Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 40
Found at i:3232488 original size:14 final size:14
Alignment explanation
Indices: 3232428--3232490 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
3232418 TTATTTATTA
3232428 AATATTAATATAAT
1 AATATTAATATAAT
3232442 AAT-TTAATATAA-
1 AATATTAATATAAT
*
3232454 AATATTTATTATTATAT
1 AATA-TTAATA-TA-AT
* *
3232471 AATATTATTTTAAT
1 AATATTAATATAAT
3232485 AATATT
1 AATATT
3232491 TTATTTACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
12 3 0.07
13 9 0.21
14 16 0.38
15 4 0.10
16 6 0.14
17 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTAATATAAT
Found at i:3232494 original size:16 final size:16
Alignment explanation
Indices: 3232449--3232496 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3232439 AATAATTTAA
*
3232449 TATAAAATATTTATTAT
1 TATATAATATTTATT-T
3232466 TATATAATA-TTATTT
1 TATATAATATTTATTT
3232481 TA-ATAATATTTTATTT
1 TATATAATA-TTTATTT
3232497 ACATGTACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.21
15 3 0.11
16 11 0.39
17 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATAATATTTATTT
Found at i:3232671 original size:19 final size:19
Alignment explanation
Indices: 3232633--3232678 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3232623 TAATAATGAA
*
3232633 TAATATTAATTTATATATT
1 TAATATTAATTAATATATT
3232652 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATATATT
*
3232671 TAGTATTA
1 TAATATTA
3232679 TGTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTAATTAATATATT
Found at i:3232685 original size:30 final size:27
Alignment explanation
Indices: 3232639--3232700 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
3232629 TGAATAATAT
*
3232639 TAATTTATATATTTAATATTAATA-TAA
1 TAATTTATATATTTAATA-AAATACTAA
3232666 TAATTTAGTATTATGTTAATAAAATACTAA
1 TAATTTA-TA-TAT-TTAATAAAATACTAA
3232696 TAATT
1 TAATT
3232701 AAAATTAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 2 0.07
29 7 0.23
30 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TAATTTATATATTTAATAAAATACTAA
Found at i:3235721 original size:29 final size:29
Alignment explanation
Indices: 3235689--3235813 Score: 125
Period size: 29 Copynumber: 4.3 Consensus size: 29
3235679 AAGATAAAAT
3235689 ATATATTTTTATATTAAAAATAAAATAAA
1 ATATATTTTTATATTAAAAATAAAATAAA
3235718 ATATATTTTTATATT-AAAATAAAAATAAA
1 ATATATTTTTATATTAAAAAT-AAAATAAA
* *
3235747 ATATA-TTTAATAATTTAAAAT--AATAAA
1 ATATATTTTTAT-ATTAAAAATAAAATAAA
** * *
3235774 ATATATTTAACAAATTAAAACA-GAAATAAA
1 ATATATTT-TTATATTAAAA-ATAAAATAAA
3235804 ATATATTTTT
1 ATATATTTTT
3235814 TAAATATAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
27 11 0.14
28 18 0.22
29 33 0.41
30 19 0.23
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (29 bp):
ATATATTTTTATATTAAAAATAAAATAAA
Found at i:3246844 original size:29 final size:29
Alignment explanation
Indices: 3246802--3246866 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
3246792 AAAAATGCTA
*
3246802 ACCCTTTGGTCTTCCCAAATCTGATCACG
1 ACCCTTTGGTCTTCCAAAATCTGATCACG
3246831 ACCCTTTGGTCTTCCAAAATCTGATCACG
1 ACCCTTTGGTCTTCCAAAATCTGATCACG
3246860 ACCCTTT
1 ACCCTTT
3246867 TCTGTAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (29 bp):
ACCCTTTGGTCTTCCAAAATCTGATCACG
Found at i:3246980 original size:25 final size:26
Alignment explanation
Indices: 3246930--3246984 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 26
3246920 TGAATGCAAA
*
3246930 TGCAAATCAATAGTTAAAAAAGTATT
1 TGCAAATCAATACTTAAAAAAGTATT
3246956 TGCAAATCAATACTT-AAAAAGTATT
1 TGCAAATCAATACTTAAAAAAGTATT
3246981 TGCA
1 TGCA
3246985 TTTGTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (26 bp):
TGCAAATCAATACTTAAAAAAGTATT
Found at i:3254803 original size:43 final size:44
Alignment explanation
Indices: 3254737--3254825 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 44
3254727 TATTATTTTT
*
3254737 TTATATAATAATAATTTAAGTAAATTACAAGGTTACTCACTGAA
1 TTATATAATAATAATTTAAGTAAATTACAAGCTTACTCACTGAA
* * *
3254781 TTATAT-ATAATAATTTAGGTAAATTATACGCTTACTCACTGAA
1 TTATATAATAATAATTTAAGTAAATTACAAGCTTACTCACTGAA
3254824 TT
1 TT
3254826 TTATTCTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 35 0.85
44 6 0.15
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (44 bp):
TTATATAATAATAATTTAAGTAAATTACAAGCTTACTCACTGAA
Found at i:3255208 original size:51 final size:51
Alignment explanation
Indices: 3255131--3255227 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
3255121 CAGTATGGCG
*
3255131 CGCCCCCTGCAGCGCGCTTTACGCTGA-TATGGCGTCACGTGGGGTAAGGCA
1 CGCCCCCTGCAGCGCGCTTTACGCTGAGT-TGGCGCCACGTGGGGTAAGGCA
* * *
3255182 CGCCCCCTGCAGCGCGTTTTATGCTGAGTTGGTGCCACGTGGGGTA
1 CGCCCCCTGCAGCGCGCTTTACGCTGAGTTGGCGCCACGTGGGGTA
3255228 TAGCGCGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.13, C:0.30, G:0.34, T:0.23
Consensus pattern (51 bp):
CGCCCCCTGCAGCGCGCTTTACGCTGAGTTGGCGCCACGTGGGGTAAGGCA
Found at i:3255663 original size:13 final size:13
Alignment explanation
Indices: 3255645--3255669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3255635 TTTTTTATTT
3255645 TTACTTTCTTTTG
1 TTACTTTCTTTTG
3255658 TTACTTTCTTTT
1 TTACTTTCTTTT
3255670 TTTGTTAATT
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:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (13 bp):
TTACTTTCTTTTG
Found at i:3266607 original size:21 final size:21
Alignment explanation
Indices: 3266560--3266646 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
3266550 AGCGGAAAAT
*
3266560 GAAGCAAGGGAAGCAGAGAGA
1 GAAGCAACGGAAGCAGAGAGA
* * *
3266581 GCAGCATCGGAAGCAGAGAAA
1 GAAGCAACGGAAGCAGAGAGA
* * *
3266602 GAAGCAGCGGCAGCACAGAGA
1 GAAGCAACGGAAGCAGAGAGA
* * *
3266623 GAAGCAACGGCAGCACAAAGA
1 GAAGCAACGGAAGCAGAGAGA
3266644 GAA
1 GAA
3266647 ACATCATATC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.45, C:0.18, G:0.36, T:0.01
Consensus pattern (21 bp):
GAAGCAACGGAAGCAGAGAGA
Found at i:3267102 original size:43 final size:43
Alignment explanation
Indices: 3267032--3267145 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
3267022 TGTATACTAG
* * * * **
3267032 AAACGCCGCTAAAA-ATCATCACATACTGCATCGTTTGTGGGGA
1 AAACGCCGC-AAAATATCAACACCTACTGCAGCGTTCGTAAGGA
* *
3267075 AAACGCTGCAAAATATCAACACCTACTGCAGCGTTCGTAAGTA
1 AAACGCCGCAAAATATCAACACCTACTGCAGCGTTCGTAAGGA
* *
3267118 AAACGCCGCTAAATCTCAACACCTACTG
1 AAACGCCGCAAAATATCAACACCTACTG
3267146 TGGCATTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 4 0.07
43 55 0.93
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCGCAAAATATCAACACCTACTGCAGCGTTCGTAAGGA
Found at i:3279204 original size:20 final size:20
Alignment explanation
Indices: 3279176--3279214 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3279166 CAAGAAATTA
3279176 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
3279196 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
3279215 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:3287739 original size:18 final size:19
Alignment explanation
Indices: 3287693--3287741 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3287683 TTGGACCCTT
*
3287693 AGTGCATCGGTGCACTAAA
1 AGTGCATCGATGCACTAAA
3287712 AGTGCATCGATGCA-TAAA
1 AGTGCATCGATGCACTAAA
3287730 A-TGCATTCGATG
1 AGTGCA-TCGATG
3287742 TTTTGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 13 0.46
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAA
Found at i:3287836 original size:45 final size:46
Alignment explanation
Indices: 3287757--3287844 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
3287747 AAAAAGCCTA
* *
3287757 AGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCACTG
1 AGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCACTG
*
3287803 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
3287845 TTTGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCACTG
Found at i:3299515 original size:45 final size:45
Alignment explanation
Indices: 3299451--3299541 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
3299441 TCAGAAGTGA
3299451 AGCTAAATGAGGCAGAGTGGGTACAGGCCAGATATGACCAATTGG
1 AGCTAAATGAGGCAGAGTGGGTACAGGCCAGATATGACCAATTGG
3299496 AGCTAAATGAGGCAGAGTGGGTACAGGCCAGATATGACCAATTGG
1 AGCTAAATGAGGCAGAGTGGGTACAGGCCAGATATGACCAATTGG
3299541 A
1 A
3299542 TTTGATTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.33, T:0.18
Consensus pattern (45 bp):
AGCTAAATGAGGCAGAGTGGGTACAGGCCAGATATGACCAATTGG
Found at i:3299847 original size:1 final size:1
Alignment explanation
Indices: 3299841--3300001 Score: 115
Period size: 1 Copynumber: 161.0 Consensus size: 1
3299831 CTTGAAGATG
* ** * * * * *
3299841 AAAAAAAGAAAAAAAATGAAAAATAAAAAATAAAAAAAAAAAAAAATAAAAAAAAATAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** ** **
3299906 AAAAAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAAATGAAAAAATGAAAAAAAATGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
3299971 AATGAAAAAAAAAACAAAAACAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3300002 CAAATAAAAT
Statistics
Matches: 119, Mismatches: 41, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 119 1.00
