0.25
30 4 0.07
31 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.03
Consensus pattern (26 bp):
AAAGAAGAAAGGAAGAAGAAGAAAGA
Found at i:1759702 original size:23 final size:21
Alignment explanation
Indices: 1759633--1759729 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 21
1759623 GAAAAACAGG
* *
1759633 AGAATAAAGAAAGAAAGGAAGA
1 AGAAGAAAAAAAGAAA-GAAGA
1759655 AGAAGAAAGAAAAG-AAGAAAGGA
1 AGAAGAAA-AAAAGAAAG-AA-GA
1759678 AGAAGAAAAAATAGGAAAGAAGA
1 AGAAGAAAAAA-A-GAAAGAAGA
* *
1759701 AGAGGAAAGATAAAGAAAGAATA
1 AGAAGAAA-A-AAAGAAAGAAGA
1759724 AGAAGA
1 AGAAGA
1759730 TAAGAAAGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
21 1 0.02
22 14 0.23
23 37 0.60
24 5 0.08
25 5 0.08
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (21 bp):
AGAAGAAAAAAAGAAAGAAGA
Found at i:1763125 original size:20 final size:20
Alignment explanation
Indices: 1763076--1763127 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1763066 TTACACAGTG
*
1763076 GTATCGATACTGTGAGCATA
1 GTATCGATATTGTGAGCATA
*
1763096 ATATCGATATTGTGAGCATA
1 GTATCGATATTGTGAGCATA
1763116 GTATCGATATTG
1 GTATCGATATTG
1763128 GTCAGGCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (20 bp):
GTATCGATATTGTGAGCATA
Found at i:1768629 original size:15 final size:17
Alignment explanation
Indices: 1768595--1768629 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1768585 TTTTTCTTTT
1768595 TATAAGTGTGTTTAATA
1 TATAAGTGTGTTTAATA
1768612 TATAAGTGT-TTTAA-A
1 TATAAGTGTGTTTAATA
1768627 TAT
1 TAT
1768630 TTCAAACGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (17 bp):
TATAAGTGTGTTTAATA
Found at i:1769176 original size:232 final size:232
Alignment explanation
Indices: 1768770--1769233 Score: 928
Period size: 232 Copynumber: 2.0 Consensus size: 232
1768760 AAGATACATT
1768770 TTTAATATATTTGAAATTCAAAAATAAACTATTATATTTTTTAAATAAAAACAGTCTCCCACTGA
1 TTTAATATATTTGAAATTCAAAAATAAACTATTATATTTTTTAAATAAAAACAGTCTCCCACTGA
1768835 CTAGAATGCACTAGAAATTAACATAGAAGAAAAACATTGGAAGTGATAAAACCATTAATACAAAC
66 CTAGAATGCACTAGAAATTAACATAGAAGAAAAACATTGGAAGTGATAAAACCATTAATACAAAC
1768900 AATGTTCATACCTAACAAAGGTGACCAAAATGGACGAGCCTTAAATTCATGTTCATCATTTGCAA
131 AATGTTCATACCTAACAAAGGTGACCAAAATGGACGAGCCTTAAATTCATGTTCATCATTTGCAA
1768965 TCCATTGGTTGCAGTTACACCACGTGATTGTATGTGA
196 TCCATTGGTTGCAGTTACACCACGTGATTGTATGTGA
1769002 TTTAATATATTTGAAATTCAAAAATAAACTATTATATTTTTTAAATAAAAACAGTCTCCCACTGA
1 TTTAATATATTTGAAATTCAAAAATAAACTATTATATTTTTTAAATAAAAACAGTCTCCCACTGA
1769067 CTAGAATGCACTAGAAATTAACATAGAAGAAAAACATTGGAAGTGATAAAACCATTAATACAAAC
66 CTAGAATGCACTAGAAATTAACATAGAAGAAAAACATTGGAAGTGATAAAACCATTAATACAAAC
1769132 AATGTTCATACCTAACAAAGGTGACCAAAATGGACGAGCCTTAAATTCATGTTCATCATTTGCAA
131 AATGTTCATACCTAACAAAGGTGACCAAAATGGACGAGCCTTAAATTCATGTTCATCATTTGCAA
1769197 TCCATTGGTTGCAGTTACACCACGTGATTGTATGTGA
196 TCCATTGGTTGCAGTTACACCACGTGATTGTATGTGA
1769234 GACCTTTTTC
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 232 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (232 bp):
TTTAATATATTTGAAATTCAAAAATAAACTATTATATTTTTTAAATAAAAACAGTCTCCCACTGA
CTAGAATGCACTAGAAATTAACATAGAAGAAAAACATTGGAAGTGATAAAACCATTAATACAAAC
AATGTTCATACCTAACAAAGGTGACCAAAATGGACGAGCCTTAAATTCATGTTCATCATTTGCAA
TCCATTGGTTGCAGTTACACCACGTGATTGTATGTGA
Found at i:1770881 original size:2 final size:2
Alignment explanation
