Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 44 of 113
Found at i:12038188 original size:11 final size:12
Alignment explanation
Indices: 12038155--12038198 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
12038145 TTCAACCCTT
12038155 TAATATATTTTA
1 TAATATATTTTA
*
12038167 TAGTATATTTTA
1 TAATATATTTTA
12038179 TAAT-TATTTTA
1 TAATATATTTTA
12038190 T-ATATATTT
1 TAATATATTT
12038199 AAATTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 13 0.45
12 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TAATATATTTTA
Found at i:12045788 original size:16 final size:15
Alignment explanation
Indices: 12045758--12045791 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12045748 CACATGACAT
12045758 ATATTATTACAAAAA
1 ATATTATTACAAAAA
*
12045773 ATATTTTTATCAAAAA
1 ATATTATTA-CAAAAA
12045789 ATA
1 ATA
12045792 ATAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATTATTACAAAAA
Found at i:12046770 original size:14 final size:14
Alignment explanation
Indices: 12046751--12046778 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12046741 AGCTGAAGGA
12046751 ATCAAAATTTCTTC
1 ATCAAAATTTCTTC
12046765 ATCAAAATTTCTTC
1 ATCAAAATTTCTTC
12046779 TTATATGACA
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:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
ATCAAAATTTCTTC
Found at i:12050204 original size:11 final size:11
Alignment explanation
Indices: 12050164--12050205 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
12050154 AATCTCATAA
12050164 GAGATTTGTTT
1 GAGATTTGTTT
* *
12050175 GTA-ATTTATTA
1 G-AGATTTGTTT
12050186 GAGATTTGTTT
1 GAGATTTGTTT
12050197 GAGATTTGT
1 GAGATTTGT
12050206 CAGATATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12050317 original size:52 final size:52
Alignment explanation
Indices: 12050231--12050361 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 52
12050221 GGACAAGAAG
* * * * * *
12050231 ACTTACAAAAGAAGAATTCTAAGA-GAAAGGAGATTCTTAATAGGT-AAGTTTG
1 ACTTACAAGAGAATAATTCTAAAAGGAAA-AAGATTCTTAATA-ATCAAGTTTA
**
12050283 ACTTGTAAGAGAATAATTCTAAAAGGAAAAAGATTCTTAATAATCAAGTTTA
1 ACTTACAAGAGAATAATTCTAAAAGGAAAAAGATTCTTAATAATCAAGTTTA
*
12050335 ACTTACAAGAGAATAATTCTAAGAGGA
1 ACTTACAAGAGAATAATTCTAAAAGGA
12050362 GAGATTTTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
51 1 0.02
52 61 0.92
53 4 0.06
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (52 bp):
ACTTACAAGAGAATAATTCTAAAAGGAAAAAGATTCTTAATAATCAAGTTTA
Found at i:12050510 original size:13 final size:13
Alignment explanation
Indices: 12050492--12050518 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12050482 GTTTTACGTC
12050492 TTATGGGTGTGTA
1 TTATGGGTGTGTA
12050505 TTATGGGTGTGTA
1 TTATGGGTGTGTA
12050518 T
1 T
12050519 GTTTGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (13 bp):
TTATGGGTGTGTA
Found at i:12058631 original size:16 final size:16
Alignment explanation
Indices: 12058612--12058645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12058602 TCATAAAACT
*
12058612 TATTTATGTTTTGTTA
1 TATTTATGTTTGGTTA
*
12058628 TATTTTTGTTTGGTTA
1 TATTTATGTTTGGTTA
12058644 TA
1 TA
12058646 GTCCCTTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (16 bp):
TATTTATGTTTGGTTA
Found at i:12060971 original size:57 final size:57
Alignment explanation
Indices: 12060883--12061322 Score: 437
Period size: 57 Copynumber: 7.7 Consensus size: 57
12060873 TTTTGTGCAG
* * * * *
12060883 GAAAAATTGATACTTTCAAATTTTTCTCAAAATATTTTTTAGAAATTTTAATCTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAATTTAATTTCAA
* * * *
12060940 GAAAAATTGATACTTTCAATTTTTTCC-CAAAATATCTTTT-GAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAA-CTTTTCCTCAAAATATTTTTTAGAAAATTTAATTTCAA
* **
12060996 GAAAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTGGAAACCTTAATTTCGAA
1 GAAAAATTGATACTTTCAACTTTTCCT-C-AAAATATTTTTTAGAAAATTTAATTTC-AA
* * * *
12061055 -AAAAATTTATACTTTCAACTTTTCCTCAAAA-ATCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATAT-TTTTTAGAAAATTTAATTTCAA
* * * * * *
12061111 GGAAAATTGATACTTTTAACTTTTCCTTAAAA-ACTGTTTTA-AAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATA-TTTTTTAGAAAATTTAATTTCAA
* * * *
12061167 GGAAAATTGATACTTTTAACTTTTCCTCAAAAAATATTTTTTGGAAACTTTAATTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC--AAAATATTTTTTAGAAAATTTAATTTCAA
* * * * * *
12061226 GGAAATTTGATACTTTCAACTTTCCCTCAAAA-ATCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATAT-TTTTTAGAAAATTTAATTTCAA
*
12061283 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTT
12061323 CTTTCTCTTC
Statistics
Matches: 328, Mismatches: 38, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.00
55 4 0.01
56 82 0.25
57 139 0.42
58 59 0.18
59 43 0.13
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAATTTAATTTCAA
Found at i:12061256 original size:172 final size:171
Alignment explanation
Indices: 12060884--12061315 Score: 539
Period size: 171 Copynumber: 2.5 Consensus size: 171
12060874 TTTGTGCAGG
* * ** * * * * **
12060884 AAAAATTGATACTTTCAAATTTTTCTCAAAATAT-TTTTTAGAAATTTTAATCTCGAGAAAAATT
1 AAAAATTTATACTTTCAACTTTCCCTCAAAA-ATCTTTTTTGAAAATTTATTTTTAAGAAAAATT
* * * * * ** *
12060948 GATACTTTCAATTTTTTCC-CAAAATA-TCTTTTGAAACTTTAATTTCGAGAAAAATTGATACTT
65 GATACTTTCAA-CTTTTCCTCAAAA-ACTGTTTTAAAAATTTATTTTTAAGGAAAATTGATACTT
*
12061011 TCAACTTTTCTCCAAAAATATTTTTTGGAAACCTTAATTTCGAA
128 TCAACTTTTCTCAAAAAATATTTTTTGGAAACCTTAATTTCGAA
* *
12061055 AAAAATTTATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAAATTTATTTTTAAGGAAAATTG
1 AAAAATTTATACTTTCAACTTTCCCTCAAAAATCTTTTTTGAAAATTTATTTTTAAGAAAAATTG
* * *
12061120 ATACTTTTAACTTTTCCTTAAAAACTGTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTTA
66 ATACTTTCAACTTTTCCTCAAAAACTGTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCA
*
12061185 ACTTTTCCTCAAAAAATATTTTTTGGAAACTTTAATTTC-AA
131 ACTTTT-CTCAAAAAATATTTTTTGGAAACCTTAATTTCGAA
**
12061226 GGAAATTTGATACTTTCAACTTTCCCTCAAAAATCTTTTTTGAAAATTTATTTTTAAGAAAAATT
1 AAAAATTT-ATACTTTCAACTTTCCCTCAAAAATCTTTTTTGAAAATTTATTTTTAAGAAAAATT
*
12061291 GATACTTTCAACTTTTTCTCAAAAA
65 GATACTTTCAACTTTTCCTCAAAAA
12061316 TATTTTTCTT
Statistics
Matches: 226, Mismatches: 30, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
170 9 0.04
171 111 0.49
172 106 0.47
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (171 bp):
AAAAATTTATACTTTCAACTTTCCCTCAAAAATCTTTTTTGAAAATTTATTTTTAAGAAAAATTG
ATACTTTCAACTTTTCCTCAAAAACTGTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCA
ACTTTTCTCAAAAAATATTTTTTGGAAACCTTAATTTCGAA
Found at i:12061753 original size:17 final size:18
Alignment explanation
Indices: 12061731--12061768 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
12061721 TTTCTTTTTC
12061731 TTTCTTCCTATTT-TCTT
1 TTTCTTCCTATTTCTCTT
*
12061748 TTTCTTCCTCTTTCTCTT
1 TTTCTTCCTATTTCTCTT
12061766 TTT
1 TTT
12061769 TACACTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTCCTATTTCTCTT
Found at i:12064122 original size:23 final size:22
Alignment explanation
Indices: 12064080--12064134 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
12064070 GGGATGAATG
*
12064080 AAAAAAAAAAAAAAAAGAAAGA-
1 AAAAAAAAATAAAAAAGAAA-AT
**
12064102 AGAAAAAAAATAAAACTGAAAAT
1 A-AAAAAAAATAAAAAAGAAAAT
12064125 AAAAAAAAAT
1 AAAAAAAAAT
12064135 CTCTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAAAAAAATAAAAAAGAAAAT
Found at i:12067131 original size:41 final size:42
Alignment explanation
Indices: 12067066--12067148 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 42
12067056 TTAACTATAA
* * *
12067066 TTTTATGAAAAATCTTAGT-TTTTTTTTTATTAAGACTACATT