ACGTcount: A:0.86, C:0.02, G:0.04, T:0.09
Consensus pattern (1 bp):
A
Found at i:3299861 original size:18 final size:18
Alignment explanation
Indices: 3299838--3299982 Score: 145
Period size: 18 Copynumber: 8.1 Consensus size: 18
3299828 TTGCTTGAAG
3299838 ATGAAAAAAAGAAAAAAA
1 ATGAAAAAAAGAAAAAAA
*
3299856 ATGAAAAATAAAAAATAAAAA
1 ATG-AAAA-AAAGAA-AAAAA
** *
3299877 AAAAAAAAAATAAAAAAAA
1 ATGAAAAAAA-GAAAAAAA
*
3299896 AT-AAAAAAATAAAAAAA
1 ATGAAAAAAAGAAAAAAA
*
3299913 AT-AAAAAAA-TAAAAAA
1 ATGAAAAAAAGAAAAAAA
*
3299929 AT-AAAAAAATAAAAAAA
1 ATGAAAAAAAGAAAAAAA
*
3299946 ATGAAAAAATGAAAAAAA
1 ATGAAAAAAAGAAAAAAA
*
3299964 ATGAAAAAATGAAAAAAA
1 ATGAAAAAAAGAAAAAAA
3299982 A
1 A
3299983 AACAAAAACA
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
16 15 0.13
17 24 0.21
18 42 0.38
19 13 0.12
20 12 0.11
21 6 0.05
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (18 bp):
ATGAAAAAAAGAAAAAAA
Found at i:3299869 original size:17 final size:16
Alignment explanation
Indices: 3299841--3300010 Score: 130
Period size: 16 Copynumber: 10.1 Consensus size: 16
3299831 CTTGAAGATG
*
3299841 AAAAAAAGAAAAA-AA
1 AAAAAAATAAAAATAA
*
3299856 ATGAAAAATAAAAAATAA
1 A-AAAAAAT-AAAAATAA
*
3299874 AAAAAAAAAAAAATAA
1 AAAAAAATAAAAATAA
*
3299890 AAAAAAATAAAAAAATA
1 AAAAAAATAAAAATA-A
3299907 AAAAAAATAAAAA-AA
1 AAAAAAATAAAAATAA
*
3299922 TAAAAAAATAAAAAAATA
1 -AAAAAAATAAAAATA-A
*
3299940 AAAAAAATGAAAAAATGA
1 AAAAAAAT--AAAAATAA
3299958 AAAAAAATGAAAAAATGAAA
1 AAAAAAAT--AAAAAT--AA
* *
3299978 AAAAAAACAAAAACAA
1 AAAAAAATAAAAATAA
* *
3299994 AACAAAA-ACAAATAA
1 AAAAAAATAAAAATAA
3300009 AA
1 AA
3300011 TGGGGGGTTC
Statistics
Matches: 130, Mismatches: 14, Indels: 22
0.78 0.08 0.13
Matches are distributed among these distances:
15 10 0.08
16 48 0.37
17 33 0.25
18 26 0.20
19 5 0.04
20 8 0.06
ACGTcount: A:0.85, C:0.02, G:0.04, T:0.09
Consensus pattern (16 bp):
AAAAAAATAAAAATAA
Found at i:3299989 original size:18 final size:16
Alignment explanation
Indices: 3299841--3300010 Score: 166
Period size: 17 Copynumber: 10.2 Consensus size: 16
3299831 CTTGAAGATG
3299841 AAAAAAAGAAAAAAAAT
1 AAAAAAA-AAAAAAAAT
* *
3299858 --GAAAAATAAAAAAT
1 AAAAAAAAAAAAAAAT
3299872 AAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAT
3299888 AAAAAAAAATAAAAAAAT
1 -AAAAAAAA-AAAAAAAT
3299906 AAAAAAAATAAAAAAAT
1 AAAAAAAA-AAAAAAAT
*
3299923 AAAAAAATAAAAAAAT
1 AAAAAAAAAAAAAAAT
*
3299939 AAAAAAAATGAAAAAAT
1 AAAAAAAA-AAAAAAAT
*
3299956 GAAAAAAAATGAAAAAAT
1 -AAAAAAAA-AAAAAAAT
3299974 GAAAAAAAAAACAAAAA-
1 -AAAAAAAAAA-AAAAAT
* * *
3299991 CAAAACAAAAACAAAT
1 AAAAAAAAAAAAAAAT
3300007 AAAA
1 AAAA
3300011 TGGGGGGTTC
Statistics
Matches: 133, Mismatches: 12, Indels: 17
0.82 0.07 0.10
Matches are distributed among these distances:
14 8 0.06
15 8 0.06
16 38 0.29
17 40 0.30
18 39 0.29
ACGTcount: A:0.85, C:0.02, G:0.04, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAT
Found at i:3300002 original size:11 final size:11
Alignment explanation
Indices: 3299975--3300005 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3299965 TGAAAAAATG
*
3299975 AAAAAAAAAAC
1 AAAAACAAAAC
3299986 AAAAACAAAAC
1 AAAAACAAAAC
3299997 AAAAACAAA
1 AAAAACAAA
3300006 TAAAATGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:3301462 original size:53 final size:53
Alignment explanation
Indices: 3301339--3302006 Score: 1114
Period size: 53 Copynumber: 12.6 Consensus size: 53
3301329 TCAACAGAAG
* *
3301339 ATTGTTCGAGTTCTACTCCCTGAAAAAAATAG-G-GCGGACTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTG-AAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301391 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGAAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* * *
3301445 ATTGTTCGAATTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAATATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301498 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301552 ATTGTTCGAGTTCTACTCCCTGAAGAAATAAAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301605 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301656 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
3301710 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301763 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301817 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301870 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301924 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301977 ATTGTTCGAGTTCTACTCCCTGAAGAAATA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATA
3302007 AGGAGCAGAC
Statistics
Matches: 585, Mismatches: 18, Indels: 25
0.93 0.03 0.04
Matches are distributed among these distances:
51 31 0.05
52 40 0.07
53 299 0.51
54 215 0.37
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:3301524 original size:107 final size:106
Alignment explanation
Indices: 3301339--3302012 Score: 1128
Period size: 107 Copynumber: 6.3 Consensus size: 106
3301329 TCAACAGAAG
* * *
3301339 ATTGTTCGAGTTCTACTCCCTGAA-AAAAATAGGGCGGACTCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
3301403 CTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGAAAGATT
66 C-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
3301445 ATTGTTCGAATTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAATATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
3301510 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 C-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301552 ATTGTTCGAGTTCTACTCCCTGAAGAAATAA-AGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
3301616 TCTACTCCCTGAAGAAATAG-G-GTGGACCCGTAGGAAGATT
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
3301656 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATTATTGTTCGAG
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAG
*
3301720 TTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
64 TTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301763 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
3301828 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301870 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
3301935 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
3301977 ATTGTTCGAGTTCTACTCCCTGAAGAAATAAG-GAGC
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AAGAGAGC
3302013 AGACACGATT
Statistics
Matches: 542, Mismatches: 16, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
104 34 0.06
105 65 0.12
106 60 0.11
107 377 0.70
108 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (106 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:3302338 original size:2 final size:2
Alignment explanation
Indices: 3302331--3302356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3302321 GTAGGTATTA
3302331 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
3302357 GCAAACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3305976 original size:27 final size:27
Alignment explanation
Indices: 3305946--3306002 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3305936 TCTTTAATCA
3305946 TTAAAGTTGAATTCATTTATTTATTTG
1 TTAAAGTTGAATTCATTTATTTATTTG
3305973 TTAAAGTTGAATTCATTTATTTATTTG
1 TTAAAGTTGAATTCATTTATTTATTTG
3306000 TTA
1 TTA
3306003 TCCTGTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.56
Consensus pattern (27 bp):
TTAAAGTTGAATTCATTTATTTATTTG
Found at i:3306135 original size:30 final size:31
Alignment explanation
Indices: 3306078--3306135 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
3306068 GGGTTCAATC
* ***
3306078 AAGAATGTACGGTTTGAGGATTGAAAGAATT
1 AAGAACGTACGGTTTGAGGACAAAAAGAATT
3306109 AAGAACGTA-GGTTTGAGGACAAAAAGA
1 AAGAACGTACGGTTTGAGGACAAAAAGA
3306136 TGCATTAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.22
Consensus pattern (31 bp):
AAGAACGTACGGTTTGAGGACAAAAAGAATT
Found at i:3306887 original size:18 final size:19
Alignment explanation
Indices: 3306856--3306899 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3306846 ATCTGTTCTG
3306856 AAATAATATATTTATT-AA
1 AAATAATATATTTATTCAA
* *
3306874 AAATATTATTTTTATTCAA
1 AAATAATATATTTATTCAA
3306893 AAA-AATA
1 AAATAATA
3306900 GGGATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATATATTTATTCAA
Found at i:3308756 original size:28 final size:28
Alignment explanation
Indices: 3308725--3308810 Score: 129
Period size: 28 Copynumber: 3.1 Consensus size: 28
3308715 AAAACTAATC
3308725 TTTAGGTATAGTTTTGAAAAATTAAAAG
1 TTTAGGTATAGTTTTGAAAAATTAAAAG
* **
3308753 TTTAGGTATAGTTTTGAAAAACT-AATC
1 TTTAGGTATAGTTTTGAAAAATTAAAAG
*
3308780 TTTAGGTATAGTTTTGAAAAATTAATAG
1 TTTAGGTATAGTTTTGAAAAATTAAAAG
3308808 TTT
1 TTT
3308811 TAATTTTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.48
28 26 0.52
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTAGGTATAGTTTTGAAAAATTAAAAG
Found at i:3308783 original size:27 final size:27
Alignment explanation
Indices: 3308714--3308805 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
3308704 AAATGAAACA
3308714 AAAAACTAATCTTTAGGTATAGTTTTG
