Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 9 of 18
Found at i:3763111 original size:27 final size:27
Alignment explanation
Indices: 3763081--3763147 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3763071 TTGTGTTTTT
*
3763081 CTAATTTTCTTTGACTTTGATTAATGG
1 CTAATTTTCTTTGACTTGGATTAATGG
3763108 CTAATTTTCTTTGACTTGGATTAATGG
1 CTAATTTTCTTTGACTTGGATTAATGG
3763135 CTAATTTTCTTTG
1 CTAATTTTCTTTG
3763148 GATGAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (27 bp):
CTAATTTTCTTTGACTTGGATTAATGG
Found at i:3763673 original size:14 final size:14
Alignment explanation
Indices: 3763654--3763684 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3763644 TTTTAGTTTA
*
3763654 AATTTTGGTTAATT
1 AATTTTAGTTAATT
3763668 AATTTTAGTTAATT
1 AATTTTAGTTAATT
3763682 AAT
1 AAT
3763685 CAATTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
AATTTTAGTTAATT
Found at i:3764685 original size:22 final size:21
Alignment explanation
Indices: 3764660--3764704 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3764650 AATTTACTGC
*
3764660 AAGTGTCTCATTAATTGGTTAA
1 AAGTGACT-ATTAATTGGTTAA
* *
3764682 AAGTGAGTGTTAATTGGTTAA
1 AAGTGACTATTAATTGGTTAA
3764703 AA
1 AA
3764705 CTTCTCTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (21 bp):
AAGTGACTATTAATTGGTTAA
Found at i:3765479 original size:17 final size:16
Alignment explanation
Indices: 3765453--3765487 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3765443 CATGTGAGGG
3765453 ATATCTCTCCCTTAAT
1 ATATCTCTCCCTTAAT
3765469 ATATGCTCTCCCTTAAT
1 ATAT-CTCTCCCTTAAT
3765486 AT
1 AT
3765488 GTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATCTCTCCCTTAAT
Found at i:3775942 original size:2 final size:2
Alignment explanation
Indices: 3775930--3775967 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3775920 ATAATATCAC
*
3775930 AT AT CAT AT AT AT AT AT AT AT AT AC 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 AT A
3775968 AGCCAGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3777299 original size:35 final size:35
Alignment explanation
Indices: 3777136--3777308 Score: 208
Period size: 36 Copynumber: 4.9 Consensus size: 35
3777126 TCTCAAGCAC
*
3777136 TTGATTAAAATTGTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* *
3777169 TTCATTTAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
3777204 TTGATTAAATATTTTTAATCAAGTTATTGGACCTAA
1 TTGATTAAAT-TGTTTAATTAAGTTATTGGGCCTAA
* * *
3777240 TTGATTAAATTTGTTCAATCAAGTTATTGGGCTTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
*
3777276 TTGATCAAATTGTTTAATTAAGTTATTGGGCCT
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCT
3777309 CNNNNNNNNN
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
32 15 0.13
33 5 0.04
35 38 0.32
36 60 0.50
37 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:3777377 original size:36 final size:36
Alignment explanation
Indices: 3777330--3777477 Score: 109
Period size: 35 Copynumber: 3.8 Consensus size: 36
3777320 NNNNNNNNTT
*
3777330 AAGTTATTGGGCCTAATTGATTAAATTTGTTTAATC
1 AAGTTATTAGGCCTAATTGATTAAATTTGTTTAATC
*
3777366 AAGTTATTGGGCCTAAGTTATTAGGCCTAATTTATTAAATTTGTTTAATC
1 AAGTTATTAGGCCT-A---ATT--G----A-TTA---AATTTGTTTAATC
* * *
3777416 AAGTTATTAGGCCTAATTAATTAAA-TTATTTAATT
1 AAGTTATTAGGCCTAATTGATTAAATTTGTTTAATC
*
3777451 AAGTTATTAGGCTTAATTGATTAAATT
1 AAGTTATTAGGCCTAATTGATTAAATT
3777478 AAATAATTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 30
0.72 0.05 0.24
Matches are distributed among these distances:
35 31 0.34
36 17 0.19
37 1 0.01
39 3 0.03
40 4 0.04
42 1 0.01
46 4 0.04
47 3 0.03
49 1 0.01
50 26 0.29
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (36 bp):
AAGTTATTAGGCCTAATTGATTAAATTTGTTTAATC
Found at i:3777385 original size:14 final size:14
Alignment explanation
Indices: 3777366--3777402 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3777356 TTGTTTAATC
*
3777366 AAGTTATTGGGCCT
1 AAGTTATTAGGCCT
3777380 AAGTTATTAGGCCT
1 AAGTTATTAGGCCT
*
3777394 AATTTATTA
1 AAGTTATTA
3777403 AATTTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (14 bp):
AAGTTATTAGGCCT
Found at i:3777393 original size:50 final size:50
Alignment explanation
Indices: 3777329--3777431 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
3777319 NNNNNNNNNT
* *
3777329 TAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCC
1 TAAGTTATTAGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTAGGCC
*
3777379 TAAGTTATTAGGCCTAATTTATTAAATTTGTTTAATCAAGTTATTAGGCC
1 TAAGTTATTAGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTAGGCC
3777429 TAA
1 TAA
3777432 TTAATTAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (50 bp):
TAAGTTATTAGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTAGGCC
Found at i:3777455 original size:35 final size:35
Alignment explanation
Indices: 3777379--3777491 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 35
3777369 TTATTGGGCC
* *
3777379 TAAGTTATTAGGCCTAATTTATTAAATTTGTTTAAT
1 TAAGTTATTAGGCCTAATTAATTAAA-TTATTTAAT
*
3777415 CAAGTTATTAGGCCTAATTAATTAAATTATTTAAT
1 TAAGTTATTAGGCCTAATTAATTAAATTATTTAAT
* * **
3777450 TAAGTTATTAGGCTTAATTGATTAAATTAAATAAT
1 TAAGTTATTAGGCCTAATTAATTAAATTATTTAAT
3777485 TAAGTTA
1 TAAGTTA
3777492 ATTAAGCTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 45 0.65
36 24 0.35
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (35 bp):
TAAGTTATTAGGCCTAATTAATTAAATTATTTAAT
Found at i:3782696 original size:63 final size:63
Alignment explanation
Indices: 3782629--3782928 Score: 275
Period size: 63 Copynumber: 4.7 Consensus size: 63
3782619 TAAAACCAAG
* *
3782629 TCCATTTTTGAATGTATCAAGCCTTAATCAAGTCAAGGAATATTCATATTTTTCAAAATTGAA
1 TCCATTTTTGAATGGATCAAGCCTTGATCAAGTCAAGGAATATTCATATTTTTCAAAATTGAA
* *
3782692 TCCATTTTTGAATGGATCGAGCCTTGATCAAGTCAAGGAATATTCATATTTTTCAAAATCGAA
1 TCCATTTTTGAATGGATCAAGCCTTGATCAAGTCAAGGAATATTCATATTTTTCAAAATTGAA
* * * * * * ** **
3782755 TTCATTTTTGAATGGATTGAA-TCTTGATCAAGTCCAGAGG--TCTTCAAAGTTATGAAAAATAA
1 TCCATTTTTGAATGGA-TCAAGCCTTGATCAAGT-CA-AGGAATATTCATA-TTTTTCAAAATTG
3782817 AA
62 AA
* ** * * * * *
3782819 TCCATTTTTGAATGAAT-AGATTCTTAATCAAGTCAAGTAGTTTTCATAATTTTTGAAAATTGAA
1 TCCATTTTTGAATGGATCA-AGCCTTGATCAAGTCAAGGAATATTCAT-ATTTTTCAAAATTGAA
* * * * *
3782883 TCCATTTCTAAATGGATCAAGCCTTGATCTACTCAAGGAATTTTCA
1 TCCATTTTTGAATGGATCAAGCCTTGATCAAGTCAAGGAATATTCA
3782929 AAGTTTATGT
Statistics
Matches: 191, Mismatches: 36, Indels: 19
0.78 0.15 0.08
Matches are distributed among these distances:
62 3 0.02
63 95 0.50
64 88 0.46
65 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (63 bp):
TCCATTTTTGAATGGATCAAGCCTTGATCAAGTCAAGGAATATTCATATTTTTCAAAATTGAA
Found at i:3784730 original size:21 final size:20
Alignment explanation
Indices: 3784706--3784744 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3784696 ACATAATCAT
3784706 CCCTAAGAGTGTTGTAGTCAA
1 CCCTAAGAGT-TTGTAGTCAA
* *
3784727 CCCTAGGAGTTTTTAGTC
1 CCCTAAGAGTTTGTAGTC
3784745 GACCTTCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
CCCTAAGAGTTTGTAGTCAA
Found at i:3796420 original size:21 final size:21
Alignment explanation
Indices: 3796396--3796448 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3796386 AGAGGCATGC
*
3796396 TAATCGGTTAAGGAA-TTTAGT
1 TAATCAGTTAA-GAAGTTTAGT
* *
3796417 TAATCAATTAAGAAGTTTGGT
1 TAATCAGTTAAGAAGTTTAGT
3796438 TAATCAGTTAA
1 TAATCAGTTAA
3796449 AGCACAAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (21 bp):
TAATCAGTTAAGAAGTTTAGT
Found at i:3798249 original size:64 final size:65
Alignment explanation
Indices: 3798168--3798289 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
3798158 AAAGAAAAGT
* *
3798168 GGTTATACCTTAGCCTTCAAAGGTAATGTCTAGAGGTTGTGCTTGATCCTT-AAAAAGGAATAGA
1 GGTTATACCTTAGCCTTCAAAGGTAATGTCTAAAGGTTGTGCTTAATCCTTGAAAAAGGAATAGA
* * *
3798232 GGTTATGCCTTCA-CCTTCAAAGGTAGTGTTTAAAGGTTGTGCTTAATCCTTGAAAAAG
1 GGTTATACCTT-AGCCTTCAAAGGTAATGTCTAAAGGTTGTGCTTAATCCTTGAAAAAG
3798290 CATAAAAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
64 44 0.86
65 7 0.14
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (65 bp):
GGTTATACCTTAGCCTTCAAAGGTAATGTCTAAAGGTTGTGCTTAATCCTTGAAAAAGGAATAGA
Found at i:3798303 original size:44 final size:44
Alignment explanation
Indices: 3798250--3798336 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
3798240 CTTCACCTTC
*
3798250 AAAGGTAGTGTTTAAAGGTTGTGCTT-AATCCTTGAAAAA-GCATA
1 AAAGGTAGTGATTAAAGGTTGTGCTTGAA-CCTT-AAAAACGCATA
* *
3798294 AAAGTTAGTGATTAGAGGTTGTGCTTGAACCTTAAAAACGCAT
1 AAAGGTAGTGATTAAAGGTTGTGCTTGAACCTTAAAAACGCAT
3798337 TGTCGTGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.13
44 31 0.82
45 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (44 bp):
AAAGGTAGTGATTAAAGGTTGTGCTTGAACCTTAAAAACGCATA
Found at i:3798966 original size:20 final size:20
Alignment explanation
Indices: 3798938--3798975 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3798928 CATTCAAAAC
3798938 CAAAAGTATCGATACATGTT
