Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 27
Found at i:2951460 original size:490 final size:490
Alignment explanation
Indices: 2950540--2951520 Score: 1953
Period size: 490 Copynumber: 2.0 Consensus size: 490
2950530 CCGTTGGAAA
2950540 TATAAGAGACAGAAGGTAGTTTCTTCAGAAGACATCTTGACCAAAAACGATCAGGGTCCCATTAA
1 TATAAGAGACAGAAGGTAGTTTCTTCAGAAGACATCTTGACCAAAAACGATCAGGGTCCCATTAA
2950605 AAAAGTCGTCTCAAGTATGCTTCAGTTCTGATCTTCTTTTCCAAAGCTTGGATGAGTGGATCATT
66 AAAAGTCGTCTCAAGTATGCTTCAGTTCTGATCTTCTTTTCCAAAGCTTGGATGAGTGGATCATT
2950670 AGAAAGAGTTATTACTTTTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTT
131 AGAAAGAGTTATTACTTTTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTT
2950735 CAAAAATATTCGACCTCGAATCTAAAACATTAAAGGGAGTAACATTAGAATAGTTTAATGATTCA
196 CAAAAATATTCGACCTCGAATCTAAAACATTAAAGGGAGTAACATTAGAATAGTTTAATGATTCA
2950800 TTCACATGATGCTTACCGAGTAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTC
261 TTCACATGATGCTTACCGAGTAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTC
2950865 GAGTAGAAATATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCACT
326 GAGTAGAAATATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCACT
2950930 CCTCAAAAGGATTCGTCCTCGAATCTGAAAATCCAAAACAAAGAGAATTAGATATGTTGAAAGGA
391 CCTCAAAAGGATTCGTCCTCGAATCTGAAAATCCAAAACAAAGAGAATTAGATATGTTGAAAGGA
2950995 AAACTTGTGAAACATTTACCAGGATCAATGTGATG
456 AAACTTGTGAAACATTTACCAGGATCAATGTGATG
*
2951030 TATAAGAGACAGACGGTAGTTTCTTCAGAAGACATCTTGACCAAAAACGATCAGGGTCCCATTAA
1 TATAAGAGACAGAAGGTAGTTTCTTCAGAAGACATCTTGACCAAAAACGATCAGGGTCCCATTAA
2951095 AAAAGTCGTCTCAAGTATGCTTCAGTTCTGATCTTCTTTTCCAAAGCTTGGATGAGTGGATCATT
66 AAAAGTCGTCTCAAGTATGCTTCAGTTCTGATCTTCTTTTCCAAAGCTTGGATGAGTGGATCATT
2951160 AGAAAGAGTTATTACTTTTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTT
131 AGAAAGAGTTATTACTTTTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTT
2951225 CAAAAATATTCGACCTCGAATCTAAAACATTAAAGGGAGTAACATTAGAATAGTTTAATGATTCA
196 CAAAAATATTCGACCTCGAATCTAAAACATTAAAGGGAGTAACATTAGAATAGTTTAATGATTCA
2951290 TTCACATGATGCTTACCGAGTAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTC
261 TTCACATGATGCTTACCGAGTAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTC
2951355 GAGTAGAAATATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCACT
326 GAGTAGAAATATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCACT
2951420 CCTCAAAAGGATTCGTCCTCGAATCTGAAAATCCAAAACAAAGAGAATTAGATATGTTGAAAGGA
391 CCTCAAAAGGATTCGTCCTCGAATCTGAAAATCCAAAACAAAGAGAATTAGATATGTTGAAAGGA
2951485 AAACTTGTGAAACATTTACCAGGATCAATGTGATG
456 AAACTTGTGAAACATTTACCAGGATCAATGTGATG
2951520 T
1 T
2951521 CTCTTTATGC
Statistics
Matches: 490, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
490 490 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (490 bp):
TATAAGAGACAGAAGGTAGTTTCTTCAGAAGACATCTTGACCAAAAACGATCAGGGTCCCATTAA
AAAAGTCGTCTCAAGTATGCTTCAGTTCTGATCTTCTTTTCCAAAGCTTGGATGAGTGGATCATT
AGAAAGAGTTATTACTTTTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTT
CAAAAATATTCGACCTCGAATCTAAAACATTAAAGGGAGTAACATTAGAATAGTTTAATGATTCA
TTCACATGATGCTTACCGAGTAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTC
GAGTAGAAATATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCACT
CCTCAAAAGGATTCGTCCTCGAATCTGAAAATCCAAAACAAAGAGAATTAGATATGTTGAAAGGA
AAACTTGTGAAACATTTACCAGGATCAATGTGATG
Found at i:2954994 original size:12 final size:13
Alignment explanation
Indices: 2954977--2955005 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2954967 TTTGGTGCTG
2954977 GAAACAAGAT-AA
1 GAAACAAGATAAA
2954989 GAAACAAGATAAA
1 GAAACAAGATAAA
2955002 GAAA
1 GAAA
2955006 AGATAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.07, G:0.17, T:0.07
Consensus pattern (13 bp):
GAAACAAGATAAA
Found at i:2958040 original size:15 final size:15
Alignment explanation
Indices: 2958020--2958054 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2958010 TATACAGTGT
2958020 GATTCCATTGCTTCA
1 GATTCCATTGCTTCA
2958035 GATTCCATTGCTTCA
1 GATTCCATTGCTTCA
2958050 GATTC
1 GATTC
2958055 ATGAACACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (15 bp):
GATTCCATTGCTTCA
Found at i:2959406 original size:15 final size:15
Alignment explanation
Indices: 2959382--2959415 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2959372 CCGTAGGACC
2959382 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
2959397 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
2959412 ACTA
1 ACTA
2959416 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:2959542 original size:29 final size:29
Alignment explanation
Indices: 2959500--2959580 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2959490 TTTTATATGT
2959500 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2959528 TCATGTAGCTCATGTCATCTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2959557 TCATGTAGCTCATGTCATCTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
2959581 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.78
30 4 0.08
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:2959592 original size:7 final size:7
Alignment explanation
Indices: 2959580--2959615 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2959570 GTCATCTTCT
2959580 CATATCA
1 CATATCA
2959587 CATATCA
1 CATATCA
2959594 CATATCA
1 CATATCA
2959601 CATAT--
1 CATATCA
2959606 CATATCA
1 CATATCA
2959613 CAT
1 CAT
2959616 GTGTATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
7 22 0.81
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
CATATCA
Found at i:2964130 original size:67 final size:65
Alignment explanation
Indices: 2964008--2964155 Score: 167
Period size: 67 Copynumber: 2.2 Consensus size: 65
2963998 CTATTGAATA
* * *
2964008 GGTACCGATACCCTCTCAAACAAGAAATTCCATAATGTCATGGGGGTACCAATTCCCCCCAG-AG
1 GGTACCGATACCCTCTCAAACAAGAAATTCCAAAATATCATAGGGGTACCAATTCCCCCCAGTA-
2964072 G
65 G
* **
2964073 GGTACCGATACCC-CTCATTGAACGAA-AAATTTCAAAATATCATAGGGGTACGGATTCCCCCCA
1 GGTACCGATACCCTCTCA---AAC-AAGAAATTCCAAAATATCATAGGGGTACCAATTCCCCCCA
2964136 GTAG
62 GTAG
*
2964140 GGTATCGATACCCTCT
1 GGTACCGATACCCTCT
2964156 AAAGGAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
64 4 0.06
65 13 0.19
67 48 0.69
68 5 0.07
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (65 bp):
GGTACCGATACCCTCTCAAACAAGAAATTCCAAAATATCATAGGGGTACCAATTCCCCCCAGTAG
Found at i:2965313 original size:22 final size:21
Alignment explanation
Indices: 2965288--2965337 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2965278 TATGAGGATG
2965288 TTATAGGAATTAGATATATAAA
1 TTATAGGAATTA-ATATATAAA
* * *
2965310 TTATATGGCATTAATGTATCAA
1 TTATA-GGAATTAATATATAAA
2965332 TTATAG
1 TTATAG
2965338 AAAAAAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (21 bp):
TTATAGGAATTAATATATAAA
Found at i:2965895 original size:22 final size:23
Alignment explanation
Indices: 2965828--2965895 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2965818 CAATCTTATA
2965828 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
2965851 TGGCACTAT-GGTGCAATTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
*
2965874 T-GCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
2965896 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 1 0.03
22 17 0.43
23 21 0.52
24 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:2970972 original size:35 final size:36
Alignment explanation
Indices: 2970906--2970973 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
2970896 GAAAATATTT
* *
2970906 ATATATTTTCTTTAAAAAATTAAATTCATAAAATTG
1 ATATATTGTCTTTAAAAAATTAAAATCATAAAATTG
*
2970942 ATATATTGT-TTTATAAAATTGAAAAT-ATAAAA
1 ATATATTGTCTTTAAAAAATT-AAAATCATAAAA
2970974 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 16 0.57
36 12 0.43
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (36 bp):
ATATATTGTCTTTAAAAAATTAAAATCATAAAATTG
Found at i:2971433 original size:22 final size:22
Alignment explanation
Indices: 2971386--2971441 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2971376 TTTTTTTAAT
* **
2971386 AAAATTAAAAAATAATTTTTGA
1 AAAATTAAAAAAAAATAATTGA
2971408 AAAATTAAATAAAAAATAATTG-
1 AAAATTAAA-AAAAAATAATTGA
2971430 AAAATATAAAAA
1 AAAAT-TAAAAA
2971442 CATAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATTAAAAAAAAATAATTGA
Found at i:2971668 original size:14 final size:15
Alignment explanation
Indices: 2971650--2971744 Score: 61
Period size: 14 Copynumber: 6.2 Consensus size: 15
2971640 ACATTAATTT
2971650 TTTAATAATTTAAT-
1 TTTAATAATTTAATA
* *
2971664 TTTAATACTTTTATA
1 TTTAATAATTTAATA
*
2971679 TTTAATATATTAAATA
1 TTTAATA-ATTTAATA
*
2971695 TCTTAATAATTATTTATA
1 T-TTAATAA-T-TTAATA
* *
2971713 TTTTAT-ATTTTATA
1 TTTAATAATTTAATA
*
2971727 TTTTA-AATTTAAATA
1 TTTAATAATTT-AATA
2971742 TTT
1 TTT
2971745 TTTATTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
14 27 0.42
15 14 0.22
16 8 0.12
17 11 0.17
18 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATAATTTAATA
Found at i:2971719 original size:7 final size:7
Alignment explanation
Indices: 2971707--2971752 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
2971697 TTAATAATTA
2971707 TTTATAT
1 TTTATAT
2971714 TTTATAT
1 TTTATAT
2971721 TTTATAT
1 TTTATAT
*
2971728 TTTAAAT
1 TTTATAT
*
2971735 TTAAATAT
1 TT-TATAT
*
2971743 TTTTTAT
1 TTTATAT
2971750 TTT