Indices: 1770874--1770901 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1770864 AACTCTTCAA
1770874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1770902 GATGTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1771411 original size:21 final size:22
Alignment explanation
Indices: 1771376--1771419 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1771366 AAAGAAGATG
*
1771376 ACAGTAACTTTTCATTATCAAC
1 ACAGTAACTTTTCATTAACAAC
1771398 ACAGTAAC-TTTCATTAACAAC
1 ACAGTAACTTTTCATTAACAAC
1771419 A
1 A
1771420 GAAAGGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (22 bp):
ACAGTAACTTTTCATTAACAAC
Found at i:1775012 original size:17 final size:18
Alignment explanation
Indices: 1774980--1775017 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1774970 ATATTTTTAT
*
1774980 ATTTTATATCAATAATAA
1 ATTTTAAATCAATAATAA
*
1774998 ATTTTAAAT-AATAATGA
1 ATTTTAAATCAATAATAA
1775015 ATT
1 ATT
1775018 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTTTAAATCAATAATAA
Found at i:1776226 original size:20 final size:21
Alignment explanation
Indices: 1776201--1776243 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1776191 CGGTAAAAAA
1776201 TTACCTAAAACATTATT-TTT
1 TTACCTAAAACATTATTGTTT
1776221 TTACCTAAAACATTATTGTTT
1 TTACCTAAAACATTATTGTTT
1776242 TT
1 TT
1776244 TAACATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (21 bp):
TTACCTAAAACATTATTGTTT
Found at i:1781435 original size:26 final size:26
Alignment explanation
Indices: 1781399--1781448 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1781389 AAGGACCACT
1781399 ATGTCCCGAAGGACCACATAGAACAC
1 ATGTCCCGAAGGACCACATAGAACAC
*
1781425 ATGTCCCGAAGGACCACGTAGAAC
1 ATGTCCCGAAGGACCACATAGAAC
1781449 CCTTGACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.30, G:0.22, T:0.12
Consensus pattern (26 bp):
ATGTCCCGAAGGACCACATAGAACAC
Found at i:1782438 original size:21 final size:23
Alignment explanation
Indices: 1782409--1782461 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
1782399 AGTTTCCCAA
*
1782409 GTATTGATACCCTC-TACATA-G
1 GTATCGATACCCTCTTACATATG
*
1782430 GTATCGATA-CCTCTTCCATATG
1 GTATCGATACCCTCTTACATATG
1782452 GTATCGATAC
1 GTATCGATAC
1782462 TGTTCATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 10 0.37
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (23 bp):
GTATCGATACCCTCTTACATATG
Found at i:1785118 original size:96 final size:98
Alignment explanation
Indices: 1785003--1785196 Score: 374
Period size: 96 Copynumber: 2.0 Consensus size: 98
1784993 TGGAAAATCA
1785003 CAACCAAAGAAAGATTCAAAAATTTCAACTCATCAATTAAATTAATTCAGATACACTTCGGCATC
1 CAACCAAAGAAAGATTCAAAAATTTCAACTCATCAATTAAATTAATTCAGATACACTTCGGCATC
1785068 TAGTATTTTTATTTTTGA-GG-TTAGTATGATT
66 TAGTATTTTTATTTTTGATGGTTTAGTATGATT
1785099 CAACCAAAGAAAGATTCAAAAATTTCAACTCATCAATTAAATTAATTCAGATACACTTCGGCATC
1 CAACCAAAGAAAGATTCAAAAATTTCAACTCATCAATTAAATTAATTCAGATACACTTCGGCATC
1785164 TAGTATTTTTATTTTTGATGGTTTAGTATGATT
66 TAGTATTTTTATTTTTGATGGTTTAGTATGATT
1785197 TGATCTTGAG
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 83 0.86
97 2 0.02
98 11 0.11
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (98 bp):
CAACCAAAGAAAGATTCAAAAATTTCAACTCATCAATTAAATTAATTCAGATACACTTCGGCATC
TAGTATTTTTATTTTTGATGGTTTAGTATGATT
Found at i:1785457 original size:21 final size:21