1 AAAAACTAATCTTTAGGTATAGTTTTG
* **
3308741 AAAAATTAAAAGTTTAGGTATAGTTTTG
1 AAAAACT-AATCTTTAGGTATAGTTTTG
3308769 AAAAACTAATCTTTAGGTATAGTTTTG
1 AAAAACTAATCTTTAGGTATAGTTTTG
*
3308796 AAAAATTAAT
1 AAAAACTAAT
3308806 AGTTTTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 33 0.58
28 24 0.42
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.39
Consensus pattern (27 bp):
AAAAACTAATCTTTAGGTATAGTTTTG
Found at i:3310574 original size:19 final size:18
Alignment explanation
Indices: 3310550--3310588 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
3310540 CAAATACAAT
*
3310550 AAAATAATATTATTTATTA
1 AAAATAATAATATTT-TTA
3310569 AAAATAATAATATTTTTA
1 AAAATAATAATATTTTTA
3310587 AA
1 AA
3310589 TATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATAATAATATTTTTA
Found at i:3310690 original size:27 final size:25
Alignment explanation
Indices: 3310626--3310692 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 25
3310616 TATGTCAATA
3310626 TTATTAAAATATTATATCTATAATT
1 TTATTAAAATATTATATCTATAATT
3310651 TTATAAATAAAAATATTATGAT-TAATATATT
1 TTAT---T-AAAATATTAT-ATCT-ATA-ATT
3310682 TTATTAAAATA
1 TTATTAAAATA
3310693 AAATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
25 4 0.11
27 6 0.17
28 2 0.06
29 11 0.31
30 5 0.14
31 7 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TTATTAAAATATTATATCTATAATT
Found at i:3310764 original size:46 final size:46
Alignment explanation
Indices: 3310695--3310782 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
3310685 TTAAAATAAA
3310695 ATTATTATAAATTATAGTAAATTATTTATTAAAATAAGAATAATAT
1 ATTATTATAAATTATAGTAAATTATTTATTAAAATAAGAATAATAT
* * *
3310741 ATTATTAATTAATTATA-TTAATTATTTATTAAAATAATAATA
1 ATTATT-ATAAATTATAGTAAATTATTTATTAAAATAAGAATA
3310783 TTTTTAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
46 29 0.76
47 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (46 bp):
ATTATTATAAATTATAGTAAATTATTTATTAAAATAAGAATAATAT
Found at i:3310783 original size:43 final size:39
Alignment explanation
Indices: 3310665--3310791 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 39
3310655 AAATAAAAAT
3310665 ATTATGATTAATATATTTTATTAAAATAA-AAT-TATTATAA
1 ATTAT-ATTAAT-TA-TTTATTAAAATAATAATATATTATAA
*
3310705 ATTATAGTAAATTATTTATTAAAATAAGAATAATATATTATTAATTA
1 ATTATA-TTAATTATTTATTAAAAT---AATAATATATTA-T-A--A
*
3310752 ATTATATTAATTATTTATTAAAATAATAATAT-TTTTAA
1 ATTATATTAATTATTTATTAAAATAATAATATATTATAA
3310790 AT
1 AT
3310792 ATTGAAAAGT
Statistics
Matches: 74, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
38 14 0.19
39 3 0.04
40 10 0.14
41 3 0.04
42 5 0.07
43 13 0.18
44 1 0.01
45 1 0.01
46 17 0.23
47 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (39 bp):
ATTATATTAATTATTTATTAAAATAATAATATATTATAA
Found at i:3310915 original size:29 final size:29
Alignment explanation
Indices: 3310881--3310936 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
3310871 ATAATTTATC
3310881 ATATATTATTAA-AATA-AATGTATAATATT
1 ATATATTA-TAATAATATAAT-TATAATATT
3310910 ATATATTATAATAATATAATTATAATA
1 ATATATTATAATAATATAATTATAATA
3310937 ATAAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 19 0.76
30 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
ATATATTATAATAATATAATTATAATATT
Found at i:3310962 original size:21 final size:19
Alignment explanation
Indices: 3310904--3310964 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 19
3310894 ATAAATGTAT
*
3310904 AATATTATATATTATAATA
1 AATATTATATATTAAAATA
*
3310923 ATATAATTATAATAATAAAATA
1 A-AT-ATTAT-ATATTAAAATA
3310945 CAATATTATATTATTAAAAT
1 -AATATTATA-TATTAAAAT
3310965 TATCAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 18 0.53
22 11 0.32
23 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTATATATTAAAATA
Found at i:3311278 original size:88 final size:89
Alignment explanation
Indices: 3311129--3311306 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 89
3311119 CATTTTCTAA
3311129 AAAATGCAAAGCAAATTCAATTGACCAGGAAAATAAATTACATTAACCATCTATTTTTCGCCAAC
1 AAAATGCAAAGCAAATTCAATTGACCAGGAAAATAAATTACATTAACCATCTATTTTTCGCCAAC
3311194 CAAACACTG-AAAATGAAGAAAAC
66 CAAACACTGAAAAATGAAGAAAAC
* * * *
3311217 AAAATGCAAAGCAAATTCAGTTGACCAGGAAAATGAATTACATTGACCATCTGTTTTTCGCCAAC
1 AAAATGCAAAGCAAATTCAATTGACCAGGAAAATAAATTACATTAACCATCTATTTTTCGCCAAC
* *
3311282 TAAACACTGAAAAATGAGGAAAAC
66 CAAACACTGAAAAATGAAGAAAAC
3311306 A
1 A
3311307 TTTTCCGGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 69 0.83
89 14 0.17
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
AAAATGCAAAGCAAATTCAATTGACCAGGAAAATAAATTACATTAACCATCTATTTTTCGCCAAC
CAAACACTGAAAAATGAAGAAAAC
Found at i:3314174 original size:16 final size:16
Alignment explanation
Indices: 3314153--3314187 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3314143 CGAAACTTTC
3314153 TTGGATTTTCAAAACT
1 TTGGATTTTCAAAACT
*
3314169 TTGGATTTTCGAAACT
1 TTGGATTTTCAAAACT
3314185 TTG
1 TTG
3314188 ACCCAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (16 bp):
TTGGATTTTCAAAACT
Found at i:3315684 original size:23 final size:21
Alignment explanation
Indices: 3315650--3315697 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
3315640 TAAAATATAA
3315650 AAATCATATAAAATCAT-ATTT
1 AAATCATAT-AAATCATAATTT
*
3315671 AAATCATATTTAAATTATAATTT
1 AAATCATA--TAAATCATAATTT
3315694 AAAT
1 AAAT
3315698 AATTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 9 0.39
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATCATATAAATCATAATTT
Found at i:3315695 original size:12 final size:11
Alignment explanation
Indices: 3315650--3315697 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
3315640 TAAAATATAA
*
3315650 AAATCATA-TA
1 AAATCATATTT
3315660 AAATCATATTT
1 AAATCATATTT
3315671 AAATCATATTT
1 AAATCATATTT
*
3315682 AAATTATAATTT
1 AAATCAT-ATTT
3315694 AAAT
1 AAAT
3315698 AATTTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 8 0.24
11 18 0.53
12 8 0.24
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATCATATTT
Found at i:3317253 original size:2 final size:2
Alignment explanation
Indices: 3317246--3317276 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3317236 TTGTAATAGT
3317246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3317277 TTTTGCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3318753 original size:15 final size:15
Alignment explanation
Indices: 3318735--3318771 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3318725 TGGTGGATAT
*
3318735 GGGGCGGGTAGATGC
1 GGGGCGGGCAGATGC
*
3318750 GGGGCGGGCGGATGC
1 GGGGCGGGCAGATGC
3318765 GGGGCGG
1 GGGGCGG
3318772 ATAAGGTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGGCGGGCAGATGC
Found at i:3319103 original size:7 final size:7
Alignment explanation
Indices: 3319091--3319115 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3319081 ATTCTTCTTT
3319091 GAAAAGA
1 GAAAAGA
3319098 GAAAAGA
1 GAAAAGA
3319105 GAAAAGA
1 GAAAAGA
3319112 GAAA
1 GAAA
3319116 CGATATGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
GAAAAGA
Found at i:3320162 original size:35 final size:35
Alignment explanation
Indices: 3320116--3320196 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
3320106 AACACGATTT
* *
3320116 TGACTATCGCATTGTGATTTTCCAAATTCGCGTTC
1 TGACTATCGCATTGTGATTTTCCAAAATCGCATTC
3320151 TGACTATCGCATTGTGATTTTCCAAAATCGCATTC
1 TGACTATCGCATTGTGATTTTCCAAAATCGCATTC
3320186 TGACTATCGCA
1 TGACTATCGCA
3320197 ACGCGATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (35 bp):
TGACTATCGCATTGTGATTTTCCAAAATCGCATTC
Found at i:3320217 original size:21 final size:21
Alignment explanation
Indices: 3320191--3320348 Score: 157
Period size: 21 Copynumber: 7.7 Consensus size: 21
3320181 CATTCTGACT
*
3320191 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATTATACATA
*
3320212 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATTAT-ACATA
* *
3320232 ATGGCAACGCGATAATACATA
1 ATCGCAACGCGATTATACATA
*
3320253 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATTAT-ACATA
* *
3320273 ATGGCAACGCGATAATACATA
1 ATCGCAACGCGATTATACATA
*
3320294 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATTAT-ACATA
*
3320314 ATCGCAACGCGATTATACAAA
1 ATCGCAACGCGATTATACATA
*
3320335 ATCGCAATGCGATT
1 ATCGCAACGCGATT
3320349 TTCAAAGCGC
Statistics
Matches: 111, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
19 6 0.05
20 43 0.39
21 56 0.50
22 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTATACATA
Found at i:3320239 original size:41 final size:41
Alignment explanation
Indices: 3320182--3320348 Score: 289
Period size: 41 Copynumber: 4.1 Consensus size: 41
3320172 CCAAAATCGC
3320182 ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
1 ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
*
3320223 ATTCTGACTATGGCAACGCGATAATACATAATCGCAACGCG
1 ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
*
3320264 ATTCTGACTATGGCAACGCGATAATACATAATCGCAACGCG
1 ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
* * *
3320305 ATTCTGACTATCGCAACGCGATTATACAAAATCGCAATGCG
1 ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
