Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008022.1 Hibiscus syriacus cultivar Beakdansim tig00110495_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: 1039607
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:652414 original size:5 final size:5
Alignment explanation
Indices: 652404--652458 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
652394 GAACTTCTCT
652404 TTTTC TTTTC TTTTC TTATT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
652451 -TTTC TTTT
1 TTTTC TTTT
652459 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
4 5 0.12
5 29 0.67
6 9 0.21
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:652425 original size:8 final size:8
Alignment explanation
Indices: 652411--652458 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
652401 TCTTTTTCTT
652411 TTCTTTTC
1 TTCTTTTC
*
652419 TTATTTTC
1 TTCTTTTC
652427 TTCTTTTC
1 TTCTTTTC
652435 TTCTTTT-
1 TTCTTTTC
652442 TGTCTTTTC
1 T-TCTTTTC
652451 TTTCTTTT
1 -TTCTTTT
652459 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.77
9 6 0.17
10 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:652458 original size:16 final size:15
Alignment explanation
Indices: 652405--652459 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
652395 AACTTCTCTT
652405 TTTC-TTTTCTTTTC
1 TTTCTTTTTCTTTTC
652419 TTAT-TTTCTTCTTTTC
1 TT-TCTTT-TTCTTTTC
652435 -TTCTTTTTGTCTTTTC
1 TTTC-TTTT-TCTTTTC
652451 TTTCTTTTT
1 TTTCTTTTT
652460 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 22 0.65
17 3 0.09
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:654517 original size:52 final size:52
Alignment explanation
Indices: 654400--654552 Score: 195
Period size: 52 Copynumber: 3.0 Consensus size: 52
654390 ATATTTGAAT
* ** * *
654400 TCATTTGTTTTGTTAATTTCACGTGCATTCACATT--CATAGTAGCAT-TCTA
1 TCATTTGTTTTGTTAA-TTCACGTGCACTCACATTCACATAACAACATGTTTA
* *
654450 TCATTTGTTTTGTTAATTCACGTGCACTCGCATTCACATAACATCATGTTTA
1 TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAACATGTTTA
* *
654502 TCATTTATTTTGTTAATTTACGTGCACTCACATTCACATAACAACATGTTT
1 TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAACATGTTT
654553 TTATTTAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
49 16 0.18
50 16 0.18
51 8 0.09
52 50 0.56
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (52 bp):
TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAACATGTTTA
Found at i:656021 original size:24 final size:23
Alignment explanation
Indices: 655994--656053 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
655984 TCATCTTGAA
* *
655994 AAAAAAAAAGAATTCTGAAAATTT
1 AAAAAAAAAGAATTC-CAAAAATT
656018 AAAAAAATACA-AATTCCAAAAATT
1 AAAAAAA-A-AGAATTCCAAAAATT
656042 AAAAAAAAAGAA
1 AAAAAAAAAGAA
656054 GAAGAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 3 0.10
24 20 0.65
25 6 0.19
26 1 0.03
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAGAATTCCAAAAATT
Found at i:656639 original size:20 final size:21
Alignment explanation
Indices: 656602--656640 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
656592 GATGGTCTTG
*
656602 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
656623 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
656641 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:679656 original size:52 final size:52
Alignment explanation
Indices: 679550--679710 Score: 236
Period size: 52 Copynumber: 3.1 Consensus size: 52
679540 ATATTTGAAT
* * * *
679550 TCATTTGTTTTGTTAATTTCACGAGCATTCACATT--CATAACAACATGTCTA
1 TCATTTGTTTTGTTAA-TTCACGTGCACTCACATTCACATAACAGCATGTTTA
679601 TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAGCATGTTTA
1 TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAGCATGTTTA
* * *
679653 TCATTTGTTTTGTTAATTTACGTGCACTCACATTCACATAACAGCGTGTTTT
1 TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAGCATGTTTA
679705 TCATTT
1 TCATTT
679711 AATTATAATT
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
50 16 0.16
51 16 0.16
52 69 0.68
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (52 bp):
TCATTTGTTTTGTTAATTCACGTGCACTCACATTCACATAACAGCATGTTTA
Found at i:680273 original size:23 final size:25
Alignment explanation
Indices: 680228--680280 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
680218 TAATAAAGGT
*
680228 AATAATAATATAAGTAATGAAAATA
1 AATAATAATATAAGAAATGAAAATA
*
680253 AATAATAATA-ATGAAAT-AAAATA
1 AATAATAATATAAGAAATGAAAATA
680276 AATAA
1 AATAA
680281 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 11 0.42
24 5 0.19
25 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (25 bp):
AATAATAATATAAGAAATGAAAATA
Found at i:680274 original size:19 final size:20
Alignment explanation
Indices: 680228--680276 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
680218 TAATAAAGGT
680228 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
680248 AA-ATAAATAATAA-TAATGA
1 AATA-AAATAATAAGTAATGA
680267 AATAAAATAA
1 AATAAAATAA
680277 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:680689 original size:19 final size:21
Alignment explanation
Indices: 680646--680697 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
680636 GAAACCCCTT
680646 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
680667 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
680686 TGAAGATACATG
1 TGAAAATACATG
680698 TTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:681540 original size:17 final size:19
Alignment explanation
Indices: 681504--681541 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
681494 AACTATATAA
681504 TGCATATAATATAATGATG
1 TGCATATAATATAATGATG
*
681523 TGCATATTATA-AAT-ATG
1 TGCATATAATATAATGATG
681540 TG
1 TG
681542 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TGCATATAATATAATGATG
Found at i:683886 original size:34 final size:32
Alignment explanation
Indices: 683820--683891 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
683810 CTTGGCTTGC
* *
683820 TTTC-TTTTTGAATTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTTGAATTTCTTCTTATTTTCTTCT
683851 TTTCTTTTTCTGAATTTTCTTCTTATTTT-TATCT
1 TTTCTTTTT-TGAA-TTTCTTCTTATTTTCT-TCT
683885 TTTCTTT
1 TTTCTTT
683892 CTTTTTGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 22 0.63
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTATTTTCTTCT
Found at i:684190 original size:19 final size:20
Alignment explanation
Indices: 684144--684192 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
684134 TAATAAAGGG
684144 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
684164 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
684183 AATAAAATAA
1 AATAAAATAA
684193 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:684647 original size:19 final size:21
Alignment explanation
Indices: 684604--684655 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
684594 GAAACCCCTT
*
684604 TGAAAATATATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
684625 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
684644 TGAAGATACATG
1 TGAAAATACATG
684656 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:688262 original size:19 final size:20
Alignment explanation
Indices: 688238--688280 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
688228 AGCATTTATC
*
688238 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
688257 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