1 TTT
2971753 TTATAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:2972365 original size:8 final size:8
Alignment explanation
Indices: 2972351--2972383 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
2972341 ATCAAATATA
2972351 TTTTAATT
1 TTTTAATT
*
2972359 ATTTAATT
1 TTTTAATT
2972367 TTTTAATT
1 TTTTAATT
2972375 TTTTAATT
1 TTTTAATT
2972383 T
1 T
2972384 AATTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTAATT
Found at i:2974224 original size:59 final size:59
Alignment explanation
Indices: 2974160--2974341 Score: 364
Period size: 59 Copynumber: 3.1 Consensus size: 59
2974150 AAAATTCTCA
2974160 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
1 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
2974219 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
1 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
2974278 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
1 TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
2974337 TATAA
1 TATAA
2974342 ATTCATCCCT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 123 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (59 bp):
TATAATTTAAATAGTATTTTATAATTTTTATTAAAAATTAATTTTAATCATTAAAATTT
Found at i:2993100 original size:12 final size:12
Alignment explanation
Indices: 2993075--2993167 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
2993065 ACGGAGATAT
* *
2993075 CAGAAATCAAAA
1 CAGAATTCAGAA
2993087 CAGAATTCAGAA
1 CAGAATTCAGAA
2993099 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
2993111 CAGAATCCATATA
1 CAGAATTCAGA-A
* *
2993124 -AGAAATCAAAA
1 CAGAATTCAGAA
**
2993135 CAGAATTCAGGT
1 CAGAATTCAGAA
*
2993147 CATGTATT-AGAA
1 CA-GAATTCAGAA
2993159 CAGAATTCA
1 CAGAATTCA
2993168 AGTCGAAAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
11 5 0.08
12 52 0.84
13 5 0.08
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2993102 original size:24 final size:25
Alignment explanation
Indices: 2993069--2993144 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 25
2993059 CATTAAACGG
2993069 AGATATCAGAAATCAAAACAGAATTC
1 AGATA-CAGAAATCAAAACAGAATTC
* * *
2993095 AGA-ACAGAATTCAGAACAGAATCC
1 AGATACAGAAATCAAAACAGAATTC
*
2993119 ATATA-AGAAATCAAAACAGAATTC
1 AGATACAGAAATCAAAACAGAATTC
2993143 AG
1 AG
2993145 GTCATGTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 36 0.88
25 2 0.05
26 3 0.07
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (25 bp):
AGATACAGAAATCAAAACAGAATTC
Found at i:2999515 original size:2 final size:2
Alignment explanation
Indices: 2999508--2999557 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2999498 TGAAAATGAG
2999508 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
2999550 AT AT AT AT
1 AT AT AT AT
2999558 CTGTGTGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3000741 original size:87 final size:87
Alignment explanation
Indices: 3000595--3000772 Score: 347
Period size: 87 Copynumber: 2.0 Consensus size: 87
3000585 CTCATAGGAA
3000595 ATTCTGAACCGGGAACTGAGTTACCGCCTCCTCCACCGTTACCCTCAAACTTCAAACCGACTCGA
1 ATTCTGAACCGGGAACTGAGTTACCGCCTCCTCCACCGTTACCCTCAAACTTCAAACCGACTCGA
*
3000660 GTTGTTCGTGTTGACTGCACTG
66 GTTATTCGTGTTGACTGCACTG
3000682 ATTCTGAACCGGGAACTGAGTTACCGCCTCCTCCACCGTTACCCTCAAACTTCAAACCGACTCGA
1 ATTCTGAACCGGGAACTGAGTTACCGCCTCCTCCACCGTTACCCTCAAACTTCAAACCGACTCGA
3000747 GTTATTCGTGTTGACTGCACTG
66 GTTATTCGTGTTGACTGCACTG
3000769 ATTC
1 ATTC
3000773 AGATCGATCC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (87 bp):
ATTCTGAACCGGGAACTGAGTTACCGCCTCCTCCACCGTTACCCTCAAACTTCAAACCGACTCGA
GTTATTCGTGTTGACTGCACTG
Found at i:3011033 original size:14 final size:14
Alignment explanation
Indices: 3011014--3011040 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3011004 AACAGACTAT
3011014 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
3011028 TCTGTTTTCTACA
1 TCTGTTTTCTACA
3011041 TATACCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:3011822 original size:28 final size:28
Alignment explanation
Indices: 3011782--3011840 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
3011772 TAAGATATAG
3011782 AAGAGGGATGGGATAAGCTTCTTGGGCA
1 AAGAGGGATGGGATAAGCTTCTTGGGCA
3011810 AAGAGGGATGGGATAAGCTTCTTGGGCA
1 AAGAGGGATGGGATAAGCTTCTTGGGCA
3011838 AAG
1 AAG
3011841 TACGATCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.39, T:0.20
Consensus pattern (28 bp):
AAGAGGGATGGGATAAGCTTCTTGGGCA
Found at i:3014152 original size:35 final size:37
Alignment explanation
Indices: 3014086--3014157 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 37
3014076 TATGTGCAGG
* *
3014086 GGGAACAGATTCCCCCCTATGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCACCTAGGGGGGTATCGATTCCCC
3014123 GGGAACAGATT-CCACCT-GGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCACCTAGGGGGGTATCGATTCCCC
3014158 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 17 0.52
36 5 0.15
37 11 0.33
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (37 bp):
GGGAACAGATTCCCACCTAGGGGGGTATCGATTCCCC
Found at i:3014761 original size:31 final size:31
Alignment explanation
Indices: 3014721--3014884 Score: 310
Period size: 31 Copynumber: 5.3 Consensus size: 31
3014711 AGGGTCGAGG
3014721 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3014752 GCTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3014783 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3014814 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3014845 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3014876 GATTACCTA
1 GTTTACCTA
3014885 GATTATTCGA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3014903 original size:93 final size:93
Alignment explanation
Indices: 3014721--3014907 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 93
3014711 AGGGTCGAGG
*
3014721 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGTT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
* **
3014786 TACCTATGTTCTTCGGGACATATGGACT
66 TACCTATGTTATTCGAAACATATGGACT
*
3014814 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGAT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
3014879 TACCTA-GATTATTCGAAATC-TATGGACT
66 TACCTATG-TTATTCGAAA-CATATGGACT
3014907 G
1 G
3014908 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
92 1 0.01
93 85 0.98
94 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (93 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
TACCTATGTTATTCGAAACATATGGACT
Found at i:3018711 original size:36 final size:35
Alignment explanation
Indices: 3018646--3018716 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
3018636 TATGTGCAGG
*
3018646 GGGAACAGATTCCCCCCTGGGGGTGTCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
3018681 GGGAACAGATT-CCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCT--GGGGGTATCGATTCCCC
3018717 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 6 0.18
35 11 0.33
36 16 0.48
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
Found at i:3019315 original size:31 final size:31
Alignment explanation
Indices: 3019275--3019438 Score: 310
Period size: 31 Copynumber: 5.3 Consensus size: 31
3019265 AGGGTCGAGG
3019275 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3019306 GCTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3019337 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3019368 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3019399 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3019430 GATTACCTA
1 GTTTACCTA
3019439 GATTATTCGA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3019457 original size:93 final size:93
Alignment explanation
Indices: 3019275--3019461 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 93
3019265 AGGGTCGAGG
*
3019275 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGTT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
* **
3019340 TACCTATGTTCTTCGGGACATATGGACT
66 TACCTATGTTATTCGAAACATATGGACT
*
3019368 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGAT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
3019433 TACCTA-GATTATTCGAAATC-TATGGACT
66 TACCTATG-TTATTCGAAA-CATATGGACT
3019461 G
1 G
3019462 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
92 1 0.01
93 85 0.98
94 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (93 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGCTTACCTATGTTCTTCGGGACATATGGACTGAT
TACCTATGTTATTCGAAACATATGGACT
Found at i:3020134 original size:103 final size:105
Alignment explanation
Indices: 3019953--3020160 Score: 402
Period size: 103 Copynumber: 2.0 Consensus size: 105
3019943 TAAACGTATT
3019953 ATAAGTATAAATGCAAAGAAATGAACGGTTAAATTTGTACGAGTGTTTATGTACAATTTACGAAA
1 ATAAGTATAAATGCAAAGAAATGAACGGTTAAATTTGTACGAGTGTTTATGTACAATTTACGAAA
3020018 ATCACTGTAGCGCTGTAGCAGGTTACTGTAGTGCTGTTCA
66 ATCACTGTAGCGCTGTAGCAGGTTACTGTAGTGCTGTTCA
3020058 ATAAGTATAAATGCAAAGAAATGAACGGTT-AATTTGTACGAGTG-TTATGTACAATTTACGAAA
1 ATAAGTATAAATGCAAAGAAATGAACGGTTAAATTTGTACGAGTGTTTATGTACAATTTACGAAA
3020121 ATCACTGTAGCGCTGTAGCAGGTTACTGTAGTGCTGTTCA
66 ATCACTGTAGCGCTGTAGCAGGTTACTGTAGTGCTGTTCA
3020161 TACCGTATTT
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 59 0.57
104 14 0.14
105 30 0.29
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (105 bp):