Alignment explanation
Indices: 1785431--1785489 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1785421 ATTTACCGTG
*
1785431 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCATCGCGGGCGCT
*
1785452 ATTGCGGCCATCGCGGACGCT
1 ATTGCGGCCATCGCGGGCGCT
* * *
1785473 ATTACGACCTTCGCGGG
1 ATTGCGGCCATCGCGGG
1785490 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.12, C:0.32, G:0.36, T:0.20
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGGCGCT
Found at i:1793814 original size:2 final size:2
Alignment explanation
Indices: 1793807--1793880 Score: 118
Period size: 2 Copynumber: 38.0 Consensus size: 2
1793797 AAAACATTAT
1793807 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
1793849 TA T- TA CTA TA TA TA TA TA TA TA -A TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1793881 GTTAATGATA
Statistics
Matches: 68, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.04
2 63 0.93
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1795663 original size:15 final size:15
Alignment explanation
Indices: 1795643--1795684 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1795633 ATAAAACACT
1795643 AATTATATAAATATA
1 AATTATATAAATATA
*
1795658 AATTATATAAACATA
1 AATTATATAAATATA
*
1795673 AATTATTTAAAT
1 AATTATATAAAT
1795685 TACGTAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTATATAAATATA
Found at i:1795778 original size:10 final size:10
Alignment explanation
Indices: 1795759--1795804 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1795749 AAAATTTCAC
1795759 TAAT-TAAAA
1 TAATATAAAA
1795768 TAATATAAAA
1 TAATATAAAA
1795778 TAATA-AAAA
1 TAATATAAAA
1795787 TTAA-ATAAAA
1 -TAATATAAAA
1795797 TAAT-TAAA
1 TAATATAAA
1795805 TTTGATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAATATAAAA
Found at i:1795786 original size:19 final size:19
Alignment explanation
Indices: 1795759--1795800 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1795749 AAAATTTCAC
*
1795759 TAATTAAAA-TAATATAAAA
1 TAATAAAAATTAA-ATAAAA
1795778 TAATAAAAATTAAATAAAA
1 TAATAAAAATTAAATAAAA
1795797 TAAT
1 TAAT
1795801 TAAATTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAATAAAAATTAAATAAAA
Found at i:1796478 original size:104 final size:104
Alignment explanation
Indices: 1796369--1796579 Score: 422
Period size: 104 Copynumber: 2.0 Consensus size: 104
1796359 GAAAAAGTAA
1796369 AAAAAAAGTAATCCCAATACAAATGTTATAGAAATTAATATTAGAAAGTAATCCTTGATTTATAG
1 AAAAAAAGTAATCCCAATACAAATGTTATAGAAATTAATATTAGAAAGTAATCCTTGATTTATAG
1796434 GTGACTCCCATTAATGAATTATTTAATATGCAATTGATC
66 GTGACTCCCATTAATGAATTATTTAATATGCAATTGATC
1796473 AAAAAAAGTAATCCCAATACAAATGTTATAGAAATTAATATTAGAAAGTAATCCTTGATTTATAG
1 AAAAAAAGTAATCCCAATACAAATGTTATAGAAATTAATATTAGAAAGTAATCCTTGATTTATAG
1796538 GTGACTCCCATTAATGAATTATTTAATATGCAATTGATC
66 GTGACTCCCATTAATGAATTATTTAATATGCAATTGATC
1796577 AAA
1 AAA
1796580 GAGCTTTAAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (104 bp):
AAAAAAAGTAATCCCAATACAAATGTTATAGAAATTAATATTAGAAAGTAATCCTTGATTTATAG
GTGACTCCCATTAATGAATTATTTAATATGCAATTGATC
Found at i:1800184 original size:14 final size:14
Alignment explanation
Indices: 1800167--1800198 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1800157 GGTCATTTGA
*
1800167 ATTAATATATAATT
1 ATTAATATATAAAT
1800181 ATTAATATATAAAT
1 ATTAATATATAAAT