688277 TTCA
1 TTCA
688281 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:688707 original size:35 final size:36
Alignment explanation
Indices: 688620--688707 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
688610 TACAATCTGT
* **
688620 TCATCACCATCTTCCATCACCATTATCATTCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
688656 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
688691 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
688708 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 26 0.57
36 20 0.43
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:690932 original size:36 final size:36
Alignment explanation
Indices: 690880--690992 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
690870 GATACTATTT
*
690880 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
690916 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
690952 TCATCACCATATTCCATCACCA-TATCTCGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
690987 ACATCA
1 TCATCA
690993 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:690935 original size:13 final size:11
Alignment explanation
Indices: 690880--690977 Score: 65
Period size: 13 Copynumber: 8.2 Consensus size: 11
690870 GATACTATTT
690880 TCATCACCATAA
1 TCATCACCAT-A
*
690892 TCCATCTCCATTA
1 T-CATCACCA-TA
*
690905 TCA-CGCCTATA
1 TCATCACC-ATA
690916 TCATCACCATA
1 TCATCACCATA
690927 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
690941 TCA-CGCCTATA
1 TCATCACC-ATA
690952 TCATCACCATA
1 TCATCACCATA
690963 TTCCATCACCATA
1 -T-CATCACCATA
690976 TC
1 TC
690978 TCGCCAATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 23
0.71 0.05 0.23
Matches are distributed among these distances:
11 23 0.33
12 16 0.23
13 28 0.40
14 3 0.04
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:691007 original size:33 final size:33
Alignment explanation
Indices: 690963--691031 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
690953 CATCACCATA
*
690963 TTCCATCACCATATC-TCGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
690996 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
691029 TTC
1 TTC
691032 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.29, C:0.36, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:691427 original size:13 final size:14
Alignment explanation
Indices: 691396--691427 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
691386 GAAGACGAAA
691396 TGGTGGGATCAGTT
1 TGGTGGGATCAGTT
691410 TGGTGGGATCAG-T
1 TGGTGGGATCAGTT
691423 TGGTG
1 TGGTG
691428 AGTTCAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.12, C:0.06, G:0.47, T:0.34
Consensus pattern (14 bp):
TGGTGGGATCAGTT
Found at i:700686 original size:24 final size:22
Alignment explanation
Indices: 700647--700700 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
700637 GGTGATGCAC
*
700647 AAGATATGTCCTTTGACATTTC-A
1 AAGA-ATGTCCTTTGA-AATTCAA
700670 AAGAATGTACCTCTTGAAATTCAA
1 AAGAATGT-CCT-TTGAAATTCAA
700694 AAGAATG
1 AAGAATG
700701 AGCCAATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 11 0.41
24 12 0.44
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTCAA
Found at i:700980 original size:24 final size:21
Alignment explanation
Indices: 700945--700987 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
700935 GGCTCATTCT
*
700945 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
700968 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
700988 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:701642 original size:14 final size:14
Alignment explanation
Indices: 701625--701674 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
701615 ACGCCTATAA
*
701625 CATCACCATCTTTT
1 CATCACCATCTTTC
701639 CATCACCATCTTTC
1 CATCACCATCTTTC
*
701653 CATCACCAT-TCTC
1 CATCACCATCTTTC
*
701666 TATCACCAT
1 CATCACCAT
701675 TCACGCCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:703732 original size:20 final size:22
Alignment explanation
Indices: 703707--703746 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
703697 GTGTAAGACC
703707 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
703727 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
703747 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:711309 original size:5 final size:5
Alignment explanation
Indices: 711295--711326 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
711285 GTGCTTCAAC
711295 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
711327 TCTTCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:711365 original size:23 final size:25
Alignment explanation
Indices: 711325--711378 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
711315 TTCTTTTCTT
711325 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
711350 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
711373 TTTCTT
1 TTTCTT
711379 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:712904 original size:20 final size:22
Alignment explanation
Indices: 712879--712918 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
712869 GTGTAAGACC
712879 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
712899 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
712919 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:722278 original size:13 final size:13
Alignment explanation
Indices: 722260--722285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
722250 AACACCTTTT
722260 ACATACCTTTTCA
1 ACATACCTTTTCA
722273 ACATACCTTTTCA
1 ACATACCTTTTCA
722286 TCTTTTTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:728751 original size:16 final size:16
Alignment explanation
Indices: 728730--728764 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
728720 ATGAAAGAAG
728730 AAAGGAAAT-GATAAGA
1 AAAGGAAATGGAT-AGA
728746 AAAGGAAATGGATAGA
1 AAAGGAAATGGATAGA
728762 AAA
1 AAA
728765 TGTTATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (16 bp):
AAAGGAAATGGATAGA
Found at i:732915 original size:19 final size:20
Alignment explanation
Indices: 732891--732941 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
732881 CGGCCAAGAG
* *
732891 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
732910 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
732930 CATGTATTTTCA
1 CATGTATTTTCA
732942 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:747826 original size:91 final size:91
Alignment explanation
Indices: 747654--747836 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
747644 GGTAGTTGAT
* *
747654 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATACAAGGCACATA
1 GCTTGGACGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATA
*
747719 GGGGATGATCACATGCAAAACACATG
66 GGGGATGATCAAATGCAAAACACATG
* * *
747745 GCTTGGACGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGACGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATA
* * **
747810 GGGGCTGGTCAAATGCAAGGCACATG
66 GGGGATGATCAAATGCAAAACACATG
747836 G
1 G
747837 GTGTTCTAGG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (91 bp):
GCTTGGACGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATA
GGGGATGATCAAATGCAAAACACATG
Found at i:751307 original size:91 final size:91
Alignment explanation
Indices: 751152--751334 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
751142 GGTAGTTGAT
* *