3320346 ATT
1 ATT
3320349 TTCAAAGCGC
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 121 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
ATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCG
Found at i:3320240 original size:20 final size:20
Alignment explanation
Indices: 3320182--3320327 Score: 145
Period size: 20 Copynumber: 7.2 Consensus size: 20
3320172 CCAAAATCGC
3320182 ATTCTGACTATCGCAACGCG
1 ATTCTGACTATCGCAACGCG
**
3320202 ATAAT-ACATAATCGCAACGCG
1 ATTCTGAC-T-ATCGCAACGCG
*
3320223 ATTCTGACTATGGCAACGCG
1 ATTCTGACTATCGCAACGCG
**
3320243 ATAAT-ACATAATCGCAACGCG
1 ATTCTGAC-T-ATCGCAACGCG
*
3320264 ATTCTGACTATGGCAACGCG
1 ATTCTGACTATCGCAACGCG
**
3320284 ATAAT-ACATAATCGCAACGCG
1 ATTCTGAC-T-ATCGCAACGCG
3320305 ATTCTGACTATCGCAACGCG
1 ATTCTGACTATCGCAACGCG
3320325 ATT
1 ATT
3320328 ATACAAAATC
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.06
20 46 0.46
21 43 0.43
22 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATTCTGACTATCGCAACGCG
Found at i:3320516 original size:22 final size:22
Alignment explanation
Indices: 3320491--3320541 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3320481 CTACGGCGAC
3320491 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
3320513 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
3320535 ATCCGTC
1 ATCCGTC
3320542 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:3320941 original size:20 final size:20
Alignment explanation
Indices: 3320916--3320981 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
3320906 AAAATCGCAA
*
3320916 CGATAGTTTAATTCGCGTTG
1 CGATAGTTTAATTCGAGTTG
* *
3320936 CGATAG-TTATGTTCGTGTTG
1 CGATAGTTTA-ATTCGAGTTG
*
3320956 CGAT--TTTCATTTCGAGTTG
1 CGATAGTTT-AATTCGAGTTG
3320975 CGATAGT
1 CGATAGT
3320982 CATTTTCGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 17 0.46
20 19 0.51
21 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
CGATAGTTTAATTCGAGTTG
Found at i:3320990 original size:39 final size:40
Alignment explanation
Indices: 3320927--3321018 Score: 141
Period size: 39 Copynumber: 2.3 Consensus size: 40
3320917 GATAGTTTAA
* *
3320927 TTCGCGTTGCGATAGTTATGTTCGTGTTGCGATTTTCA-T
1 TTCGAGTTGCGATAGTCATGTTCGTGTTGCGATTTTCATT
*
3320966 TTCGAGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATT
1 TTCGAGTTGCGATAGTCATGTTCGTGTTGCGATTTTCATT
*
3321006 TTCGTGTTGCGAT
1 TTCGAGTTGCGAT
3321019 TTTAAGTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 35 0.73
40 13 0.27
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.47
Consensus pattern (40 bp):
TTCGAGTTGCGATAGTCATGTTCGTGTTGCGATTTTCATT
Found at i:3320994 original size:20 final size:20
Alignment explanation
Indices: 3320927--3321018 Score: 105
Period size: 20 Copynumber: 4.7 Consensus size: 20
3320917 GATAGTTTAA
* * *
3320927 TTCGCGTTGCGATAGTTATG
1 TTCGTGTTGCGATAGTCATT
**
3320947 TTCGTGTTGCGATTTTCA-T
1 TTCGTGTTGCGATAGTCATT
*
3320966 TTCGAGTTGCGATAGTCATT
1 TTCGTGTTGCGATAGTCATT
**
3320986 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATAGTCATT
3321006 TTCGTGTTGCGAT
1 TTCGTGTTGCGAT
3321019 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.25
20 45 0.75
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.47
Consensus pattern (20 bp):
TTCGTGTTGCGATAGTCATT
Found at i:3321028 original size:20 final size:20
Alignment explanation
Indices: 3320947--3321021 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
3320937 GATAGTTATG
3320947 TTCGTGTTGCGATTTTCA-T
1 TTCGTGTTGCGATTTTCATT
* **
3320966 TTCGAGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
3320986 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
3321006 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
3321022 AAGTTTCAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 15 0.31
20 34 0.69
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:3322957 original size:20 final size:20
Alignment explanation
Indices: 3322932--3323014 Score: 70
Period size: 20 Copynumber: 4.5 Consensus size: 20
3322922 AAACTTAAAA
3322932 ATCGCAACGTGAAAATGACT
1 ATCGCAACGTGAAAATGACT
* **
3322952 ATCGCAACGCGAATTTGACT
1 ATCGCAACGTGAAAATGACT
**
3322972 ATCGCAA--TG-GGAT-A--
1 ATCGCAACGTGAAAATGACT
*
3322986 ATCGCAATGTGAAAATGACT
1 ATCGCAACGTGAAAATGACT
3323006 ATCGCAACG
1 ATCGCAACG
3323015 CGAATTTAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
14 7 0.15
16 3 0.06
17 3 0.06
18 2 0.04
20 32 0.68
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGTGAAAATGACT
Found at i:3323036 original size:19 final size:19
Alignment explanation
Indices: 3323014--3323055 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3323004 CTATCGCAAC
3323014 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* * *
3323033 GCGATTTTGGTTTTGCGTT
1 GCGAATTTAGTTTCGCGTT
3323052 GCGA
1 GCGA
3323056 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.14, G:0.31, T:0.43
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:3323056 original size:19 final size:19
Alignment explanation
Indices: 3323023--3323059 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3323013 CGCGAATTTA
3323023 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
3323042 GTTTTGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
3323060 CTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:3323071 original size:33 final size:33
Alignment explanation
Indices: 3323024--3323103 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
3323014 GCGAATTTAG
* * * *
3323024 TTTCGCGTTGCGATTTTGGTTTTGCGTTGCGAT
1 TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
* *
3323057 TTTCTCGTTGCGATTTTTATTTCGCATTGCGAT
1 TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
*
3323090 TATCCCGTTGCGAT
1 TTTCCCGTTGCGAT
3323104 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
Found at i:3323112 original size:33 final size:33
Alignment explanation
Indices: 3323047--3323164 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 33
3323037 TTTTGGTTTT
* * ** *
3323047 GCGTTGCGATTTTCTCGTTGCGATTTTTATTTC
1 GCGTTGCGATTATCCCGTTGCGATAGTCATTTC
*
3323080 GCATTGCGATTATCCCGTTGCGATAGTCATTTCC
1 GCGTTGCGATTATCCCGTTGCGATAGTCATTT-C
*
3323114 GCGTTGCGATAGTCATTTCTGCGTTGCGATAGTCATTTTC
1 GCGTTGCGAT--T-A--TC-CCGTTGCGATAGTCA-TTTC
3323154 GCGTTGCGATT
1 GCGTTGCGATT
3323165 TAAGTTTCAG
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
33 26 0.38
34 10 0.14
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.03
40 25 0.36
41 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (33 bp):
GCGTTGCGATTATCCCGTTGCGATAGTCATTTC
Found at i:3323120 original size:20 final size:20
Alignment explanation
Indices: 3323095--3323163 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
3323085 GCGATTATCC
3323095 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
3323115 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
3323135 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
3323155 CGTTGCGAT
1 CGTTGCGAT
3323164 TTAAGTTTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:3323741 original size:21 final size:21
Alignment explanation
Indices: 3323650--3323753 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
3323640 GACTCACCTG
*
3323650 TCATCGTTCAAGAGGCCTCT-
1 TCATCGTTCAAGAGGCCCCTA
* *
3323670 CCTATCATTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTA
** * *
3323692 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
3323713 CCACCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
3323734 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
3323754 CCCACTATTC
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:3323768 original size:42 final size:42
Alignment explanation
Indices: 3323650--3323768 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
3323640 GACTCACCTG
*
3323650 TCATCGTTCAAGAGG-CCTCTCCTA-TCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGTCC-CTCCCACT-ATTCAAGAGGCCCCTA
** ** *
3323692 TCATCCCTCAAGA-GTCCCCTCCCACCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGT-CCCTCCCACTATTCAAGAGGCCCCTA
*
3323734 TCATCGTTGAAGAGGTCCCTCCCACTATTCAAGAG
1 TCATCGTTCAAGAGGTCCCTCCCACTATTCAAGAG
3323769 CTCGATTAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.02
42 56 0.92
43 4 0.07
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGTCCCTCCCACTATTCAAGAGGCCCCTA
Found at i:3325151 original size:72 final size:63
Alignment explanation
Indices: 3325075--3325305 Score: 241
Period size: 65 Copynumber: 3.5 Consensus size: 63
3325065 CTTTTTTTTA
3325075 TTGTTTAATTGATTCT-TAAAAGTCTGATTTGTTTAATTGATGAGGAAAATAAGAATTATTAGCA
1 TTGTTTAATTGATT-TGTAAAAGT-TGATTTGTTTAATTGATG-GGAAAAT---AATTATT---A
*
3325139 TTTTTTGC
57 -TTTGTGC
* * *
3325147 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTT-A-ATTGATGGGAAAATAATTATTATTTGTGC
* * *
3325212 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGGGAAAATAATTATTATTTGTGC
* * **
3325275 TT-ATTGATTGAAATGTAAAAGTTGATTTGTT
1 TTGTTTAATTGATTTGTAAAAGTTGATTTGTT
3325306 GATTTCAATC
Statistics
Matches: 148, Mismatches: 8, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