1 CAAAAGTATCGATACATGTT
* *
3798958 CAAATGTATTGATACATG
1 CAAAAGTATCGATACATG
3798976 AAATCCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
CAAAAGTATCGATACATGTT
Found at i:3800452 original size:15 final size:15
Alignment explanation
Indices: 3800432--3800462 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3800422 GATTTGTTTC
3800432 AATTTTGATGTTTGA
1 AATTTTGATGTTTGA
3800447 AATTTTGATGTTTGA
1 AATTTTGATGTTTGA
3800462 A
1 A
3800463 TGTGAAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
AATTTTGATGTTTGA
Found at i:3801066 original size:13 final size:13
Alignment explanation
Indices: 3801048--3801072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3801038 TTTTATAAAT
3801048 AAAATAATAATAA
1 AAAATAATAATAA
3801061 AAAATAATAATA
1 AAAATAATAATA
3801073 TTTGATCTAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:3801390 original size:30 final size:30
Alignment explanation
Indices: 3801356--3801413 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3801346 TAAGAAGTTG
3801356 AGGGGTGGAA-TTGTCAATAATGAA-AAGTAA
1 AGGGGT-GAAGTTGT-AATAATGAACAAGTAA
*
3801386 AGGGGTGAAGTTGTAATTATGAACAAGT
1 AGGGGTGAAGTTGTAATAATGAACAAGT
3801414 CGAAGGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (30 bp):
AGGGGTGAAGTTGTAATAATGAACAAGTAA
Found at i:3803665 original size:25 final size:25
Alignment explanation
Indices: 3803613--3803665 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3803603 TGATTATACA
* ** *
3803613 TGGCAAGGCCACGGGTTGTTATACG
1 TGGCAAGGCCACGAGTTAATAAACG
*
3803638 TGGCAAGGCCACGAGTTAATAAATG
1 TGGCAAGGCCACGAGTTAATAAACG
3803663 TGG
1 TGG
3803666 TTACGACCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (25 bp):
TGGCAAGGCCACGAGTTAATAAACG
Found at i:3805817 original size:31 final size:31
Alignment explanation
Indices: 3805782--3805862 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
3805772 GCCAAATCAC
** *
3805782 AGGGACTAAATTTTACAAAATTGC-AAAGCAT
1 AGGGACTAAATTGAACAAAA-TACTAAAGCAT
* *
3805813 AGGGACTAAATTGAACAAAATACTATAGTAT
1 AGGGACTAAATTGAACAAAATACTAAAGCAT
3805844 AGGGACTAAATTGAACAAA
1 AGGGACTAAATTGAACAAA
3805863 GCTCTCTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.23
Consensus pattern (31 bp):
AGGGACTAAATTGAACAAAATACTAAAGCAT
Found at i:3809888 original size:17 final size:17
Alignment explanation
Indices: 3809858--3809890 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3809848 TTCTTGATAA
3809858 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
3809875 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
3809891 TTATTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:3810127 original size:58 final size:60
Alignment explanation
Indices: 3810042--3810171 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
3810032 TCTTGTCTTT
* * * * *
3810042 AATTAAGAC-AAAAATGTTTTATCTTATC-TAAATTGAGACATATA-AGTTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTATCTTAAATTAAGACAAACATA-TTTTCTTATCTA
*
3810100 GATTAAGACAAAAAATAATTTT-T-TTATCTTAAATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAAAAAT-ATTTTATCTTATCTTAAATTAAGACAAACATATTTTCTTATCTA
3810159 AATTAAGATCAAA
1 AATTAAGA-CAAA
3810172 CATGTTGTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
58 13 0.22
59 38 0.63
60 9 0.15
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (60 bp):
AATTAAGACAAAAAATATTTTATCTTATCTTAAATTAAGACAAACATATTTTCTTATCTA
Found at i:3810161 original size:28 final size:28
Alignment explanation
Indices: 3810042--3810202 Score: 144
Period size: 29 Copynumber: 5.5 Consensus size: 28
3810032 TCTTGTCTTT
* *
3810042 AATTAAGACAAAAATGTTTTATCTTATCTA
1 AATTAAGACAAACAT-ATTT-TCTTATCTA
* * * *
3810072 AATTGAGACATATA-AGTTTTCTTGTCTA
1 AATTAAGACAAACATA-TTTTCTTATCTA
* * *
3810100 GATTAAGACAAAAAATAATTTTTTTATCTTA
1 AATTAAGAC-AAACAT-ATTTTCTTATC-TA
3810131 AATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAACATATTTTCTTATCTA
* * *
3810159 AATTAAGATCAAACATGTTGTCTTGTCTA
1 AATTAAGA-CAAACATATTTTCTTATCTA
3810188 AATTAAGACAAACAT
1 AATTAAGACAAACAT
3810203 GTTAATGCTA
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
28 32 0.30
29 41 0.38
30 24 0.22
31 11 0.10
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTATCTA
Found at i:3812206 original size:45 final size:45
Alignment explanation
Indices: 3812155--3812242 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
3812145 TTTTAAAGAC
3812155 CAAACCACCTTCCAAGCATGGGAAAGACATTTTATTCCAAGCCTT
1 CAAACCACCTTCCAAGCATGGGAAAGACATTTTATTCCAAGCCTT
*** *
3812200 CAAACCACCTTTTGAGCATGGGAAAGAGATTTTATTCCAAGCC
1 CAAACCACCTTCCAAGCATGGGAAAGACATTTTATTCCAAGCC
3812243 ACCCAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (45 bp):
CAAACCACCTTCCAAGCATGGGAAAGACATTTTATTCCAAGCCTT
Found at i:3829122 original size:26 final size:26
Alignment explanation
Indices: 3829093--3829180 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
3829083 CCTATGTAAC
3829093 TATCATCCAATGTTCTTCTAGAAGTA
1 TATCATCCAATGTTCTTCTAGAAGTA
* * * * *
3829119 TATCAACCCAT-TTCTACCTCACTACTGTAA
1 TATCATCCAATGTTCT-TCT-A-GA-AGT-A
3829149 CTATCATCCAATGTTCTTCTAGAAGTA
1 -TATCATCCAATGTTCTTCTAGAAGTA
3829176 TATCA
1 TATCA
3829181 ACCCATTTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 4 0.09
26 16 0.36
27 2 0.04
28 3 0.07
29 3 0.07
30 2 0.04
31 11 0.24
32 4 0.09
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (26 bp):
TATCATCCAATGTTCTTCTAGAAGTA
Found at i:3829175 original size:57 final size:57
Alignment explanation
Indices: 3829087--3829201 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
3829077 ACTTTACCTA
3829087 TGTAACTATCATCCAATGTTCTTCTAGAAGTATATCAACCCATTTCTACCTCACTAC
1 TGTAACTATCATCCAATGTTCTTCTAGAAGTATATCAACCCATTTCTACCTCACTAC
3829144 TGTAACTATCATCCAATGTTCTTCTAGAAGTATATCAACCCATTTCTACCTCACTAC
1 TGTAACTATCATCCAATGTTCTTCTAGAAGTATATCAACCCATTTCTACCTCACTAC
3829201 T
1 T
3829202 TCTTTCTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36
Consensus pattern (57 bp):
TGTAACTATCATCCAATGTTCTTCTAGAAGTATATCAACCCATTTCTACCTCACTAC
Found at i:3833379 original size:15 final size:13
Alignment explanation
Indices: 3833358--3833409 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 13
3833348 TCCAAAACCC
3833358 AAAAAAAAAGAATG
1 AAAAAAAAA-AATG
3833372 ATAAAAAATAAAATG
1 A-AAAAAA-AAAATG
3833387 -AAAAAAAAAAT-
1 AAAAAAAAAAATG
3833398 AAAAAAAGAAAA
1 AAAAAAA-AAAA
3833410 AATAATACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.32
13 10 0.29
14 1 0.03
15 10 0.29
16 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAAATG
Found at i:3833410 original size:15 final size:16
Alignment explanation
Indices: 3833374--3833414 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3833364 AAAGAATGAT
3833374 AAAAAATAAAATGAAAA
1 AAAAAATAAAA-GAAAA
*
3833391 AAAAAATAAAA-AAAG
1 AAAAAATAAAAGAAAA
3833406 AAAAAATAA
1 AAAAAATAA
3833415 TACCTTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
17 11 0.48
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAGAAAA
Found at i:3837274 original size:31 final size:31
Alignment explanation
Indices: 3837236--3837299 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3837226 TACGTCGACT
3837236 CATTGGGACAATTGACACTCTAATAAAGTAC
1 CATTGGGACAATTGACACTCTAATAAAGTAC
3837267 CATTGGGACAATTGACACTCTAATAAAGTAC
1 CATTGGGACAATTGACACTCTAATAAAGTAC
3837298 CA
1 CA
3837300 GAATGCTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (31 bp):
CATTGGGACAATTGACACTCTAATAAAGTAC
Found at i:3860343 original size:21 final size:21
Alignment explanation
Indices: 3860319--3860371 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
3860309 AGTATTTATT
3860319 ATTTTGATTTTTCTTAGTTTA
1 ATTTTGATTTTTCTTAGTTTA
* * ** *
3860340 ATTTTGCTATAACTTAGTTTG
1 ATTTTGATTTTTCTTAGTTTA
3860361 A-TTTGATTTTT
1 ATTTTGATTTTT
3860372 TTGATATCGT
Statistics
Matches: 23, Mismatches: 9, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62
Consensus pattern (21 bp):
ATTTTGATTTTTCTTAGTTTA
Found at i:3867257 original size:17 final size:17
Alignment explanation
Indices: 3867237--3867286 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
3867227 GAAGCTTCTG
3867237 TCTTTTTCTTTCTTTTA
1 TCTTTTTCTTTCTTTTA
*
3867254 TCTTTTTCTTTATCTTTA
1 TCTTTTTCTTTCT-TTTA
3867272 TC-TTTTCTTTTCTTT
1 TCTTTTTC-TTTCTTT
3867287 CCATGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTTTCTTTCTTTTA
Found at i:3867267 original size:12 final size:12
Alignment explanation
Indices: 3867245--3867286 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3867235 TGTCTTTTTC
3867245 TTTCTTTTATCTT
1 TTTC-TTTATCTT
3867258 TTTCTTTATCTT
1 TTTCTTTATCTT
*
3867270 TATCTTT-TC-T
1 TTTCTTTATCTT
3867280 TTTCTTT
1 TTTCTTT
3867287 CCATGTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
12 14 0.52
13 4 0.15
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTTATCTT
Found at i:3872448 original size:23 final size:23
Alignment explanation
Indices: 3872422--3872466 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3872412 TAAATAATGC