751152 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATG
751217 GGGGATGATCACATGCAAAACACATG
66 GGGGATGATCACATGCAAAACACATG
*
751243 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATACAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATG
* * **
751308 GGGGCTGGTCACATGCAAGGCACATG
66 GGGGATGATCACATGCAAAACACATG
751334 G
1 G
751335 GTGTTCTAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATACAAGGCACATG
GGGGATGATCACATGCAAAACACATG
Found at i:752253 original size:24 final size:25
Alignment explanation
Indices: 752207--752261 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
752197 ACAGTTATGC
*
752207 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
752231 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
752256 CA-TTGA
1 CACTTGA
752262 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:754255 original size:625 final size:625
Alignment explanation
Indices: 753066--754318 Score: 2461
Period size: 625 Copynumber: 2.0 Consensus size: 625
753056 ATTCACATGT
753066 TAGTATAAATTATCATATTATTATTTCCATCCTATGCTTAGTTGATAATGTCTTTCATATCATTC
1 TAGTATAAATTATCATATTATTATTTCCATCCTATGCTTAGTTGATAATGTCTTTCATATCATTC
753131 AAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATT
66 AAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATT
753196 TATGAATACCATGTTATATGATATTCATGCATACAACATATACCCACTTCTTTATGATTGATACA
131 TATGAATACCATGTTATATGATATTCATGCATACAACATATACCCACTTCTTTATGATTGATACA
753261 CAATGTTATAAGTATGTTAGATTAATCTTACATCCATTTAAGTATGATTCAATACATTCATGAAA
196 CAATGTTATAAGTATGTTAGATTAATCTTACATCCATTTAAGTATGATTCAATACATTCATGAAA
753326 TGGCAGCATGCTTAATCATTCATTTGTTAGCTCATATGCATTCATTTTAGCTCCTAGGTCTTACA
261 TGGCAGCATGCTTAATCATTCATTTGTTAGCTCATATGCATTCATTTTAGCTCCTAGGTCTTACA
753391 CATTAGCTTACATATGTTATATCATTATGTACTTAGCTCATGATATGCATTCATAGCTTATATCA
326 CATTAGCTTACATATGTTATATCATTATGTACTTAGCTCATGATATGCATTCATAGCTTATATCA
753456 CTCAAACACCTCACAGAAGGATGCATTTTACCTTAAATAAGCTCACACATTACTTATTTTATTTG
391 CTCAAACACCTCACAGAAGGATGCATTTTACCTTAAATAAGCTCACACATTACTTATTTTATTTG
*
753521 TTTGGTGATTTCTATAGTTGAAACACAGAGCAAGGCATATTATGGTAGCTTAGTTAGCTTAAAGG
456 TTTGGTGATTTCTATAGTTGAAACACAGAGCAAGGCATATTATGGTAGCTTAGTTAGCTAAAAGG
*
753586 ACAAGTATAGCAACTCACACTAGCTCGTGAACATTATGGCAGCTCATTTCATCACATATGGAGCT
521 ACAAGTATAGCAACTCACACTAGCTCATGAACATTATGGCAGCTCATTTCATCACATATGGAGCT
753651 TCAACTTAGCTGGAGGAGCTAGCATGTAGTTGAACTTAGC
586 TCAACTTAGCTGGAGGAGCTAGCATGTAGTTGAACTTAGC
753691 TAGTATAAATTATCATATTATTATTTCCATCCTATGCTTAGTTGATAATGTCTTTCATATCATTC
1 TAGTATAAATTATCATATTATTATTTCCATCCTATGCTTAGTTGATAATGTCTTTCATATCATTC
753756 AAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATT
66 AAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATT
753821 TATGAATACCATGTTATATGATATTCATGCATACAACATATACCCACTTCTTTATGATTGATACA
131 TATGAATACCATGTTATATGATATTCATGCATACAACATATACCCACTTCTTTATGATTGATACA
753886 CAATGTTATAAGTATGTTAGATTAATCTTACATCCATTTAAGTATGATTCAATACATTCATGAAA
196 CAATGTTATAAGTATGTTAGATTAATCTTACATCCATTTAAGTATGATTCAATACATTCATGAAA
753951 TGGCAGCATGCTTAATCATTCATTTGTTAGCTCATATGCATTCATTTTAGCTCCTAGGTCTTACA
261 TGGCAGCATGCTTAATCATTCATTTGTTAGCTCATATGCATTCATTTTAGCTCCTAGGTCTTACA
*
754016 TATTAGCTTACATATGTTATATCATTATGTACTTAGCTCATGATATGCATTCATAGCTTATATCA
326 CATTAGCTTACATATGTTATATCATTATGTACTTAGCTCATGATATGCATTCATAGCTTATATCA
*
754081 CTCAAACACCTCACAGCAGGATGCATTTTACCTTAAATAAGCTCACACATTACTTATTTTATTTG
391 CTCAAACACCTCACAGAAGGATGCATTTTACCTTAAATAAGCTCACACATTACTTATTTTATTTG
754146 TTTGGTGATTTCTATAGTTGAAACACAGAGCAAGGCATATTATGGTAGCTTAGTTAGCTAAAAGG
456 TTTGGTGATTTCTATAGTTGAAACACAGAGCAAGGCATATTATGGTAGCTTAGTTAGCTAAAAGG
*
754211 ACAAGTATAGCAACTCACACTAGCTCATGAACATTATGGCAGCTCATTTCATCACATATGGTGCT
521 ACAAGTATAGCAACTCACACTAGCTCATGAACATTATGGCAGCTCATTTCATCACATATGGAGCT
754276 TCAACTTAGCTGGAGGAGCTAGCATGTAGTTGAACTTAGC
586 TCAACTTAGCTGGAGGAGCTAGCATGTAGTTGAACTTAGC
754316 TAG
1 TAG
754319 AGGAGAGCTT
Statistics
Matches: 623, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
625 623 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (625 bp):
TAGTATAAATTATCATATTATTATTTCCATCCTATGCTTAGTTGATAATGTCTTTCATATCATTC
AAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATT
TATGAATACCATGTTATATGATATTCATGCATACAACATATACCCACTTCTTTATGATTGATACA
CAATGTTATAAGTATGTTAGATTAATCTTACATCCATTTAAGTATGATTCAATACATTCATGAAA
TGGCAGCATGCTTAATCATTCATTTGTTAGCTCATATGCATTCATTTTAGCTCCTAGGTCTTACA
CATTAGCTTACATATGTTATATCATTATGTACTTAGCTCATGATATGCATTCATAGCTTATATCA
CTCAAACACCTCACAGAAGGATGCATTTTACCTTAAATAAGCTCACACATTACTTATTTTATTTG
TTTGGTGATTTCTATAGTTGAAACACAGAGCAAGGCATATTATGGTAGCTTAGTTAGCTAAAAGG
ACAAGTATAGCAACTCACACTAGCTCATGAACATTATGGCAGCTCATTTCATCACATATGGAGCT
TCAACTTAGCTGGAGGAGCTAGCATGTAGTTGAACTTAGC
Found at i:758911 original size:22 final size:23
Alignment explanation
Indices: 758883--758934 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
758873 ATTTATAAGT
758883 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
758905 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
758928 TGGTGAT
1 TGGTGAT
758935 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:758927 original size:36 final size:38
Alignment explanation
Indices: 758885--758964 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 38
758875 TTATAAGTTG
758885 GTGATAATATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGCGATGGACTATGGTGATGATATAGGC
*
758921 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
*
758957 ATGATAAT
1 GTGATAAT
758965 GGTGATGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.08
34 3 0.08
35 3 0.08
36 27 0.73
37 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
Found at i:758965 original size:36 final size:36
Alignment explanation
Indices: 758903--758974 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
758893 ATAGGCGTGA
*
758903 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
758939 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
758975 AGATTGTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCATGATAATGGTGATGGAC
Found at i:762625 original size:22 final size:23
Alignment explanation
Indices: 762597--762648 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
762587 ATTTATAAGT
*
762597 TGGTGATAATATATGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
762619 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
762642 TGGTGAT
1 TGGTGAT
762649 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:762640 original size:36 final size:36
Alignment explanation
Indices: 762617--762688 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
762607 ATATGCGTGA
*
762617 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGATGATGGAC
*
762653 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGATGATGGAC
762689 AGATTGTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGATGATGGAC
Found at i:776039 original size:28 final size:26
Alignment explanation
Indices: 775984--776041 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
775974 CTTTCTTTCT
* *
775984 TTTCTTCTTTTTTTTAAGTGTTGGAA
1 TTTCTTCTTTCTTTTAAGTGTTGCAA
776010 TTTCTTTCTTTCTTTTAGAGTGCTT-CAA
1 TTTC-TTCTTTCTTTTA-AGTG-TTGCAA
776038 TTTC
1 TTTC
776042 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 11 0.41
28 10 0.37
29 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTCTTTTAAGTGTTGCAA
Found at i:793742 original size:120 final size:118
Alignment explanation