1800195 ATTA
1 ATTA
1800199 TAACATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTAATATATAAAT
Found at i:1802271 original size:58 final size:59
Alignment explanation
Indices: 1802169--1802303 Score: 159
Period size: 58 Copynumber: 2.3 Consensus size: 59
1802159 ATCCAAAAAG
* * * ** *
1802169 GAACCCAAACA-AAATGCAATAATCAGGAAACAAGAAGGGAACGTTACCCTTTGAAGAG
1 GAACCCAAACATGAATACAGTAATCAGGAAACAAGAAGGGAACGTTACCCTCCGAAGAA
* * *
1802227 GAATCCAAATA-GAATACAGTAATCAGGAAATAAGATAGGG-ACGTTACCCTCCGAAGAA
1 GAACCCAAACATGAATACAGTAATCAGGAAACAAGA-AGGGAACGTTACCCTCCGAAGAA
1802285 GAACCCAAACATGAATACA
1 GAACCCAAACATGAATACA
1802304 ATATTACATC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 53 0.83
59 11 0.17
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (59 bp):
GAACCCAAACATGAATACAGTAATCAGGAAACAAGAAGGGAACGTTACCCTCCGAAGAA
Found at i:1802407 original size:2 final size:2
Alignment explanation
Indices: 1802400--1802432 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1802390 CACAACATGA
1802400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1802433 TACAGAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1821861 original size:48 final size:48
Alignment explanation
Indices: 1821803--1822076 Score: 363
Period size: 48 Copynumber: 5.7 Consensus size: 48
1821793 TAGATAGTGG
* * *
1821803 ATCAAGAGTTTTACTTGCAAAGTCAATTGTAAGGTATATAGATCATGA
1 ATCACGAGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
** * * *
1821851 ATCACGAGTTTTGTTTGCAAGGTCAATTGTAATGTTCATAGATCTTGA
1 ATCACGAGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
* * * *
1821899 ATCACAAGTTTTTCTTGCAAGTTCAATTGTAAGGTACATAGATCGTGA
1 ATCACGAGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
* *
1821947 ATCACGGGTTTTACTTACAAGGTCAATTGTAAGGTACATAGATCATGA
1 ATCACGAGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
*
1821995 ATCAC-AGGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCGTGA
1 ATCACGA-GTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
* *
1822043 ATCAC-AGATTTTACTTGCAATGTCAATTGAAAGG
1 ATCACGAG-TTTTACTTGCAAGGTCAATTGTAAGG
1822077 GTGTAATTGT
Statistics
Matches: 198, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
47 1 0.01
48 197 0.99
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (48 bp):
ATCACGAGTTTTACTTGCAAGGTCAATTGTAAGGTACATAGATCATGA
Found at i:1830331 original size:2 final size:2
Alignment explanation
Indices: 1830326--1830350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1830316 AGTTTTTTGT
1830326 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1830351 TTATCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1839994 original size:24 final size:24
Alignment explanation
Indices: 1839962--1840019 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
1839952 TGCAAAATAT
*
1839962 GTATCGATACTATTTTACACGGTA
1 GTATCGATACTACTTTACACGGTA
*
1839986 GTATCGATACTACTTTACATGGTA
1 GTATCGATACTACTTTACACGGTA
1840010 GTATCGATAC
1 GTATCGATAC
1840020 CATTATCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
GTATCGATACTACTTTACACGGTA
Found at i:1845089 original size:23 final size:23
Alignment explanation
Indices: 1845036--1845097 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1845026 CAAAACCCGT
* *
1845036 GGAGGGTATTGGTACCTATTCAA
1 GGAGGGTATTGGTACCCATGCAA
*
1845059 GGATGGTATTGGTACCCATGCAAA