1 TTTTATGAAAAATCATAGTATTTTTGTATATT-AGACTACATT
* *
12067108 TTTTATG-AAAATGATAGTATTTTTGTATATTATACTACATT
1 TTTTATGAAAAATCATAGTATTTTTGTATATTAGACTACATT
12067149 ATATAGATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (42 bp):
TTTTATGAAAAATCATAGTATTTTTGTATATTAGACTACATT
Found at i:12068477 original size:15 final size:15
Alignment explanation
Indices: 12068457--12068486 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12068447 AAGTATATTG
*
12068457 ATATTATAATACTTT
1 ATATTATAAGACTTT
12068472 ATATTATAAGACTTT
1 ATATTATAAGACTTT
12068487 TGTTATACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATTATAAGACTTT
Found at i:12087391 original size:62 final size:60
Alignment explanation
Indices: 12087254--12087396 Score: 148
Period size: 62 Copynumber: 2.4 Consensus size: 60
12087244 CATTTAACTT
* * * *
12087254 TTAAAGAAATGTAATAATTAATTAATTTTTAAAAAATAATATATAATTACTGCATTTATC
1 TTAAAAAAATGTAATAATTAATTAATTTTAAAAAAATAATATATAATAACTACATTTATC
* * * *
12087314 TT-GAAAAATCATAATATTTGATT-ATTTTAAATAAATTATAATGAT-TAATAACTACATTTATC
1 TTAAAAAAAT-GTAATAATTAATTAATTTTAAA-AAA--ATAAT-ATATAATAACTACATTTATC
12087376 TTAAAAAAATGTAATAATTAA
1 TTAAAAAAATGTAATAATTAA
12087397 GATTTTTTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
59 12 0.18
60 15 0.23
62 30 0.46
63 8 0.12
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (60 bp):
TTAAAAAAATGTAATAATTAATTAATTTTAAAAAAATAATATATAATAACTACATTTATC
Found at i:12089811 original size:24 final size:24
Alignment explanation
Indices: 12089766--12089812 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12089756 TTAAAAATAG
* **
12089766 CAAAAAATAAAAAGAAGCTAAAAT
1 CAAAAAATAAAAAAAAAATAAAAT
12089790 CAAAAAATAAAAAAAAAATAAAA
1 CAAAAAATAAAAAAAAAATAAAA
12089813 AGGGTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (24 bp):
CAAAAAATAAAAAAAAAATAAAAT
Found at i:12090173 original size:17 final size:17
Alignment explanation
Indices: 12090146--12090188 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
12090136 AAATTAATGC
*
12090146 ATTAA-ATAATAAATTT
1 ATTAATATAATAAATAT
*
12090162 ATTAATATAATACATAT
1 ATTAATATAATAAATAT
*
12090179 ATAAATATAA
1 ATTAATATAA
12090189 AATTAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAATATAATAAATAT
Found at i:12090431 original size:7 final size:7
Alignment explanation
Indices: 12090419--12090454 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
12090409 TTTACCTAAT
12090419 TAAAAAA
1 TAAAAAA
12090426 TAAAAAAA
1 T-AAAAAA
12090434 CTAAAAAA
1 -TAAAAAA
12090442 TAAAAAA
1 TAAAAAA
12090449 TAAAAA
1 TAAAAA
12090455 GAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 12 0.44
9 1 0.04
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:12098717 original size:11 final size:11
Alignment explanation
Indices: 12098701--12098725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12098691 ATTCAGTTTG
12098701 TTTTTTCTTTT
1 TTTTTTCTTTT
12098712 TTTTTTCTTTT
1 TTTTTTCTTTT
12098723 TTT
1 TTT
12098726 CAAAGTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:12099874 original size:18 final size:18
Alignment explanation
Indices: 12099851--12099887 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12099841 TTTTTATCAT
*
12099851 CCTCTTATAATAGGGTGA
1 CCTCTTATAATAGGATGA
*
12099869 CCTCTTGTAATAGGATGA
1 CCTCTTATAATAGGATGA
12099887 C
1 C
12099888 TTTAGAGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (18 bp):
CCTCTTATAATAGGATGA
Found at i:12103519 original size:22 final size:22
Alignment explanation
Indices: 12103494--12103536 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12103484 GTATATATAC
* *
12103494 AATAAATAATTAAGCAAATATG
1 AATAAATAAATAAACAAATATG
12103516 AATAAATAAATAAACAAATAT
1 AATAAATAAATAAACAAATAT
12103537 ACACAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (22 bp):
AATAAATAAATAAACAAATATG
Found at i:12104198 original size:24 final size:24
Alignment explanation
Indices: 12104125--12104202 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
12104115 GATAAAATTA
*
12104125 TTATTGTTTATTTAAAAATATATTTT
1 TTATTTTTTATTTAAAAA-A-ATTTT
* * *** *
12104151 TTATCTTTTATTGAAGGGATTTTT
1 TTATTTTTTATTTAAAAAAATTTT
12104175 TTATTTTTTATTTAAAAAAATTTT
1 TTATTTTTTATTTAAAAAAATTTT
12104199 TTAT
1 TTAT
12104203 AAGAATATAT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
24 26 0.67
25 1 0.03
26 12 0.31
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (24 bp):
TTATTTTTTATTTAAAAAAATTTT
Found at i:12104779 original size:21 final size:21
Alignment explanation
Indices: 12104755--12104810 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
12104745 AAAAAAACCT
*
12104755 AGATTTCT-TCAAACTTTCCCC
1 AGATTTCTCCCAAA-TTTCCCC
*
12104776 AGATTTCTCCCAAATTTGCCC
1 AGATTTCTCCCAAATTTCCCC
*
12104797 AGATTACTCCCAAA
1 AGATTTCTCCCAAA
12104811 ATCTTCCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (21 bp):
AGATTTCTCCCAAATTTCCCC
Found at i:12105226 original size:5 final size:5
Alignment explanation
Indices: 12105201--12105260 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 5
12105191 AAAACAAGTA
*
12105201 ATAAT AATAAT AATAAT ATAAC ATAAT ATAAT ATAAT GATAAT GATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT
*
12105250 GATAAC ATAAT
1 -ATAAT ATAAT
12105261 GTACTAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
5 22 0.45
6 27 0.55
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (5 bp):
ATAAT
Found at i:12105460 original size:26 final size:26
Alignment explanation
Indices: 12105426--12105498 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
12105416 AGCCTACTAG
*
12105426 ACACCAATGGGCCTAATTGGGCCTAA
1 ACACAAATGGGCCTAATTGGGCCTAA
* * * *
12105452 ACACTAATGGGCTTACTTGGGCCTGA
1 ACACAAATGGGCCTAATTGGGCCTAA
*
12105478 ACACAAATGGTCCTAATTGGG
1 ACACAAATGGGCCTAATTGGG
12105499 TTCAAACACC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (26 bp):
ACACAAATGGGCCTAATTGGGCCTAA
Found at i:12105526 original size:19 final size:19
Alignment explanation
Indices: 12105502--12105558 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
12105492 AATTGGGTTC
12105502 AAACACCAATGAGCCTACT
1 AAACACCAATGAGCCTACT
*
12105521 AAACACCAATGAACCTACT
1 AAACACCAATGAGCCTACT
*
12105540 AGACACCAAT-AGGCCTACT
1 AAACACCAATGA-GCCTACT
12105559 TGGGCTCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 1 0.03
19 33 0.97
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (19 bp):
AAACACCAATGAGCCTACT
Found at i:12108696 original size:16 final size:16
Alignment explanation
Indices: 12108675--12108710 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
12108665 ATTGGAATAG
12108675 AAAAAGAA-AGCAAAAA
1 AAAAAGAACAG-AAAAA
12108691 AAAAAGAACAGAAAAA
1 AAAAAGAACAGAAAAA
12108707 AAAA
1 AAAA
12108711 TGAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAGAACAGAAAAA
Found at i:12108734 original size:13 final size:13
Alignment explanation
Indices: 12108716--12108767 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
12108706 AAAAATGAAT
12108716 AATAATAATAAAA
1 AATAATAATAAAA
12108729 AATAATAATATAACA
1 AATAATAATA-AA-A
*
12108744 TAAT-ATAATATAA
1 -AATAATAATAAAA
*
12108757 AATAATGATAA
1 AATAATAATAA
12108768 TGATAACATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.09
13 16 0.50
14 3 0.09
15 7 0.22
16 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:12108751 original size:15 final size:16
Alignment explanation
Indices: 12108733--12108780 Score: 71
Period size: 15 Copynumber: 3.0 Consensus size: 16
12108723 ATAAAAAATA
12108733 ATAATATAACATAAT-
1 ATAATATAACATAATG
*
12108748 ATAATATAAAATAATG
1 ATAATATAACATAATG