Indices: 793516--793756 Score: 455
Period size: 120 Copynumber: 2.0 Consensus size: 118
793506 CTCACTTTTC
793516 AGGACCAATCACGTAAAGGTCACTTCCAAAAGGATATCCTTAGATAAAGATCATTCCCAAAAGGT
1 AGGACCAATCACGTAAAGGTCACTTCCAAAAGGATATCCTTAGATAAAGATCATTCCCAAAAGGT
793581 ATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
66 ATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
*
793634 AGGACCAATCATGTAAAAGGTCACTTCCAAAAGGGATATCCTTAGATAAAGATCATTCCCAAAAG
1 AGGACCAATCACGT-AAAGGTCACTTCCAAAA-GGATATCCTTAGATAAAGATCATTCCCAAAAG
793699 GTATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
64 GTATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
793754 AGG
1 AGG
793757 TACCTAATGG
Statistics
Matches: 120, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
118 13 0.11
119 17 0.14
120 90 0.75
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (118 bp):
AGGACCAATCACGTAAAGGTCACTTCCAAAAGGATATCCTTAGATAAAGATCATTCCCAAAAGGT
ATCTGTTGGTAAATCATATTCCAAAGAAAGACCTAAAAGGAAATCTTACGAAA
Found at i:796865 original size:20 final size:19
Alignment explanation
Indices: 796840--796891 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
796830 GCTGCTGGAA
* *
796840 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
796860 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
796879 AACCGGGTTGACC
1 AACCGGTTTGACC
796892 CGACCCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:796869 original size:10 final size:10
Alignment explanation
Indices: 796840--796889 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
796830 GCTGCTGGAA
796840 AACCGGTTTG
1 AACCGGTTTG
*
796850 -ACCAGTTTTG
1 AACC-GGTTTG
796860 AACCGGTTTG
1 AACCGGTTTG
*
796870 -ACCGGTCTG
1 AACCGGTTTG
*
796879 AACCGGGTTG
1 AACCGGTTTG
796889 A
1 A
796890 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:796906 original size:14 final size:14
Alignment explanation
Indices: 796887--796914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
796877 TGAACCGGGT
796887 TGACCCGACCCGAC
1 TGACCCGACCCGAC
796901 TGACCCGACCCGAC
1 TGACCCGACCCGAC
796915 CGTTGACCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:796924 original size:7 final size:7
Alignment explanation
Indices: 796912--796942 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
796902 GACCCGACCC
796912 GACCGTT
1 GACCGTT
796919 GACCGTT
1 GACCGTT
*
796926 GACTGTT
1 GACCGTT
796933 GACCGTT
1 GACCGTT
796940 GAC
1 GAC
796943 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:797787 original size:60 final size:60
Alignment explanation
Indices: 797719--797840 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 60
797709 CTAATGTGAC
* *
797719 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGC-CTGC-GGCCCTAAGATGT
1 TCTTAGGTAGGCCTC-ACGGCCC-GAAATCTA-TCTCGGGTAGGCTCT-CAGGCCCTAAGATGT
*
797779 TCTTAGGTAGGCCTCACGGCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCGAAATCTATCTCGGGTAGGCTCTCAGGCCCTAAGATGT
797839 TC
1 TC
797841 CCTTAGGGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
59 17 0.31
60 35 0.64
61 3 0.05
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (60 bp):
TCTTAGGTAGGCCTCACGGCCCGAAATCTATCTCGGGTAGGCTCTCAGGCCCTAAGATGT
Found at i:797799 original size:30 final size:30
Alignment explanation
Indices: 797719--797840 Score: 99
Period size: 30 Copynumber: 4.1 Consensus size: 30
797709 CTAATGTGAC
* * *
797719 TCTTAGGTAGG-CTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCTC-ACGGCCCTAAGAT-GT
** *
797750 TCTCGGGTAGGCCT-GCGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCTAAGATGT
* *
797779 TCTTAGGTAGGCCTCACGGCCCGAA-ATCT
1 TCTTAGGTAGGCCTCACGGCCCTAAGATGT
*
797808 ATCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 -TCTTAGGTAGGC-CTCACGGCCCTAAGATGT
797839 TC
1 TC
797841 CCTTAGGGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
29 16 0.22
30 40 0.54
31 16 0.22
32 2 0.03
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (30 bp):
TCTTAGGTAGGCCTCACGGCCCTAAGATGT
Found at i:804025 original size:9 final size:9
Alignment explanation
Indices: 804011--804079 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
804001 CTGCTGGAAA
804011 ACCGGTTTG
1 ACCGGTTTG
*
804020 ACCGGTCTG
1 ACCGGTTTG
804029 AACCGGTTTG
1 -ACCGGTTTG
*
804039 ACCGGTCTG
1 ACCGGTTTG
*
804048 AATCGGTTTG
1 -ACCGGTTTG
*
804058 ACCGGTCTG
1 ACCGGTTTG
*
804067 AACCGGGTTG
1 -ACCGGTTTG
804077 ACC
1 ACC
804080 CGACCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:804034 original size:19 final size:19
Alignment explanation
Indices: 804010--804079 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
804000 GCTGCTGGAA
804010 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
804029 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
804048 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
804067 AACCGGGTTGACC
1 AACCGGTTTGACC
804080 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:804094 original size:14 final size:14
Alignment explanation
Indices: 804075--804102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
804065 TGAACCGGGT
804075 TGACCCGACCCGAC
1 TGACCCGACCCGAC
804089 TGACCCGACCCGAC
1 TGACCCGACCCGAC
804103 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:804117 original size:17 final size:17
Alignment explanation
Indices: 804073--804132 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
804063 TCTGAACCGG
804073 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
804090 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
*
804109 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
804126 GTTGACC
1 GTTGACC
804133 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 21 0.58
19 15 0.42
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:804117 original size:22 final size:19
Alignment explanation
Indices: 804076--804125 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
804066 GAACCGGGTT
804076 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
804095 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC---TGACCC
804117 GACCCGACC
1 GACCCGACC
804126 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.46
22 15 0.54
ACGTcount: A:0.20, C:0.50, G:0.22, T:0.08
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:804134 original size:7 final size:7
Alignment explanation
Indices: 804122--804159 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
804112 GACCCGACCC
804122 GACCGTT
1 GACCGTT
804129 GACCGTT
1 GACCGTT
804136 GACCGTT
1 GACCGTT
*
804143 GACTGTT
1 GACCGTT
804150 GACCGTT
1 GACCGTT
804157 GAC
1 GAC
804160 TTCCTTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:805094 original size:32 final size:30
Alignment explanation
Indices: 805058--805132 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
805048 GTAGGCCCTG
*
805058 CGGCCCTAAGATGTGTTCTTAGGTAGGCCTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGG-CTCA
* * *
805090 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCA
1 CGG-CCCTAAGATGTATCTTAGGTAGGCTCA
805120 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
805133 TCCCTTAGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
28 5 0.14
29 5 0.14
30 4 0.11
31 10 0.29
32 6 0.17
33 5 0.14
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (30 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCA
Found at i:805094 original size:63 final size:61
Alignment explanation