1 GGAGGGTATTGGTACCCATGC-AA
*
1845083 GG-GGGTATTGATACC
1 GGAGGGTATTGGTACC
1845098 TAGCGCGCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (23 bp):
GGAGGGTATTGGTACCCATGCAA
Found at i:1856906 original size:46 final size:46
Alignment explanation
Indices: 1856854--1856959 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
1856844 TTATTCGTTA
1856854 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1856900 ATTTCATTTATGGCATTCTTTCATGCCTTAATTCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1856946 ATTTCATTTATGGC
1 ATTTCATTTATGGC
1856960 TTCGTTTTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1856920 original size:26 final size:26
Alignment explanation
Indices: 1856854--1856959 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 26
1856844 TTATTCGTTA
1856854 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
*
1856880 ----C-TTAAT-GCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
*
1856900 ATTTCATTTATGGCATTCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1856926 ----C-TTAAT-TCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1856946 ATTTCATTTATGGC
1 ATTTCATTTATGGC
1856960 TTCGTTTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
20 26 0.43
21 8 0.13
22 2 0.03
24 2 0.03
25 8 0.13
26 14 0.23
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTTCATTTATGGCATCCTTTCATGC
Found at i:1858711 original size:14 final size:14
Alignment explanation
Indices: 1858692--1858723 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1858682 CGTTCGTGAA
1858692 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1858706 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1858720 CGTT
1 CGTT
1858724 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1858740 original size:24 final size:24
Alignment explanation
Indices: 1858693--1858740 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1858683 GTTCGTGAAC
* *
1858693 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
1858717 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
1858741 ATTTAACCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.54
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:1859551 original size:16 final size:16
Alignment explanation
Indices: 1859495--1859549 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1859485 GGGTCTCCAA
1859495 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1859511 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
1859527 CGTTTATTTTCATGTT
1 CGTTTATGTTCGTGTT
1859543 CGTTTAT
1 CGTTTAT
1859550 TTATTAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.09, C:0.13, G:0.20, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1868972 original size:12 final size:12
Alignment explanation
Indices: 1868955--1868979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1868945 GTCAAATAAT
1868955 TTAGGCACCAAA
1 TTAGGCACCAAA
1868967 TTAGGCACCAAA
1 TTAGGCACCAAA
1868979 T
1 T
1868980 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:1873588 original size:12 final size:12
Alignment explanation
Indices: 1873571--1873595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1873561 GTCAAATAAT
1873571 TTAGGCACCAAA
1 TTAGGCACCAAA
1873583 TTAGGCACCAAA
1 TTAGGCACCAAA
1873595 T
1 T
1873596 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Done.