12108764 ATAATGATAACATAATG
1 ATAAT-ATAACATAATG
12108781 TACTAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 5 0.17
17 10 0.34
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (16 bp):
ATAATATAACATAATG
Found at i:12108946 original size:45 final size:45
Alignment explanation
Indices: 12108891--12108978 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
12108881 TTGAGCCCAA
* *
12108891 ACACAAATGGGCCTAATTGGGTCC-GGACACTAATGAGCCTACTAG
1 ACACAAATGGGCCTAATTGGG-CCTAGACACCAATGAGCCTACTAG
* * * *
12108936 ACACCAATGGGCTTACTTGGGCCTAGACACCAATGGGCCTACT
1 ACACAAATGGGCCTAATTGGGCCTAGACACCAATGAGCCTACT
12108979 TGGGCTCAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (45 bp):
ACACAAATGGGCCTAATTGGGCCTAGACACCAATGAGCCTACTAG
Found at i:12108966 original size:26 final size:25
Alignment explanation
Indices: 12108932--12108996 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
12108922 AATGAGCCTA
*
12108932 CTAGACACCAATGGGCTTACTTGGG
1 CTAGACACCAATGGGCCTACTTGGG
12108957 CCTAGACACCAATGGGCCTACTTGGG
1 -CTAGACACCAATGGGCCTACTTGGG
*
12108983 CTCAGACACAAATG
1 CT-AGACACCAATG
12108997 AGTGTCATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 2 0.06
26 34 0.94
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (25 bp):
CTAGACACCAATGGGCCTACTTGGG
Found at i:12113728 original size:5 final size:5
Alignment explanation
Indices: 12113709--12113743 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12113699 GAAAAATTAA
* *
12113709 AAAAA AAAAC AAAAC AAAAC AAGAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
12113744 TTAAAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:12114528 original size:128 final size:127
Alignment explanation
Indices: 12114182--12114526 Score: 396
Period size: 129 Copynumber: 2.7 Consensus size: 127
12114172 TATCTTTTAT
* * *
12114182 TAAAATATTTTTAGCATTACTTTATAGAAATTTGACATGTGGCATTTTATTTAAAAATTATTATA
1 TAAAATATTTTTATCATTAGTTTATA-AAATTTGACATGTAGCATTTTATTT-AAAATTATTATA
* *
12114247 ATATTCCTATTAAATTACATGTTAAATTTTAACATAATATAAAATCAGCTACATATTAAATTAC
64 ATATTCTTATTAAATTACATATTAAATTTTAACATAATATAAAATCAGCTACATATTAAATTAC
* * ** * *
12114311 TAAAATATTTTTGTCATT-GTTTCATAAAAATTTGATATGTAGTTTTTTGTTTAAAATTGACTAT
1 TAAAATATTTTTATCATTAGTTT-AT-AAAATTTGACATGTAGCATTTTATTTAAAATT-ATTAT
* * * * **
12114375 AATATCCTTATTAAATTACATATTAAATTTTAACATAGTATAAAATTA-TTATGTATTAAATTAC
63 AATATTCTTATTAAATTACATATTAAATTTTAACATAATATAAAATCAGCTACATATTAAATTAC
** * *
12114439 TAAAATACCTTTATCATTAGTTTATGAAAATTTGACATAT-G-ATATT-TTTAAAATTATTATAA
1 TAAAATATTTTTATCATTAGTTTAT-AAAATTTGACATGTAGCATTTTATTTAAAATTATTATAA
*
12114501 TATTCTTATTAAATTATATA-TAAATT
65 TATTCTTATTAAATTACATATTAAATT
12114527 AATTACATAT
Statistics
Matches: 184, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
123 6 0.03
124 24 0.13
125 9 0.05
126 3 0.02
127 1 0.01
128 51 0.28
129 89 0.48
130 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (127 bp):
TAAAATATTTTTATCATTAGTTTATAAAATTTGACATGTAGCATTTTATTTAAAATTATTATAAT
ATTCTTATTAAATTACATATTAAATTTTAACATAATATAAAATCAGCTACATATTAAATTAC
Found at i:12114536 original size:15 final size:15
Alignment explanation
Indices: 12114512--12114551 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
12114502 ATTCTTATTA
*
12114512 AATTATATATAAATT
1 AATTACATATAAATT
*
12114527 AATTACATATAACTT
1 AATTACATATAAATT
*
12114542 AACTACATAT
1 AATTACATAT
12114552 TAAAAGACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTACATATAAATT
Found at i:12114880 original size:25 final size:23
Alignment explanation
Indices: 12114827--12114880 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
12114817 AAATATATTT
* *
12114827 AAAATAATAAAAATTTTGATAAT
1 AAAATAATAAAAATTTTGACAAA
*
12114850 ATAATAATAAAATAATTTTGACAAA
1 AAAATAAT-AAA-AATTTTGACAAA
12114875 AAAATA
1 AAAATA
12114881 GTTTAACCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 15 0.60
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAATAATAAAAATTTTGACAAA
Found at i:12120717 original size:13 final size:13
Alignment explanation
Indices: 12120699--12120724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12120689 CAACCACATA
12120699 GTCCAAATTCATG
1 GTCCAAATTCATG
12120712 GTCCAAATTCATG
1 GTCCAAATTCATG
12120725 ATTCCACGTA
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GTCCAAATTCATG
Found at i:12121903 original size:7 final size:7
Alignment explanation
Indices: 12121893--12121924 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
12121883 AATAAAATAC
12121893 AAATTAA
1 AAATTAA
12121900 AAATTAA
1 AAATTAA
12121907 AAATTAA
1 AAATTAA
12121914 AAATTATA
1 AAATTA-A
12121922 AAA
1 AAA
12121925 CATATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:12123055 original size:24 final size:24
Alignment explanation
Indices: 12123023--12123069 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12123013 GAAAATAAAA
12123023 TTATATGTTAAATGAATAAATAAT
1 TTATATGTTAAATGAATAAATAAT
* *
12123047 TTATATGTTAAATTATTAAATAA
1 TTATATGTTAAATGAATAAATAA
12123070 ATAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TTATATGTTAAATGAATAAATAAT
Found at i:12123085 original size:31 final size:32
Alignment explanation
Indices: 12123030--12123090 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
12123020 AAATTATATG
*
12123030 TTAAATGAATAAATAATTTATATGTTAAATTA
1 TTAAATAAATAAATAATTTATATGTTAAATTA
12123062 TTAAATAAATAAATAA-TTATATGTTAAAT
1 TTAAATAAATAAATAATTTATATGTTAAAT
12123091 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (32 bp):
TTAAATAAATAAATAATTTATATGTTAAATTA
Found at i:12124277 original size:28 final size:28
Alignment explanation
Indices: 12124231--12124306 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
12124221 TTTATTTTAA
* * *
12124231 ATAAATAAATTATTTATTTATGTAACCT
1 ATAAATTATTTATTTATTTATGTAACAT
* *
12124259 ATGAATTATTT-TTGTATTTATTTAACAT
1 ATAAATTATTTATT-TATTTATGTAACAT
*
12124287 GTAAATTATTTATTTATTTA
1 ATAAATTATTTATTTATTTA
12124307 ACATATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (28 bp):
ATAAATTATTTATTTATTTATGTAACAT
Found at i:12124305 original size:24 final size:24
Alignment explanation
Indices: 12124236--12124315 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
12124226 TTTAAATAAA
*
12124236 TAAATTATTTATTTATGTAACCTATG
1 TAAATTATTTATTTATTTAA-C-ATG
*
12124262 -AATTATTTTTGTATTTATTTAACATG
1 TAA--ATTATT-TATTTATTTAACATG
*
12124288 TAAATTATTTATTTATTTAACATA
1 TAAATTATTTATTTATTTAACATG
12124312 TAAA
1 TAAA
12124316 AATAACTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 18 0.39
25 7 0.15
26 3 0.07
27 8 0.17
28 10 0.22
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (24 bp):
TAAATTATTTATTTATTTAACATG
Found at i:12130791 original size:24 final size:24
Alignment explanation
Indices: 12130759--12130805 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12130749 GAAAATAAAA
12130759 TTATATGTTAAATGAATAAATAAT
1 TTATATGTTAAATGAATAAATAAT
* *
12130783 TTATATGTTAAATTATTAAATAA
1 TTATATGTTAAATGAATAAATAA
12130806 ATAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TTATATGTTAAATGAATAAATAAT
Found at i:12130821 original size:31 final size:32
Alignment explanation
Indices: 12130766--12130826 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
12130756 AAATTATATG
*
12130766 TTAAATGAATAAATAATTTATATGTTAAATTA
1 TTAAATAAATAAATAATTTATATGTTAAATTA
12130798 TTAAATAAATAAATAA-TTATATGTTAAAT
1 TTAAATAAATAAATAATTTATATGTTAAAT
12130827 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (32 bp):
TTAAATAAATAAATAATTTATATGTTAAATTA
Found at i:12131072 original size:22 final size:22
Alignment explanation