Indices: 805011--805132 Score: 140
Period size: 63 Copynumber: 2.0 Consensus size: 61
805001 CTAATGTGAC
* ** * *
805011 TCTTAGGTAGTCCTTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTA-TCTCGGGTAGG--CT-CAGGCCCTAAGATGTGT
*
805074 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCTCAGGCCCTAAGATGT
805133 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
60 1 0.02
61 15 0.29
63 34 0.67
64 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (61 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCTCAGGCCCTAAGATGTGT
Found at i:805745 original size:24 final size:21
Alignment explanation
Indices: 805711--805753 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
805701 TGCACAAGAT
*
805711 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
805733 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
805754 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:809760 original size:20 final size:19
Alignment explanation
Indices: 809724--809762 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
809714 AGTAAAGATG
* *
809724 TGAAAACATATATTATGCA
1 TGAAAACATAAAGTATGCA
809743 TGAAAATCATAAAGTATGCA
1 TGAAAA-CATAAAGTATGCA
809763 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (19 bp):
TGAAAACATAAAGTATGCA
Found at i:817928 original size:19 final size:18
Alignment explanation
Indices: 817901--817967 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
817891 CCTTGGCTTG
*
817901 CTTTCTCTTTTTGAATTTT
1 CTTTTTCTTTTTG-ATTTT
817920 CTTTTTCTTTTCTGATTTT
1 CTTTTTCTTTT-TGATTTT
*
817939 C--TTTCTTTTTG-TCTT
1 CTTTTTCTTTTTGATTTT
817954 CTCTTTTCTTTTTG
1 CT-TTTTCTTTTTG
817968 CACTCCAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.10
16 2 0.05
17 8 0.19
18 10 0.24
19 16 0.38
20 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.06, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTGATTTT
Found at i:817955 original size:23 final size:22
Alignment explanation
Indices: 817917--817964 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
817907 CTTTTTGAAT
*
817917 TTTCTTTTTCTTTTCTGATTTTC
1 TTTCTTTTTCTCTTCT-ATTTTC
* *
817940 TTTCTTTTTGTCTTCTCTTTTC
1 TTTCTTTTTCTCTTCTATTTTC
817962 TTT
1 TTT
817965 TTGCACTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTCTTTTTCTCTTCTATTTTC
Found at i:824337 original size:23 final size:25
Alignment explanation
Indices: 824310--824373 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
824300 GAAAAATCAG
824310 CAAAGAAAATAAAAGCACTC-AAAA
1 CAAAGAAAATAAAAGCACTCGAAAA
* *
824334 -AAAGAAATTGAAAGCACTCGAAAA
1 CAAAGAAAATAAAAGCACTCGAAAA
*
824358 CAAGAGAAAAAAAAAG
1 CAA-AGAAAATAAAAG
824374 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 17 0.53
24 4 0.12
25 2 0.06
26 9 0.28
ACGTcount: A:0.66, C:0.12, G:0.14, T:0.08
Consensus pattern (25 bp):
CAAAGAAAATAAAAGCACTCGAAAA
Found at i:826528 original size:19 final size:19
Alignment explanation
Indices: 826504--826541 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
826494 AACATGATGG
826504 TTCAATTCTGGAAAATGAA
1 TTCAATTCTGGAAAATGAA
826523 TTCAATTCTGGAAAATGAA
1 TTCAATTCTGGAAAATGAA
826542 GGGTCTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
TTCAATTCTGGAAAATGAA
Found at i:836964 original size:16 final size:16
Alignment explanation
Indices: 836943--836985 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
836933 TTTTAACTTC
836943 TCTTTTTCTT-TTCTTT
1 TCTTTTT-TTCTTCTTT
836959 TCTTTTTTTCTTCTTT
1 TCTTTTTTTCTTCTTT
*
836975 TCTTCTTTTCT
1 TCTTTTTTTCT
836986 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTTTCTTCTTT
Found at i:836980 original size:11 final size:11
Alignment explanation
Indices: 836943--836981 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
836933 TTTTAACTTC
*
836943 TCTTTTTCTTT
1 TCTTCTTCTTT
836954 TCTT-TTCTTT
1 TCTTCTTCTTT
*
836964 TTTTCTTCTTT
1 TCTTCTTCTTT
836975 TCTTCTT
1 TCTTCTT
836982 TTCTGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:848174 original size:20 final size:19
Alignment explanation
Indices: 848138--848176 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
848128 AGTAAAGATG
* *
848138 TGAAAACATATATTATGCA
1 TGAAAACATAAAGTATGCA
848157 TGAAAATCATAAAGTATGCA
1 TGAAAA-CATAAAGTATGCA
848177 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (19 bp):
TGAAAACATAAAGTATGCA
Found at i:850485 original size:13 final size:12
Alignment explanation
Indices: 850467--850508 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
850457 GCTTGCTTTC
850467 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
850480 TCTTTTT-CTTT
1 TCTTTTTGATTT
850491 TCTTTTCTGATTT
1 TCTTTT-TGATTT
850504 TCTTT
1 TCTTT
850509 CTTTTTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:850495 original size:24 final size:25
Alignment explanation
Indices: 850462--850508 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
850452 CCTTGGCTTG
850462 CTTTCTCTTTT-TGAATTTTCTTTTT
1 CTTTCTCTTTTCTG-ATTTTCTTTTT
850487 CTTT-TCTTTTCTGATTTTCTTT
1 CTTTCTCTTTTCTGATTTTCTTT
850509 CTTTTTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.72
Consensus pattern (25 bp):
CTTTCTCTTTTCTGATTTTCTTTTT
Found at i:856871 original size:23 final size:25
Alignment explanation
Indices: 856843--856905 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 25
856833 AAAAATCAGC
856843 AAAGAAAATAAAAGCACTC-AAAA-
1 AAAGAAAATAAAAGCACTCGAAAAG
* *
856866 AAAGAAATTGAAAGCACTCGAAAAG
1 AAAGAAAATAAAAGCACTCGAAAAG
*
856891 AAGAGAAAAAAAAAG
1 AA-AGAAAATAAAAG
856906 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 17 0.53
24 4 0.12
25 2 0.06
26 9 0.28
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.08
Consensus pattern (25 bp):
AAAGAAAATAAAAGCACTCGAAAAG
Found at i:856906 original size:15 final size:14
Alignment explanation
Indices: 856886--856915 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
856876 AAAGCACTCG
856886 AAAAGAAGAGAAAAA
1 AAAAGAA-AGAAAAA
856901 AAAAGAAAGAAAAA
1 AAAAGAAAGAAAAA
856915 A
1 A
856916 GTTGGAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:862129 original size:36 final size:36
Alignment explanation
Indices: 862055--862170 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
862045 AAATGGAATT
* **
862055 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
862090 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
862126 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
862162 TGGTGATGA
1 TGGTGATGA
862171 ACAGATTGTA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.26
36 57 0.74
ACGTcount: A:0.28, C:0.02, G:0.41, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
Found at i:866482 original size:72 final size:71
Alignment explanation
Indices: 866364--866501 Score: 163
Period size: 72 Copynumber: 1.9 Consensus size: 71
866354 AATACATCCT
** * * * * *
866364 TTGGCTGAATTCATCCCACCTTGTGTGAAGTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
866429 ATGTATC
65 ATGTATC
*
866436 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
866499 AAT
64 AAT
866502 CGATGAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
71 16 0.29
72 30 0.54
73 10 0.18
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:883500 original size:16 final size:16
Alignment explanation
Indices: 883479--883521 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
883469 TTTTAACTTC
883479 TCTTTTTCTT-TTCTTT
1 TCTTTTT-TTCTTCTTT