*
3872422 CTTACTAACTAGTCACGCAATAT
1 CTTACTAACAAGTCACGCAATAT
*
3872445 CTTACTAACAAGTCACGTAATA
1 CTTACTAACAAGTCACGCAATA
3872467 CCTGTCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (23 bp):
CTTACTAACAAGTCACGCAATAT
Found at i:3872576 original size:65 final size:65
Alignment explanation
Indices: 3872504--3872649 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 65
3872494 TCAACCAGTT
*** * * *
3872504 ACGCAATACTTAAAAATTAATCACGTGATGTCCAAAGTTAGCCATGTAATACTTAAAAATTAATC
1 ACGCAATACTTAAAAATTAATCACACAATGTCCAAAGTCAGCCATGTAATACCTAAAAACTAATC
** ** * *
3872569 ACGCAATACTTAAAAATTGGTCACACAATGTCCAAAGTCAGTTATGTAATTCCTAAAAACTAGTC
1 ACGCAATACTTAAAAATTAATCACACAATGTCCAAAGTCAGCCATGTAATACCTAAAAACTAATC
*
3872634 ACGAAATACTTAAAAA
1 ACGCAATACTTAAAAA
3872650 CTACCAAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (65 bp):
ACGCAATACTTAAAAATTAATCACACAATGTCCAAAGTCAGCCATGTAATACCTAAAAACTAATC
Found at i:3872592 original size:22 final size:22
Alignment explanation
Indices: 3872551--3872597 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3872541 TTAGCCATGT
*
3872551 AATACTTAAAAATTAATCACGC
1 AATACTTAAAAATTAATCACAC
**
3872573 AATACTTAAAAATTGGTCACAC
1 AATACTTAAAAATTAATCACAC
3872595 AAT
1 AAT
3872598 GTCCAAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (22 bp):
AATACTTAAAAATTAATCACAC
Found at i:3879383 original size:33 final size:36
Alignment explanation
Indices: 3879338--3879407 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 36
3879328 AATGAATATT
*
3879338 TTATATTTAAATAT-T-AT-TTTATTT-TTTTATTTA
1 TTATATTAAAATATGTGATCTTT-TTTGTTTTATTTA
3879371 TTATATTAAAATATGTGATCTTTTTTGTTTTATTTA
1 TTATATTAAAATATGTGATCTTTTTTGTTTTATTTA
3879407 T
1 T
3879408 CACATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 13 0.41
34 1 0.03
35 5 0.16
36 13 0.41
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (36 bp):
TTATATTAAAATATGTGATCTTTTTTGTTTTATTTA
Found at i:3884472 original size:2 final size:2
Alignment explanation
Indices: 3884465--3884492 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3884455 AGGAATGTTC
3884465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3884493 ATTCAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3889140 original size:48 final size:48
Alignment explanation
Indices: 3889069--3889166 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3889059 TTTGGTACTT
3889069 AAATGTATCATATATGGATCAAATAAAGGTCATGCTCAAATTGCTTTC
1 AAATGTATCATATATGGATCAAATAAAGGTCATGCTCAAATTGCTTTC
3889117 AAATGTATCATATATGGATCAAATAAAGGTCATGCTCAAATTGCTTTC
1 AAATGTATCATATATGGATCAAATAAAGGTCATGCTCAAATTGCTTTC
3889165 AA
1 AA
3889167 TTCTGGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (48 bp):
AAATGTATCATATATGGATCAAATAAAGGTCATGCTCAAATTGCTTTC
Found at i:3891648 original size:33 final size:32
Alignment explanation
Indices: 3891584--3891648 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
3891574 GAGACCATAG
* *
3891584 AAACAACACCCAGAAAATGATGTCATCATGTT
1 AAACAACACCCAGAAAATGACGTCATAATGTT
* *
3891616 AAACAACACCCGATAAAATGACGTTATAATGTT
1 AAACAACACCC-AGAAAATGACGTCATAATGTT
3891649 TTTGAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (32 bp):
AAACAACACCCAGAAAATGACGTCATAATGTT
Found at i:3892944 original size:23 final size:22
Alignment explanation
Indices: 3892892--3892950 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
3892882 TTTAAGTTTT
* * *
3892892 TAATTATATATTATAAAAATAA
1 TAATTAAATTTTAAAAAAATAA
*
3892914 TATTTTAAATTTTAAAAAAATTAA
1 TA-ATTAAATTTTAAAAAAA-TAA
3892938 TAATTAATATTTT
1 TAATTAA-ATTTT
3892951 CATCATAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.07
23 17 0.59
24 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTAAATTTTAAAAAAATAA
Found at i:3893055 original size:27 final size:26
Alignment explanation
Indices: 3892992--3893045 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
3892982 TGATAATATT
* *
3892992 TAAATGATCAATTATTAATATTTTAAA
1 TAAAT-ATAAATTATTAATATTTAAAA
3893019 TAAATTATAAATTATTAATATTTAAAA
1 TAAA-TATAAATTATTAATATTTAAAA
3893046 CATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATATAAATTATTAATATTTAAAA
Found at i:3893145 original size:15 final size:15
Alignment explanation
Indices: 3893116--3893266 Score: 66
Period size: 15 Copynumber: 9.9 Consensus size: 15
3893106 TTAAAAATAA
*
3893116 TATTAA-ATTTAAAT
1 TATTAATATTTTAAT
3893130 TATTAATATTTTAAT
1 TATTAATATTTTAAT
*
3893145 TATAATAATATTTAAAT
1 TAT--TAATATTTTAAT
* *
3893162 TATAAATAAAATATTACTAT
1 TAT---TAATATTTTA--AT
* *
3893182 T-TTAAAATATTAAT
1 TATTAATATTTTAAT
*
3893196 GATTAA-ATTATTAA-
1 TATTAATATT-TTAAT
* *
3893210 TATTTAAAATTTCAAT
1 TA-TTAATATTTTAAT
3893226 TATTAATATTTTAA-
1 TATTAATATTTTAAT
*
3893240 -A-TAA-ATTATAAGT
1 TATTAATATTTTAA-T
3893253 TATTAATATTTTAA
1 TATTAATATTTTAA
3893267 AAATAAAACA
Statistics
Matches: 108, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
11 6 0.06
12 3 0.03
13 1 0.01
14 12 0.11
15 38 0.35
16 21 0.19
17 14 0.13
18 9 0.08
19 1 0.01
20 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
TATTAATATTTTAAT
Found at i:3893155 original size:17 final size:17
Alignment explanation
Indices: 3893122--3893166 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
3893112 ATAATATTAA
3893122 ATTTAAATTAT--TAAT
1 ATTTAAATTATAATAAT
*
3893137 ATTTTAATTATAATAAT
1 ATTTAAATTATAATAAT
3893154 ATTTAAATTATAA
1 ATTTAAATTATAA
3893167 ATAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 10 0.38
17 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATTATAATAAT
Found at i:3893183 original size:43 final size:42
Alignment explanation
Indices: 3893125--3893211 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
3893115 ATATTAAATT
* *
3893125 TAAATTATTAATATTTTAATTATAATAAT-ATTTAAATTATAAA
1 TAAAATATTAATATTTTAA-AATAATAATGA-TTAAATTATAAA
* * *
3893168 TAAAATATTACTATTTTAAAATATTAATGATTAAATTATTAA
1 TAAAATATTAATATTTTAAAATAATAATGATTAAATTATAAA
3893210 TA
1 TA
3893212 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
42 20 0.53
43 18 0.47
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TAAAATATTAATATTTTAAAATAATAATGATTAAATTATAAA
Found at i:3893217 original size:57 final size:55
Alignment explanation
Indices: 3893099--3893217 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 55
3893089 ATTTTAATTT
* *
3893099 TTTAAATTTAAAAATAATATTAAATTTAAATTATTAATATTTTAATTATAATAATA
1 TTTAAATTTAAAAATAATATTAAATTTAAAATATTAATATTTAAATTAT-ATAATA
*
3893155 TTTAAATTATAAATAA-AATATTACTATTTTAAAATATTAATGA-TTAAATTAT-TAATA
1 TTTAAATT-TAAA-AATAATATTA--AATTTAAAATATTAAT-ATTTAAATTATATAATA
3893212 TTTAAA
1 TTTAAA
3893218 ATTTCAATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
56 8 0.15
57 22 0.40
58 2 0.04
59 22 0.40
60 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (55 bp):
TTTAAATTTAAAAATAATATTAAATTTAAAATATTAATATTTAAATTATATAATA
Found at i:3893272 original size:22 final size:22
Alignment explanation
Indices: 3893201--3893272 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
3893191 TTAATGATTA
*
3893201 AATTATTAATA-TTTAAAATTT
1 AATTATTAATATTTTAAAATAT
3893222 CAATTATTAATATTTTAAATAAATTAT
1 -AATTATTAATATTTT--A-AAA-TAT
3893249 AAGTTATTAATATTTTAAAA-AT
1 AA-TTATTAATATTTTAAAATAT
3893271 AA
1 AA
3893273 AACAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
22 15 0.35
23 3 0.07
24 3 0.07
25 2 0.05
26 5 0.12
27 15 0.35
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
AATTATTAATATTTTAAAATAT
Found at i:3893340 original size:15 final size:14
Alignment explanation
Indices: 3893312--3893344 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3893302 TCATAAAAGA
3893312 TATT-TTTATTTTT
1 TATTATTTATTTTT
3893325 TATTATTTATTTTTT
1 TATTATTTA-TTTTT
3893340 TATTA
1 TATTA
3893345 ATCTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTATTTATTTTT
Found at i:3899752 original size:43 final size:43
Alignment explanation
Indices: 3899691--3899777 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
3899681 CTTTGAACCA
3899691 TTCAAAGAAGTCTATTAGTATTTTATGTTTTTCCATGAATTTG
1 TTCAAAGAAGTCTATTAGTATTTTATGTTTTTCCATGAATTTG
*
3899734 TTCAAAGAAGTCTATTAGTATTTTATGTTTTTCTATGAATTTG
1 TTCAAAGAAGTCTATTAGTATTTTATGTTTTTCCATGAATTTG
3899777 T
1 T
3899778 AGTAATTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.51
Consensus pattern (43 bp):
TTCAAAGAAGTCTATTAGTATTTTATGTTTTTCCATGAATTTG
Found at i:3917036 original size:40 final size:41
Alignment explanation
Indices: 3916960--3917039 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
3916950 TTGGCTATTT
* * *
3916960 TTCACCTTAGTAGAGTTTTTTAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTAGAGGTTTCTAACCTCGCCAAGATTGGTGA
* * *
3917001 TTCACCTTAGT-GGGGTTTCTAACCTCGCTACGATTGGTG
1 TTCACCTTAGTAGAGGTTTCTAACCTCGCCAAGATTGGTG
3917040 TTTTGCACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
TTCACCTTAGTAGAGGTTTCTAACCTCGCCAAGATTGGTGA
Found at i:3921911 original size:30 final size:29
Alignment explanation