Indices: 12131038--12131111 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
12131028 AATATCCACT
*
12131038 ATTTTTGAGATATTTATATTTTA
1 ATTTTTTA-ATATTTATATTTTA
12131061 ATTTTTTAATATTTATAATATTTGA
1 ATTTTTTAATATTTAT-AT-TTT-A
* * *
12131086 ATTTTTTAA-ATATCTATTTAA
1 ATTTTTTAATATTTATATTTTA
12131107 ATTTT
1 ATTTT
12131112 AATATTACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 6 0.14
22 10 0.23
23 11 0.25
24 7 0.16
25 10 0.23
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTTTTTAATATTTATATTTTA
Found at i:12131081 original size:9 final size:8
Alignment explanation
Indices: 12131053--12131117 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
12131043 TGAGATATTT
12131053 ATATTTTA
1 ATATTTTA
*
12131061 ATTTTTTA
1 ATATTTTA
12131069 ATATTTATA
1 ATATTT-TA
*
12131078 ATATTTGA
1 ATATTTTA
*
12131086 ATTTTTTAA
1 ATATTTT-A
12131095 ATATCTATTTA
1 ATA--T-TTTA
12131106 A-ATTTTA
1 ATATTTTA
12131113 ATATT
1 ATATT
12131118 ACAATTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.11
8 22 0.49
9 11 0.24
10 1 0.02
11 3 0.07
12 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (8 bp):
ATATTTTA
Found at i:12132021 original size:24 final size:24
Alignment explanation
Indices: 12131957--12132030 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
12131947 TAAAATAAAT
* *
12131957 AAATTATTTATTTATGTAGCCTATGA
1 AAATTATTTATTTATTTA-AC-ATGA
* *
12131983 ATTATTTTTGTATTTATTTAACATGA
1 A-AATTATT-TATTTATTTAACATGA
12132009 AAATTATTTATTTATTTAACAT
1 AAATTATTTATTTATTTAACAT
12132031 ATAAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 14 0.35
25 5 0.12
26 6 0.15
27 6 0.15
28 9 0.22
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (24 bp):
AAATTATTTATTTATTTAACATGA
Found at i:12136119 original size:196 final size:198
Alignment explanation
Indices: 12135730--12136140 Score: 433
Period size: 196 Copynumber: 2.1 Consensus size: 198
12135720 AGAATTATTT
* * * * * ** *
12135730 ATTACAATTTTTTT-AAAATATGTAAAAAGCTTAATTATTATTACGTTTTTTTTTAAATAAATAC
1 ATTATAATTTTTTTAAAAACATATAAAAAACTTAATTATTATTAC-TATTTTTGAAAATAAACAC
* * * *
12135794 AATAATTGATTATTATAATTTATTTAAAATAGTTAAATATTACATTTTAAAAAATTAAATATAGT
65 AATAATTGATTATTATAAGTTATTTAAAATAGTTAAATAATACATTTTAAAAAATTAAATACAAT
* * * * *
12135859 AATTGTTTTTTGTAATTTTTAAAATAATCAATTATTATATTTATTTGAAACAAAAAGGAGTAATT
130 AATTGTTTATTGGAATTTTTAAAATAATCAATTAGTATATTTATTTAAAACAAAAAGCAGTAATT
*
12135924 GTAC
195 ATAC
* *
12135928 ATTATAATTTTTTTAAAAACATATAAAAAATTTAATTATTA-TA-TATTTTTGAAAATAAACGCA
1 ATTATAATTTTTTTAAAAACATATAAAAAACTTAATTATTATTACTATTTTTGAAAATAAACACA
* * ** *
12135991 ATAATTGATTATTGTAAGTTATTTAAAATA-TTCAAATAATGCATTTT-TTAAGTTAAATACAAT
66 ATAATTGATTATTATAAGTTATTTAAAATAGTT-AAATAATACATTTTAAAAAATTAAATACAAT
* * * **
12136054 AATTGTTTATTGGAATTTTTTGAAAATAATCGATTGGT-TCTTT-TTTAAAAGTTAAAAGCAGTA
130 AATTGTTTATTGGAA-TTTTT-AAAATAATCAATTAGTATATTTATTTAAAA-CAAAAAGCAGTA
**
12136117 ATTATTT
192 ATTATAC
12136124 ATTATAA-TTTTTTAAAA
1 ATTATAATTTTTTTAAAA
12136141 TATGTGTATA
Statistics
Matches: 176, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
195 42 0.24
196 84 0.48
197 13 0.07
198 15 0.09
199 22 0.12
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (198 bp):
ATTATAATTTTTTTAAAAACATATAAAAAACTTAATTATTATTACTATTTTTGAAAATAAACACA
ATAATTGATTATTATAAGTTATTTAAAATAGTTAAATAATACATTTTAAAAAATTAAATACAATA
ATTGTTTATTGGAATTTTTAAAATAATCAATTAGTATATTTATTTAAAACAAAAAGCAGTAATTA
TAC
Found at i:12147425 original size:28 final size:28
Alignment explanation
Indices: 12147347--12147427 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 28
12147337 ACAAAATCAT
* * *
12147347 CACTTATAAGATTTCAACCAATCTTTTG
1 CACTTGTAAGATTTCAAACAATCATTTG
* *
12147375 CCCTTGTAA-AATTCAAACAATCATTTG
1 CACTTGTAAGATTTCAAACAATCATTTG
12147402 CACTTGTAAGATTTCAAACAATCATT
1 CACTTGTAAGATTTCAAACAATCATT
12147428 CTTAACCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (28 bp):
CACTTGTAAGATTTCAAACAATCATTTG
Found at i:12147910 original size:26 final size:27
Alignment explanation
Indices: 12147881--12147944 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
12147871 CAAAGAATCT
*
12147881 ATTGAATCATTGA-TACTT-CAAAATTC
1 ATTGAATCATTAACTA-TTCCAAAATTC
* *
12147907 ATTGAAACTTTAACTATTCCAAAATTC
1 ATTGAATCATTAACTATTCCAAAATTC
*
12147934 ATCGAATCATT
1 ATTGAATCATT
12147945 TATTTGTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (27 bp):
ATTGAATCATTAACTATTCCAAAATTC
Found at i:12148972 original size:16 final size:16
Alignment explanation
Indices: 12148951--12148990 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12148941 ACCATTAAAA
*
12148951 ATCATCGTAAATCATC
1 ATCATCATAAATCATC
12148967 ATCATCATAAATCATC
1 ATCATCATAAATCATC
*
12148983 ATTATCAT
1 ATCATCAT
12148991 TGGTTTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
ATCATCATAAATCATC
Found at i:12154364 original size:16 final size:16
Alignment explanation
Indices: 12154339--12154369 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12154329 TGAAAAGGTT
12154339 AAAGGCTTAACCCAAA
1 AAAGGCTTAACCCAAA
*
12154355 AAAGGTTTAACCCAA
1 AAAGGCTTAACCCAA
12154370 CAACATTTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAGGCTTAACCCAAA
Found at i:12155511 original size:20 final size:19
Alignment explanation
Indices: 12155476--12155516 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12155466 GATACATTTG
*
12155476 GATAAAAAATTTAATTATT
1 GATAAAAAAATTAATTATT
*
12155495 GATAAATAAAATTAATTTTT
1 GATAAA-AAAATTAATTATT
12155515 GA
1 GA
12155517 ATTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
GATAAAAAAATTAATTATT
Found at i:12160892 original size:18 final size:18
Alignment explanation
Indices: 12160871--12160924 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
12160861 TTAAATGTTG
12160871 AAAAAAAAAT-AATTTTT
1 AAAAAAAAATGAATTTTT
*
12160888 AAAAAAATATGAATTTTT
1 AAAAAAAAATGAATTTTT
* * *
12160906 AAGAAAAGATAAATTTTT
1 AAAAAAAAATGAATTTTT
12160924 A
1 A
12160925 TAATATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
AAAAAAAAATGAATTTTT
Found at i:12162010 original size:34 final size:34
Alignment explanation
Indices: 12161960--12162044 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
12161950 GTTGTGTATT
** *
12161960 TTTTTATGCTAATGTGATTTTTTTACCTTATGAA
1 TTTTTATGCTCTTGTGATTTTTATACCTTATGAA
* * *
12161994 TTTTTATTCTCTTGTGATTTTTATGCCTTGTGAA
1 TTTTTATGCTCTTGTGATTTTTATACCTTATGAA
*
12162028 TTTTTATGCTTTTGTGA
1 TTTTTATGCTCTTGTGA
12162045 ACAATGCTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (34 bp):
TTTTTATGCTCTTGTGATTTTTATACCTTATGAA
Found at i:12162042 original size:18 final size:18
Alignment explanation
Indices: 12161960--12162045 Score: 81
Period size: 17 Copynumber: 5.0 Consensus size: 18
12161950 GTTGTGTATT
**
12161960 TTTTTATGCTAATGTG-A
1 TTTTTATGCTCTTGTGAA
* * *
12161977 TTTTTTTAC-CTTATGAA
1 TTTTTATGCTCTTGTGAA
*
12161994 TTTTTATTCTCTTGTG-A
1 TTTTTATGCTCTTGTGAA
12162011 TTTTTATGC-CTTGTGAA
1 TTTTTATGCTCTTGTGAA
*
12162028 TTTTTATGCTTTTGTGAA
1 TTTTTATGCTCTTGTGAA
12162046 CAATGCTGAC
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
16 9 0.16
17 34 0.62
18 12 0.22
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (18 bp):
TTTTTATGCTCTTGTGAA
Found at i:12162109 original size:18 final size:18
Alignment explanation
Indices: 12162058--12162109 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
12162048 ATGCTGACAA
12162058 TGCCTTGTG-ATTTTTTT
1 TGCCTTGTGAATTTTTTT
*
12162075 TG-CTAATGTGATTTTTTTTT
1 TGCCT--TGTGA-ATTTTTTT
12162095 TGCCTTGTGAATTTT
1 TGCCTTGTGAATTTT
12162110 ATTCTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 8 0.29
19 5 0.18
20 9 0.32