ATAAGTATAAATGCAAAGAAATGAACGGTTAAATTTGTACGAGTGTTTATGTACAATTTACGAAA
ATCACTGTAGCGCTGTAGCAGGTTACTGTAGTGCTGTTCA
Found at i:3023274 original size:20 final size:20
Alignment explanation
Indices: 3023249--3023287 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3023239 CAGTATGTGC
3023249 AGGGGG-AACAGATTCCCCCT
1 AGGGGGTAAC-GATTCCCCCT
*
3023269 AGGGGGTATCGATTCCCCC
1 AGGGGGTAACGATTCCCCC
3023288 CTAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (20 bp):
AGGGGGTAACGATTCCCCCT
Found at i:3023888 original size:31 final size:31
Alignment explanation
Indices: 3023848--3024001 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
3023838 AGGGTCGAGG
3023848 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3023879 GCTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3023910 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3023941 GTTTACCTATGTTCTTCGGG--ATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3023970 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3024001 G
1 G
3024002 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
29 26 0.23
31 89 0.77
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3025788 original size:9 final size:9
Alignment explanation
Indices: 3025774--3025801 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3025764 GTATAATGGT
3025774 AAAATTAAA
1 AAAATTAAA
3025783 AAAATTAAA
1 AAAATTAAA
3025792 AAAATTAAA
1 AAAATTAAA
3025801 A
1 A
3025802 TATGATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:3026371 original size:21 final size:20
Alignment explanation
Indices: 3026336--3026376 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3026326 GGACCGGCTG
* *
3026336 AAAACCGAGAAAAACTGGGA
1 AAAACCGAAAAAAACCGGGA
3026356 AAAACCGGAAAAAAACCGGGA
1 AAAACC-GAAAAAAACCGGGA
3026377 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.56, C:0.17, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAACCGAAAAAAACCGGGA
Found at i:3032399 original size:40 final size:40
Alignment explanation
Indices: 3032355--3032438 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
3032345 AACAAAGTAC
*
3032355 AGCACAAAGCACAATAATTCTATAAGAGCACACTAGCAAT
1 AGCACAAAGCACAATAATACTATAAGAGCACACTAGCAAT
3032395 AGCACAAAGCACAATAATACTATAAGAGCACACTAGCAAT
1 AGCACAAAGCACAATAATACTATAAGAGCACACTAGCAAT
3032435 AGCA
1 AGCA
3032439 AGTTAACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (40 bp):
AGCACAAAGCACAATAATACTATAAGAGCACACTAGCAAT
Found at i:3032426 original size:19 final size:19
Alignment explanation
Indices: 3032362--3032426 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
3032352 TACAGCACAA
*
3032362 AGCACAATAATTCTATAAG
1 AGCACAATAATACTATAAG
* *
3032381 AGCACACTAGCAATAGC-ACAA-
1 AGCACA--A-TAATA-CTATAAG
3032402 AGCACAATAATACTATAAG
1 AGCACAATAATACTATAAG
3032421 AGCACA
1 AGCACA
3032427 CTAGCAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
17 1 0.03
18 7 0.20
19 13 0.37
21 7 0.20
22 6 0.17
23 1 0.03
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (19 bp):
AGCACAATAATACTATAAG
Found at i:3034194 original size:21 final size:21
Alignment explanation
Indices: 3034170--3034219 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3034160 ATTAAATTAT
3034170 TATTTTTTATTAATAAAATAC
1 TATTTTTTATTAATAAAATAC
*
3034191 TATTTTTTATTAATAAAATAT
1 TATTTTTTATTAATAAAATAC
3034212 TATTTTTT
1 TATTTTTT
3034220 TCATCAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTTTATTAATAAAATAC
Found at i:3036889 original size:2 final size:2
Alignment explanation
Indices: 3036884--3036910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3036874 TTTTTTAAAA
3036884 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3036911 CAACACAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3040697 original size:177 final size:178
Alignment explanation
Indices: 3040401--3040755 Score: 703
Period size: 177 Copynumber: 2.0 Consensus size: 178
3040391 TGCAACAGTC
3040401 AACTCGTCGAAACTGGTTCTACAGAAAAGCTAAAATAGATGCTATTACAGAGAAAAAGGAACACA
1 AACTCGTCGAAACTGGTTCTACAGAAAAGCTAAAATAGATGCTATTACAGAGAAAAAGGAACACA
3040466 ATTTAGTTCTGCATAATCGAAGACAAGTTGGTAAACCACTTACGAAAAGCATGACGCCATAACCG
66 ATTTAGTTCTGCATAATCGAAGACAAGTTGGTAAACCACTTACGAAAAGCATGACGCCATAACCG
3040531 TGAATGTTCTGGTTCGACGTA-TTGGATTGCAGCTAGTTAATTCGAAG
131 TGAATGTTCTGGTTCGACGTATTTGGATTGCAGCTAGTTAATTCGAAG
3040578 AACTCGTCGAAACTGGTTCTACAGAAAAGCTAAAATAGATGCTATTACAGAGAAAAAGGAACACA
1 AACTCGTCGAAACTGGTTCTACAGAAAAGCTAAAATAGATGCTATTACAGAGAAAAAGGAACACA
3040643 ATTTAGTTCTGCATAATCGAAGACAAGTTGGTAAACCACTTACGAAAAGCATGACGCCATAACCG
66 ATTTAGTTCTGCATAATCGAAGACAAGTTGGTAAACCACTTACGAAAAGCATGACGCCATAACCG
3040708 TGAATGTTCTGGTTCGACGTATTTGGATTGCAGCTAGTTAATTCGAAG
131 TGAATGTTCTGGTTCGACGTATTTGGATTGCAGCTAGTTAATTCGAAG
3040756 CAAGCTGCAA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
177 151 0.85
178 26 0.15
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (178 bp):
AACTCGTCGAAACTGGTTCTACAGAAAAGCTAAAATAGATGCTATTACAGAGAAAAAGGAACACA
ATTTAGTTCTGCATAATCGAAGACAAGTTGGTAAACCACTTACGAAAAGCATGACGCCATAACCG
TGAATGTTCTGGTTCGACGTATTTGGATTGCAGCTAGTTAATTCGAAG
Found at i:3050586 original size:7 final size:7
Alignment explanation
Indices: 3050574--3050603 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3050564 AGGTAAATTA
3050574 CATCATT
1 CATCATT
3050581 CATCATT
1 CATCATT
3050588 CATCATT
1 CATCATT
3050595 CATCATT
1 CATCATT
3050602 CA
1 CA
3050604 ACTATCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (7 bp):
CATCATT
Found at i:3058290 original size:20 final size:20
Alignment explanation
Indices: 3058267--3058316 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3058257 GAATATGTAA
*
3058267 ATCGCTACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3058287 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3058307 GTCGCAACGC
1 ATCGCAACGC
3058317 TGAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3059134 original size:163 final size:163
Alignment explanation
Indices: 3058850--3059175 Score: 620
Period size: 163 Copynumber: 2.0 Consensus size: 163
3058840 GTTGTTGAAC
3058850 CTAGAAGTAGTGAAGTTGGGCCAGTAGCGGGTAGTAATCAACTAAGTTTTTCAACCCCAGTTATG
1 CTAGAAGTAGTGAAGTTGGGCCAGTAGCGGGTAGTAATCAACTAAGTTTTTCAACCCCAGTTATG
3058915 GTGCTCAAAATTTAATGGTTCCACCACAATTTCATCACCAAGCAAATTTTGTTTCACCACATTTC
66 GTGCTCAAAATTTAATGGTTCCACCACAATTTCATCACCAAGCAAATTTTGTTTCACCACATTTC
3058980 CAATACC-AACACAATCTCAAAACCCAC-ACCTT
131 CAATACCAAACACAATCTC-AAACCCACAACCTT
3059012 CTAGAAGTAGTGAAGTTGGGCCAGTAGCGGGTAGTAATCAACTAAGTTTTTCAACCCCAGTTTAT
1 CTAGAAGTAGTGAAGTTGGGCCAGTAGCGGGTAGTAATCAACTAAGTTTTTCAACCCCAG-TTAT
3059077 GGTGCTCAAAATTTAATGGTTCCACCACAATTTCATCACCAAGCAAATTTTGTTTCACCACATTT
65 GGTGCTCAAAATTTAATGGTTCCACCACAATTTCATCACCAAGCAAATTTTGTTTCACCACATTT
3059142 CCAATACCAAACACAATCTCAAACCCACAACCTT
130 CCAATACCAAACACAATCTCAAACCCACAACCTT
3059176 TTTGATCTCA
Statistics
Matches: 161, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
162 60 0.37
163 85 0.53
164 16 0.10
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (163 bp):
CTAGAAGTAGTGAAGTTGGGCCAGTAGCGGGTAGTAATCAACTAAGTTTTTCAACCCCAGTTATG
GTGCTCAAAATTTAATGGTTCCACCACAATTTCATCACCAAGCAAATTTTGTTTCACCACATTTC
CAATACCAAACACAATCTCAAACCCACAACCTT
Found at i:3059251 original size:32 final size:32
Alignment explanation
Indices: 3059215--3059279 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3059205 GTTTCAATAA
**
3059215 GAACAGATGATGCGTGTAATGATTTTGATATT
1 GAACAGACCATGCGTGTAATGATTTTGATATT
*
3059247 GAACAGACCCTGCGTGTAATGATTTTGATATT
1 GAACAGACCATGCGTGTAATGATTTTGATATT
3059279 G
1 G
3059280 GTCAATACCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (32 bp):
GAACAGACCATGCGTGTAATGATTTTGATATT
Found at i:3059438 original size:13 final size:14
Alignment explanation
Indices: 3059413--3059448 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3059403 AGAAGAAAAA
3059413 GAAGAAGAAAT-CCC
1 GAAGAA-AAATCCCC
3059427 GAAGAAAAATCCCC
1 GAAGAAAAATCCCC
3059441 GAAGAAAA
1 GAAGAAAA
3059449 TGTCACGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.56, C:0.19, G:0.19, T:0.06
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:3061815 original size:140 final size:140
Alignment explanation
Indices: 3061563--3061985 Score: 756
Period size: 140 Copynumber: 3.0 Consensus size: 140
3061553 GCAAATGTTG
3061563 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * *
3061628 TTGAACATTGTTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGATATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3061693 CGAATTTGAC
131 CGAATTTGAC
*
3061703 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
3061768 TTGAACATTGATATGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGATATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3061833 CGAATTTGAC
131 CGAATTTGAC
*
3061843 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * * *
3061908 TTGAACATTGCTATGATCTGTTCAGTTATTATCACTAATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGATATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3061973 CGAATTTGAC
131 CGAATTTGAC
3061983 TAT
1 TAT
3061986 CGCAACGCGA
Statistics
Matches: 271, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 271 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGATATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:3061981 original size:20 final size:20