883495 TCTTTTTTTCTTCTTT
1 TCTTTTTTTCTTCTTT
*
883511 TCTTCTTTTCT
1 TCTTTTTTTCT
883522 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTTTCTTCTTT
Found at i:883516 original size:11 final size:11
Alignment explanation
Indices: 883479--883517 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
883469 TTTTAACTTC
*
883479 TCTTTTTCTTT
1 TCTTCTTCTTT
883490 TCTT-TTCTTT
1 TCTTCTTCTTT
*
883500 TTTTCTTCTTT
1 TCTTCTTCTTT
883511 TCTTCTT
1 TCTTCTT
883518 TTCTGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:886190 original size:22 final size:20
Alignment explanation
Indices: 886165--886204 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
886155 ATGTTTGTTT
886165 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
886187 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
886205 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:886437 original size:15 final size:15
Alignment explanation
Indices: 886414--886449 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
886404 ACTAATATTC
* *
886414 TTATCATAATATATA
1 TTATAATAACATATA
886429 TTATAATAACATATA
1 TTATAATAACATATA
886444 TTATAA
1 TTATAA
886450 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:890450 original size:22 final size:20
Alignment explanation
Indices: 890425--890464 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
890415 ATGTTTGTTT
890425 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
890447 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
890465 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:911330 original size:19 final size:20
Alignment explanation
Indices: 911304--911356 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
911294 TTCGGCCAAG
* *
911304 AGCATGTATCTTCAT-TAAA
1 AGCATGTATTTTCATAAAAA
*
911323 ATCATGTATTTTCATAAAAA
1 AGCATGTATTTTCATAAAAA
911343 AGCATGTATTTTCA
1 AGCATGTATTTTCA
911357 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (20 bp):
AGCATGTATTTTCATAAAAA
Found at i:914047 original size:16 final size:16
Alignment explanation
Indices: 914026--914057 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
914016 TAGTTAGCTC
914026 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
914042 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
914058 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:917448 original size:16 final size:16
Alignment explanation
Indices: 917427--917458 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
917417 TAGTTAGCTC
917427 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
917443 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
917459 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:932944 original size:28 final size:28
Alignment explanation
Indices: 932880--932944 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
932870 CTTTTATTTT
*
932880 CTTTGCTTTTCTTCTTTTTGAGTGCTGGA
1 CTTTG-TTTTCTTCTTTTTGAGTGCTGCA
* *
932909 -TTTTTTTTCTT-TCTTTTGAGTGCTTCA
1 CTTTGTTTTCTTCT-TTTTGAGTGCTGCA
932936 CTTTGTTTT
1 CTTTGTTTT
932945 ATGATTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 10 0.33
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.63
Consensus pattern (28 bp):
CTTTGTTTTCTTCTTTTTGAGTGCTGCA
Found at i:937796 original size:33 final size:33
Alignment explanation
Indices: 937754--937822 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
937744 GTTGATGAAT
*
937754 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
937787 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
937820 GAA
1 GAA
937823 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:937827 original size:13 final size:12
Alignment explanation
Indices: 937808--937904 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
937798 TTATTGGCGT
937808 GATATGGTGATG
1 GATATGGTGATG
937820 GAATATGGTGAT-
1 G-ATATGGTGATG
*
937832 GATATAGGCG-T-
1 GATAT-GGTGATG
937843 GATAATGGTGATG
1 GAT-ATGGTGATG
937856 GACTATGGTGAT-
1 GA-TATGGTGATG
*
937868 GATATAGGCG-T-
1 GATAT-GGTGATG
*
937879 GATAATGGAGATG
1 GAT-ATGGTGATG
937892 GATTATGGTGATG
1 GA-TATGGTGATG
937905 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:937863 original size:36 final size:36
Alignment explanation
Indices: 937793--937905 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
937783 AATGGAAGGA
* *
937793 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
937828 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
937864 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
937900 TGATGA
1 TGATGA
937906 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:938291 original size:19 final size:20
Alignment explanation
Indices: 938244--938294 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
938234 GAAATCCCTT
**
938244 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
938264 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
938283 TGAAGATACATG
1 TGAAAATACATG
938295 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:941346 original size:26 final size:24
Alignment explanation
Indices: 941315--941385 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
941305 AGTTGCTTCA
941315 CTTTTCTTTTGCTTTTGATTTTCTT
1 CTTTTCTTTTGCTTTTG-TTTTCTT
*
941340 CTTTTTCTTTTCTCTTTTGTTTTCTT
1 C-TTTTCTTTT-GCTTTTGTTTTCTT
941366 C-TTTCTTGTTGCTTTT-TTTT
1 CTTTTCTT-TTGCTTTTGTTTT
941386 GTAGCACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 4 0.10
24 11 0.27
25 3 0.07
26 17 0.41
27 6 0.15
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (24 bp):
CTTTTCTTTTGCTTTTGTTTTCTT
Found at i:941368 original size:13 final size:13
Alignment explanation
Indices: 941326--941369 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
941316 TTTTCTTTTG
941326 CTTTTGATTTTCTT
1 CTTTTG-TTTTCTT
*
941340 CTTTTTCTTTTC-T
1 C-TTTTGTTTTCTT
941353 CTTTTGTTTTCTT
1 CTTTTGTTTTCTT
941366 CTTT
1 CTTT
941370 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.35
13 7 0.27
14 6 0.23
15 4 0.15
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (13 bp):
CTTTTGTTTTCTT
Found at i:941767 original size:33 final size:33
Alignment explanation
Indices: 941725--941793 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
941715 GTTGATGAAT
*
941725 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
941758 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
941791 GAA
1 GAA
941794 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:941834 original size:36 final size:36
Alignment explanation
Indices: 941775--941876 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
941765 GATGTTATTG
941775 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
941810 GCGTGATAATGGTGATGGACTATGGTGATGATATAG
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
941846 GCGTGATAATGGAGATGGATTATGGTGATGA
1 GCGTGATAATGGTGATGGAATATGGTGATGA
941877 AAATAGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.11
36 55 0.89
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGAATATGGTGATGATATAA
Found at i:947207 original size:27 final size:27
Alignment explanation
Indices: 947173--947229 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
947163 TTTCTTTGCT
* *
947173 TTTCTTCTTTTTGAATGC-TGAATTTC
1 TTTCTTCTTTTGGAATGCTTCAATTTC
*
947199 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAATGCTTCAATTTC
947227 TTT
1 TTT
947230 TCTGATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAATGCTTCAATTTC
Found at i:956957 original size:17 final size:16
Alignment explanation
Indices: 956932--957005 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 16
956922 CCTTGGCTTG
956932 CTTTCTTTTTTACTTTT
1 CTTTCTTTTTT-CTTTT
*
956949 CTTTTTTTTTTC-TTT
1 CTTTCTTTTTTCTTTT
**
956964 -TTTCTGAATTT-TTTT
1 CTTTCT-TTTTTCTTTT
956979 C-TTCTTTTTGTCTTTT
1 CTTTCTTTTT-TCTTTT
956995 CTTTTCTTTTT
1 C-TTTCTTTTT
957006 GTACTATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
14 6 0.14
15 14 0.32
16 6 0.14
17 10 0.23
18 8 0.18
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (16 bp):
CTTTCTTTTTTCTTTT
Found at i:956958 original size:16 final size:17
Alignment explanation
Indices: 956932--956964 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
956922 CCTTGGCTTG
956932 CTTTCTTTTTTACTTTT
1 CTTTCTTTTTTACTTTT
*
956949 CTTT-TTTTTTTCTTTT
1 CTTTCTTTTTTACTTTT
956965 TTCTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTCTTTTTTACTTTT
Found at i:956959 original size:11 final size:11
Alignment explanation
Indices: 956933--957005 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 11
956923 CTTGGCTTGC
956933 TTTCTTTTTTACT
1 TTTCTTTTTT--T
956946 TTTCTTTTTTT
1 TTTCTTTTTTT
*
956957 TTTCTTTTTTC
1 TTTCTTTTTTT
***
956968 TGAATTTTTTT
1 TTTCTTTTTTT
*
956979 CTTCTTTTTGTCT
1 TTTCTTTTT-T-T
956992 TTTCTTTTCTTT
1 TTTCTTTT-TTT
957004 TT
1 TT
957006 GTACTATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
11 23 0.49
12 4 0.09
13 19 0.40
14 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:956994 original size:19 final size:19
Alignment explanation
Indices: 956953--957008 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
956943 ACTTTTCTTT
*
956953 TTTTTTTCTT-TTTTCTGAA
1 TTTTTTTCTTCTTTT-TGTA
*
956972 TTTTTTTCTTCTTTTTGTC
1 TTTTTTTCTTCTTTTTGTA
*
956991 TTTTCTT-TTCTTTTTGTA
1 TTTTTTTCTTCTTTTTGTA
957009 CTATAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.31
19 18 0.56
20 4 0.12
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTCTTTTTGTA
Found at i:960293 original size:35 final size:36
Alignment explanation
Indices: 960254--960333 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
960244 AAATGGAATT
* **
960254 TGGTGATGATATAGGCATGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATAGAAGA
*
960289 TGGTGATGATATAGGCGTGATAATGGTGATAGAAGA
1 TGGTGATGATATAGGCATGATAATGGTGATAGAAGA
960325 TGGTGATGA
1 TGGTGATGA
960334 ACAGATTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATAGAAGA
Found at i:964381 original size:19 final size:18
Alignment explanation
Indices: 964336--964382 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
964326 GATGTAGGAG
* *
964336 TCTTTTTCTTTTTTTTTT
1 TCTTTTTGTTTTTTTTCT
*
964354 TGTTTTTGTTTTTTTTCT
1 TCTTTTTGTTTTTTTTCT
964372 TCTTTCTTGTT
1 TCTTT-TTGTT
964383 AATTTTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TCTTTTTGTTTTTTTTCT
Found at i:970978 original size:41 final size:41
Alignment explanation
Indices: 970886--970971 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
970876 AGAAAAATAC
*
970886 AAAAAGAAGTGCTAAGTGAAGTGCAAAGTCAAAGCACTCAA
1 AAAAAGAAGTGCAAAGTGAAGTGCAAAGTCAAAGCACTCAA
*
970927 AAAAAGAAGTGCAAAGTGAAGTGCAAAGTCAAAGCACTCAG
1 AAAAAGAAGTGCAAAGTGAAGTGCAAAGTCAAAGCACTCAA
970968 AAAA
1 AAAA
970972 CAAAGTGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.13
Consensus pattern (41 bp):
AAAAAGAAGTGCAAAGTGAAGTGCAAAGTCAAAGCACTCAA
Found at i:976438 original size:10 final size:9
Alignment explanation
Indices: 976395--976456 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 9
976385 GCTTGTTTTC
976395 TTTTTCTTT
1 TTTTTCTTT
976404 TCTTTTCTTT
1 T-TTTTCTTT
*
976414 TTTTTCTGATA
1 TTTTTCT--TT
976425 TTTTTCTTCT
1 TTTTTCTT-T
976435 TTTTGTCTTT
1 TTTT-TCTTT
976445 TTCTTTCTTT
1 TT-TTTCTTT
976455 TT
1 TT
976457 GCACTCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 8 0.18
10 23 0.51
11 14 0.31
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:976456 original size:11 final size:10
Alignment explanation
Indices: 976390--976456 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 10
976380 CCTTGGCTTG
976390 TTTTCTTTTTC
1 TTTT-TTTTTC
*
976401 TTTTCTTTTC
1 TTTTTTTTTC
976411 -TTTTTTTTC
1 TTTTTTTTTC
* *
976420 TGATATTTTTC
1 T-TTTTTTTTC
*
976431 TTCTTTTTGTC
1 TT-TTTTTTTC
*
976442 TTTTTCTTTC
1 TTTTTTTTTC
976452 TTTTT
1 TTTTT
976457 GCACTCCAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 8 0.18
10 16 0.36
11 20 0.45
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:981667 original size:35 final size:36
Alignment explanation
Indices: 981580--981667 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 36
981570 TACAATCTGT
* *
981580 TCATCACCATCTTCCATCACCATTATTACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
981616 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
981651 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
981668 TTCCATTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 27 0.57
36 20 0.43
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:981836 original size:15 final size:17
Alignment explanation
Indices: 981800--981833 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
981790 TTTGATAACA
981800 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
981816 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
981832 TT
1 TT
981834 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:982080 original size:6 final size:6
Alignment explanation
Indices: 982033--982082 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
982023 GTGCTACAAC
*
982033 AAAAAG AAACAAG AAAGAAG AAGAAA- AAAAAC AAAAAG -AAAAG AAAAAG
1 AAAAAG AAA-AAG AAA-AAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG
982082 A
1 A
982083 CTCCTACATC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 8 0.21
6 16 0.42
7 13 0.34
8 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:987178 original size:35 final size:36
Alignment explanation
Indices: 987091--987178 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 36
987081 TACAATCTGT
* * *
987091 TCATCACCATCTTCCATCACCATTATTATGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* *
987127 TCATCACTATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
987162 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
987179 TTCCATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 25 0.57
36 19 0.43
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.32
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:989905 original size:11 final size:11
Alignment explanation
Indices: 989881--989925 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
989871 TTGGTGCTGG
989881 AAACAAGATAA
1 AAACAAGATAA
* *
989892 AAATAAGATTA
1 AAACAAGATAA
989903 AAACAAGATAA
1 AAACAAGATAA
989914 AGAA-AAGATAA
1 A-AACAAGATAA
989925 A
1 A
989926 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:989909 original size:22 final size:22
Alignment explanation
Indices: 989881--989922 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
989871 TTGGTGCTGG
989881 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
989903 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
989923 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:990065 original size:20 final size:20
Alignment explanation
Indices: 990040--990082 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