62 25 0.17
63 31 0.21
64 1 0.01
65 39 0.26
66 1 0.01
69 6 0.04
71 11 0.07
72 27 0.18
73 7 0.05
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.50
Consensus pattern (63 bp):
TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGGGAAAATAATTATTATTTGTGC
Found at i:3325177 original size:27 final size:27
Alignment explanation
Indices: 3325147--3325258 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
3325137 CATTTTTTGC
*
3325147 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAAAGTTGAT
* *
3325174 TTGTTTAATATTGATGTGTAAATAATTCTTATTTGT
1 TTGTTT-A-ATTGATGTGT-AA-AAGT-TGA----T
*
3325210 GCTTGTTTAATTGATTTGTAAAAGTTGAT
1 --TTGTTTAATTGATGTGTAAAAGTTGAT
3325239 TTGTTTAATTGATGTGTAAA
1 TTGTTTAATTGATGTGTAAA
3325259 TAATTCTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
27 25 0.37
28 1 0.01
29 10 0.15
30 2 0.03
31 3 0.04
32 2 0.03
33 2 0.03
34 3 0.04
35 2 0.03
36 10 0.15
37 1 0.01
38 6 0.09
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.52
Consensus pattern (27 bp):
TTGTTTAATTGATGTGTAAAAGTTGAT
Found at i:3325382 original size:20 final size:20
Alignment explanation
Indices: 3325357--3325410 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
3325347 AGGTACACTT
*
3325357 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
3325377 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
3325397 TCGCAACGAGAAAG
1 TCGCAACGCGAAAG
3325411 TCAATTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:3325478 original size:20 final size:20
Alignment explanation
Indices: 3325453--3325663 Score: 263
Period size: 20 Copynumber: 10.8 Consensus size: 20
3325443 GCGATTTTCC
* *
3325453 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
3325473 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
3325493 CGTTACGATGGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
3325513 GGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3325533 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
3325553 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3325573 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
3325587 AGTTGCTATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3325607 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
3325627 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3325647 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
3325664 GAATGTGTAA
Statistics
Matches: 164, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
14 10 0.06
16 1 0.01
18 1 0.01
20 152 0.93
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3325601 original size:134 final size:133
Alignment explanation
Indices: 3325409--3325663 Score: 357
Period size: 134 Copynumber: 1.9 Consensus size: 133
3325399 GCAACGAGAA
* * *
3325409 AGTCAATTCGAGTTACGATAGTCTAATACGCTTTGCGATTTTCCCGTTGCGATAATCAAATTCAC
1 AGTCAATTCGAGTTACGATAGTCAAATACGCGTTGCGATTTTCCAGTTGCGATAATCAAATTCAC
* *
3325474 GTTGCGATAGTCAAATTCGCGTTACGATGGTCAAATTCGGGTTGCAATAGTCAAATTCGCGTTGC
66 GTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC
3325539 GAT
131 GAT
* * * ** * *
3325542 AGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCTATAATCAAATTCG
1 AGTCA-ATTCGAGTTACGATAGTCAAATACGCGTTGCGATTTTCCAGTTGCGATAATCAAATTCA
* * * *
3325607 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
65 CGTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCAATAGTCAAAT
3325664 GAATGTGTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
133 5 0.05
134 100 0.95
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (133 bp):
AGTCAATTCGAGTTACGATAGTCAAATACGCGTTGCGATTTTCCAGTTGCGATAATCAAATTCAC
GTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC
GAT
Found at i:3325626 original size:74 final size:76
Alignment explanation
Indices: 3325453--3325655 Score: 275
Period size: 74 Copynumber: 2.6 Consensus size: 76
3325443 GCGATTTTCC
* * * *
3325453 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTACGATGGTCAAATTCGGGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT-GT---ATTCGAGTTG
*
3325518 CAATAGTCAAATTCG
62 CAATAATCAAATTCG
* * *
3325533 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT-T-TTTGAGTTGCTAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTATTCGAGTTGCAAT
3325596 AATCAAATTCG
66 AATCAAATTCG
*
3325607 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
3325656 ATTCAAATGA
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
74 67 0.59
78 1 0.01
80 45 0.40
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (76 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTATTCGAGTTGCAAT
AATCAAATTCG
Found at i:3325886 original size:140 final size:140
Alignment explanation
Indices: 3325634--3325916 Score: 557
Period size: 140 Copynumber: 2.0 Consensus size: 140
3325624 TCGCGTTGCG
3325634 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
3325699 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
3325764 AATACACATA
131 AATACACATA
3325774 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
3325839 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
3325904 AATACACATA
131 AATACACATA
3325914 ATA
1 ATA
3325917 CAATGTTTGC
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:3325997 original size:18 final size:18
Alignment explanation
Indices: 3325974--3326008 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3325964 AAGCCGGTTG
*
3325974 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3325992 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
3326009 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3328291 original size:24 final size:24
Alignment explanation
Indices: 3328257--3328310 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3328247 CTGAAACATC
3328257 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3328281 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3328305 ATCAAA
1 ATCAAA
3328311 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3329156 original size:20 final size:20
Alignment explanation
Indices: 3329131--3329214 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
3329121 AAATTCAGCA
*
3329131 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
3329151 TTGCGATAGTCAGAATCGAG
1 TTGCGATAGTCAGAATCGCG
**
3329171 TTGCGATTATGT-ATTATCGCG
1 TTGCGA-TA-GTCAGAATCGCG
*
3329192 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCG
3329212 TTG
1 TTG
3329215 TGAATCTGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 2 0.04
20 36 0.67
21 14 0.26
22 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:3334747 original size:44 final size:44
Alignment explanation
Indices: 3334697--3334786 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
3334687 TACACATAGA
*
3334697 CTCTGCTGAAAGAAGTAAACTTGATGCAAAGTCTAACAAATATG
1 CTCTGCTGAAAGAAGTAAACTTGATGCAAAGTCCAACAAATATG
* * *
3334741 CTCTGCTGAAAGAAGTAAATTTGATGCTAAGTCCAACAAATGTG
1 CTCTGCTGAAAGAAGTAAACTTGATGCAAAGTCCAACAAATATG
3334785 CT
1 CT
3334787 TTTGTTGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (44 bp):
CTCTGCTGAAAGAAGTAAACTTGATGCAAAGTCCAACAAATATG
Found at i:3344217 original size:21 final size:22
Alignment explanation
Indices: 3344188--3344228 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3344178 TTATACCAAG
*
3344188 GACAAGAAGA-CCCTTCATAAA
1 GACAAGAAGATCACTTCATAAA
*
3344209 GACATGAAGATCACTTCATA
1 GACAAGAAGATCACTTCATA
3344229 TTGAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (22 bp):
GACAAGAAGATCACTTCATAAA
Found at i:3345377 original size:260 final size:260
Alignment explanation
Indices: 3344911--3345435 Score: 960
Period size: 260 Copynumber: 2.0 Consensus size: 260
3344901 TCAGATACGC
* *
3344911 AAGGAACTACTTTAGAACCTGTTGATTCTAGTTAGTATGAGAAATCATGCACAATCATTGTTCGT
1 AAGGAACTACTTTAGAACCTGTTGATTCTAGTCAGTATGAGAAATCACGCACAATCATTGTTCGT
*
3344976 ATCAACAAGTTATTTGGAAATGCCAAGGAAATAGTGGCAACTATAGAAGTTCAGAAGGATGAAAA
66 ATCAACAAGTTATTTGGAAATGCCAAGGAAATAGTGGAAACTATAGAAGTTCAGAAGGATGAAAA
* *
3345041 GAAGACATGCAGTCAGAACTCGTTAGTGCTTGATATTCTACTCCCAACAACAGGGGAAATAAAAC
131 GAAGACATACAGTCAGAACTCGTTAGTGCTTGATATTCTACTCCCAACAACAAGGGAAATAAAAC
3345106 CGGAAACTCTAGTTCAACCCAAGTTGAGAGGTGGCTCTCGTTGTGATTACATCCCAATATCATAT
196 CGGAAACTCTAGTTCAACCCAAGTTGAGAGGTGGCTCTCGTTGTGATTACATCCCAATATCATAT
*
3345171 AAGGGACTACTTTAGAACCTGTTGATTCTAGTCAGTATGAGAAATCACGCACAATCATTGTTCGT
1 AAGGAACTACTTTAGAACCTGTTGATTCTAGTCAGTATGAGAAATCACGCACAATCATTGTTCGT
*
3345236 ATCAACAAGTTGTTTGGAAATGCCAAGGAAATAGTGGAAACTATAGAAGTTCAGAAGGATGAAAA
66 ATCAACAAGTTATTTGGAAATGCCAAGGAAATAGTGGAAACTATAGAAGTTCAGAAGGATGAAAA
* * *
3345301 GAATACATACAGTCAGAACTCGTTGGTGTTTGATATTCTACTCCCAACAACAAGGGAAATAAAAC
131 GAAGACATACAGTCAGAACTCGTTAGTGCTTGATATTCTACTCCCAACAACAAGGGAAATAAAAC
3345366 CGGAAACTCTAGTTCAACCCAAGTTGAGAGGTGGCTCTCGTTGTGATTACATCCCAATATCATAT
196 CGGAAACTCTAGTTCAACCCAAGTTGAGAGGTGGCTCTCGTTGTGATTACATCCCAATATCATAT
3345431 AAGGA
1 AAGGA
3345436 GTTGTATGAT
Statistics
Matches: 254, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
260 254 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (260 bp):