21 2 0.07
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (18 bp):
TGCCTTGTGAATTTTTTT
Found at i:12162138 original size:107 final size:107
Alignment explanation
Indices: 12161959--12162304 Score: 376
Period size: 107 Copynumber: 3.1 Consensus size: 107
12161949 TGTTGTGTAT
* *
12161959 TTTTTTATGCTAATGTGA-TTTTTTTACCTTATGAATTTTTATTCTCTTGTGATTTTTATGCCTT
1 TTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTTATTCTC---TGATTTTTATGCCTT
12162023 GTGAATTTTTATGCTTTTGTGAACAATG-CTGACAATGCCTTGTGA
63 GTGAATTTTTATGCTTTTGTGAACAATGTC-GACAATGCCTTGTGA
* *
12162068 TTTTTTTTGCTAATGTGATTTTTTTTTTGCCTTGTGAA-TTTTATTCTCT-ATTTTTATACCTTG
1 TTTTTTATGCTAATGTGA--TTTTTTTTGCCTTGTGAATTTTTATTCTCTGATTTTTATGCCTTG
* ** *
12162131 TAAATTTTTATGCCCTTGTGAACAATGTCGAGCAATGTCTTGTGA
64 TGAATTTTTATGCTTTTGTGAACAATGTCGA-CAATGCCTTGTGA
* ** * * *
12162176 TTTTTTATACTAACATGATTTTATTTGCCTAGTGAATTTTTGATCTCTTGTGATTTTTCATGCCT
1 TTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTT-AT-TC-TCTGATTTTT-ATGCCT
* ** * *
12162241 TTTGAATTCATATTACTTTAGTGAACAATGTCGAACAATGCCTTGTGA
62 TGTGAATTTTTA-TGCTTTTGTGAACAATGTCG-ACAATGCCTTGTGA
12162289 TTTTTTATGCTAATGT
1 TTTTTTATGCTAATGT
12162305 AAAAGTTTGA
Statistics
Matches: 196, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
106 16 0.08
107 43 0.22
108 30 0.15
109 19 0.10
110 2 0.01
111 16 0.08
112 28 0.14
113 41 0.21
114 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (107 bp):
TTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTTATTCTCTGATTTTTATGCCTTGTG
AATTTTTATGCTTTTGTGAACAATGTCGACAATGCCTTGTGA
Found at i:12167704 original size:61 final size:60
Alignment explanation
Indices: 12167646--12167772 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 60
12167636 CAATAATTGA
* *
12167646 TTATTGTAAGTTATTT-AAAATATTCAAATAATGCATTTTTTAAGTTAAATACAGTAATTAT
1 TTATTGGAA-TTATTTGAAAATAATCAAATAATGCATTTTTTAAGTTAAA-ACAGTAATTAT
* * * ** *
12167707 TTATTGGAATTTTTTGAAAATAATCGATTGGTGCTTTTTTTAAGTTAAAAGCAGTAATTAT
1 TTATTGGAATTATTTGAAAATAATCAAATAATGCATTTTTTAAGTTAAAA-CAGTAATTAT
12167768 TTATT
1 TTATT
12167773 ATAATTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 6 0.11
61 50 0.89
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (60 bp):
TTATTGGAATTATTTGAAAATAATCAAATAATGCATTTTTTAAGTTAAAACAGTAATTAT
Found at i:12167776 original size:193 final size:194
Alignment explanation
Indices: 12167375--12167782 Score: 486
Period size: 194 Copynumber: 2.1 Consensus size: 194
12167365 TAAAAATAAG
* * *
12167375 AATTATTTATTATAAATTTTTTAAAATATGTAAAAAGCTTAATTATTACGTTTTTTTAAAATAAA
1 AATTATTTATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTTTTTAAAATAAA
* * * *
12167440 TACAATAATTGATTATTATAATTTATTTAAAATAATTAAATACTGCATTTTAAAAAATTAAATAT
66 CACAATAATTGATTATTATAAGTTATTTAAAATAATTAAATAATGCATTTTAAAAAATTAAATAC
* * * * *
12167505 AGTAATTGTTTTTTGTAATTTTTAAAATAATCAATTATTATGTTTATTTGAAACAAAAAGGAGT
131 AGTAATTATTTATTGGAATTTTTAAAATAATCAATTATGATGTTTATTTGAAACAAAAAGCAGT
* ** * *
12167569 AATTGTACATTATAATTTTTTTAAAACATATAAAAA-TTTAATTATTATGTTTTTTTGAAAATAA
1 AATTATTTATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTTTTT-AAAATAA
* ** *
12167633 ACACAATAATTGATTATTGTAAGTTATTTAAAAT-ATTCAAATAATGCATTTT-TTAAGTTAAAT
65 ACACAATAATTGATTATTATAAGTTATTTAAAATAATT-AAATAATGCATTTTAAAAAATTAAAT
* * * ***
12167696 ACAGTAATTATTTATTGGAATTTTTTGAAAATAATCGA-T-TGGTGCTTT-TTTTAAGTTAAAAG
129 ACAGTAATTATTTATTGGAA-TTTTT-AAAATAATCAATTATGATG-TTTATTTGAAACAAAAAG
12167758 CAGT
191 CAGT
12167762 AATTATTTATTATAATTTTTT
1 AATTATTTATTATAATTTTTT
12167783 AAATATGTGT
Statistics
Matches: 179, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
193 79 0.44
194 90 0.50
195 10 0.06
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (194 bp):
AATTATTTATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTTTTTAAAATAAA
CACAATAATTGATTATTATAAGTTATTTAAAATAATTAAATAATGCATTTTAAAAAATTAAATAC
AGTAATTATTTATTGGAATTTTTAAAATAATCAATTATGATGTTTATTTGAAACAAAAAGCAGT
Found at i:12181201 original size:16 final size:16
Alignment explanation
Indices: 12181164--12181194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12181154 CATTAAAAAT
*
12181164 CATCGTAAATCATCAG
1 CATCATAAATCATCAG
12181180 CATCATAAATCATCA
1 CATCATAAATCATCA
12181195 TTATCATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
CATCATAAATCATCAG
Found at i:12184396 original size:28 final size:28
Alignment explanation
Indices: 12184320--12184400 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 28
12184310 ACAAAATCAT
* * * *
12184320 CACTTATAAGATTTCAACCAATCTTTTG
1 CACTTGTAAGATTTCAAACAATCATTTA
* *
12184348 CCCTTGTAA-AATTCAAACAATCATTTA
1 CACTTGTAAGATTTCAAACAATCATTTA
12184375 CACTTGTAAGATTTCAAACAATCATT
1 CACTTGTAAGATTTCAAACAATCATT
12184401 CTTAACCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 22 0.50
28 22 0.50
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (28 bp):
CACTTGTAAGATTTCAAACAATCATTTA
Found at i:12184885 original size:26 final size:27
Alignment explanation
Indices: 12184855--12184918 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
12184845 AAAAGAATCT
*
12184855 ATTGAATCATTGA-TACTT-CAAAATTC
1 ATTGAATCATTAACTA-TTCCAAAATTC
* *
12184881 ATTGAAACTTTAACTATTCCAAAATTC
1 ATTGAATCATTAACTATTCCAAAATTC
*
12184908 ATCGAATCATT
1 ATTGAATCATT
12184919 TATTTGTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (27 bp):
ATTGAATCATTAACTATTCCAAAATTC
Found at i:12185946 original size:16 final size:16
Alignment explanation
Indices: 12185925--12185964 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12185915 ACCATTAAAA
*
12185925 ATCATCGTAAATCATC
1 ATCATCATAAATCATC
12185941 ATCATCATAAATCATC
1 ATCATCATAAATCATC
*
12185957 ATTATCAT
1 ATCATCAT
12185965 TGGTTTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
ATCATCATAAATCATC
Found at i:12197882 original size:18 final size:18
Alignment explanation
Indices: 12197861--12197914 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
12197851 TTAAATGTTG
12197861 AAAAAAAAAT-AATTTTT
1 AAAAAAAAATGAATTTTT
*
12197878 AAAAAAATATGAATTTTT
1 AAAAAAAAATGAATTTTT
* * *
12197896 AAGAAAAGATAAATTTTT
1 AAAAAAAAATGAATTTTT
12197914 A
1 A
12197915 TAATATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
AAAAAAAAATGAATTTTT
Found at i:12198541 original size:88 final size:90
Alignment explanation
Indices: 12198174--12198559 Score: 249
Period size: 88 Copynumber: 4.3 Consensus size: 90
12198164 ATTATAGTCA
* * *
12198174 TTGTATTTAAAAAATACTAC-AAAAA-AATTCATAAATATTGAATTTTAAATCCTAAAAAC-A-A
1 TTGTA-TTAAAAAATAC-ACAAAAAATAATCCACAAATATTGAATTTCAAATCCTAAAAACTATA
** * *
12198235 TGATGTTTATTAATGAAAAATGTCGTTG
64 ACAT-TTTATTCATGAAAAACGTCGTTG
* * * *
12198263 TTGTATTAAAAAA-ATCATAAAAAGATAATCCACAAATATT-ACATTTTAAATGCTAGAAACT-T
1 TTGTATTAAAAAATA-CACAAAAA-ATAATCCACAAATATTGA-ATTTCAAATCCTAAAAACTAT
* * * *
12198325 CAACATTTTATTTATAAAAAACCTCATTG
63 -AACATTTTATTCATGAAAAACGTCGTTG
* * ***
12198354 TTGTA-TAAAAAATTTTCACAAAACAATAATCCATAAATATT-AAGTTTCAAATCCTTGGAA-TG
1 TTGTATTAAAAAA--TACACAAAA-AATAATCCACAAATATTGAA-TTTCAAATCCTAAAAACT-
** * * **
12198416 ACGACATTTTGA-TCATGAAAAATGTTGTCA
61 ATAACATTTT-ATTCATGAAAAACGTCGTTG
* * *
12198446 TTATATTAAAAAA-ACACAAAAAA-AACCCACAAATATTGCATTTCAAATCCTAAAAACTATAAC
1 TTGTATTAAAAAATACACAAAAAATAATCCACAAATATTGAATTTCAAATCCTAAAAACTATAAC
* * *
12198509 GTTTTATCCATGAAAAACATCGTTG
66 ATTTTATTCATGAAAAACGTCGTTG
*
12198534 TTGTATTAAAAATATTTCACAAAAAA
1 TTGTATTAAAAA-A-TACACAAAAAA
12198560 ATCCGTAATT
Statistics
Matches: 226, Mismatches: 48, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
87 3 0.01
88 68 0.30
89 12 0.05
90 42 0.19