990030 GGATAATGTC
990040 CTATATATAGGGGCTGAGTT
1 CTATATATAGGGGCTGAGTT
990060 CTATATATAGGGGCTGAGTT
1 CTATATATAGGGGCTGAGTT
990080 CTA
1 CTA
990083 AAGGTCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (20 bp):
CTATATATAGGGGCTGAGTT
Found at i:994372 original size:11 final size:11
Alignment explanation
Indices: 994348--994392 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
994338 TTGGTGCTGG
994348 AAACAAGATAA
1 AAACAAGATAA
* *
994359 AAATAAGATTA
1 AAACAAGATAA
994370 AAACAAGATAA
1 AAACAAGATAA
994381 AGAA-AAGATAA
1 A-AACAAGATAA
994392 A
1 A
994393 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:994376 original size:22 final size:22
Alignment explanation
Indices: 994348--994389 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
994338 TTGGTGCTGG
994348 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
994370 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
994390 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:998936 original size:15 final size:15
Alignment explanation
Indices: 998916--998962 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
998906 TTACTACCTT
998916 CATCATTCCATTTTC
1 CATCATTCCATTTTC
998931 CATCATTCCATTTTC
1 CATCATTCCATTTTC
998946 CATCATTCCATTTTC
1 CATCATTCCATTTTC
998961 CA
1 CA
998963 ACATATTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (15 bp):
CATCATTCCATTTTC
Found at i:998941 original size:8 final size:8
Alignment explanation
Indices: 998916--998956 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
998906 TTACTACCTT
998916 CATCATTC
1 CATCATTC
*
998924 CAT-TTTC
1 CATCATTC
998931 CATCATTC
1 CATCATTC
*
998939 CAT-TTTC
1 CATCATTC
998946 CATCATTC
1 CATCATTC
998954 CAT
1 CAT
998957 TTTCCAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 12 0.44
8 15 0.56
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (8 bp):
CATCATTC
Found at i:1005008 original size:36 final size:35
Alignment explanation
Indices: 1004916--1005025 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
1004906 GGTGGTTATA
* * * *
1004916 ATAGGCATGAAATGGTGATAGAAGATGGTAATGAT
1 ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
* *
1004951 ATAGGCGTGCAATGGTAATGGAAGATGGTGATGTT
1 ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
1004986 ATAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT
1 ATAGGCGTG-AAATGGTGATGGAAGATGGTGATGTT
1005022 -TAGG
1 ATAGG
1005026 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (35 bp):
ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
Found at i:1013629 original size:15 final size:15
Alignment explanation
Indices: 1013611--1013655 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1013601 ATGTAGGAGA
*
1013611 TTTTTTTTCTTTTTG
1 TTTTTCTTCTTTTTG
1013626 TTTTTCTTCTTTTT-
1 TTTTTCTTCTTTTTG
*
1013640 TTTCTC-TCTTTTTG
1 TTTTTCTTCTTTTTG
1013654 TT
1 TT
1013656 GCTTTTGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 7 0.26
14 7 0.26
15 13 0.48
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (15 bp):
TTTTTCTTCTTTTTG
Found at i:1013631 original size:12 final size:12
Alignment explanation
Indices: 1013611--1013652 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
1013601 ATGTAGGAGA
1013611 TTTTTTTTCTT-
1 TTTTTTTTCTTC
1013622 TTTGTTTTTCTTC
1 TTT-TTTTTCTTC
1013635 TTTTTTTTCTCTC
1 TTTTTTTTCT-TC
1013648 TTTTT
1 TTTTT
1013653 GTTGCTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.11
12 15 0.54
13 10 0.36
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:1014137 original size:36 final size:35
Alignment explanation
Indices: 1014045--1014154 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
1014035 GGTGGTTATA
* * * *
1014045 ATAGGCGTGAAATGGTGATAGAATATGGTAATGAT
1 ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
* *
1014080 ATAGGCGTGTAATGGTAATGGAAGATGGTGATGTT
1 ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
*
1014115 ATAGGCATGAAAATGGTGATGGAAGATGGTGATGTT
1 ATAGGCGTG-AAATGGTGATGGAAGATGGTGATGTT
1014151 -TAGG
1 ATAGG
1014155 TAGTTTCTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 41 0.63
36 24 0.37
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.29
Consensus pattern (35 bp):
ATAGGCGTGAAATGGTGATGGAAGATGGTGATGTT
Found at i:1018118 original size:19 final size:20
Alignment explanation
Indices: 1018080--1018130 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1018070 GAAACCCCTT
1018080 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1018100 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1018119 TGAAGATACATG
1 TGAAAATACATG
1018131 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1020438 original size:35 final size:35
Alignment explanation
Indices: 1020332--1020448 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
1020322 TACTATCTGT
* *
1020332 TCATCA-TCATCTTCCATCACCATTTTTACGCCTATA
1 TCATCACT-ATCTTCTATCACCA-TTTCACGCCTATA
* * *
1020368 ACATCACCATCTTCTATCACCATTGCACGCCTATA
1 TCATCACTATCTTCTATCACCATTTCACGCCTATA
* * *
1020403 TCATTACTATCTTCTATCACCATTTCACACATATA
1 TCATCACTATCTTCTATCACCATTTCACGCCTATA
*
1020438 TAATCACTATC
1 TCATCACTATC
1020449 CCATTACCAT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
35 49 0.73
36 18 0.27
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.36
Consensus pattern (35 bp):
TCATCACTATCTTCTATCACCATTTCACGCCTATA
Found at i:1024438 original size:16 final size:16
Alignment explanation
Indices: 1024404--1024437 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1024394 TTCAACTTTC
*
1024404 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
1024420 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
1024435 TTT
1 TTT
1024438 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:1024465 original size:23 final size:25
Alignment explanation
Indices: 1024426--1024479 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
1024416 TTCTTTTCTT
1024426 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
1024451 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
1024474 TTTCTT
1 TTTCTT
1024480 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:1026806 original size:23 final size:24
Alignment explanation
Indices: 1026780--1026829 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1026770 ATCAGCAAAT
1026780 AAATTAAAAGCACTC-AAAAGAAG
1 AAATTAAAAGCACTCGAAAAGAAG
* *
1026803 AAATTGAAATCACTCGAAAAGAAG
1 AAATTAAAAGCACTCGAAAAGAAG
1026827 AAA
1 AAA
1026830 AAGAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14
Consensus pattern (24 bp):
AAATTAAAAGCACTCGAAAAGAAG
Found at i:1026835 original size:24 final size:23
Alignment explanation
Indices: 1026790--1026835 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1026780 AAATTAAAAG
**
1026790 CACTCAAAAGAAGAAATTGAAAT
1 CACTCAAAAGAAGAAAAAGAAAT
1026813 CACTCGAAAAGAAGAAAAAGAAA
1 CACTC-AAAAGAAGAAAAAGAAA
1026836 GAAATAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (23 bp):
CACTCAAAAGAAGAAAAAGAAAT
Found at i:1035874 original size:11 final size:13
Alignment explanation
Indices: 1035842--1035871 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1035832 TTGCCAAAGA
1035842 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1035855 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1035867 TGAAA
1 TGAAA
1035872 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Done.