Indices: 3921875--3921932 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3921865 AGTTAAAAGG
3921875 TTTTTAA-AGTTAAATATTAATATTTTTATT
1 TTTTTAATAGTTAAA-ATTAA-ATTTTTATT
* *
3921905 TTTTTAATATTTTAAATTAAATTTTTAT
1 TTTTTAATAGTTAAAATTAAATTTTTAT
3921933 ATTCATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTTAATAGTTAAAATTAAATTTTTATT
Found at i:3922852 original size:10 final size:10
Alignment explanation
Indices: 3922839--3922874 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3922829 ATTTTAATTT
*
3922839 TAATTAATAG
1 TAATTAATAA
3922849 TAATTAATCAA
1 TAATTAAT-AA
3922860 TAATTAATAA
1 TAATTAATAA
3922870 TAATT
1 TAATT
3922875 TTTTAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (10 bp):
TAATTAATAA
Found at i:3924631 original size:30 final size:30
Alignment explanation
Indices: 3924578--3924634 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3924568 AATTGTAGAA
* * *
3924578 ATTTAAAATATTAAGTTGGAACAAAATATC
1 ATTTAAAATATAAACTTGAAACAAAATATC
*
3924608 ATTTCAAATATAAACTTGAAACAAAAT
1 ATTTAAAATATAAACTTGAAACAAAAT
3924635 TTTTATCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (30 bp):
ATTTAAAATATAAACTTGAAACAAAATATC
Found at i:3925720 original size:2 final size:2
Alignment explanation
Indices: 3925713--3925758 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3925703 TTTTTGTTCC
3925713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3925755 TA TA
1 TA TA
3925759 GAAAATTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3929243 original size:15 final size:14
Alignment explanation
Indices: 3929225--3929265 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3929215 AAAATAATTT
3929225 TTTTAAAAAATAAAA
1 TTTTAAAAAA-AAAA
3929240 TTTTAAAAAAAAAA
1 TTTTAAAAAAAAAA
*
3929254 -GTTAAAAAAAAA
1 TTTTAAAAAAAAA
3929266 CTCCAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.44
14 4 0.16
15 10 0.40
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
TTTTAAAAAAAAAA
Found at i:3929243 original size:17 final size:17
Alignment explanation
Indices: 3929208--3929250 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3929198 TGTTAGAAGC
3929208 TTTTAAAAAAAT-AATT
1 TTTTAAAAAAATAAATT
* *
3929224 TTTTTAAAAAATAAA-A
1 TTTTAAAAAAATAAATT
3929240 TTTTAAAAAAA
1 TTTTAAAAAAA
3929251 AAAGTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTTAAAAAAATAAATT
Found at i:3929251 original size:17 final size:15
Alignment explanation
Indices: 3929208--3929263 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
3929198 TGTTAGAAGC
*
3929208 TTTTAAAAAAATAATT
1 TTTTAAAAAAATAA-A
*
3929224 TTTTTAAAAAATAAAA
1 TTTTAAAAAAAT-AAA
3929240 TTTTAAAAAAA-AAA
1 TTTTAAAAAAATAAA
*
3929254 -GTTAAAAAAA
1 TTTTAAAAAAA
3929264 AACTCCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
16 21 0.60
17 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAATAAA
Found at i:3929520 original size:17 final size:17
Alignment explanation
Indices: 3929484--3929525 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3929474 CTTTCAAATA
*
3929484 TTATTTCTACTTTTTCTT
1 TTATTT-TACTTTTTATT
*
3929502 TTATTTTATTTTTTATT
1 TTATTTTACTTTTTATT
3929519 TTATTTT
1 TTATTTT
3929526 TTATCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTACTTTTTATT
Found at i:3929537 original size:12 final size:12
Alignment explanation
Indices: 3929500--3929529 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3929490 CTACTTTTTC
3929500 TTTTATTTTATT
1 TTTTATTTTATT
3929512 TTTTATTTTATT
1 TTTTATTTTATT
3929524 TTTTAT
1 TTTTAT
3929530 CTTTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:3930886 original size:12 final size:11
Alignment explanation
Indices: 3930869--3930908 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
3930859 GAATAGTTTC
3930869 TTGCTGCCTCCT
1 TTGCTGCCT-CT
3930881 TTGCTGCCTCT
1 TTGCTGCCTCT
3930892 CTTGCTGCCTTCT
1 -TTGCTGCC-TCT
3930905 TTGC
1 TTGC
3930909 CTTCAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.08
12 21 0.81
13 3 0.12
ACGTcount: A:0.00, C:0.38, G:0.17, T:0.45
Consensus pattern (11 bp):
TTGCTGCCTCT
Found at i:3935389 original size:11 final size:11
Alignment explanation
Indices: 3935363--3935407 Score: 72
Period size: 12 Copynumber: 3.9 Consensus size: 11
3935353 GAATAGTTTC
3935363 TTGCTGCCTCCT
1 TTGCTGCCT-CT
3935375 TTGCTGCCTCT
1 TTGCTGCCTCT
3935386 TTGCTGCCTCT
1 TTGCTGCCTCT
3935397 CTTGCTGCCTC
1 -TTGCTGCCTC
3935408 AAAAATCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 13 0.41
12 19 0.59
ACGTcount: A:0.00, C:0.40, G:0.18, T:0.42
Consensus pattern (11 bp):
TTGCTGCCTCT
Found at i:3935393 original size:23 final size:23
Alignment explanation
Indices: 3935363--3935407 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3935353 GAATAGTTTC
3935363 TTGCTGCCTC-CTTTGCTGCCTCT
1 TTGCTGCCTCTC-TTGCTGCCTCT
3935386 TTGCTGCCTCTCTTGCTGCCTC
1 TTGCTGCCTCTCTTGCTGCCTC
3935408 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.00, C:0.40, G:0.18, T:0.42
Consensus pattern (23 bp):
TTGCTGCCTCTCTTGCTGCCTCT
Found at i:3944710 original size:36 final size:36
Alignment explanation
Indices: 3944663--3944734 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
3944653 AAAAGATAGA
* *
3944663 TGTTTTCACCATTACACACGACTGCATATATGCAAG
1 TGTTTTCACCATTACACACAACTGCATATATACAAG
3944699 TGTTTTCACCATTACACACAACTGCATATATACAAG
1 TGTTTTCACCATTACACACAACTGCATATATACAAG
3944735 CTATATCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (36 bp):
TGTTTTCACCATTACACACAACTGCATATATACAAG
Found at i:3949896 original size:20 final size:21
Alignment explanation
Indices: 3949871--3949913 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
3949861 GTGAATAGAG
*
3949871 ATCATAATTAT-ACCAATATA
1 ATCATAATGATGACCAATATA
3949891 ATCATAATGATGGACCAATATA
1 ATCATAATGAT-GACCAATATA
3949913 A
1 A
3949914 GGAAATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (21 bp):
ATCATAATGATGACCAATATA
Found at i:3949922 original size:21 final size:22
Alignment explanation
Indices: 3949882--3949923 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3949872 TCATAATTAT
*
3949882 ACCAATATAATCATAATGATGG
1 ACCAATATAAGCATAATGATGG
*
3949904 ACCAATATAAGGA-AATGATG
1 ACCAATATAAGCATAATGATG
3949924 TTCCAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (22 bp):
ACCAATATAAGCATAATGATGG
Found at i:3954130 original size:74 final size:74
Alignment explanation
Indices: 3953976--3954115 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 74
3953966 AAACCTATAC
* * *
3953976 TTATAAATATGTATTCATTAAATGATGATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
1 TTATAAATATGCATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
3954041 TTAAACCTA
66 TTAAACCTA
* *
3954050 TTATAAATGTGCATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGCATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
3954115 T
66 T
3954116 AATTCCATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (74 bp):
TTATAAATATGCATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
TTAAACCTA
Found at i:3962368 original size:29 final size:29
Alignment explanation
Indices: 3962336--3962392 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3962326 TAAATTTGCA
*
3962336 TTTTTAATCTCATATAATATAAATATTTT
1 TTTTTAAGCTCATATAATATAAATATTTT
* *
3962365 TTTTTGAGCTCATATAATATCAATATTT
1 TTTTTAAGCTCATATAATATAAATATTT
3962393 AATTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (29 bp):
TTTTTAAGCTCATATAATATAAATATTTT
Found at i:3963445 original size:22 final size:23
Alignment explanation
Indices: 3963407--3963452 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3963397 AAATAATTTA
3963407 ATATTGTTTTGTATTTTATAAAT
1 ATATTGTTTTGTATTTTATAAAT
* *
3963430 ATATT-TTTTGTTTTTTATTAAT
1 ATATTGTTTTGTATTTTATAAAT
3963452 A
1 A
3963453 GAAACGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (23 bp):
ATATTGTTTTGTATTTTATAAAT
Found at i:3965467 original size:35 final size:35
Alignment explanation
Indices: 3965412--3965479 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3965402 TTCAAGAGTG
* *
3965412 TGGATTTGGAATTGACCTTGAACATGTTTTGGGTT
1 TGGACTTGGAATTGACCTTGAACATGTTCTGGGTT
* *
3965447 TGGACTTGGACTTGATCTTGAACATGTTCTGGG
1 TGGACTTGGAATTGACCTTGAACATGTTCTGGG
3965480 CTTGAGAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (35 bp):
TGGACTTGGAATTGACCTTGAACATGTTCTGGGTT
Found at i:3968417 original size:36 final size:30
Alignment explanation
Indices: 3968354--3968427 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
3968344 TATATTAATT
3968354 ATATAATAATTTATTTAATTTAAAATAAAA
1 ATATAATAATTTATTTAATTTAAAATAAAA
*
3968384 ATATAATAATTTAATTTAA--TATAATAAAA
1 ATATAATAATTT-ATTTAATTTAAAATAAAA
3968413 A-ATAA-AATTT-TTTAA
1 ATATAATAATTTATTTAA
3968428 ATAATTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 5 0.12
27 5 0.12
28 4 0.10
29 10 0.24
30 12 0.29
31 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATAATTTATTTAATTTAAAATAAAA
Found at i:3968420 original size:35 final size:30
Alignment explanation