91 34 0.15
92 58 0.26
93 9 0.04
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.33
Consensus pattern (90 bp):
TTGTATTAAAAAATACACAAAAAATAATCCACAAATATTGAATTTCAAATCCTAAAAACTATAAC
ATTTTATTCATGAAAAACGTCGTTG
Found at i:12198983 original size:18 final size:17
Alignment explanation
Indices: 12198957--12199019 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
12198947 TTTATGCTAA
*
12198957 TGTG-ATTTTTTTACCT
1 TGTGAATTTTTTTTCCT
* *
12198973 TATGAATTTTTATTCTCT
1 TGTGAATTTTTTTTC-CT
*
12198991 TGTG-ATTTTTTATGCCT
1 TGTGAATTTTTT-TTCCT
12199008 TGTGAATTTTTT
1 TGTGAATTTTTT
12199020 ATGCTTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.08
17 20 0.54
18 14 0.38
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.62
Consensus pattern (17 bp):
TGTGAATTTTTTTTCCT
Found at i:12199029 original size:19 final size:19
Alignment explanation
Indices: 12198944--12199032 Score: 82
Period size: 18 Copynumber: 5.0 Consensus size: 19
12198934 TGTTGTGTAT
**
12198944 TTTTTTATGCTAATGTG-A
1 TTTTTTATGCTCTTGTGAA
* *
12198962 TTTTTT-TAC-CTTATGAA
1 TTTTTTATGCTCTTGTGAA
*
12198979 -TTTTTATTCTCTTGTG-A
1 TTTTTTATGCTCTTGTGAA
12198996 TTTTTTATGC-CTTGTGAA
1 TTTTTTATGCTCTTGTGAA
*
12199014 TTTTTTATGCTTTTGTGAA
1 TTTTTTATGCTCTTGTGAA
12199033 CAATGCTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 8 0.14
17 12 0.21
18 30 0.53
19 7 0.12
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (19 bp):
TTTTTTATGCTCTTGTGAA
Found at i:12199092 original size:20 final size:21
Alignment explanation
Indices: 12199056--12199098 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
12199046 TGCCTTGTGA
12199056 TTTTTTTTGCTAATGTG-ATTT
1 TTTTTTTTGCT-ATGTGAATTT
12199077 TTTTTTTTGCCT-TGTGAATTT
1 TTTTTTTTG-CTATGTGAATTT
12199098 T
1 T
12199099 ATTCTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (21 bp):
TTTTTTTTGCTATGTGAATTT
Found at i:12199163 original size:110 final size:109
Alignment explanation
Indices: 12198928--12199294 Score: 368
Period size: 110 Copynumber: 3.3 Consensus size: 109
12198918 ATGCTTTTGT
* *
12198928 GAACAATG--TTGTGTATTTTTTTATGCTAATGTGA-TTTTTTTACCTTATGAATTTTTATTCTC
1 GAACAATGCCTTGTG-A-TTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTTATTCTC
* *
12198990 TTGTGATTTTTTATGCCTTGTGAATTTTTTATGCTTTTGTGAACAATG-C
64 ---TGATTTTTTATGCCTTGT-AAATTTTTATGCCTTTGTGAACAATGTC
*
12199039 TGAACAATGCCTTGTGATTTTTTTTGCTAATGTGATTTTTTTTTTTGCCTTGTGAA-TTTTATTC
1 -GAACAATGCCTTGTGATTTTTTATGCTAATGTGA---TTTTTTTTGCCTTGTGAATTTTTATTC
* *
12199103 TCT-ATTTTTTATACCTTGTAAATTTTTATGCCCTTGTGAACAATGTC
62 TCTGATTTTTTATGCCTTGTAAATTTTTATGCCTTTGTGAACAATGTC
* * * ** * *
12199150 GAGCAATGTCTTGTGATTTTTTATACTAACATGATTTTATTTGCCTAGTGAATTTTTGATCTCTT
1 GAACAATGCCTTGTGATTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTT-AT-TC-T
* * * * ** **
12199215 GTGATTTTTCATGCCTTTTGAATTCATATTACTTTAGTGAACAATGTC
63 CTGATTTTTTATGCCTTGTAAATTTTTATGCCTTT-GTGAACAATGTC
12199263 GAACAATGCCTTGTGATTTTTTATGCTAATGT
1 GAACAATGCCTTGTGATTTTTTATGCTAATGT
12199295 AAAAGTTTGA
Statistics
Matches: 212, Mismatches: 30, Indels: 25
0.79 0.11 0.09
Matches are distributed among these distances:
107 16 0.08
108 4 0.02
109 2 0.01
110 53 0.25
111 18 0.08
112 49 0.23
113 40 0.19
114 5 0.02
115 10 0.05
116 15 0.07
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (109 bp):
GAACAATGCCTTGTGATTTTTTATGCTAATGTGATTTTTTTTGCCTTGTGAATTTTTATTCTCTG
ATTTTTTATGCCTTGTAAATTTTTATGCCTTTGTGAACAATGTC
Found at i:12206584 original size:26 final size:27
Alignment explanation
Indices: 12206555--12206618 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
12206545 CAAAGAATCT
*
12206555 ATTGAATCATTGA-TACTT-CAAAATTC
1 ATTGAATCATTAACTA-TTCCAAAATTC
* *
12206581 ATTGAAACTTTAACTATTCCAAAATTC
1 ATTGAATCATTAACTATTCCAAAATTC
*
12206608 ATCGAATCATT
1 ATTGAATCATT
12206619 TATTTGTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (27 bp):
ATTGAATCATTAACTATTCCAAAATTC
Found at i:12207646 original size:16 final size:16
Alignment explanation
Indices: 12207625--12207664 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12207615 ACCATTAAAA
*
12207625 ATCATCGTAAATCATC
1 ATCATCATAAATCATC
12207641 ATCATCATAAATCATC
1 ATCATCATAAATCATC
*
12207657 ATTATCAT
1 ATCATCAT
12207665 TGGTTTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
ATCATCATAAATCATC
Found at i:12219548 original size:18 final size:17
Alignment explanation
Indices: 12219527--12219581 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
12219517 ATCTTAAATA
12219527 TTGAAAAAATAATAATTT
1 TTGAAAAAAT-ATAATTT
12219545 TTGAAAAAATATAAATTT
1 TTGAAAAAATAT-AATTT
*
12219563 TT-AAGAAAAGATAATTT
1 TTGAA-AAAATATAATTT
12219580 TT
1 TT
12219582 TATGATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TTGAAAAAATATAATTT
Found at i:12219804 original size:20 final size:20
Alignment explanation
Indices: 12219776--12219815 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12219766 AATGAAATAT
*
12219776 TATGTTTATAAATATAAAAA
1 TATGATTATAAATATAAAAA
**
12219796 TATGATTATTGATATAAAAA
1 TATGATTATAAATATAAAAA
12219816 CAATAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
TATGATTATAAATATAAAAA
Found at i:12219938 original size:89 final size:90
Alignment explanation
Indices: 12219829--12220172 Score: 237
Period size: 92 Copynumber: 3.8 Consensus size: 90
12219819 TAAAAAATTC
* * *
12219829 ATGAAAAATGTCGTCATTGTATTTAAAAAAT-ACTACAAAA-A-AATTCATAAATATTGCATTTT
1 ATGAAAAATGTCGTCATTGTATTAAAAAAATCA-TA-AAAAGATAATCCACAAATATTGCATTTT
12219891 AAATCCTAAAAACAATGATGTTTATTA
64 AAATCCTAAAAACAATGATGTTTATTA
**
12219918 ATGAAAAATGTCGTTGTTGTATTAAAAAAATCATAAAAAGATAATCCACAAATATTGCATTTTAA
1 ATGAAAAATGTCGTCATTGTATTAAAAAAATCATAAAAAGATAATCCACAAATATTGCATTTTAA
* *
12219983 ATCCTAGAAACTTCAAT-AT-TTTATTT
66 ATCCTA-AAA--ACAATGATGTTTATTA
** * ** * * *
12220009 ATGAAAAACCTCATTGTTGTA-TAAAAAATTTTCACAAAACA-ATAATCCACAAATATT-AAGTT
1 ATGAAAAATGTCGTCATTGTATTAAAAAA--ATCATAAAA-AGATAATCCACAAATATTGCA-TT
* ** * * *
12220071 TCAAATCCTTGGAATGACGA-CAT-TTTGA-TC
62 TTAAATCC-T--AAAAACAATGATGTTT-ATTA
* * * * * *
12220101 ATGAAAAATGTTGTCATTATATT-AAAAAATCA-AAAAATAAAACCCACAAATATTGCATTTCAA
1 ATGAAAAATGTCGTCATTGTATTAAAAAAATCATAAAAAGATAATCCACAAATATTGCATTTTAA
12220164 ATCCTAAAA
66 ATCCTAAAA
12220173 GCTACAACGT
Statistics
Matches: 205, Mismatches: 32, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
86 2 0.01
88 6 0.03
89 59 0.29
90 39 0.19
91 28 0.14
92 61 0.30
93 8 0.04
94 1 0.00
95 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (90 bp):
ATGAAAAATGTCGTCATTGTATTAAAAAAATCATAAAAAGATAATCCACAAATATTGCATTTTAA
ATCCTAAAAACAATGATGTTTATTA
Found at i:12220034 original size:90 final size:91
Alignment explanation
Indices: 12219845--12220065 Score: 235
Period size: 90 Copynumber: 2.5 Consensus size: 91
12219835 AATGTCGTCA
* *
12219845 TTGTATTTAAAAAATA-CTAC-AAA-AA-AATTCATAAATATTGCATTTTAAATCCTAAAAACAA
1 TTGTA-TTAAAAAATATC-ACAAAACAATAATCCACAAATATTGCATTTTAAATCCTAAAAACAA
** *
12219906 TGATGTTTATTAATGAAAAATGTCGTTG
64 TGATGTTTATTAATGAAAAACCTCATTG
* *
12219934 TTGTATTAAAAAA-ATCATAAAA-AGATAATCCACAAATATTGCATTTTAAATCCTAGAAACTTC
1 TTGTATTAAAAAATATCACAAAACA-ATAATCCACAAATATTGCATTTTAAATCCTA-AAA--AC
*
12219997 AAT-AT-TTTATTTATGAAAAACCTCATTG
62 AATGATGTTTATTAATGAAAAACCTCATTG
*
12220025 TTGTA-TAAAAAATTTTCACAAAACAATAATCCACAAATATT
1 TTGTATTAAAAAA-TATCACAAAACAATAATCCACAAATATT
12220066 AAGTTTCAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
87 2 0.02
88 13 0.12
89 6 0.05
90 34 0.30
91 27 0.24
92 25 0.22
93 5 0.04
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (91 bp):