AAGGAACTACTTTAGAACCTGTTGATTCTAGTCAGTATGAGAAATCACGCACAATCATTGTTCGT
ATCAACAAGTTATTTGGAAATGCCAAGGAAATAGTGGAAACTATAGAAGTTCAGAAGGATGAAAA
GAAGACATACAGTCAGAACTCGTTAGTGCTTGATATTCTACTCCCAACAACAAGGGAAATAAAAC
CGGAAACTCTAGTTCAACCCAAGTTGAGAGGTGGCTCTCGTTGTGATTACATCCCAATATCATAT
Found at i:3351073 original size:42 final size:42
Alignment explanation
Indices: 3351018--3351103 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
3351008 AAGTCCTTCA
* * *
3351018 GGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAG
1 GGCCATCAATAAGTCTTTCAAGCATAATGATTAAATCCTTAG
*
3351060 GGCCATCAGTAAGTCTTTCAAGCATAATGATTAAATCCTTAG
1 GGCCATCAATAAGTCTTTCAAGCATAATGATTAAATCCTTAG
3351102 GG
1 GG
3351104 TAATTTGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
GGCCATCAATAAGTCTTTCAAGCATAATGATTAAATCCTTAG
Found at i:3351160 original size:13 final size:13
Alignment explanation
Indices: 3351142--3351166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3351132 TGAAGCGAAC
3351142 CCATTAGTAAGTG
1 CCATTAGTAAGTG
3351155 CCATTAGTAAGT
1 CCATTAGTAAGT
3351167 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CCATTAGTAAGTG
Found at i:3351194 original size:22 final size:21
Alignment explanation
Indices: 3351162--3351225 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
3351152 GTGCCATTAG
3351162 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
3351183 TGAAGTCATTCGGGCCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
3351204 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
3351225 T
1 T
3351226 TAAATCCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 3 0.09
22 11 0.33
23 4 0.12
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:3351204 original size:135 final size:135
Alignment explanation
Indices: 3351027--3351288 Score: 418
Period size: 135 Copynumber: 1.9 Consensus size: 135
3351017 AGGCCATCAA
* * *
3351027 TAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCAAGCATAATGATT
1 TAAGTCTTTCGAGCATGATGATGAAATCATTAGGGCCATCAGTAAGTCTTTCAAGCATAATGATT
* * *
3351092 AAATCCTT-AGGGTAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCGAACCCATTAGTAAGTGC
66 AAATCCTTCA-GGAAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCAAACCCATCAGTAAGTGC
3351156 CATTAG
130 CATTAG
* * * *
3351162 TAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATT
1 TAAGTCTTTCGAGCATGATGATGAAATCATTAGGGCCATCAGTAAGTCTTTCAAGCATAATGATT
3351227 AAATCCTTCAGGAAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCAAACCCATCAGTAAGT
66 AAATCCTTCAGGAAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCAAACCCATCAGTAAGT
3351289 CTTTCGAGCA
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
135 115 0.99
136 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (135 bp):
TAAGTCTTTCGAGCATGATGATGAAATCATTAGGGCCATCAGTAAGTCTTTCAAGCATAATGATT
AAATCCTTCAGGAAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCAAACCCATCAGTAAGTGCC
ATTAG
Found at i:3351213 original size:42 final size:42
Alignment explanation
Indices: 3351154--3351480 Score: 196
Period size: 42 Copynumber: 8.0 Consensus size: 42
3351144 ATTAGTAAGT
*
3351154 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
* * * *
3351196 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
** ** * * * **
3351238 GAAATTTGTAAG-CCTTC-ATGGAAGA-GTAGTGAAG-CAAAC--
1 GCCATCAGTAAGTCTTTCGA-GCATGATG-A-TGAAGTCATTCGG
* *
3351277 -CCATCAGTAAGTCTTTCGAGCATTATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
* * *
3351318 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
** ** * * * **
3351360 GAAATTTGTAAG-CCTTC-ACGAAAGA-GTAGTGAAG-CAAAC--
1 GCCATCAGTAAGTCTTTCGA-GCATGATG-A-TGAAGTCATTCGG
* * *
3351399 -CCATCAGTAAGTCTTTCGAGTATGATGATGAAGTCCTTTGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
* * *
3351440 GCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCATTCG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCG
3351481 AGTAATTTGT
Statistics
Matches: 205, Mismatches: 60, Indels: 40
0.67 0.20 0.13
Matches are distributed among these distances:
38 24 0.12
39 20 0.10
40 8 0.04
41 22 0.11
42 131 0.64
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGG
Found at i:3351214 original size:20 final size:20
Alignment explanation
Indices: 3351154--3351217 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3351144 ATTAGTAAGT
*
3351154 GCCATTAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
* * *
3351174 G-CATGATGATGAAGTCATTCGG
1 GCCATCA-G-T-AAGTCTTTCGA
3351196 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
3351216 GC
1 GC
3351218 ATGATGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:3351310 original size:22 final size:21
Alignment explanation
Indices: 3351284--3351347 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
3351274 AACCCATCAG
*
3351284 TAAGTCTTTCGAGCATTATGA
1 TAAGTCTTTCGAGCATCATGA
* *
3351305 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCTTTCGAG-CATCATGA
*
3351326 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATCATGA
3351347 T
1 T
3351348 TAAATCCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 3 0.09
22 11 0.33
23 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATCATGA
Found at i:3351336 original size:20 final size:20
Alignment explanation
Indices: 3351277--3351339 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
3351267 TGAAGCAAAC
3351277 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
* * *
3351297 -CATTATGATGAAGTCCTTCGGG
1 CCATCA-G-T-AAGTCTTTCGAG
3351319 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
3351339 C
1 C
3351340 ATGATGATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 2 0.06
22 11 0.33
23 4 0.12
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (20 bp):
CCATCAGTAAGTCTTTCGAG
Found at i:3351377 original size:122 final size:122
Alignment explanation
Indices: 3351155--3351562 Score: 672
Period size: 122 Copynumber: 3.3 Consensus size: 122
3351145 TTAGTAAGTG
* *
3351155 CCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
3351220 GATGATTAAATCCTTCAGGAAATTTGTAAGCCTTCATGGAAGAGTAGTGAAGCAAAC
66 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
*
3351277 CCATCAGTAAGTCTTTCGAGCATTATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
*
3351342 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGAAAGAGTAGTGAAGCAAAC
66 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
* * *
3351399 CCATCAGTAAGTCTTTCGAGTATGATGATGAAGTCCTTTGGGCCATTAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * *
3351464 GATGATTAAATCATTCGAGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
* *
3351521 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
3351563 TAATTTGTAA
Statistics
Matches: 266, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 266 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
Found at i:3351544 original size:80 final size:80
Alignment explanation
Indices: 3351441--3351653 Score: 363
Period size: 80 Copynumber: 2.7 Consensus size: 80
3351431 GTCCTTTGGG
* * *
3351441 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGAGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
3351506 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
*
3351521 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACTGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
3351586 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* * *
3351601 CCATCAGTAAGTCTTTCGAGTATGATGATGAAATCCTTCGGGTCATTTGTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
3351654 TCTTTCAAGC
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 126 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAGCAAAT
Found at i:3351670 original size:42 final size:41
Alignment explanation
Indices: 3351607--3351693 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
3351597 AAATCCATCA
* * * *
3351607 GTAAGTCTTTCGAGTATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCAAGCAAGATGAT-AAATCCTTCGGGCCATTT
*
3351649 GTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCAAGCAAGATGATAAATCCTTCGGGCCATTT
3351690 -TAAG
1 GTAAG
3351694 CCTTCTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.10
41 16 0.40
42 20 0.50
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (41 bp):
GTAAGTCTTTCAAGCAAGATGATAAATCCTTCGGGCCATTT
Found at i:3352129 original size:53 final size:53
Alignment explanation
Indices: 3352063--3352380 Score: 406
Period size: 53 Copynumber: 5.9 Consensus size: 53
3352053 AGAATCACAC
* *
3352063 CAGAAGATTGTTCGAGTTCTACTCCCTTAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* *
3352116 CAAAAGATTGTTCGAGTTCTACTCTCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * *
3352169 TAGAAGATTGTTCGAGTTCTACACTCCATTAAGCAAGTGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCT--ACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * *
3352224 CAGAAGATCGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAGCAAACCCGTAAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * **
3352277 CAGAAGATTGTTTGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCAGT-TT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC-GTAAG