Indices: 3968354--3968414 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
3968344 TATATTAATT
*
3968354 ATATAATAATTTATTTAATTTAAAATAAAA
1 ATATAATAATTTATTTAATTTAAAAAAAAA
* *
3968384 ATATAATAATTTAATTTAATATAATAAAAAA
1 ATATAATAATTT-ATTTAATTTAAAAAAAAA
3968415 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATAATAATTTATTTAATTTAAAAAAAAA
Found at i:3969392 original size:29 final size:29
Alignment explanation
Indices: 3969360--3969417 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3969350 TTGTTTAAAA
* *
3969360 ATATTTAAAT-AAATTTTTATTTTTTTATT
1 ATATTT-AATCAAATTATTATATTTTTATT
3969389 ATATTTAATCAAATTATTATATTTTTATT
1 ATATTTAATCAAATTATTATATTTTTATT
3969418 TTAGATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATATTTAATCAAATTATTATATTTTTATT
Found at i:3972791 original size:21 final size:19
Alignment explanation
Indices: 3972767--3972817 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 19
3972757 TAAAATTTTA
3972767 ATATAATTAATTAATTATATT
1 ATATAATT-ATTAATTAT-TT
*
3972788 ATAT--TTA-TATTTATTT
1 ATATAATTATTAATTATTT
3972804 ATATAATTATTAAT
1 ATATAATTATTAAT
3972818 GCTTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
16 6 0.24
17 6 0.24
18 4 0.16
19 5 0.20
21 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATAATTATTAATTATTT
Found at i:3977693 original size:29 final size:30
Alignment explanation
Indices: 3977631--3977695 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
3977621 GCTGTTTGCC
*
3977631 CAATTA-TTTTGTTGCTTTAATTTGTAATT
1 CAATTAGTTTTGTTGCTATAATTTGTAATT
* *
3977660 AAATTAGTTTTAGTTG-TATAATTT-TAGTT
1 CAATTAGTTTT-GTTGCTATAATTTGTAATT
3977689 CAATTAG
1 CAATTAG
3977696 AATTAAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 15 0.50
30 11 0.37
31 4 0.13
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (30 bp):
CAATTAGTTTTGTTGCTATAATTTGTAATT
Found at i:3981117 original size:20 final size:20
Alignment explanation
Indices: 3981092--3981162 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
3981082 ACGAATGAAC
3981092 ATCTATCGATAAATTTGGCG
1 ATCTATCGATAAATTTGGCG
* * *
3981112 ATCTATCGATAGA--TGACTAA
1 ATCTATCGATAAATTTGGC--G
*
3981132 ATCTATCAATAAATTTGGCG
1 ATCTATCGATAAATTTGGCG
*
3981152 ATCTATTGATA
1 ATCTATCGATA
3981163 GATGACTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
18 3 0.08
20 32 0.84
22 3 0.08
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (20 bp):
ATCTATCGATAAATTTGGCG
Found at i:3981147 original size:40 final size:40
Alignment explanation
Indices: 3981092--3981182 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
3981082 ACGAATGAAC
*
3981092 ATCTATCGATAAATTTGGCGATCTATCGATAGATGACTAA
1 ATCTATCAATAAATTTGGCGATCTATCGATAGATGACTAA
*
3981132 ATCTATCAATAAATTTGGCGATCTATTGATAGATGACTAA
1 ATCTATCAATAAATTTGGCGATCTATCGATAGATGACTAA
3981172 ATCTATCAATA
1 ATCTATCAATA
3981183 GATCGACTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (40 bp):
ATCTATCAATAAATTTGGCGATCTATCGATAGATGACTAA
Found at i:3981183 original size:20 final size:20
Alignment explanation
Indices: 3981112--3981209 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
3981102 AAATTTGGCG
*
3981112 ATCTATCGATAGATGACTAA
1 ATCTATCAATAGATGACTAA
* * *
3981132 ATCTATCAATAAATTTGGC--G
1 ATCTATCAATAGA--TGACTAA
**
3981152 ATCTATTGATAGATGACTAA
1 ATCTATCAATAGATGACTAA
**
3981172 ATCTATCAATAGATCGACTCG
1 ATCTATCAATAGAT-GACTAA
* *
3981193 ATTTATCAATAAATGAC
1 ATCTATCAATAGATGAC
3981210 ATCCAAAGTG
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
18 3 0.05
20 36 0.62
21 16 0.28
22 3 0.05
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCTATCAATAGATGACTAA
Found at i:3982490 original size:40 final size:40
Alignment explanation
Indices: 3982445--3982594 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
3982435 TTTTCTTGAT
3982445 TGAATGTCTAATATGGTGATTTAGACTAAGTGCTAATGAA
1 TGAATGTCTAATATGGTGATTTAGACTAAGTGCTAATGAA
* **
3982485 TGAATGTCTAATATGGTGATTTAGGCTAAGTGCTCTTGAA
1 TGAATGTCTAATATGGTGATTTAGACTAAGTGCTAATGAA
* *
3982525 TGAATGTCTAATGTGGTGATTTAGGCTAAGTGCTAATGAA
1 TGAATGTCTAATATGGTGATTTAGACTAAGTGCTAATGAA
* *
3982565 TGAATGTCTAATGTGGTGGTTTAGACTAAG
1 TGAATGTCTAATATGGTGATTTAGACTAAG
3982595 ACATTGTTGA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (40 bp):
TGAATGTCTAATATGGTGATTTAGACTAAGTGCTAATGAA
Found at i:3987747 original size:32 final size:32
Alignment explanation
Indices: 3987706--3987769 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3987696 GTATGATTAA
3987706 TACGAACAAAAAAGTTTCAAAAAAAAAAATGC
1 TACGAACAAAAAAGTTTCAAAAAAAAAAATGC
*
3987738 TACGAACAAAAAAGTTTCAAAAAAGAAAATGC
1 TACGAACAAAAAAGTTTCAAAAAAAAAAATGC
3987770 CTTGAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.61, C:0.12, G:0.11, T:0.16
Consensus pattern (32 bp):
TACGAACAAAAAAGTTTCAAAAAAAAAAATGC
Found at i:4003149 original size:89 final size:89
Alignment explanation
Indices: 4002998--4003176 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
4002988 TAAAGGCTTT
4002998 AAGGGATAGTAAAAGTCTTAGTAAAAATGAGGTAGTCCTAAAAGTGGGCAATGGTGCAAACATTG
1 AAGGGATAGTAAAAGTCTTAGTAAAAATGAGGTAGTCCTAAAAGTGGGCAATGGTGCAAACATTG
4003063 CAGTAGTTGTCGTTGGGACTTGTG
66 CAGTAGTTGTCGTTGGGACTTGTG
4003087 AAGGGATAGTAAAAGTCTTAGTAAAAATGAGGTAGTCCTAAAAGTGGGCAATGGTGCAAACATTG
1 AAGGGATAGTAAAAGTCTTAGTAAAAATGAGGTAGTCCTAAAAGTGGGCAATGGTGCAAACATTG
4003152 CAGTAGTTGTCGTTGGGACTTGTG
66 CAGTAGTTGTCGTTGGGACTTGTG
4003176 A
1 A
4003177 TCTTATTTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (89 bp):
AAGGGATAGTAAAAGTCTTAGTAAAAATGAGGTAGTCCTAAAAGTGGGCAATGGTGCAAACATTG
CAGTAGTTGTCGTTGGGACTTGTG
Found at i:4016747 original size:12 final size:13
Alignment explanation
Indices: 4016730--4016759 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4016720 AGAAGCTCTT
4016730 CTTCTTCTT-CTC
1 CTTCTTCTTCCTC
4016742 CTTCTTCTTCCTC
1 CTTCTTCTTCCTC
4016755 CTTCT
1 CTTCT
4016760 CTCCAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (13 bp):
CTTCTTCTTCCTC
Found at i:4022753 original size:118 final size:120
Alignment explanation
Indices: 4022560--4022795 Score: 352
Period size: 118 Copynumber: 2.0 Consensus size: 120
4022550 TGAGTCAAAT
* * *
4022560 GTTCTAACTAAGCTTGAAAAAGTTAGTTGTTGGGTTTTGGTTGATCCCGAAAAAAAAATCATTGT
1 GTTCTAACTAAGCCTGAAAAAGTTAGTTGTTGGGTTTTGGTTGATCCCCAAAAAAAAACCATTGT
**
4022625 TGAAGGTTGTGGCTGAGCCTGTGAAAAGGTATCGTAAAAGCTTGGTGAAAGCTTAG
66 TGAAGGTTGTGGCTGAGCCTGTG-AAAGCCATCGTAAAAGCTTGGTGAAAGCTTAG
* *
4022681 GTTCTAACTCAGCCT-AAAAA-TTAGTTTTTGGGTTTTGG-TGATCCCCAAAAAAAAACCATTGT
1 GTTCTAACTAAGCCTGAAAAAGTTAGTTGTTGGGTTTTGGTTGATCCCCAAAAAAAAACCATTGT
* **
4022743 TGAAGGTTGTGGTTGAGCCTGTGAAAGCCATTTTAAAAGCTTGGTGAAAGCTT
66 TGAAGGTTGTGGCTGAGCCTGTGAAAGCCATCGTAAAAGCTTGGTGAAAGCTT
4022796 GAGAATTTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
117 26 0.25
118 44 0.42
119 17 0.16
120 5 0.05
121 13 0.12
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (120 bp):
GTTCTAACTAAGCCTGAAAAAGTTAGTTGTTGGGTTTTGGTTGATCCCCAAAAAAAAACCATTGT
TGAAGGTTGTGGCTGAGCCTGTGAAAGCCATCGTAAAAGCTTGGTGAAAGCTTAG
Found at i:4038920 original size:74 final size:73
Alignment explanation
Indices: 4038759--4038899 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 73
4038749 AACCTTTCTA
* *
4038759 CTTAGTTAATTAAGTCATCTCTATCTCTGAACCCAGTTTTTGGCAATAAGCTCTTAGTCGACTAA
1 CTTAGTCAACTAAGTCATCTCTATCTCTGAACCCAGTTTTTGGCAATAAGCTCTTAGTCGACTAA
4038824 CAACGCTT
66 CAACGCTT
* * * * * * * *
4038832 CTTAGTCGATTAAGTCATTTTCTGTCTCTGAATCCAGTTTTTGGTAGTAAGCTCTTTGTCGACTA
1 CTTAGTCAACTAAGTCA-TCTCTATCTCTGAACCCAGTTTTTGGCAATAAGCTCTTAGTCGACTA
4038897 ACA
65 ACA
4038900 TTGTCTCTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 15 0.25
74 44 0.75
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (73 bp):
CTTAGTCAACTAAGTCATCTCTATCTCTGAACCCAGTTTTTGGCAATAAGCTCTTAGTCGACTAA
CAACGCTT
Found at i:4041447 original size:21 final size:19
Alignment explanation
Indices: 4041405--4041450 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
4041395 GGTTTTCCTT
*
4041405 TTTCTTTCTTTTTCTTCGA
1 TTTCTTTCCTTTTCTTCGA
*
4041424 TTTCTGTTCCTTTTCTCTCTA
1 TTTCT-TTCCTTTTCT-TCGA
4041445 TTTCTT
1 TTTCTT
4041451 CCTAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 10 0.43
21 8 0.35
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTCTTTCCTTTTCTTCGA
Found at i:4047697 original size:73 final size:73
Alignment explanation
Indices: 4047615--4047759 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
4047605 CGACTAACCT
* *
4047615 TGCTACTTAGTTAATTAAGTCATCTTTGTCTTTGAATCC-AGTTTCTGGC-AGTAAGCTCTTAGT
1 TGCTACTTAGTCAATTAAGTCATCTTTGTCTCTGAA-CCTAGTTT-TGGCTAGTAAGCTCTTAGT
4047678 CAACTAATAA
64 CAACTAATAA
* * * * *
4047688 TGCTTCTTAGTCGATTAAGTCATTTTTGTCTCTGAACCTAGTTTTTGCTAGTAAGCTCTTAGTCG
1 TGCTACTTAGTCAATTAAGTCATCTTTGTCTCTGAACCTAGTTTTGGCTAGTAAGCTCTTAGTCA
4047753 ACTAATA
66 ACTAATA
4047760 TTGTCTCTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
72 5 0.08
73 58 0.92
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (73 bp):