Alignment explanation
Indices: 3061956--3062052 Score: 124
Period size: 20 Copynumber: 4.8 Consensus size: 20
3061946 TTACACATTC
3061956 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
3061976 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
3061996 ATTT-AACTATCGTAACGTGA
1 ATTTGAA-TATCGCAACGCGA
* *
3062016 ATTTGATTATCGCAACGGGA
1 ATTTGAATATCGCAACGCGA
*
3062036 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
3062053 AGAAAATCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:3062083 original size:20 final size:19
Alignment explanation
Indices: 3062058--3062102 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3062048 CAACGAGAAA
*
3062058 ATCGCAAAGTGTATTAGACT
1 ATCGCAAAGTGAATT-GACT
*
3062078 ATCGCAACGTGAATTGACT
1 ATCGCAAAGTGAATTGACT
*
3062097 TTCGCA
1 ATCGCA
3062103 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (19 bp):
ATCGCAAAGTGAATTGACT
Found at i:3062271 original size:14 final size:14
Alignment explanation
Indices: 3062252--3062284 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3062242 AATTAAACAT
3062252 ATCAACTTTTACAA
1 ATCAACTTTTACAA
3062266 ATCAACTTTTACAA
1 ATCAACTTTTACAA
3062280 ATCAA
1 ATCAA
3062285 TTAAACAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCAACTTTTACAA
Found at i:3062306 original size:77 final size:78
Alignment explanation
Indices: 3062181--3062347 Score: 264
Period size: 77 Copynumber: 2.1 Consensus size: 78
3062171 ATTGAAATCA
* *
3062181 ACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTGTTTACACATCAATT
1 ACAAATCAACTTTTACA--T-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATT
* *
3062246 AAACATATCAACTTTT
63 AAACAAATAAACTTTT
3062262 ACAAATCAACTTTTACA-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAA
3062326 CAAATAAACTTTT
66 CAAATAAACTTTT
3062339 ACAAATCAA
1 ACAAATCAA
3062348 TTAAACAAGC
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
77 65 0.79
81 17 0.21
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (78 bp):
ACAAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAA
CAAATAAACTTTT
Found at i:3062326 original size:36 final size:36
Alignment explanation
Indices: 3062203--3062328 Score: 119
Period size: 36 Copynumber: 3.4 Consensus size: 36
3062193 TTACATTTCA
* *
3062203 ATCAATTAAATAAGCACAAATAAGAATTGTTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
* *** * *
3062239 ATCAATTAAACATATCAACTTTTACA-AATCAACTTTTACAA
1 ATCAATTAAACA-AGC-ACAAATA-AGAAT-TA--TTTACAC
3062280 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
3062316 ATCAATTAAACAA
1 ATCAATTAAACAA
3062329 ATAAACTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
36 30 0.43
37 2 0.03
38 9 0.13
39 8 0.12
40 2 0.03
41 18 0.26
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.29
Consensus pattern (36 bp):
ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
Found at i:3064374 original size:19 final size:20
Alignment explanation
Indices: 3064342--3064384 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
3064332 AATAGTTTCT
3064342 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
3064362 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
3064381 GAAA
1 GAAA
3064385 ATGACTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3064419 original size:20 final size:21
Alignment explanation
Indices: 3064370--3064423 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
3064360 ACGAAACTTA
3064370 AATCGCAACGCGAAAATGACT
1 AATCGCAACGCGAAAATGACT
** *
3064391 -ATCAAAACGCGGAAATGA-T
1 AATCGCAACGCGAAAATGACT
3064410 AATCGCAACGCGAA
1 AATCGCAACGCGAA
3064424 TTTGACTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (21 bp):
AATCGCAACGCGAAAATGACT
Found at i:3064434 original size:20 final size:19
Alignment explanation
Indices: 3064371--3064439 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
3064361 CGAAACTTAA
3064371 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
**
3064391 ATCAAAACGCGGAAATGA-T
1 ATCGCAACGC-GAAATGACT
*
3064410 AATCGCAACGCGAATTTGACT
1 -ATCGCAACGCGAA-ATGACT
*
3064431 ATCGTAACG
1 ATCGCAACG
3064440 GGATAATCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.10
20 33 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3064506 original size:19 final size:19
Alignment explanation
Indices: 3064444--3064506 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
3064434 GTAACGGGAT
*
3064444 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
*
3064463 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
3064482 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
3064501 ATTCGC
1 AATCGC
3064507 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:3064563 original size:33 final size:34
Alignment explanation
Indices: 3064506--3064581 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
3064496 ACTAAATTCG
3064506 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
3064540 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
3064573 CGTTGCGAT
1 CGTTGCGAT
3064582 AGTCAAATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:3064598 original size:20 final size:20
Alignment explanation
Indices: 3064573--3064621 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3064563 GCGATTATCC
3064573 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3064593 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3064613 CGTTGCGAT
1 CGTTGCGAT
3064622 TTTTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3066539 original size:20 final size:20
Alignment explanation
Indices: 3066519--3066661 Score: 144
Period size: 20 Copynumber: 7.2 Consensus size: 20
3066509 GAAATTTAAA
* **
3066519 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
3066539 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3066559 ATAGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
3066579 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
3066599 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
* *
3066618 ATCACAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3066638 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3066658 ATCG
1 ATCG
3066662 TTGCGATTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.13
20 90 0.87
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3067090 original size:22 final size:22
Alignment explanation
Indices: 3067035--3067091 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
3067025 GATGGAGATA
* *
3067035 GACGGATTTCGCCTGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
3067057 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
3067079 GACGGATGTCGTC
1 GACGGATTTCGTC
3067092 ATAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:3067276 original size:20 final size:20
Alignment explanation
Indices: 3067253--3067338 Score: 111
Period size: 20 Copynumber: 4.2 Consensus size: 20
3067243 TTATCGCAAC
*
3067253 GCGATAGTCATAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
3067273 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
** *
3067293 GCGATTATGT-ATTATTGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
3067314 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
3067334 GCGAT
1 GCGAT
3067339 TTACATATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 2 0.04
20 38 0.68
21 14 0.25
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:3067356 original size:61 final size:61
Alignment explanation
Indices: 3067223--3067419 Score: 164
Period size: 61 Copynumber: 3.2 Consensus size: 61
3067213 GCACTTTGAA
* * *
3067223 AATCGCATTGAGATTTTGTATTATCGCAACGCGATAGTCATAATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAG
* * *** * *
3067284 AATCGCGTTGCGATTATGTATTATTGCGTTGCGATAGTCAGAATCGCGTTGCGAT-TTACAT
1 AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGT-CAG
* * * ** * * * **
3067345 ATTCGCATTGCGATTTTCTAAAATCGCAACGCGA-ATTTGGAAAATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCAACGCGATA-GT-CAGAATCGCGTTGCGATAGTCAG
*
3067407 AATCGCGTTGCGA
1 AATCGCATTGCGA
3067420 ATCTGGAAAC
Statistics
Matches: 103, Mismatches: 29, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
60 2 0.02
61 74 0.72
62 26 0.25
63 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (61 bp):
AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAG
Found at i:3067378 original size:21 final size:21
Alignment explanation
Indices: 3067354--3067400 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3067344 TATTCGCATT
*
3067354 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
3067375 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
3067396 GCGAT
1 GCGAT
3067401 AGTCAGAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:3067420 original size:41 final size:41
Alignment explanation
Indices: 3067272--3067464 Score: 126
Period size: 41 Copynumber: 4.7 Consensus size: 41
3067262 ATAATCGCGT
* ** * **
3067272 TGCGATAGTCAGAATCGCGTTGCG-ATTATGTATTATTGCGT
1 TGCGATAGTCAGAATCGCGTTGCGAATT-TGGAAAATCGCAA
** * * *
3067313 TGCGATAGTCAGAATCGCGTTGCG-ATTTACATATTCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGAATTTGGAAAATCGCAA
** * ***
3067353 TGCGATTTTCTAAAATCGCAACGCGAATTTGGAAAATCGCAA
1 TGCGATAGTC-AGAATCGCGTTGCGAATTTGGAAAATCGCAA
* *
3067395 TGCGATAGTCAGAATCGCGTTGCGAATCTGGAAACT-G-AA