TTGTATTAAAAAATATCACAAAACAATAATCCACAAATATTGCATTTTAAATCCTAAAAACAATG
ATGTTTATTAATGAAAAACCTCATTG
Found at i:12220213 original size:89 final size:87
Alignment explanation
Indices: 12219825--12220218 Score: 267
Period size: 89 Copynumber: 4.4 Consensus size: 87
12219815 ACAATAAAAA
* * ** * * * *
12219825 ATTCATGAAAAATGTCGTCATTGTATTTAAAAAATACTACAAA-AAAATTCATAAATATTGCATT
1 ATTCATGAAAAACGTCATTGTTGTA-TTAAAAAAT-CAAAAAACAAAATCCACAAATATTGCATT
* *
12219889 TTAAATCCTAAAA-ACAATGATGTTT
64 TCAAATCCTAAAATACAA-CAT-TTT
* * * * *
12219914 ATTAATGAAAAATGTCGTTGTTGTATTAAAAAAATCATAAAAAGATAATCCACAAATATTGCATT
1 ATTCATGAAAAACGTCATTGTTGTATT-AAAAAATCA-AAAAACAAAATCCACAAATATTGCATT
* * *
12219979 TTAAATCCTAGAAACTTCAATATTTT
64 TCAAATCCTA-AAA-TACAACATTTT
* * * *
12220005 ATTTATGAAAAACCTCATTGTTGTA-TAAAAAATTTTCACAAAACAATAATCCACAAATATT-AA
1 ATTCATGAAAAACGTCATTGTTGTATTAAAAAA---TCAAAAAACAA-AATCCACAAATATTGCA
** *
12220068 GTTTCAAATCCTTGGAATGACGACATTTT
62 -TTTCAAATCC-TAAAAT-ACAACATTTT
* ** ** * * *
12220097 GA-TCATGAAAAATGTTGTCATTATATTAAAAAATCAAAAAATAAAACCCACAAATATTGCATTT
1 -ATTCATGAAAAACGTCATTGTTGTATTAAAAAATCAAAAAACAAAATCCACAAATATTGCATTT
*
12220161 CAAATCCTAAAAGCTACAACGTTTT
65 CAAATCCTAAAA--TACAACATTTT
* *
12220186 ATCCATGAAAAACATCATTGTTGTATTAAAAAA
1 ATTCATGAAAAACGTCATTGTTGTATTAAAAAA
12220219 ATTTCACAAA
Statistics
Matches: 238, Mismatches: 48, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
88 7 0.03
89 93 0.39
90 40 0.17
91 34 0.14
92 52 0.22
93 12 0.05
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (87 bp):
ATTCATGAAAAACGTCATTGTTGTATTAAAAAATCAAAAAACAAAATCCACAAATATTGCATTTC
AAATCCTAAAATACAACATTTT
Found at i:12220653 original size:18 final size:17
Alignment explanation
Indices: 12220627--12220689 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
12220617 TTTGTGCTAA
*
12220627 TGTG-ATTTTTTTACCT
1 TGTGAATTTTTTTTCCT
* *
12220643 TATGAATTTTTATTCTCT
1 TGTGAATTTTTTTTC-CT
*
12220661 TGTG-ATTTTTTATGCCT
1 TGTGAATTTTTT-TTCCT
12220678 TGTGAATTTTTT
1 TGTGAATTTTTT
12220690 ATGCTTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.08
17 20 0.54
18 14 0.38
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.62
Consensus pattern (17 bp):
TGTGAATTTTTTTTCCT
Found at i:12220690 original size:18 final size:17
Alignment explanation
Indices: 12220627--12220693 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 17
12220617 TTTGTGCTAA
*
12220627 TGTGATTTTTT-TACCT
1 TGTGATTTTTTATGCCT
* * *
12220643 TATGAATTTTTATTCTCT
1 TGTGATTTTTTATGC-CT
12220661 TGTGATTTTTTATGCCT
1 TGTGATTTTTTATGCCT
12220678 TGTGAATTTTTTATGC
1 TGTG-ATTTTTTATGC
12220694 TTTTGTGAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.21
17 8 0.19
18 25 0.60
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.60
Consensus pattern (17 bp):
TGTGATTTTTTATGCCT
Found at i:12220699 original size:19 final size:19
Alignment explanation
Indices: 12220645--12220702 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
12220635 TTTTACCTTA
*
12220645 TGAA-TTTTTATTCTCTTG
1 TGAATTTTTTATGCTCTTG
12220663 TG-ATTTTTTATGC-CTTG
1 TGAATTTTTTATGCTCTTG
*
12220680 TGAATTTTTTATGCTTTTG
1 TGAATTTTTTATGCTCTTG
12220699 TGAA
1 TGAA
12220703 CAATGCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 7 0.20
18 21 0.60
19 7 0.20
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.59
Consensus pattern (19 bp):
TGAATTTTTTATGCTCTTG
Found at i:12220700 original size:36 final size:34
Alignment explanation
Indices: 12220627--12220701 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 34
12220617 TTTGTGCTAA
*
12220627 TGTGATTTTTTTACCTTATGAATTTTTATTCTCT
1 TGTGATTTTTTTACCTTATGAATTTTTATGCTCT
* * *
12220661 TGTGATTTTTTATGCCTTGTGAATTTTTTATGCTTT
1 TGTGATTTTTT-TACCTTATGAA-TTTTTATGCTCT
12220697 TGTGA
1 TGTGA
12220702 ACAATGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 11 0.31
35 9 0.26
36 15 0.43
ACGTcount: A:0.16, C:0.09, G:0.15, T:0.60
Consensus pattern (34 bp):
TGTGATTTTTTTACCTTATGAATTTTTATGCTCT
Found at i:12220804 original size:17 final size:18
Alignment explanation
Indices: 12220782--12220816 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12220772 TATTCTCTAT
12220782 TTTTTAT-ACCTTGTAAA
1 TTTTTATGACCTTGTAAA
*
12220799 TTTTTATGCCCTTGTAAA
1 TTTTTATGACCTTGTAAA
12220817 CAATGTCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTTTATGACCTTGTAAA
Found at i:12220819 original size:114 final size:118
Alignment explanation
Indices: 12220632--12220852 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 118
12220622 GCTAATGTGA
* * **
12220632 TTTTTTTACCTTATGAATTTTTATTCTCTTGTGATTTTTTATGCCTTGTGAATTTTTTATGCTTT
1 TTTTTTTACCTTATGAATTTTTATTCTC-T-TGATTTTTTATACCTTGTGAAATTTTTATGCCCT
* *
12220697 TGTGAACAATG-CTAAACAATGTCTTGTGATTTTTTATGCTAATGTAATTTTTTTT
64 TGTAAACAATGTC-AAACAATGTCTTGTGATTTTTTATACTAATGTAATTTTTTTT
* *
12220752 TTTTTTTGCCTTGTGAA-TTTTATTCTC-T-ATTTTTTATACCTTGT-AAATTTTTATGCCCTTG
1 TTTTTTTACCTTATGAATTTTTATTCTCTTGATTTTTTATACCTTGTGAAATTTTTATGCCCTTG
* *
12220813 TAAACAATGTCGAGCAATGTCTTGTGATTTTTTATACTAA
66 TAAACAATGTCAAACAATGTCTTGTGATTTTTTATACTAA
12220853 CATGATTTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
114 48 0.53
115 16 0.18
116 1 0.01
119 10 0.11
120 15 0.17
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (118 bp):
TTTTTTTACCTTATGAATTTTTATTCTCTTGATTTTTTATACCTTGTGAAATTTTTATGCCCTTG
TAAACAATGTCAAACAATGTCTTGTGATTTTTTATACTAATGTAATTTTTTTT
Found at i:12225780 original size:16 final size:16
Alignment explanation
Indices: 12225759--12225798 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
12225749 ACCATTAAAA
* *
12225759 ATCATCGTAAATGATC
1 ATCATCATAAATCATC
12225775 ATCATCATAAATCATC
1 ATCATCATAAATCATC
*
12225791 ATTATCAT
1 ATCATCAT
12225799 TGGTTTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (16 bp):
ATCATCATAAATCATC
Found at i:12231175 original size:16 final size:16
Alignment explanation
Indices: 12231150--12231180 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12231140 TGAAAAGGTT
12231150 AAAGGCTTAACCCAAA
1 AAAGGCTTAACCCAAA
*
12231166 AAAGGTTTAACCCAA
1 AAAGGCTTAACCCAA
12231181 CAACATTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAGGCTTAACCCAAA
Found at i:12237690 original size:18 final size:17
Alignment explanation
Indices: 12237667--12237725 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
12237657 TAAAATTTTA
12237667 AATTTTGAAAGAAAAAAT
1 AATTTT-AAAGAAAAAAT
*
12237685 AATTTTTAAA-AAAATAT
1 AA-TTTTAAAGAAAAAAT
* *
12237702 AAATTTTTAAGAAAAGAT
1 -AATTTTAAAGAAAAAAT
12237720 AATTTT
1 AATTTT
12237726 TTTATGATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 18 0.51
18 13 0.37
19 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (17 bp):
AATTTTAAAGAAAAAAT
Found at i:12237703 original size:17 final size:17
Alignment explanation
Indices: 12237667--12237726 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
12237657 TAAAATTTTA
*
12237667 AATTTTGAAAGAAAAAAT
1 AATTTTTAAA-AAAAAAT
*
12237685 AATTTTTAAAAAAATAT
1 AATTTTTAAAAAAAAAT
* *
12237702 AAATTTTTAAGAAAAGAT
1 -AATTTTTAAAAAAAAAT
12237720 AATTTTT
1 AATTTTT
12237727 TTATGATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 13 0.35
18 24 0.65
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
AATTTTTAAAAAAAAAT
Found at i:12237727 original size:18 final size:17
Alignment explanation
Indices: 12237675--12237726 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
12237665 TAAATTTTGA
12237675 AAGAAAAAATAATTTTT
1 AAGAAAAAATAATTTTT
12237692 AA-AAAAATATAAATTTTT
1 AAGAAAAA-AT-AATTTTT
*
12237710 AAGAAAAGATAATTTTT
1 AAGAAAAAATAATTTTT