TGCTACTTAGTCAATTAAGTCATCTTTGTCTCTGAACCTAGTTTTGGCTAGTAAGCTCTTAGTCA
ACTAATAA
Found at i:4047780 original size:73 final size:73
Alignment explanation
Indices: 4047630--4047789 Score: 191
Period size: 73 Copynumber: 2.2 Consensus size: 73
4047620 CTTAGTTAAT
*
4047630 TAAGTCATCTTTGTCTTTGAATCCAGTTTCTGGCAGTAAGCTCTTAGTCAACTAATAATGCTTCT
1 TAAGTCATCTTTGTCTCTGAATCCAGTTTCTGGCAGTAAGCTCTTAGTCAACTAATAATGCTTCT
*
4047695 TAGTCGAT
66 TAGTCGAC
* * * *
4047703 TAAGTCATTTTTGTCTCTGAA-CCTAGTTT-TTGCTAGTAAGCTCTTAGTCGACTAATATTG-TC
1 TAAGTCATCTTTGTCTCTGAATCC-AGTTTCTGGC-AGTAAGCTCTTAGTCAACTAATAATGCT-
*
4047765 TCTTGGTCGAC
63 TCTTAGTCGAC
**
4047776 TAAGTGTTCTTTGT
1 TAAGTCATCTTTGT
4047790 TTCACAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
72 6 0.08
73 68 0.92
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.42
Consensus pattern (73 bp):
TAAGTCATCTTTGTCTCTGAATCCAGTTTCTGGCAGTAAGCTCTTAGTCAACTAATAATGCTTCT
TAGTCGAC
Found at i:4057576 original size:2 final size:2
Alignment explanation
Indices: 4057569--4057599 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4057559 TTTCTTTGTT
*
4057569 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4057600 TGTTGTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4062247 original size:68 final size:67
Alignment explanation
Indices: 4062092--4062282 Score: 251
Period size: 68 Copynumber: 2.8 Consensus size: 67
4062082 CATAGTATAT
* * *
4062092 GAGATAAGAATGAGCACATGATATATACTATGTTGCAATGTACGTGATAAGGATTCGTATACCAT
1 GAGATAAAAATGAGCACATGATGTATGCTATGTTGCAATGTACGTGATAAGGATTCGTATACCAT
4062157 AC
66 AC
* *
4062159 AAGATAAAAATGAGCACATGATGTATGTTATGTTGCAATGTACGTGA-AGAGGATTC-TACATAC
1 GAGATAAAAATGAGCACATGATGTATGCTATGTTGCAATGTACGTGATA-AGGATTCGT--ATAC
4062222 CATAC
63 CATAC
* * * * *
4062227 GAGATAATAATGAGCACATGATGTGTGCTATGTTACAATGTATGTGATAATGATTC
1 GAGATAAAAATGAGCACATGATGTATGCTATGTTGCAATGTACGTGATAAGGATTC
4062283 CACATACTGT
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 2 0.02
67 49 0.45
68 56 0.52
69 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (67 bp):
GAGATAAAAATGAGCACATGATGTATGCTATGTTGCAATGTACGTGATAAGGATTCGTATACCAT
AC
Found at i:4062299 original size:68 final size:68
Alignment explanation
Indices: 4062077--4062289 Score: 250
Period size: 68 Copynumber: 3.1 Consensus size: 68
4062067 GTGATGCTGT
** * * * * *
4062077 TTCCACATAGTATATGAGATAAGAATGAGCACATGATATATACTATGTTGCAATGTACGTGATAA
1 TTCCACATACCATACGAGATAAAAATGAGCACATGATGTATGCTATGTTACAATGTACGTGATAA
4062142 GGA
66 GGA
** * * *
4062145 TT-CGTATACCATACAAGATAAAAATGAGCACATGATGTATGTTATGTTGCAATGTACGTGA-AG
1 TTCCACATACCATACGAGATAAAAATGAGCACATGATGTATGCTATGTTACAATGTACGTGATA-
4062208 AGGA
65 AGGA
* * * *
4062212 TTCTACATACCATACGAGATAATAATGAGCACATGATGTGTGCTATGTTACAATGTATGTGATAA
1 TTCCACATACCATACGAGATAAAAATGAGCACATGATGTATGCTATGTTACAATGTACGTGATAA
*
4062277 TGA
66 GGA
4062280 TTCCACATAC
1 TTCCACATAC
4062290 TGTATGAGAT
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
66 1 0.01
67 55 0.45
68 64 0.53
69 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (68 bp):
TTCCACATACCATACGAGATAAAAATGAGCACATGATGTATGCTATGTTACAATGTACGTGATAA
GGA
Found at i:4073738 original size:26 final size:25
Alignment explanation
Indices: 4073709--4073761 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
4073699 GCAAATTAGG
*
4073709 ATCATGTTATC-ATAATCAAAACTATA
1 ATCATGTTAACGATAA-CAAAAC-ATA
*
4073735 ATCATTTTAACGATAACAAAACATA
1 ATCATGTTAACGATAACAAAACATA
4073760 AT
1 AT
4073762 AAACATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 15 0.62
27 4 0.17
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (25 bp):
ATCATGTTAACGATAACAAAACATA
Found at i:4081683 original size:21 final size:20
Alignment explanation
Indices: 4081648--4081686 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4081638 TAATATGTTA
4081648 TAATAAATGATATAATATAT
1 TAATAAATGATATAATATAT
*
4081668 TAATATAATTATATAATAT
1 TAATA-AATGATATAATAT
4081687 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TAATAAATGATATAATATAT
Found at i:4084320 original size:7 final size:7
Alignment explanation
Indices: 4084308--4084362 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
4084298 TGTAAACTAA
4084308 AAATATT
1 AAATATT
*
4084315 AAATATA
1 AAATATT
4084322 AAACTA-T
1 AAA-TATT
4084329 AATATATT
1 AA-ATATT
4084337 AAATA-T
1 AAATATT
4084343 AAATAATT
1 AAAT-ATT
*
4084351 AAATATG
1 AAATATT
4084358 AAATA
1 AAATA
4084363 CATGATTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.12
7 24 0.60
8 11 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (7 bp):
AAATATT
Found at i:4084320 original size:22 final size:22
Alignment explanation
Indices: 4084301--4084345 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4084291 ATTTATATGT
4084301 AAACTA-AAAATATTAAATATA
1 AAACTATAAAATATTAAATATA
*
4084322 AAACTATAATATATTAAATATA
1 AAACTATAAAATATTAAATATA
4084344 AA
1 AA
4084346 TAATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAACTATAAAATATTAAATATA
Found at i:4089003 original size:7 final size:7
Alignment explanation
Indices: 4088984--4089014 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
4088974 AAACATAAAT
4088984 TAAAAAA
1 TAAAAAA
4088991 TGAAAAAA
1 T-AAAAAA
4088999 TAAAAAA
1 TAAAAAA
4089006 TAAAAAA
1 TAAAAAA
4089013 TA
1 TA
4089015 TATTAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:4089307 original size:16 final size:17
Alignment explanation
Indices: 4089286--4089320 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4089276 AATTATAAAT
*
4089286 AAAATATTCAT-TTTTA
1 AAAATATTAATATTTTA
4089302 AAAATATTAATATTTTA
1 AAAATATTAATATTTTA
4089319 AA
1 AA
4089321 TAAATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAATATTAATATTTTA
Found at i:4091392 original size:16 final size:15
Alignment explanation
Indices: 4091371--4091404 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4091361 GCAACCAAAA
4091371 TTTAGATTTTGATTAT
1 TTTAGATTTTGATT-T
4091387 TTTAGATTTTGATTT
1 TTTAGATTTTGATTT
4091402 TTT
1 TTT
4091405 GGATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (15 bp):
TTTAGATTTTGATTT
Found at i:4091684 original size:12 final size:12
Alignment explanation
Indices: 4091667--4091703 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4091657 TTTCTGATGA
4091667 ACATGTATCGAT
1 ACATGTATCGAT
4091679 ACATGT-TC-AT
1 ACATGTATCGAT
4091689 A-ATGTATCGAT
1 ACATGTATCGAT
4091700 ACAT
1 ACAT
4091704 TTTTCTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:4092855 original size:80 final size:80
Alignment explanation
Indices: 4092722--4093048 Score: 403
Period size: 80 Copynumber: 4.1 Consensus size: 80
4092712 CATGAGTTCT
* * *
4092722 ATTTATGAGATTGT-AACATATATGCCTTGAGATGTATGTGTTAAGTATA-TCATGTACACTATG
1 ATTTATGAGGTTATGAA-ATATATGCCATGAGATGTATGTGTTAAG-ATAGTCATGTACACTATG
4092785 GGCTAAGCATGTAAGTG
64 GGCTAAGCATGTAAGTG
*
4092802 ATTTATGA-GTCTATGAAATATATGCCATGAGATGTATGTGCTAAGTATA-TCATGTACACTATG
1 ATTTATGAGGT-TATGAAATATATGCCATGAGATGTATGTGTTAAG-ATAGTCATGTACACTATG
4092865 GGCTAAGCATGTAAGTG
64 GGCTAAGCATGTAAGTG
* * * * * *
4092882 ATTTATAAGGTTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTTATATACACTATGAG
1 ATTTATGAGGTTATGAAATATATGCCATGAGATGTATGTGTTAAGATAGTCATGTACACTATGGG
*
4092947 TTAAGCATGTAAGTG
66 CTAAGCATGTAAGTG
* * ** **
4092962 ATTTTTGAGGTTATGAAATGTATGCTGTGAGATGTATAAGTTAAGATAGTCATGTACACTATGGG
1 ATTTATGAGGTTATGAAATATATGCCATGAGATGTATGTGTTAAGATAGTCATGTACACTATGGG
* *
4093027 CTAAGTATG-ATGATG
66 CTAAGCATGTAAG-TG
4093042 ATTTATG
1 ATTTATG
4093049 GAAATGTTAT
Statistics
Matches: 216, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
79 6 0.03
80 206 0.95
81 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (80 bp):
ATTTATGAGGTTATGAAATATATGCCATGAGATGTATGTGTTAAGATAGTCATGTACACTATGGG
CTAAGCATGTAAGTG
Found at i:4095591 original size:2 final size:2
Alignment explanation
Indices: 4095584--4095609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4095574 AGTATGTCAC
4095584 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
4095610 GAATGTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4105028 original size:20 final size:22
Alignment explanation
Indices: 4105000--4105044 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4104990 ATTTGTATTT
*
4105000 AAACTTATAAT-ATTAAATATA
1 AAACTTATAATCATAAAATATA
4105021 AAAC-TATAATGCATAAAATATA
1 AAACTTATAAT-CATAAAATATA
4105043 AA
1 AA
4105045 TAGTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 4 0.19
22 11 0.52
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
AAACTTATAATCATAAAATATA
Found at i:4111523 original size:10 final size:11
Alignment explanation
Indices: 4111493--4111523 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4111483 TTTTGAGGAT
4111493 AAATGTTTTTC
1 AAATGTTTTTC
4111504 AAATGTTTTTC
1 AAATGTTTTTC
*
4111515 AATTGTTTT
1 AAATGTTTT
4111524 ATCACTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (11 bp):
AAATGTTTTTC
Found at i:4111568 original size:37 final size:37