1 TGCGATAGTCAGAATCGCGTTGCGAATTTGGAAAATCGCAA
* *
3067434 TTGCGATACT-AGAGATCGCGTTGCGATTTTG
1 -TGCGATAGTCAGA-ATCGCGTTGCGAATTTG
3067465 TTGGTCATTT
Statistics
Matches: 120, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
39 5 0.04
40 39 0.32
41 57 0.47
42 19 0.16
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (41 bp):
TGCGATAGTCAGAATCGCGTTGCGAATTTGGAAAATCGCAA
Found at i:3068113 original size:23 final size:23
Alignment explanation
Indices: 3068086--3068138 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
3068076 AAGAGCTTAT
*
3068086 TTATTTT-TTTTTAAAAATAAAA
1 TTATTTTAATTTTAAAAATAAAA
*
3068108 GTTATTTTAAATTTTAAATATAAAA
1 -TTATTTT-AATTTTAAAAATAAAA
3068133 TTATTT
1 TTATTT
3068139 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 6 0.23
25 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTTAATTTTAAAAATAAAA
Found at i:3068139 original size:23 final size:25
Alignment explanation
Indices: 3068094--3068155 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 25
3068084 ATTTATTTTT
*
3068094 TTTTAAAAATAAAAGTTATTTTAAA
1 TTTTAAATATAAAAGTTATTTTAAA
3068119 TTTTAAATATAAAA-TTA-TTTAAA
1 TTTTAAATATAAAAGTTATTTTAAA
**
3068142 AATTAAATATAAAA
1 TTTTAAATATAAAA
3068156 ATACTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 18 0.53
24 3 0.09
25 13 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTTAAATATAAAAGTTATTTTAAA
Found at i:3068165 original size:23 final size:23
Alignment explanation
Indices: 3068121--3068165 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3068111 ATTTTAAATT
* * *
3068121 TTAAATATAAAATTATTTAAAAA
1 TTAAATATAAAAATACTAAAAAA
3068144 TTAAATATAAAAATACTAAAAA
1 TTAAATATAAAAATACTAAAAA
3068166 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAATATAAAAATACTAAAAAA
Found at i:3068172 original size:23 final size:23
Alignment explanation
Indices: 3068123--3068170 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3068113 TTTAAATTTT
* * *
3068123 AAATATAAAATTATTTAAAAATT
1 AAATATAAAAATATCTAAAAATA
3068146 AAATATAAAAATA-CTAAAAATA
1 AAATATAAAAATATCTAAAAATA
3068168 AAA
1 AAA
3068171 ATTAAATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAAAAATATCTAAAAATA
Found at i:3074486 original size:18 final size:17
Alignment explanation
Indices: 3074460--3074494 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3074450 GTAAATCATG
*
3074460 TGTTTTATGTCACTCTTA
1 TGTTATATGTCA-TCTTA
3074478 TGTTATATGTCATCTTA
1 TGTTATATGTCATCTTA
3074495 AATGTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (17 bp):
TGTTATATGTCATCTTA
Found at i:3074998 original size:19 final size:19
Alignment explanation
Indices: 3074974--3075047 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
3074964 TATGCATTGG
* * *
3074974 GCTATGAATCTTAAAGTAA
1 GCTATGAATATGAAAATAA
3074993 GCTATGAATATGAAAATAA
1 GCTATGAATATGAAAATAA
* * *
3075012 GTTATGAATTTGGAAATAA
1 GCTATGAATATGAAAATAA
* * *
3075031 GTTCTGAATCTGAAAAT
1 GCTATGAATATGAAAAT
3075048 GATTTCTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:3075094 original size:7 final size:6
Alignment explanation
Indices: 3075075--3075117 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
3075065 AGTACTTGTT
* * *
3075075 ATGAAA ATGAAA AGTGAAA ATGAAC ATGTAA ATGAAT ATGAAA
1 ATGAAA ATGAAA A-TGAAA ATGAAA ATGAAA ATGAAA ATGAAA
3075118 GGGAAAGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (6 bp):
ATGAAA
Found at i:3083751 original size:3 final size:3
Alignment explanation
Indices: 3083715--3083812 Score: 55
Period size: 3 Copynumber: 32.3 Consensus size: 3
3083705 GACGCGACAA
* *
3083715 CTT CTT TTT CTT CCTT C-T CTT -TT GTT -TT -TT CTT CTT CTT CCTT
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT
*
3083758 CATC CTT CTTT CTT CTT CTT CCTT CTTT CTT CTT CTT CCTT -TT -TT
1 C-TT CTT C-TT CTT CTT CTT -CTT C-TT CTT CTT CTT -CTT CTT CTT
*
3083803 CTT ATT CTT C
1 CTT CTT CTT C
3083813 AAAGTAATCT
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
2 12 0.15
3 46 0.59
4 20 0.26
ACGTcount: A:0.02, C:0.31, G:0.01, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:3083765 original size:17 final size:17
Alignment explanation
Indices: 3083745--3083812 Score: 93
Period size: 17 Copynumber: 4.0 Consensus size: 17
3083735 TTTGTTTTTT
*
3083745 CTTC-TTCTTCCTTCATC
1 CTTCTTTCTT-CTTCTTC
3083762 CTTCTTTCTTCTTCTTC
1 CTTCTTTCTTCTTCTTC
3083779 CTTCTTTCTTCTTCTTC
1 CTTCTTTCTTCTTCTTC
* *
3083796 CTTTTTTCTTATTCTTC
1 CTTCTTTCTTCTTCTTC
3083813 AAAGTAATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
17 42 0.89
18 5 0.11
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTCTTTCTTCTTCTTC
Found at i:3083769 original size:24 final size:24
Alignment explanation
Indices: 3083742--3083795 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
3083732 TCTTTTGTTT
3083742 TTTCTTCTTCTTCCTTCATCCTTC
1 TTTCTTCTTCTTCCTTCATCCTTC
* *
3083766 TTTCTTCTTCTTCCTTCTTTCTTC
1 TTTCTTCTTCTTCCTTCATCCTTC
3083790 -TTCTTC
1 TTTCTTC
3083796 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCTTCTTCTTCCTTCATCCTTC
Found at i:3083773 original size:27 final size:27
Alignment explanation
Indices: 3083715--3083794 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
3083705 GACGCGACAA
* * *
3083715 CTTCTTTTTCTTCCTTCTCTTTTGTTT
1 CTTCTTCTTCTTCCTTCTCTCTTCTTT
*
3083742 TTTCTTCTTCTTCCTTCATC-CTTCTTT
1 CTTCTTCTTCTTCCTTC-TCTCTTCTTT
*
3083769 CTTCTTCTTCCTTCTTTCT-TCTTCTT
1 CTTCTTCTT-CTTCCTTCTCTCTTCTT
3083795 CCTTTTTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 35 0.80
28 9 0.20
ACGTcount: A:0.01, C:0.31, G:0.01, T:0.66
Consensus pattern (27 bp):
CTTCTTCTTCTTCCTTCTCTCTTCTTT
Found at i:3093812 original size:27 final size:25
Alignment explanation
Indices: 3093762--3093813 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
3093752 AATATATACT
*
3093762 TATTAAATATAAATACATAAAAATA
1 TATTAAATATAAATACAAAAAAATA
3093787 TATTAATATTATAAATA-AAAACAAATA
1 TATTAA-A-TATAAATACAAAA-AAATA
3093814 CTAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.26
26 4 0.17
27 13 0.57
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
TATTAAATATAAATACAAAAAAATA
Found at i:3094129 original size:31 final size:31
Alignment explanation
Indices: 3094087--3094152 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
3094077 TAGACCTGTT
3094087 TTAA-ATTCAACGGCCCAAATGCAACATAGA
1 TTAAGATTCAACGGCCCAAATGCAACATAGA
3094117 TTAAGATTCAACGGCCCAAATGCAACATAGA
1 TTAAGATTCAACGGCCCAAATGCAACATAGA
3094148 TTAAG
1 TTAAG
3094153 GTTTTAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (31 bp):
TTAAGATTCAACGGCCCAAATGCAACATAGA
Found at i:3095934 original size:20 final size:16
Alignment explanation
Indices: 3095874--3095925 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
3095864 TCTCATGTTG
3095874 TTTCCTTTATTTAATC
1 TTTCCTTTATTTAATC
3095890 TTTCCTTTATTTAATC
1 TTTCCTTTATTTAATC
3095906 TTTCCTTTATTTAATC
1 TTTCCTTTATTTAATC
3095922 TTTC
1 TTTC
3095926 ATTCCTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCCTTTATTTAATC
Found at i:3099517 original size:19 final size:21
Alignment explanation
Indices: 3099493--3099539 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3099483 TATATGTTTG
3099493 ATGAACAGT-AA-AATA-CGGT
1 ATGAACAGTGAACAATATC-GT
3099512 ATGAACAGTGAACAATATCGT
1 ATGAACAGTGAACAATATCGT
3099533 ATGAACA
1 ATGAACA
3099540 ATAATGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 13 0.52
22 1 0.04
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (21 bp):
ATGAACAGTGAACAATATCGT
Found at i:3100345 original size:21 final size:21
Alignment explanation
Indices: 3100319--3100387 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
3100309 TCCCGTAGGG
3100319 CCACTGTATTGTCCTGAAGGA
1 CCACTGTATTGTCCTGAAGGA
* *
3100340 CCACTGTATTATCCTAAAGGA
1 CCACTGTATTGTCCTGAAGGA
* *
3100361 CCAC--TA-TGTCCCGTAGGA
1 CCACTGTATTGTCCTGAAGGA
3100379 CCACTGTAT
1 CCACTGTAT
3100388 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 12 0.31
19 2 0.05
20 2 0.05
21 23 0.59
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
CCACTGTATTGTCCTGAAGGA
Found at i:3103136 original size:20 final size:20
Alignment explanation
Indices: 3103108--3103150 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3103098 TTTTCTTCTG
3103108 AAATAAAAAATG-AACTTTGA
1 AAAT-AAAAATGAAACTTTGA
* *
3103128 AAATCAAAATGAAATTTTGA
1 AAATAAAAATGAAACTTTGA
3103148 AAA
1 AAA
3103151 AGGATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (20 bp):
AAATAAAAATGAAACTTTGA
Found at i:3105274 original size:27 final size:26
Alignment explanation
Indices: 3105244--3105305 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
3105234 AAACCTTTGA
3105244 ATATTAATATTTAATATAAAATTTGTT
1 ATATTAATATTT-ATATAAAATTTGTT
* * *
3105271 ATATCAATA-TTATATATAATTTTTT
1 ATATTAATATTTATATAAAATTTGTT
3105296 ATATTAATAT
1 ATATTAATAT
3105306 ATCGGTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 20 0.67
26 2 0.07
27 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTAATATTTATATAAAATTTGTT
Found at i:3106156 original size:24 final size:23
Alignment explanation
Indices: 3106129--3106178 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3106119 TACCCTCCAC
3106129 TTCTCGTTACTCTTGTCTTTTTAT
1 TTCTCGTTAC-CTTGTCTTTTTAT
* * * *
3106153 TTCTTGTTTCCTTTTGTTTTTAT
1 TTCTCGTTACCTTGTCTTTTTAT