* * *
3352330 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGGACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
3352381 CATTTGAAGA
Statistics
Matches: 230, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
53 155 0.67
54 18 0.08
55 57 0.25
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:3352211 original size:108 final size:106
Alignment explanation
Indices: 3352063--3352380 Score: 408
Period size: 108 Copynumber: 3.0 Consensus size: 106
3352053 AGAATCACAC
* * *
3352063 CAGAAGATTGTTCGAGTTCTACTCCCTTAAGCAAGAGGGAGCGAACCCGTAGGCAAAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTTAAGCAAGTGGGAGCGAACCCGTAAGCAGAAGATTGTT
* *
3352128 CGAGTTCTACTCTCTGAAGCAAGAGGGAGCGAACCCGTAAG
66 CGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAA
* * *
3352169 TAGAAGATTGTTCGAGTTCTACACTCCATTAAGCAAGTGGGAGCGAACCCGTAAGCAGAAGATCG
1 CAGAAGATTGTTCGAGTTCT--ACTCCCTTAAGCAAGTGGGAGCGAACCCGTAAGCAGAAGATTG
* *
3352234 TTCGAGTTCTACTCCCTGAAGCAAGAAGGAGCAAACCCGTAAA
64 TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAA
* * ***
3352277 CAGAAGATTGTTTGAGTTCTACTCCCTGAAGCAA-TAGGGAGCGAACCCAGT-TTTAGAAGATTG
1 CAGAAGATTGTTCGAGTTCTACTCCCTTAAGCAAGT-GGGAGCGAACCC-GTAAGCAGAAGATTG
* *
3352340 TTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGGACCCGT
64 TTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
3352381 CATTTGAAGA
Statistics
Matches: 184, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.01
106 59 0.32
107 19 0.10
108 105 0.57
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (106 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTTAAGCAAGTGGGAGCGAACCCGTAAGCAGAAGATTGTT
CGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAA
Found at i:3359760 original size:2 final size:2
Alignment explanation
Indices: 3359753--3359787 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3359743 TTATTTTTCT
3359753 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3359788 TATTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3360510 original size:22 final size:22
Alignment explanation
Indices: 3360483--3360527 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3360473 TATCTAATTA
3360483 TATAAATAATAATTTAAAATAT
1 TATAAATAATAATTTAAAATAT
*
3360505 TATAAATAATAATTTAATATAT
1 TATAAATAATAATTTAAAATAT
3360527 T
1 T
3360528 GTAATATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAAATAATAATTTAAAATAT
Found at i:3360647 original size:22 final size:23
Alignment explanation
Indices: 3360617--3360659 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3360607 CATACCAATT
3360617 GTTTAGAAGACCTATGTACTAAG
1 GTTTAGAAGACCTATGTACTAAG
3360640 GTTT-GAAGACCTATGTACTA
1 GTTTAGAAGACCTATGTACTA
3360660 TCTATTAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (23 bp):
GTTTAGAAGACCTATGTACTAAG
Found at i:3369767 original size:14 final size:14
Alignment explanation
Indices: 3369745--3369784 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3369735 TTTTATTTTT
3369745 TTTATTATATTTATA
1 TTTA-TATATTTATA
*
3369760 TTTATATAATTATA
1 TTTATATATTTATA
3369774 TTTAT-TATTTA
1 TTTATATATTTA
3369785 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:3373036 original size:25 final size:25
Alignment explanation
Indices: 3373003--3373072 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 25
3372993 TGGCATTTGA
3373003 ATGCAAACGGATGACCCTTTTGTCT
1 ATGCAAACGGATGACCCTTTTGTCT
* *
3373028 CAT-CCAAC-GA--ATCCTTTTGTCT
1 -ATGCAAACGGATGACCCTTTTGTCT
*
3373050 ATGCAAACGGATGACCATTTTGT
1 ATGCAAACGGATGACCCTTTTGT
3373073 GATTTTGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 2 0.06
24 2 0.06
25 12 0.34
26 2 0.06
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (25 bp):
ATGCAAACGGATGACCCTTTTGTCT
Found at i:3376324 original size:3 final size:3
Alignment explanation
Indices: 3376316--3376350 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3376306 TATTTTAATC
3376316 TAT TAT TAT TA- TATT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA
3376351 ATTTTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 26 0.87
4 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3376335 original size:12 final size:12
Alignment explanation
Indices: 3376318--3376354 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3376308 TTTTAATCTA
3376318 TTATTATTATAT
1 TTATTATTATAT
3376330 TTATTATTAT-T
1 TTATTATTATAT
3376341 ATTATTATTA-AT
1 -TTATTATTATAT
3376353 TT
1 TT
3376355 TGTTTACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:3377731 original size:29 final size:29
Alignment explanation
Indices: 3377698--3377758 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3377688 TCTTTGCTAT
*
3377698 TTTAGTCCC-TTAAGTTTCTA-TTTTTGTTG
1 TTTAG-CCCTTTAAGTTTC-AGTTTATGTTG
*
3377727 TTTAGCCCTTTCAGTTTCAGTTTATGTTG
1 TTTAGCCCTTTAAGTTTCAGTTTATGTTG
3377756 TTT
1 TTT
3377759 TGGTCCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.57
Consensus pattern (29 bp):
TTTAGCCCTTTAAGTTTCAGTTTATGTTG
Found at i:3377773 original size:30 final size:30
Alignment explanation
Indices: 3377733--3377796 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3377723 GTTGTTTAGC
* *
3377733 CCTTTCAGTTTCA-GTTTATGTTGTTTTGGT
1 CCTTTCAGTTT-ATGTTTATGCTATTTTGGT
* *
3377763 CCTTTGAGTTTATGTTTTTGCTATTTTGGT
1 CCTTTCAGTTTATGTTTATGCTATTTTGGT
3377793 CCTT
1 CCTT
3377797 GTAAGTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.09, C:0.14, G:0.19, T:0.58
Consensus pattern (30 bp):
CCTTTCAGTTTATGTTTATGCTATTTTGGT
Found at i:3377908 original size:22 final size:21
Alignment explanation
Indices: 3377883--3377925 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3377873 TGTATGTACG
*
3377883 TGTTGTAAATGTTATTATTTTA
1 TGTTGTAAATATT-TTATTTTA
3377905 TGTTGTAAATATTTTATTTTA
1 TGTTGTAAATATTTTATTTTA
3377926 CATCGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
TGTTGTAAATATTTTATTTTA
Found at i:3378729 original size:4 final size:4
Alignment explanation
Indices: 3378699--3378749 Score: 57
Period size: 4 Copynumber: 11.5 Consensus size: 4
3378689 GAAACAAAGA
3378699 AAAT AAAT GAAAT GAAAT GAGAAT AAAT AAAT AAAT AAAT GAAAT AAAT
1 AAAT AAAT -AAAT -AAAT -A-AAT AAAT AAAT AAAT AAAT -AAAT AAAT
3378748 AA
1 AA
3378750 GGTATAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 25 0.57
5 16 0.36
6 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3378824 original size:9 final size:9
Alignment explanation
Indices: 3378806--3378843 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3378796 AAGTAGAAGC
3378806 AAAA-AAAA
1 AAAAGAAAA
3378814 AAAAGAAAAA
1 AAAAG-AAAA
3378824 AAAAGAAAA
1 AAAAGAAAA
*
3378833 AAAGGAAAA
1 AAAAGAAAA
3378842 AA
1 AA
3378844 TGAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.52
10 9 0.33
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:3378843 original size:10 final size:10
Alignment explanation
Indices: 3378809--3378835 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3378799 TAGAAGCAAA
3378809 AAAAAAAAAG
1 AAAAAAAAAG
3378819 AAAAAAAAAG
1 AAAAAAAAAG
3378829 AAAAAAA
1 AAAAAAA
3378836 GGAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3385441 original size:19 final size:19
Alignment explanation
Indices: 3385395--3385451 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
3385385 CTAGCCCAAG
*
3385395 AGTATCGATACTTATGTAAA
1 AGTATCGATACTT-TATAAA
* *
3385415 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTATAAA
3385434 AGTATCGATACTTT-TAAA
1 AGTATCGATACTTTATAAA
3385452 CATTATGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 3 0.09
19 17 0.53
20 12 0.38
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (19 bp):
AGTATCGATACTTTATAAA
Found at i:3392279 original size:20 final size:18
Alignment explanation
Indices: 3392233--3392275 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3392223 TTTTGTATCA
*
3392233 GTACTTTGTGTGCTTTTG
1 GTACTATGTGTGCTTTTG
3392251 GTACTATGTGTGCTTTTG
1 GTACTATGTGTGCTTTTG
3392269 GTACTAT
1 GTACTAT
3392276 ATGTAATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.51
Consensus pattern (18 bp):
GTACTATGTGTGCTTTTG
Found at i:3392435 original size:54 final size:54
Alignment explanation
Indices: 3392377--3392481 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
3392367 TGGCACTAAA
* * * *
3392377 TGTGCAACCCATGGTATTTATAATGCGTTTATGAATGACCATTTCATCACTATG
1 TGTGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCAACACTATG
** **
3392431 TGTGCAATGCATGGAATTCATAATGAGTTTATGAATTTCCATTTCAACACT
1 TGTGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCAACACT
3392482 TCGGTGAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (54 bp):
TGTGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCAACACTATG
Found at i:3396366 original size:18 final size:19
Alignment explanation
Indices: 3396334--3396372 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3396324 ATTTACTTTG
* *
3396334 TTTTTAGTTTATCTTTATA
1 TTTTAAGTTTATCTTAATA
3396353 TTTTAAGTTT-TCTTAATA
1 TTTTAAGTTTATCTTAATA
3396371 TT
1 TT
3396373 ATAATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTAAGTTTATCTTAATA
Found at i:3396487 original size:17 final size:20
Alignment explanation
Indices: 3396448--3396490 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3396438 AATCATTTTA
3396448 TTATATATAATATTCTATTAT
1 TTATATATAATATTCTA-TAT
3396469 TTATATATAA-ATT-TA-AT
1 TTATATATAATATTCTATAT
3396486 TTATA
1 TTATA
3396491 AATTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
20 3 0.14
21 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATAATATTCTATAT
Found at i:3398582 original size:32 final size:27
Alignment explanation
Indices: 3398523--3398586 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
3398513 AAATTTTTTT
3398523 TATATATTATGTTTTATTATATATATA
1 TATATATTATGTTTTATTATATATATA
3398550 TATATATTATTGTTATTATTAT-TATACGTA
1 TATATATTA-TGTT-TTATTATATATA--TA
3398580 TATATAT
1 TATATAT
3398587 GTATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
27 9 0.27
28 8 0.24
29 7 0.21
30 9 0.27
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (27 bp):
TATATATTATGTTTTATTATATATATA
Found at i:3398654 original size:18 final size:18
Alignment explanation
Indices: 3398624--3398690 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
3398614 TTTACCATCT
*
3398624 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
3398642 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
3398660 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
*
3398678 TTTTTTAT-TTATT
1 TTATTTATATTATT
3398691 CATGTAATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 5 0.13
18 33 0.87
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:3400431 original size:10 final size:10
Alignment explanation
Indices: 3400416--3400449 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3400406 TTCATTTACC
3400416 ATTTATTTTT
1 ATTTATTTTT
3400426 ATTTATTTTT
1 ATTTATTTTT
* *
3400436 ATCTATTTCT
1 ATTTATTTTT
3400446 ATTT
1 ATTT
3400450 TACTAACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:3409917 original size:48 final size:49
Alignment explanation
Indices: 3409840--3409933 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
3409830 AATACTTCGC
* ** * *
3409840 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGGAAAAA-AAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAACGT
*
3409888 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
3409934 AGAGGGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 34 0.87
49 5 0.13
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (49 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAACGT
Found at i:3410868 original size:105 final size:105
Alignment explanation
Indices: 3410686--3411460 Score: 1424
Period size: 105 Copynumber: 7.4 Consensus size: 105
3410676 AGGTTTTACC
*
3410686 CAGAGCCAATTTCAACTTCCCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3410751 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3410791 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3410856 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3410896 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
3410961 ACGAAGGGACCGCTGGTTGTCAACGAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3411001 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3411066 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3411106 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
3411171 ACGAAGGGACCGCTGGTTGTCAACGAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
3411211 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
3411276 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3411316 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
3411381 ACGAAGGAACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3411421 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3411461 AAAAACAACA
Statistics
Matches: 649, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 649 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:3413209 original size:3 final size:3
Alignment explanation
Indices: 3413203--3413250 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
3413193 ATATTACGTT
*
3413203 TTA TTA -TA TATA TATA TATA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3413250 T
1 T
3413251 ACGTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 28 0.68
4 11 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3413331 original size:18 final size:18
Alignment explanation
Indices: 3413301--3413367 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
3413291 TTTACCATCT
*
3413301 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
3413319 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
3413337 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
*
3413355 TTTTTTAT-TTATT
1 TTATTTATATTATT
3413368 CATGTAATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 5 0.13
18 33 0.87
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:3418123 original size:24 final size:26
Alignment explanation
Indices: 3418069--3418123 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
3418059 AAACATGGGT
* *
3418069 GGCTGGAAAAACAAATGCAAATGGGGT
1 GGCTGGAAAAAC-AATGCAAATGAGGC
*
3418096 GGCTGGAAAAAC-A-GTAAATGAGGC
1 GGCTGGAAAAACAATGCAAATGAGGC
3418120 GGCT
1 GGCT
3418124 AATTGTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 12 0.48
25 1 0.04
27 12 0.48
ACGTcount: A:0.38, C:0.13, G:0.35, T:0.15
Consensus pattern (26 bp):
GGCTGGAAAAACAATGCAAATGAGGC
Found at i:3424280 original size:6 final size:6
Alignment explanation
Indices: 3424269--3424339 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
3424259 ATTTAAATAT
* * * * *
3424269 GTATGC GCATGC GTATGC GTATGC GTATGC GCATGC GTATGT ATATGT
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
* * *
3424317 GTATGT GTATGT GTATGT GTATG
1 GTATGC GTATGC GTATGC GTATG
3424340 TATATATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.38
Consensus pattern (6 bp):
GTATGC
Found at i:3424320 original size:12 final size:12
Alignment explanation
Indices: 3424305--3424350 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3424295 ATGCGCATGC
3424305 GTATGTATATGT
1 GTATGTATATGT
*
3424317 GTATGTGTATGT
1 GTATGTATATGT
*
3424329 GTATGTGTATGT
1 GTATGTATATGT
* *
3424341 ATATATATAT
1 GTATGTATAT
3424351 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (12 bp):
GTATGTATATGT
Found at i:3424326 original size:18 final size:18
Alignment explanation
Indices: 3424305--3424350 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
3424295 ATGCGCATGC
3424305 GTATGTATATGTGTATGT
1 GTATGTATATGTGTATGT
*
3424323 GTATGTGTATGTGTATGT
1 GTATGTATATGTGTATGT
* *
3424341 ATATATATAT
1 GTATGTATAT
3424351 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (18 bp):
GTATGTATATGTGTATGT
Found at i:3424347 original size:2 final size:2
Alignment explanation
Indices: 3424340--3424366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3424330 TATGTGTATG
3424340 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3424367 TGTTATTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3431758 original size:3 final size:3
Alignment explanation
Indices: 3431750--3431801 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
3431740 TTTCTTATAT
*
3431750 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TG TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3431796 TTA TTA
1 TTA TTA
3431802 AATAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3432294 original size:26 final size:26
Alignment explanation
Indices: 3432259--3432314 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3432249 ACCTATGCAA
*
3432259 CCTCCTTGGGACCGGTCTGAGAGCAT
1 CCTCCTTGGGACCGGTCTGAGAGAAT
3432285 CCTCCTTGGGACCGGTCTGAGAGAAT
1 CCTCCTTGGGACCGGTCTGAGAGAAT
3432311 CCTC
1 CCTC
3432315 GGTAGTGGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (26 bp):
CCTCCTTGGGACCGGTCTGAGAGAAT
Found at i:3433421 original size:2 final size:2
Alignment explanation
Indices: 3433408--3433455 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3433398 TATATTAGTC
*
3433408 AT AT AA 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
3433450 AT AT AT
1 AT AT AT
3433456 TTGTTCAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3434433 original size:30 final size:28
Alignment explanation
Indices: 3434383--3434439 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
3434373 TAATTCTTTC
*
3434383 TTTTCAAAAATTTGTATATATACTTATTA
1 TTTTCAAAAATTTATATATATA-TTATTA
*
3434412 TTTTCATAATATTTATATATATATTATT
1 TTTTCA-AAAATTTATATATATATTATT
3434440 TTATTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTCAAAAATTTATATATATATTATTA
Found at i:3436145 original size:14 final size:14
Alignment explanation
Indices: 3436126--3436173 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3436116 ACATTTATAT
*
3436126 TTTTTGCGTTTGCA
1 TTTTTGCATTTGCA
3436140 TTTTTGCATTTTGCA
1 TTTTTGCA-TTTGCA
* *
3436155 TCTTTGCATTTGTA
1 TTTTTGCATTTGCA
3436169 TTTTT
1 TTTTT
3436174 ATGTTTGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.10, C:0.12, G:0.15, T:0.62
Consensus pattern (14 bp):
TTTTTGCATTTGCA
Done.