Alignment explanation
Indices: 4111506--4111588 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
4111496 TGTTTTTCAA
* * * *
4111506 ATGTTTTTCAATTGTTTTATCACTTTTGGATTTAGA-
1 ATGTTTTTCAATTATATCATAACTTTTGGATTTAGAG
4111542 AGTGTTTTTCAATTATATCATAACTTTTGGATTTAGAG
1 A-TGTTTTTCAATTATATCATAACTTTTGGATTTAGAG
4111580 ATGTTTTTC
1 ATGTTTTTC
4111589 TAATACGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 39 0.95
38 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.53
Consensus pattern (37 bp):
ATGTTTTTCAATTATATCATAACTTTTGGATTTAGAG
Found at i:4111767 original size:36 final size:36
Alignment explanation
Indices: 4111700--4111769 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
4111690 AAATAATCAC
*
4111700 AACTTTTCATATGAAAAAGTATAATTCTTTATTTGT
1 AACTTTTCATATGAAAAAGCATAATTCTTTATTTGT
*
4111736 AACTTTTTATATGAAAATA-CATAACTT-TTTATTT
1 AACTTTTCATATGAAAA-AGCATAA-TTCTTTATTT
4111770 TGAAACGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (36 bp):
AACTTTTCATATGAAAAAGCATAATTCTTTATTTGT
Found at i:4114755 original size:14 final size:14
Alignment explanation
Indices: 4114736--4114763 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4114726 CAATAACAAA
4114736 ATTATATATATAAT
1 ATTATATATATAAT
4114750 ATTATATATATAAT
1 ATTATATATATAAT
4114764 GATAAATTTG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATATATATAAT
Found at i:4118403 original size:14 final size:16
Alignment explanation
Indices: 4118377--4118414 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
4118367 ATTTTTCCCC
4118377 AAATATTTCCCCT-CA
1 AAATATTTCCCCTCCA
4118392 AAATATTT-CCCTCCA
1 AAATATTTCCCCTCCA
4118407 AAATATTT
1 AAATATTT
4118415 GAGAGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATTTCCCCTCCA
Found at i:4118686 original size:30 final size:30
Alignment explanation
Indices: 4118630--4118686 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4118620 TGCATGCCGC
* *
4118630 GCACCTGCGTGCCGCTCGCCCATGCTGTGT
1 GCACCTGCGTGCCGCGCACCCATGCTGTGT
*
4118660 GCACCTGCGTGCCGCGCACCCCTGCTG
1 GCACCTGCGTGCCGCGCACCCATGCTG
4118687 GGCCGGCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.07, C:0.44, G:0.30, T:0.19
Consensus pattern (30 bp):
GCACCTGCGTGCCGCGCACCCATGCTGTGT
Found at i:4120010 original size:250 final size:249
Alignment explanation
Indices: 4119452--4120099 Score: 761
Period size: 250 Copynumber: 2.6 Consensus size: 249
4119442 TAAAGGTATT
* * * * * * *
4119452 TTTACTTTGTTTAAATTGACTTGTTATGGTAATTATCACACATTTACGTCAATATTTTAACAATA
1 TTTATTTTGTTTAAATTGACTTTTTACGGTAACTCTCACTCATTTACGTAAATATTTTAACAAT-
* * *
4119517 CTTATTTCAACTTTATGATTTTTTACATTCATTCTAATCAATTTATGTC-ATGATTTTTAAATGA
65 CTTATTTCAACTTTATGATTTTTTACATTCATTCTTATAAATTTACGTCAAT-ATTTTTAAATGA
* * * * *
4119581 CAATTTTCACTGTAATTATTTTTATCTTTGCTATTATTCATTTATAAATTAATATTTCTAAATAA
129 TAATTTTCACTATAATTATTTTTATCTTTG--ATTATTCATTTATAAAGTAAAATTTATAAATAA
* * *
4119646 TTAATTTCTTTTTGCTTGAGAATATAAATGTAAATGATTAATTTTCACTTAAAATATA
192 TTAATATCATTTTGCTCGAGAATATAAATGTAAATGATTAATTTTCACTTAAAATATA
* * * *
4119704 TTTATTTTGTTTAAATTGACATTTTACGAG-AGCACTCACTCATTTACGTTAATATTTTAACAAT
1 TTTATTTTGTTTAAATTGACTTTTTACG-GTAACTCTCACTCATTTACGTAAATATTTTAACAAT
* * * * *
4119768 GCTTGTTTCAAATTTATGATTTTTCTCATATTCATTCTTATTAGTTTACGTCAATATTTTTAAAT
65 -CTTATTTCAACTTTATGATTTTT-T-ACATTCATTCTTATAAATTTACGTCAATATTTTTAAAT
* *
4119833 GGTTAATTTTCACTATAATTATTTTTAT-TCTTG-TTATTCATTTATAAAGTAAAATTTATATAT
127 -GATAATTTTCACTATAATTATTTTTATCT-TTGATTATTCATTTATAAAGTAAAATTTATAAAT
* * ** *
4119896 GATTAA-AT-ATTTTGCTCGAGAGTATAAATGTAGGTGATTAATTTTCACTTAAAATATG
190 AATTAATATCATTTTGCTCGAGAATATAAATGTAAATGATTAATTTTCACTTAAAATATA
* * *
4119954 TTTATTTTGTTTAAATTGACTTTTTGCGGTAACTCTCACTTATTTATGTAAATATTTTAACAAAT
1 TTTATTTTGTTTAAATTGACTTTTTACGGTAACTCTCACTCATTTACGTAAATATTTTAAC-AAT
* * * *
4120019 TTTATTTCAACTTTATGATTTTTTACATTCATTCTTATAAATTTACATCTAA-AATTTTAAATTA
65 CTTATTTCAACTTTATGATTTTTTACATTCATTCTTATAAATTTACGTC-AATATTTTTAAATGA
4120083 CTAATTTTCACTATAAT
129 -TAATTTTCACTATAAT
4120100 GTTATGGAAT
Statistics
Matches: 336, Mismatches: 50, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
248 46 0.14
249 4 0.01
250 116 0.35
251 4 0.01
252 104 0.31
253 2 0.01
254 31 0.09
255 29 0.09
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (249 bp):
TTTATTTTGTTTAAATTGACTTTTTACGGTAACTCTCACTCATTTACGTAAATATTTTAACAATC
TTATTTCAACTTTATGATTTTTTACATTCATTCTTATAAATTTACGTCAATATTTTTAAATGATA
ATTTTCACTATAATTATTTTTATCTTTGATTATTCATTTATAAAGTAAAATTTATAAATAATTAA
TATCATTTTGCTCGAGAATATAAATGTAAATGATTAATTTTCACTTAAAATATA
Found at i:4125954 original size:40 final size:40
Alignment explanation
Indices: 4125845--4125954 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
4125835 TTTGCTTGAT
* * *
4125845 TGAATGTCTAATGTGGTGATTTAGATTAAATATTATGATA
1 TGAATGTCTAATGTGGTGATTTAGACTAAGTATTAAGATA
*
4125885 TGAATGTCTAATATGGTGATTTAGACTAAGTATTAAG-TA
1 TGAATGTCTAATGTGGTGATTTAGACTAAGTATTAAGATA
4125924 GTGAATGTCTAATGTGGTGATTTAGACTAAG
1 -TGAATGTCTAATGTGGTGATTTAGACTAAG
4125955 ACATTGTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 2 0.03
40 62 0.97
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (40 bp):
TGAATGTCTAATGTGGTGATTTAGACTAAGTATTAAGATA
Found at i:4131612 original size:248 final size:249
Alignment explanation
Indices: 4130727--4131944 Score: 1284
Period size: 248 Copynumber: 4.9 Consensus size: 249
4130717 GTGCTAGCTC
* * *
4130727 ATAAATTAAAATTTGTAAAT-TTGTAAATATTTTTAACTTGAA-AATATAAATGTAAATGATTAA
1 ATAAAGTAAAATTTGTAAATGGT-TAAATATTTTT-AC-TCAAGAATATAAATGTAAATGATTAA
* * * * * *
4130790 TTTTCACAAAAATTATGTTTATTTTGTCTAAATTGACGTTTTAC-GATAACT-TTCAATCATTTA
63 TTTTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAG-TAAGTCTT-ACTCATTTA
* * * * * * *
4130853 TGTCAATATTTTTACAATATTTATTTTAACTTTATTATTTTTTACGTTTATTTTTATAAATTTAT
126 CGTCAATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACATTTATTCTTATAAATTTAC
* ** * * *
4130918 ATTAAGATTTTTAAATGGTTAATTTTCACTCTAATT-TTTTTATCTTTATTATTATTCATTT
191 ATCAAGATTTTTAAATGACTAATTTTCACTATAATTATTTGTATCCTTATTATTA---ATTT
* * ** *
4130979 ATAAATTAAAATTTATAAATATTTAAATATTTTTAACTCAAAAATATAAATGTAAATGATTAATT
1 ATAAAGTAAAATTTGTAAATGGTTAAATATTTTT-ACTCAAGAATATAAATGTAAATGATTAATT
* * * * * * * *
4131044 TTCACAAAAATTATGTTTATTTTGTCTAGATTGA-ATTTT-TA-TATGTCTCT-CGTTTATTTAT
65 TTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAGTCT-TAC--TCATTTAC
* * *
4131105 GTCAATATTCTAACAACATTTATTTCAACTTTATGA-TTTTTA-ATGCTCATTCTTATAAATTTA
127 GTCAATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACAT--TTATTCTTATAAATTTA
*
4131168 CATCAAGATTTTTAAAT-AGCTAATTTTCACTATAATTATTTGTATCCTTATGATTATTTATTT
190 CATCAAGATTTTTAAATGA-CTAATTTTCACTATAATTATTTGTATCC-T-T-ATTATTAATTT
* * * ** *
4131231 ATAAAGTGAAATTTGTAAATGGTTAAATATTTTTTAATCAAGTATATAAATGTAAACAATTGATT
1 ATAAAGTAAAATTTGTAAATGGTTAAATA-TTTTTACTCAAGAATATAAATGTAAATGATTAATT
* * * * *
4131296 TTCACTAAAAGTATGTTTAATTT-TTTAAATTGACATTTCACAGTAAATCTCACTCATTTACATC
65 TTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAGTCTTACTCATTTACGTC
* ** * *
4131360 AATATTTTAACAATACTTATTTCAACTAAATGATTTTTTACATTTATTCTGATAAATTTACGTCA
130 AATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACATTTATTCTTATAAATTTACATCA
* *
4131425 AGA-TTTTAAATGACTAATTTTCTCTATAATTATTTTTATCCTTATTATTAATTT
195 AGATTTTTAAATGACTAATTTTCACTATAATTATTTGTATCCTTATTATTAATTT
* * * *
4131479 ATAAAGAAAAATTTGTAAATGGTCAAATATCTTTTGCTCAAGAATATAAATTTAAATGATTAATT
1 ATAAAGTAAAATTTGTAAATGGTTAAATAT-TTTTACTCAAGAATATAAATGTAAATGATTAATT
* * * ** *
4131544 TTCACTTAAAGCATATTTATTTTGTTTAAATTGAC-TTTTATGGTAAGTCTTACTTATTTACGTC
65 TTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAGTCTTACTCATTTACGTC
** ** *
4131608 AATATTTTAATGATGCTTATTTCAACTTTATGATTTTTTA-AGTTCATTCTTATAAATTTACATC
130 AATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACA-TTTATTCTTATAAATTTACATC
* * *
4131672 GAGATTTTTAAATGACTAATTTTCATTATAATTATTTGTATCTTTATTATTAATTT
194 AAGATTTTTAAATGACTAATTTTCACTATAATTATTTGTATCCTTATTATTAATTT
* * *
4131728 ATAAAGTAAAATTTGTAAATGGTTAAATA-TATTGCTCAAGAATATAAATTTAAATGATTAATTT
1 ATAAAGTAAAATTTGTAAATGGTTAAATATTTTTACTCAAGAATATAAATGTAAATGATTAATTT
* * * * * *
4131792 TCACTTAAAGTATATTTATTTTGTTTAAATTGGCTTTTTACAGTAAGTCTCACTCATTTACATCA
66 TCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAGTCTTACTCATTTACGTCA
* * * * * * *
4131857 ATATATTAATAATATTTATTTGAACTTTTTGATGTTTTACATTTATTCTTATAAATTTA-AGCCC
131 ATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACATTTATTCTTATAAATTTACA-TCA
*
4131921 AGATTTTTAAATGGCTAATTTTCA
195 AGATTTTTAAATGACTAATTTTCA
4131945 TTACAAGTTT
Statistics
Matches: 822, Mismatches: 115, Indels: 62
0.82 0.12 0.06
Matches are distributed among these distances:
247 69 0.08
248 259 0.32
249 91 0.11
250 8 0.01
251 134 0.16
252 231 0.28
253 15 0.02
254 9 0.01
255 6 0.01
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (249 bp):
ATAAAGTAAAATTTGTAAATGGTTAAATATTTTTACTCAAGAATATAAATGTAAATGATTAATTT
TCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAGTCTTACTCATTTACGTCA
ATATTTTAACAATATTTATTTCAACTTTATGATTTTTTACATTTATTCTTATAAATTTACATCAA
GATTTTTAAATGACTAATTTTCACTATAATTATTTGTATCCTTATTATTAATTT
Found at i:4131981 original size:500 final size:500
Alignment explanation
Indices: 4130727--4131983 Score: 1436
Period size: 500 Copynumber: 2.5 Consensus size: 500
4130717 GTGCTAGCTC
* * * *
4130727 ATAAATTAAAATTTGTAAAT-TTGTAAATATTTTTAACTTGAA-AATATAAATGTAAATGATTAA
1 ATAAAGTAAAATTTGTAAATGGT-TAAATATTATTAA--TCAAGAATATAAATGTAAATGATTAA
* * * * * * * *
4130790 TTTTCACAAAAATTATGTTTATTTTGTCTAAATTGACGTTTTAC-GATAACTTTCAATCATTTAT
63 TTTTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAG-TAAATCTCACTCATTTAC
* * * * *
4130854 GTCAATATTTTTACAATATTTATTTTAACTTTATT-ATTTTTTACGTTTATTTTTATAAATTTAT
127 ATCAATATTTTAACAATATTTATTTCAACTTT-TTGATTTTTTACATTTATTCTTATAAATTTA-
* * *
4130918 A-TTAAGATTTTTAAATGGTTAATTTTCACT-CTAATTTTTTTATCTTTATTATTATTCATTTAT
190 AGTCAAGATTTTTAAATGGCTAATTTTCATTAC-AATTTTTTTATCTTTATTATTA--CATTTAT
** * *
4130981 AAATTAAAATTTATAAATATTTAAATATTTTTAACTCAAAAATATAAATGTAAATGATTAATTTT
252 AAAGAAAAATTTATAAATAGTCAAATATTTTTAACTCAAAAATATAAATGTAAATGATTAATTTT
** * * * *
4131046 CACAAAAATTATGTTTATTTTGTCTAGATTGAATTTTTATATGTCTCTCGTTTATTTATGTCAAT
317 CACAAAAAGCATATTTATTTTGTCTAAATTGAATTTTTATAAGTCTCTCG-TTATTTACGTCAAT
*
4131111 ATTCTAACAACATTTATTTCAACTTTATGATTTTTAATGCTCATTCTTATAAATTTACATCAAGA
381 ATTCTAACAACACTTATTTCAACTTTATGATTTTTAATGCTCATTCTTATAAATTTACATCAAGA
*
4131176 TTTTTAAATAGCTAATTTTCACTATAATTATTTGTATCCTTATGATTATTTATTT
446 TTTTTAAATAGCTAATTTTCACTATAATTATTTGTATCCTTATGATTATTAATTT
* * * ** *
4131231 ATAAAGTGAAATTTGTAAATGGTTAAATATTTTTTAATCAAGTATATAAATGTAAACAATTGATT
1 ATAAAGTAAAATTTGTAAATGGTTAAATA-TTATTAATCAAGAATATAAATGTAAATGATTAATT
* *
4131296 TTCACTAAAAGTATGTTTAATTT-TTTAAATTGACATTTCACAGTAAATCTCACTCATTTACATC
65 TTCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAATCTCACTCATTTACATC
* *** * *
4131360 AATATTTTAACAATACTTATTTCAACTAAATGATTTTTTACATTTATTCTGATAAATTTACGTCA
130 AATATTTTAACAATATTTATTTCAACTTTTTGATTTTTTACATTTATTCTTATAAATTTAAGTCA
* * *
4131425 AGA-TTTTAAATGACTAATTTTC-TCTATAATTATTTTTATCCTTATTATTA-ATTTATAAAGAA
195 AGATTTTTAAATGGCTAATTTTCAT-TACAATT-TTTTTATCTTTATTATTACATTTATAAAGAA
* * * * * **
4131487 AAATTTGTAAATGGTCAAATATCTTTT-GCTCAAGAATATAAATTTAAATGATTAATTTTCACTT
258 AAATTTATAAATAGTCAAATAT-TTTTAACTCAAAAATATAAATGTAAATGATTAATTTTCACAA
* * *
4131551 AAAGCATATTTATTTTGTTTAAATTGACTTTTATGGTAAGTCT-TAC-TTATTTACGTCAATATT
322 AAAGCATATTTATTTTGTCTAAATTGAATTTT-T-ATAAGTCTCT-CGTTATTTACGTCAATATT
* ** ** * *
4131614 TTAATGATGCTTATTTCAACTTTATGATTTTTTAA-GTTCATTCTTATAAATTTACATCGAGATT
384 CTAACAACACTTATTTCAACTTTATGA-TTTTTAATGCTCATTCTTATAAATTTACATCAAGATT
*
4131678 TTTAAAT-GACTAATTTTCATTATAATTATTTGTAT-CTT-T-ATTATTAATTT
448 TTTAAATAG-CTAATTTTCACTATAATTATTTGTATCCTTATGATTATTAATTT
** *
4131728 ATAAAGTAAAATTTGTAAATGGTTAAATA-TATTGCTCAAGAATATAAATTTAAATGATTAATTT
1 ATAAAGTAAAATTTGTAAATGGTTAAATATTATTAATCAAGAATATAAATGTAAATGATTAATTT
* * * * *
4131792 TCACTTAAAGTATATTTATTTTGTTTAAATTGGCTTTTTACAGTAAGTCTCACTCATTTACATCA
66 TCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAATCTCACTCATTTACATCA
* * * * * *
4131857 ATATATTAATAATATTTATTTGAACTTTTTGATGTTTTACATTTATTCTTATAAATTTAAGCCCA
131 ATATTTTAACAATATTTATTTCAACTTTTTGATTTTTTACATTTATTCTTATAAATTTAAGTCAA
* *
4131922 GATTTTTAAATGGCTAATTTTCATTACAAGTTTCTTTATTTTTATTAGTCTACATTTATAAA
196 GATTTTTAAATGGCTAATTTTCATTACAA-TTTTTTTATCTTTATTA-T-TACATTTATAAA
4131984 TGGTTTTTTT
Statistics
Matches: 633, Mismatches: 98, Indels: 48
0.81 0.13 0.06
Matches are distributed among these distances:
495 46 0.07
496 93 0.15
497 72 0.11
498 5 0.01
499 6 0.01
500 191 0.30
501 13 0.02
502 30 0.05
503 105 0.17
504 64 0.10
505 8 0.01
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (500 bp):
ATAAAGTAAAATTTGTAAATGGTTAAATATTATTAATCAAGAATATAAATGTAAATGATTAATTT
TCACTAAAAGTATGTTTATTTTGTTTAAATTGACATTTTACAGTAAATCTCACTCATTTACATCA
ATATTTTAACAATATTTATTTCAACTTTTTGATTTTTTACATTTATTCTTATAAATTTAAGTCAA
GATTTTTAAATGGCTAATTTTCATTACAATTTTTTTATCTTTATTATTACATTTATAAAGAAAAA
TTTATAAATAGTCAAATATTTTTAACTCAAAAATATAAATGTAAATGATTAATTTTCACAAAAAG
CATATTTATTTTGTCTAAATTGAATTTTTATAAGTCTCTCGTTATTTACGTCAATATTCTAACAA
CACTTATTTCAACTTTATGATTTTTAATGCTCATTCTTATAAATTTACATCAAGATTTTTAAATA
GCTAATTTTCACTATAATTATTTGTATCCTTATGATTATTAATTT
Found at i:4133970 original size:22 final size:23
Alignment explanation
Indices: 4133928--4133970 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4133918 TTTTTTGTAC
*
4133928 TTGAAAAAAATACTTTATTAATT
1 TTGAAAAAAATAATTTATTAATT
*
4133951 TTGAAAAAATTAATTT-TTAA
1 TTGAAAAAAATAATTTATTAA
4133971 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
TTGAAAAAAATAATTTATTAATT
Found at i:4134020 original size:33 final size:31
Alignment explanation
Indices: 4133955--4134020 Score: 78
Period size: 33 Copynumber: 2.1 Consensus size: 31
4133945 TTAATTTTGA
* * *
4133955 AAAAATTAATTTTTAAATATATATATTTATT
1 AAAAATTAATTTTCAAATATATATAATAATT
*
4133986 AAAAATTAATTTAATCAAATATTTATAATAATT
1 AAAAATTAATTT--TCAAATATATATAATAATT
4134019 AA
1 AA
4134021 GATCAAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.41
33 17 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (31 bp):
AAAAATTAATTTTCAAATATATATAATAATT
Found at i:4142365 original size:21 final size:22
Alignment explanation
Indices: 4142319--4142365 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
4142309 CAGGATGGTT
*
4142319 TTTTGATAGGTTAAATTTTGAA
1 TTTTGATAGGTTAAATTTTAAA
*
4142341 TTTTGATTGGTTAAA-TTTAAA
1 TTTTGATAGGTTAAATTTTAAA
4142362 TTTT
1 TTTT
4142366 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (22 bp):
TTTTGATAGGTTAAATTTTAAA
Found at i:4145117 original size:3 final size:3
Alignment explanation
Indices: 4145109--4145165 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
4145099 TTCAAATATC
4145109 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4145157 ATT ATT ATT
1 ATT ATT ATT
4145166 TTGAATTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4148363 original size:6 final size:6
Alignment explanation
Indices: 4148352--4148376 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4148342 TTAGACATCA
4148352 CTCCAT CTCCAT CTCCAT CTCCAT C
1 CTCCAT CTCCAT CTCCAT CTCCAT C
4148377 CACTTGCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCCAT
Found at i:4154717 original size:23 final size:23
Alignment explanation
Indices: 4154691--4154737 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4154681 AGCATATTGC
4154691 TTGTTAGAATAAAGATCCACTGT
1 TTGTTAGAATAAAGATCCACTGT
4154714 TTGTTAGAATAAAGATCCACTGT
1 TTGTTAGAATAAAGATCCACTGT
4154737 T
1 T
4154738 GCTTCATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (23 bp):
TTGTTAGAATAAAGATCCACTGT
Found at i:4156875 original size:72 final size:72
Alignment explanation
Indices: 4156755--4156893 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
4156745 TCTTTGAAAC
* * * *
4156755 CCATTTCCATTTACATACTTTCAAAATGTCTAAAGTATTTCCAGCATTTAATCATTCTCTTCCTT
1 CCATTTCCATGTACATACTTTCAAAATGTCTAAAGAATTCCCAGCATTTAACCATTCTCTTCCTT
4156820 CCTAAAT
66 CCTAAAT
* *
4156827 CCATTTCCATGTACATACTTTCAAAATGTCTGAAGAATTCCCATCATTTAACCATTCTCTTCCTT
1 CCATTTCCATGTACATACTTTCAAAATGTCTAAAGAATTCCCAGCATTTAACCATTCTCTTCCTT
4156892 CC
66 CC
4156894 CTATACTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.28, C:0.27, G:0.05, T:0.40
Consensus pattern (72 bp):
CCATTTCCATGTACATACTTTCAAAATGTCTAAAGAATTCCCAGCATTTAACCATTCTCTTCCTT
CCTAAAT
Found at i:4176570 original size:25 final size:24
Alignment explanation
Indices: 4176542--4176588 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4176532 TATCTATTGA
* *
4176542 TTGGGAATTTATCTTGATGTTATGG
1 TTGGAAATATATCTTGAT-TTATGG
*
4176567 TTGGAAATATGTCTTGATTTAT
1 TTGGAAATATATCTTGATTTAT
4176589 TGATTGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.49
Consensus pattern (24 bp):
TTGGAAATATATCTTGATTTATGG
Found at i:4181852 original size:17 final size:17
Alignment explanation
Indices: 4181830--4181863 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4181820 CCAGTAGCTT
4181830 TCGATTCTGGGTTAGTA
1 TCGATTCTGGGTTAGTA
4181847 TCGATTCTGGGTTAGTA
1 TCGATTCTGGGTTAGTA
4181864 AAACTACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (17 bp):
TCGATTCTGGGTTAGTA
Found at i:4187908 original size:31 final size:29
Alignment explanation
Indices: 4187867--4187970 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
4187857 TATAGGAACC
*
4187867 AAATTAAACAAAATTGTAAAGTACATAGACT
1 AAATTAAACAAAATT-TATAGTACA-AGACT
* * * * *
4187898 AAATTGAACAAAACTCTATACTATAGGGACT
1 AAATTAAACAAAA-TTTATAGTACA-AGACT
*
4187929 AAATTAAAAAAAATTTATAGTACAAGGACT
1 AAATTAAACAAAATTTATAGTACAA-GACT
*
4187959 AAATTGAACAAA
1 AAATTAAACAAA
4187971 GCTTTGTCGT
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
30 22 0.39
31 33 0.59
32 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (29 bp):
AAATTAAACAAAATTTATAGTACAAGACT
Done.