3106176 TTC
1 TTC
3106179 ACTAAATTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.06, C:0.18, G:0.08, T:0.68
Consensus pattern (23 bp):
TTCTCGTTACCTTGTCTTTTTAT
Found at i:3131063 original size:19 final size:17
Alignment explanation
Indices: 3131041--3131108 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 17
3131031 GGATGAAACA
*
3131041 AATATAAAAAATGAAATTG
1 AATAAAAAAAAT-AAA-TG
3131060 AATAAAATAAAATAAATG
1 AATAAAA-AAAATAAATG
* *
3131078 AAGAAAAAAAATATAT-
1 AATAAAAAAAATAAATG
3131094 AA-AAAAAAGAATAAA
1 AATAAAAAA-AATAAA
3131109 AAAGGTAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.14
16 7 0.16
17 8 0.19
18 8 0.19
19 9 0.21
20 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (17 bp):
AATAAAAAAAATAAATG
Found at i:3131089 original size:13 final size:13
Alignment explanation
Indices: 3131065--3131111 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3131055 AATTGAATAA
*
3131065 AATAAAATAAATG
1 AATAAAAAAAATG
*
3131078 AAGAAAAAAAAT-
1 AATAAAAAAAATG
3131090 ATATAAAAAAAA-G
1 A-ATAAAAAAAATG
3131103 AATAAAAAA
1 AATAAAAAA
3131112 GGTAAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AATAAAAAAAATG
Found at i:3131208 original size:29 final size:28
Alignment explanation
Indices: 3131175--3131236 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
3131165 AAACATAATG
*
3131175 AAAATAAATAAATAGTATAAATAAAATA-A
1 AAAATAAAAAAATA-TATAAA-AAAATATA
*
3131204 AAAATAAAAAAATATATATAAAAATATA
1 AAAATAAAAAAATATATAAAAAAATATA
3131232 AAAAT
1 AAAAT
3131237 GTATGTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 6 0.20
28 11 0.37
29 13 0.43
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (28 bp):
AAAATAAAAAAATATATAAAAAAATATA
Found at i:3131369 original size:29 final size:28
Alignment explanation
Indices: 3131243--3131370 Score: 70
Period size: 29 Copynumber: 4.5 Consensus size: 28
3131233 AAATGTATGT
*
3131243 ATAATATAATA-AAATATTAAAT--AGTA
1 ATAATATAATATAAA-ATAAAATAAAGTA
* *
3131269 ACAATAATAATAAATAAATGAAAAATAAA-T-
1 ATAAT-ATAATATA-AAAT--AAAATAAAGTA
* *
3131299 ATACATATAATATTAACTAAAA-AATAGTA
1 ATA-ATATAATATAAAATAAAATAA-AGTA
* *
3131328 ATTATAGAAATATAAAATAAAATAAAGTA
1 ATAATA-TAATATAAAATAAAATAAAGTA
3131357 ATAATATATATATA
1 ATAATATA-ATATA
3131371 TATAACGTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
26 6 0.08
27 11 0.14
28 8 0.11
29 33 0.43
30 14 0.18
31 3 0.04
32 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
ATAATATAATATAAAATAAAATAAAGTA
Found at i:3131402 original size:13 final size:13
Alignment explanation
Indices: 3131384--3131408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3131374 AACGTTAAGA
3131384 AAATATAGTAAAC
1 AAATATAGTAAAC
3131397 AAATATAGTAAA
1 AAATATAGTAAA
3131409 TAAGTAAACA
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:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATATAGTAAAC
Found at i:3131430 original size:21 final size:21
Alignment explanation
Indices: 3131383--3131432 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3131373 TAACGTTAAG
* *
3131383 AAAATATAGTAAACAAATATAG
1 AAAATA-AGTAAACAAAGATAA
* *
3131405 TAAATAAGTAAACATAGATAA
1 AAAATAAGTAAACAAAGATAA
3131426 AAAATAA
1 AAAATAA
3131433 TATATATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAATAAGTAAACAAAGATAA
Found at i:3132983 original size:106 final size:106
Alignment explanation
Indices: 3132799--3135861 Score: 4583
Period size: 106 Copynumber: 28.9 Consensus size: 106
3132789 GCATTGTTCC
* * * * * *
3132799 GAGTCCAATATTCTCCGTTGTGAAGTTGAAATTGGCTCTGGAATCGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3132864 CCAGTC-ATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3132905 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3132970 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3133011 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3133076 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3133117 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3133182 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3133223 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3133288 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3133329 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3133394 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
3133435 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3133500 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3133541 GAGACCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
3133606 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3133647 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3133712 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3133753 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3133818 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3133859 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3133924 CCAGTGGTACCTTCGTCGTGAAGTTTAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3133965 GAGTCCAATATTCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
3134029 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3134071 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3134136 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3134177 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3134242 CCAGCGGTCCCTTCGTCGTGAAATTGAAATTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3134283 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3134348 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3134389 TAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3134454 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3134495 GAGTCTAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
3134560 CCAGCGGTCCCTTCATCGTGAAGTTAAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
3134601 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3134666 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3134707 GA-TACCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GAGT-CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
3134771 ACCAGCGGTTCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3134813 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3134878 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
3134919 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGATGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3134984 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTGTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3135025 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCT-ATAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTGTTTGTTGACA
* * * *
3135089 ACCAGTGGTTCCTTCGTCGTGATGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135131 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG-GAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3135195 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3135236 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3135301 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135342 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGCTATGAAATTGGCAAGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG----GAAATT-----G--
* * *
3135407 ATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTGAACTTGCGTTGTCTT
55 -TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3135460 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3135525 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135566 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTC------T--GAAA---TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3135620 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3135661 GAGTCCAATATACTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTCACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3135726 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135767 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGGCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3135832 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
3135862 CCAAGTATTG
Statistics
Matches: 2701, Mismatches: 225, Indels: 62
0.90 0.08 0.02
Matches are distributed among these distances:
95 87 0.03
98 4 0.00
100 1 0.00
101 1 0.00
103 3 0.00
105 98 0.04
106 2399 0.89
107 3 0.00
110 5 0.00
114 6 0.00
115 1 0.00
118 93 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3135385 original size:12 final size:12
Alignment explanation
Indices: 3135368--3135401 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3135358 GCTGTGAAGT
3135368 TGAAATTGGCTA
1 TGAAATTGGCTA
3135380 TGAAATTGGCTA
1 TGAAATTGGCTA
3135392 TGAAATTGGC
1 TGAAATTGGC
3135402 AAGTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (12 bp):
TGAAATTGGCTA
Found at i:3135466 original size:224 final size:223
Alignment explanation
Indices: 3135157--3135610 Score: 728
Period size: 224 Copynumber: 2.0 Consensus size: 223
3135147 GCTGTGAAGT
* * * * *
3135157 TGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGGAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 TGAAATTGGCTATGAAATTGGCAAATTATTTATTGCAACCAGCGGTCCCTTCGTCGGGAAGTTGA
* * *
3135222 ACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAG
66 ACTTGCATTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAA
*
3135287 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
131 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
3135352 TCATTCGCTGTGAAGTTGAAATTGGCTA
196 TCATTCGCTGTAAAGTTGAAATTGGCTA
*
3135380 TGAAATTGGCTATGAAATTGGCAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTG
1 TGAAATTGGCTATGAAATTGGCAAATTATTTATTG-CAACCAGCGGTCCCTTCGTCGGGAAGTTG
* * * *
3135445 AACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
65 AACTTGCATTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGCCTCTGAAATTGAGAA
*
3135510 ATTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
130 ATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* * *
3135575 ATCCTTCGTTGTAAAGTTGAAATTGGCTC
195 ATCATTCGCTGTAAAGTTGAAATTGGCTA
3135604 TGAAATT
1 TGAAATT
3135611 TGTTGACAAC
Statistics
Matches: 211, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
223 31 0.15
224 180 0.85
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (223 bp):
TGAAATTGGCTATGAAATTGGCAAATTATTTATTGCAACCAGCGGTCCCTTCGTCGGGAAGTTGA
ACTTGCATTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAA
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCATTCGCTGTAAAGTTGAAATTGGCTA
Found at i:3135470 original size:118 final size:115
Alignment explanation
Indices: 3135262--3135610 Score: 500
Period size: 118 Copynumber: 3.1 Consensus size: 115
3135252 GTTGTGAAGT
* *
3135262 TGAAATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATTGGCT-TGAAATTG-GAAGTT-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* *
3135327 AACTTGCGTTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTA
63 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
3135380 TGAAATTGGCTATGAAATTGGCAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTG
1 TGAAATTGGCT-TGAAATTGG-AAGTT-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* *
3135445 AACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTC
63 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
3135498 TGAAATTGG---GAAA-T-----TTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
1 TGAAATTGGCTTGAAATTGGAAGTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
3135554 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTC
66 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
3135604 TGAAATT
1 TGAAATT
3135611 TGTTGACAAC
Statistics
Matches: 216, Mismatches: 14, Indels: 14
0.89 0.06 0.06
Matches are distributed among these distances:
106 92 0.43
107 2 0.01
113 1 0.00
114 4 0.02
117 1 0.00
118 116 0.54
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (115 bp):
TGAAATTGGCTTGAAATTGGAAGTTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:3135757 original size:201 final size:201
Alignment explanation
Indices: 3135407--3135811 Score: 702
Period size: 201 Copynumber: 2.0 Consensus size: 201
3135397 TTGGCAAGTT
* *
3135407 ATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATC
1 ATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATA
* * *
3135472 CTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTATTGACAACCAGCGGTCCCT
66 CTACGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTCACAACCAGCGGTCCCT
*
3135537 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGC
131 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGGC
3135602 TCTGAA
196 TCTGAA
* *
3135608 ATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATA
1 ATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATA
* *
3135673 CTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTCACAACCAGCGGTCCCT
66 CTACGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTCACAACCAGCGGTCCCT
* *
3135738 TCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC
131 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGGC
3135803 TCTGAA
196 TCTGAA
3135809 ATT
1 ATT
3135812 GGGAAGTTGT
Statistics
Matches: 192, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 192 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (201 bp):
ATTTATTGACAACCAGCGGTCCCTTCGTCGGGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATA
CTACGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTCACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGGC
TCTGAA
Found at i:3136753 original size:22 final size:22
Alignment explanation
Indices: 3136727--3136781 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
3136717 TTGTGTTTGG
3136727 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3136749 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3136771 TCAAAGGTTTG
1 TCAAAGGTTTG
3136782 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3137429 original size:19 final size:21
Alignment explanation
Indices: 3137393--3137436 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3137383 GTCCCTTTTC
* *
3137393 TTTTTGATTTTTGCTTCT-TT
1 TTTTTGATTCTTGATTCTCTT
3137413 TTTTTG-TTCTTGATTCTCTT
1 TTTTTGATTCTTGATTCTCTT
3137433 TTTT
1 TTTT
3137437 ATTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.05, C:0.11, G:0.09, T:0.75
Consensus pattern (21 bp):
TTTTTGATTCTTGATTCTCTT
Found at i:3137447 original size:43 final size:45
Alignment explanation
Indices: 3137387--3137473 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 45
3137377 CTTTTTGTCC
3137387 CTTTTCTTTTTGATTTTTGCTTC-TT-TTTTTTGTTCTTGATTCT
1 CTTTTCTTTTTGATTTTTGCTTCTTTCTTTTTTGTTCTTGATTCT
*
3137430 CTTTT-TTATTTGTTTTTTGCTTCTTTGCTTTTTTGTTCTTGATT
1 CTTTTCTT-TTTGATTTTTGCTTCTTT-CTTTTTTGTTCTTGATT
3137474 GGATCTTCGC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 2 0.05
43 19 0.49
44 2 0.05
46 16 0.41
ACGTcount: A:0.05, C:0.13, G:0.10, T:0.72
Consensus pattern (45 bp):
CTTTTCTTTTTGATTTTTGCTTCTTTCTTTTTTGTTCTTGATTCT
Found at i:3142022 original size:19 final size:17
Alignment explanation
Indices: 3142000--3142045 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
3141990 TGAAACAAAT
3142000 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
3142019 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
*
3142037 AGAAAAAAA
1 ATAAAAAAA
3142046 TATATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 9 0.36
20 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:3142160 original size:9 final size:9
Alignment explanation
Indices: 3142133--3142182 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
3142123 AACATAATGA
3142133 AAAT-AAAT
1 AAATAAAAT
**
3142141 AAATAGTAT
1 AAATAAAAT
3142150 AAATAAAAT
1 AAATAAAAT
3142159 AAA-AAAAT
1 AAATAAAAT
3142167 AAA-AAAAT
1 AAATAAAAT
*
3142175 ATATAAAA
1 AAATAAAA
3142183 ATATAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 19 0.54
9 16 0.46
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3142167 original size:8 final size:8
Alignment explanation
Indices: 3142148--3142192 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
3142138 AATAAATAGT
3142148 ATAAATAAA
1 ATAAA-AAA
3142157 ATAAAAAA
1 ATAAAAAA
3142165 ATAAAAAA
1 ATAAAAAA
3142173 ATATATAAAA
1 ATA-A-AAAA
*
3142183 ATATAAAA
1 ATAAAAAA
3142191 AT
1 AT
3142193 GTATGTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
8 20 0.61
9 6 0.18
10 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
ATAAAAAA
Found at i:3142184 original size:18 final size:16
Alignment explanation
Indices: 3142148--3142192 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
3142138 AATAAATAGT
3142148 ATAAATAAAATAAAAAA
1 ATAAA-AAAATAAAAAA
3142165 ATAAAAAAATATATAAAA
1 ATAAAAAAATA-A-AAAA
*
3142183 ATATAAAAAT
1 ATAAAAAAAT
3142193 GTATGTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 6 0.24
18 13 0.52
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAAAAATAAAAAA
Found at i:3142356 original size:14 final size:14
Alignment explanation
Indices: 3142337--3142391 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3142327 TAACGTTAGG
3142337 AAAATATAGTAAAA
1 AAAATATAGTAAAA
3142351 AAAATATAGTAAACA
1 AAAATATAGTAAA-A
*
3142366 AGTAAACATAGATAAAA
1 A--AAATATAG-TAAAA
3142383 AATAATATA
1 AA-AATATA
3142392 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 13 0.38
15 3 0.09
16 5 0.15
17 9 0.26
18 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATATAGTAAAA
Found at i:3142392 original size:2 final size:2
Alignment explanation
Indices: 3142387--3142413 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3142377 ATAAAAAATA
3142387 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3142414 ATAGGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3143005 original size:37 final size:37
Alignment explanation
Indices: 3142912--3143009 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
3142902 ATGCTTGTGG
* * * * *
3142912 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* *
3142949 ATCCTACTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
3142986 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
3143010 CTAATAGGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:3144746 original size:63 final size:63
Alignment explanation
Indices: 3144640--3144763 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
3144630 CCCTAAGGGA
* ** *
3144640 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCGTGGAGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
* *
3144703 ACATCTTAGGG-CTGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAGA
3144764 GTCACATTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 4 0.08
63 49 0.92
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:3145685 original size:30 final size:30
Alignment explanation
Indices: 3145651--3145755 Score: 158
Period size: 30 Copynumber: 3.5 Consensus size: 30
3145641 CACATTCGAA
*
3145651 AATTCCCATAATGTCACCTTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
*
3145681 AATTCCCAGAATGTCACATTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
* *
3145711 AATTCCCAGAATATCACC-ATTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
*
3145740 AATTCCCAAAATGTCA
1 AATTCCCAGAATGTCA
3145756 ACGGGTCAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 24 0.35
30 44 0.65
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (30 bp):
AATTCCCAGAATGTCACCTTTTTTCAAAAT
Found at i:3152085 original size:32 final size:31
Alignment explanation
Indices: 3152015--3152123 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
3152005 TTATGGCCTG
* * * * * *
3152015 AGAGCCTACCCAAGATAGATTTCGGGGCCGT
1 AGAGCCTACCTAAGAAACATCTCAGGGCCGC
*
3152046 AGAGCCTACCTAAGAACACATCTTAGGGCCGC
1 AGAGCCTACCTAAGAA-ACATCTCAGGGCCGC
* * ** *
3152078 AGGGCCTACCTGAGAATGATCTCAGGGTCGC
1 AGAGCCTACCTAAGAAACATCTCAGGGCCGC
3152109 AGAGCCTACCTAAGA
1 AGAGCCTACCTAAGA
3152124 GTCACATTAG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 38 0.61
32 24 0.39
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (31 bp):
AGAGCCTACCTAAGAAACATCTCAGGGCCGC
Found at i:3171646 original size:2 final size:2
Alignment explanation
Indices: 3171641--3171669 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3171631 GATTGTGTGC
3171641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3171670 CCTGGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3174747 original size:31 final size:31
Alignment explanation
Indices: 3174706--3174814 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
3174696 TAGGTCCCAA
* *
3174706 AGAACCTAGGTAAACTATTCATATGTTCCTT
1 AGAACATAGGTAAACTATTCATATGTTCCGT
* * * * * *
3174737 AGAACATAGGTATATTGTCCATATGTCCCGG
1 AGAACATAGGTAAACTATTCATATGTTCCGT
*
3174768 A-AGACATAGGT-AATTATGTCCATATGTTCCGT
1 AGA-ACATAGGTAAACTAT-T-CATATGTTCCGT
3174800 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
3174815 CCTCGAATTT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
30 5 0.08
31 32 0.54
32 19 0.32
33 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAACTATTCATATGTTCCGT
Found at i:3174793 original size:32 final size:32
Alignment explanation
Indices: 3174737--3174812 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
3174727 TATGTTCCTT
3174737 AGAACATAGGT-ATATTGTCCATATGTCCCGGA
1 AGAACATAGGTAATATTGTCCATATGTCCC-GA
* *
3174769 AG-ACATAGGTAAT-TATGTCCATATGTTCCGT
1 AGAACATAGGTAATAT-TGTCCATATGTCCCGA
3174800 AGAACATAGGTAA
1 AGAACATAGGTAA
3174813 ACCCTCGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 12 0.31
32 27 0.69
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (32 bp):
AGAACATAGGTAATATTGTCCATATGTCCCGA
Found at i:3176980 original size:40 final size:40
Alignment explanation
Indices: 3176925--3177016 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
3176915 TGTTCTACCT
* *
3176925 AGTTTCGATACTTTCTATGAGCTTCGACACTATGAACCAA
1 AGTTTCAATACTTTCTATGAGCTTCGAAACTATGAACCAA
*
3176965 AGTTTCAATACTTTCTATGAGCTTTGAAACTATGAACCAA
1 AGTTTCAATACTTTCTATGAGCTTCGAAACTATGAACCAA
3177005 AGTTTCAATACT
1 AGTTTCAATACT
3177017 CTTGTAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (40 bp):
AGTTTCAATACTTTCTATGAGCTTCGAAACTATGAACCAA
Found at i:3178368 original size:17 final size:16
Alignment explanation
Indices: 3178348--3178389 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3178338 TTTATGAAAA
3178348 ATTAAGACAATAGCAAG
1 ATTAAGACAA-AGCAAG
* *
3178365 ATTAAGA-AAAGGAAT
1 ATTAAGACAAAGCAAG
3178380 ATTAAGACAA
1 ATTAAGACAA
3178390 CAAAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (16 bp):
ATTAAGACAAAGCAAG
Found at i:3179952 original size:26 final size:26
Alignment explanation
Indices: 3179886--3179946 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
3179876 GTTCAAGCCT
3179886 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
3179912 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
3179938 TTTCGAGTT
1 TTTCGAGTT
3179947 TGAGTTGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:3180121 original size:11 final size:10
Alignment explanation
Indices: 3180097--3180130 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3180087 AAAATGGCTA
3180097 TTTTTCTCGGT
1 TTTTTC-CGGT
*
3180108 TTTTACCGGT
1 TTTTTCCGGT
3180118 TTTTTCCGGT
1 TTTTTCCGGT
3180128 TTT
1 TTT
3180131 CAGCCGGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (10 bp):
TTTTTCCGGT
Found at i:3180137 original size:21 final size:21
Alignment explanation
Indices: 3180097--3180138 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3180087 AAAATGGCTA
*
3180097 TTTTTCTCGGTTTTTACCGGT
1 TTTTTCTCGGTTTTCACCGGT
3180118 TTTTTC-CGGTTTTCAGCCGGT
1 TTTTTCTCGGTTTTCA-CCGGT
3180139 CCGGTTCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.05, C:0.21, G:0.21, T:0.52
Consensus pattern (21 bp):
TTTTTCTCGGTTTTCACCGGT
Found at i:3180942 original size:2 final size:2
Alignment explanation
Indices: 3180933--3180966 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3180923 AAAATATAAA
3180933 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3180967 ATCGGGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3192964 original size:5 final size:6
Alignment explanation
Indices: 3192946--3192973 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3192936 GACTTTTAAC
3192946 AATAAA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATA
3192974 GTATTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:3195514 original size:23 final size:22
Alignment explanation
Indices: 3195488--3195551 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
3195478 CAGCTCATAT
3195488 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
3195511 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
3195534 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
3195552 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:3195692 original size:103 final size:103
Alignment explanation
Indices: 3195567--3195784 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
3195557 TAATGTTCAT
* *
3195567 AAGGACCACATATCATTCCTTAAGAATTATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
3195632 GACCTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACCTCACACATGTTCCAAAGAATACATACATGTCCCG
3195670 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
3195735 GACCTCACGCATGTTCCAAAGAATACATACATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATACATGTCCCG
3195773 AAGGACCACATA
1 AAGGACCACATA
3195785 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATACATGTCCCG
Found at i:3196461 original size:21 final size:21
Alignment explanation
Indices: 3196437--3196479 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3196427 TCATATTCGT
* *
3196437 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
3196458 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
3196479 T
1 T
3196480 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:3202528 original size:23 final size:22
Alignment explanation
Indices: 3202502--3202565 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
3202492 CACCACATAT
3202502 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
3202525 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
3202548 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
3202566 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:3202701 original size:103 final size:103
Alignment explanation
Indices: 3202584--3202798 Score: 378
Period size: 103 Copynumber: 2.1 Consensus size: 103
3202574 TGTCCATAAG
*
3202584 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
* *
3202649 CTCACACATGTTCCAAAGAATATATATATGTCCCG-AA
66 CTCACACATGTTCCAAAGAATACATACATGTCCCGAAA
3202686 GAACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
1 G-ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
*
3202751 CCTTACACATGTTCCAAAGAATACATACATGTCCCGAAA
65 CCTCACACATGTTCCAAAGAATACATACATGTCCCGAAA
3202790 GACCACATA
1 GACCACATA
3202799 GACCCTCTAC
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
102 1 0.01
103 103 0.96
104 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
CTCACACATGTTCCAAAGAATACATACATGTCCCGAAA
Found at i:3203314 original size:18 final size:19
Alignment explanation
Indices: 3203277--3203313 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3203267 TTTTTCATTA
*
3203277 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
3203296 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
3203314 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:3203365 original size:21 final size:21
Alignment explanation
Indices: 3203341--3203383 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3203331 TCATATTCGT
*
3203341 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGATCGATTCCCC
* *
3203362 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGGATCGATTCCCC
3203383 T
1 T
3203384 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGGATCGATTCCCC
Done.