12237727 TTATGATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
18 11 0.35
19 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AAGAAAAAATAATTTTT
Found at i:12238354 original size:86 final size:87
Alignment explanation
Indices: 12237968--12238360 Score: 269
Period size: 90 Copynumber: 4.4 Consensus size: 87
12237958 ACAATAAAAA
* * * * *
12237968 ATTCATGAAAAATGTCATCATTGTATTAAAAAATTACTACAAAAAAAATTCATAAATATTGCATT
1 ATTCATGAAAAACGTCATCGTTGTATTAAAAAA--AC-A-AAAAATAATCCACAAATATTGCATT
* **
12238033 TTAAATCCTAAAAAC-A-ATGATATTT
62 TCAAATCCTAAAAACTACAACAT-TTT
* *
12238058 ATTAATGAAAAATGTCATCGTTGTATTAAAAAAATCATAAAATGATAATCCACAAATATTGCATT
1 ATTCATGAAAAACGTCATCGTTGTATTAAAAAAA-CA-AAAA--ATAATCCACAAATATTGCATT
* * * *
12238123 TTAAATCATAGAAACTTCAACATTTT
62 TCAAATCCTAAAAACTACAACATTTT
* * * * * *
12238149 ATTTATGAAAAACCTCATTGTTGTA-TAAAAATTTTTCATAAAACAATAATCCACAAATATT-AA
1 ATTCATGAAAAACGTCATCGTTGTATTAAAAA-----AACAAAA-AATAATCCACAAATATTGCA
***
12238212 GTTTCAAATCCTTGGAA-TGACAACATTTT
60 -TTTCAAATCCTAAAAACT-ACAACATTTT
** ** * * *
12238241 GA-TCATGAAAAACGTTGTCAATATATTAAAAAAACCAAAAA-AACCCACAAATATTGCATTTCA
1 -ATTCATGAAAAACGTCATCGTTGTATTAAAAAAACAAAAAATAATCCACAAATATTGCATTTCA
12238304 AATCCTAAAAACTACAACATTTT
65 AATCCTAAAAACTACAACATTTT
* * * *
12238327 ATCCATGAAAAACATCGTTGTTGTATTAAAAAAA
1 ATTCATGAAAAACGTCATCGTTGTATTAAAAAAA
12238361 TTTCCCAAAA
Statistics
Matches: 239, Mismatches: 46, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
85 1 0.00
86 61 0.26
87 4 0.02
88 10 0.04
89 1 0.00
90 68 0.28
91 26 0.11
92 55 0.23
93 10 0.04
94 2 0.01
95 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (87 bp):
ATTCATGAAAAACGTCATCGTTGTATTAAAAAAACAAAAAATAATCCACAAATATTGCATTTCAA
ATCCTAAAAACTACAACATTTT
Found at i:12238802 original size:17 final size:17
Alignment explanation
Indices: 12238764--12238840 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 17
12238754 TGCTGTGTAT
12238764 TTTTTTTATGCTAATGTG-A
1 TTTTTTTAT-CT--TGTGAA
*
12238783 TTTTTTTATCTTATGAA
1 TTTTTTTATCTTGTGAA
*
12238800 TTTTTATTCTCTTGTG-A
1 TTTTT-TTATCTTGTGAA
12238817 -TTTTTTATGCCTTGTGAA
1 TTTTTTTAT--CTTGTGAA
12238835 TTTTTT
1 TTTTTT
12238841 ATGCTTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.06
16 7 0.15
17 13 0.27
18 11 0.23
19 14 0.29
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.64
Consensus pattern (17 bp):
TTTTTTTATCTTGTGAA
Found at i:12238850 original size:19 final size:19
Alignment explanation
Indices: 12238765--12238853 Score: 82
Period size: 18 Copynumber: 5.0 Consensus size: 19
12238755 GCTGTGTATT
**
12238765 TTTTTTATGCTAATGTG-A
1 TTTTTTATGCTCTTGTGAA
* *
12238783 TTTTTT-T-ATCTTATGAA
1 TTTTTTATGCTCTTGTGAA
*
12238800 -TTTTTATTCTCTTGTG-A
1 TTTTTTATGCTCTTGTGAA
12238817 TTTTTTATGC-CTTGTGAA
1 TTTTTTATGCTCTTGTGAA
*
12238835 TTTTTTATGCTTTTGTGAA
1 TTTTTTATGCTCTTGTGAA
12238854 CATTGCTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 9 0.16
17 10 0.18
18 31 0.54
19 7 0.12
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (19 bp):
TTTTTTATGCTCTTGTGAA
Found at i:12238985 original size:111 final size:110
Alignment explanation
Indices: 12238765--12239116 Score: 356
Period size: 112 Copynumber: 3.1 Consensus size: 110
12238755 GCTGTGTATT
* *
12238765 TTTTTTATGCTAATGTGATTTTTTTAT--CTTATGAATTTTTATTCTCTTGTGATTTTTTATGCC
1 TTTTTTAAGCTAATGTGATTTTTTTATGCCTTGTGAATTTTTATTCTC---TGATTTTTTATGCC
* * *
12238828 TTGTGAATTTTTTATGCTTTTGTGAACATTG-CTGAACAATGCCTTGTGA
63 TTGT-AAATTTTTATGCCTTTGTGAACAATGTC-GAACAATGCCTTGTGA
* *
12238877 TTTTTTAAGCTAATGTGATTTTTTTTTATGCCTTGTGAATTTGTATTCTCT-ATTTTTTATACCT
1 TTTTTTAAGCTAATGTGA--TTTTTTTATGCCTTGTGAATTTTTATTCTCTGATTTTTTATGCCT
* *
12238941 TGTAAATTTTTATGCCCTTGTGAACAATGTCGAACAATGTCTTGTGA
64 TGTAAATTTTTATGCCTTTGTGAACAATGTCGAACAATGCCTTGTGA
* * * * *
12238988 TTTTTTATA-CTAACGTGATTTTATT-TGCCTAGTGAATTTTTGATCTCTTGTGATTTTTCATGC
1 TTTTTTA-AGCTAATGTGATTTTTTTATGCCTTGTGAATTTTT-AT-TC-TCTGATTTTTTATGC
* * ** ** *
12239051 CTTTTGAATTCATATTACTTTAGTGAACAATGTTGAACAATGCCTTGTGA
62 CTTGTAAATTTTTATGCCTTT-GTGAACAATGTCGAACAATGCCTTGTGA
*
12239101 TTTTTTATGCTAATGT
1 TTTTTTAAGCTAATGT
12239117 AAACTTTGAT
Statistics
Matches: 201, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
108 14 0.07
109 8 0.04
110 2 0.01
111 54 0.27
112 57 0.28
113 40 0.20
114 9 0.04
116 17 0.08
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (110 bp):
TTTTTTAAGCTAATGTGATTTTTTTATGCCTTGTGAATTTTTATTCTCTGATTTTTTATGCCTTG
TAAATTTTTATGCCTTTGTGAACAATGTCGAACAATGCCTTGTGA
Found at i:12242299 original size:25 final size:24
Alignment explanation
Indices: 12242238--12242288 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
12242228 CAAGTGGTGC
* *
12242238 ATTGTATCATATA-ACGAAGTCTAA
1 ATTGTATCATTTACAC-AAGTCCAA
12242262 ATTGTATCATTTACACAAGTCCAA
1 ATTGTATCATTTACACAAGTCCAA
12242286 ATT
1 ATT
12242289 TGTTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (24 bp):
ATTGTATCATTTACACAAGTCCAA
Found at i:12242383 original size:84 final size:85
Alignment explanation
Indices: 12242242--12242411 Score: 279
Period size: 84 Copynumber: 2.0 Consensus size: 85
12242232 TGGTGCATTG
* * *
12242242 TATCATATAACGAAGTCTAAATTGTATCATTTACACAAGTCCAAATTTGTTCTATTTATACAAAT
1 TATCACATAAAGAAGTCTAAATTGCATCATTTACACAAGTCCAAATTTGTTCTATTTATACAAAT
*
12242307 AAACACA-TTTCATTTATAA
66 AAACAAATTTTCATTTATAA
*
12242326 TATCACATAAAGAAGTCTAAATTGCATCATTTACACAAGTCCAAATTTGTTTTATTTATACAAAT
1 TATCACATAAAGAAGTCTAAATTGCATCATTTACACAAGTCCAAATTTGTTCTATTTATACAAAT
*
12242391 CAACAAATTTTCATTTATAA
66 AAACAAATTTTCATTTATAA
12242411 T
1 T
12242412 TTATGTAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 66 0.84
85 13 0.16
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (85 bp):
TATCACATAAAGAAGTCTAAATTGCATCATTTACACAAGTCCAAATTTGTTCTATTTATACAAAT
AAACAAATTTTCATTTATAA
Found at i:12242473 original size:94 final size:94
Alignment explanation
Indices: 12242361--12242544 Score: 368
Period size: 94 Copynumber: 2.0 Consensus size: 94
12242351 ATCATTTACA
12242361 CAAGTCCAAATTTGTTTTATTTATACAAATCAACAAATTTTCATTTATAATTTATGTAAGTTTAA
1 CAAGTCCAAATTTGTTTTATTTATACAAATCAACAAATTTTCATTTATAATTTATGTAAGTTTAA
12242426 TTACAAAATGCCAATGTAATTATAATATT
66 TTACAAAATGCCAATGTAATTATAATATT
12242455 CAAGTCCAAATTTGTTTTATTTATACAAATCAACAAATTTTCATTTATAATTTATGTAAGTTTAA
1 CAAGTCCAAATTTGTTTTATTTATACAAATCAACAAATTTTCATTTATAATTTATGTAAGTTTAA
12242520 TTACAAAATGCCAATGTAATTATAA
66 TTACAAAATGCCAATGTAATTATAA
12242545 CATTGAAACA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (94 bp):
CAAGTCCAAATTTGTTTTATTTATACAAATCAACAAATTTTCATTTATAATTTATGTAAGTTTAA
TTACAAAATGCCAATGTAATTATAATATT
Found at i:12246274 original size:20 final size:20
Alignment explanation
Indices: 12246230--12246285 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
12246220 TCATATATCG
* *
12246230 ATTAAAACAAA-TG-AATCT
1 ATTAAAATAAATTGAAATCA
*
12246248 ATCAAAATAAATTGAAATCA
1 ATTAAAATAAATTGAAATCA
* *
12246268 ATTAAAATTAATTAAAAT
1 ATTAAAATAAATTGAAAT
12246286 AATCGATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 9 0.30
19 2 0.07
20 19 0.63
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (20 bp):
ATTAAAATAAATTGAAATCA
Found at i:12247257 original size:15 final size:14
Alignment explanation
Indices: 12247233--12247263 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
12247223 TTAATAACTT
12247233 TTTTTATTATATTA
1 TTTTTATTATATTA
12247247 TTTTTAGTTATATTA
1 TTTTTA-TTATATTA
12247262 TT
1 TT
12247264 ATTTGATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTATTATATTA
Found at i:12247369 original size:31 final size:32
Alignment explanation
Indices: 12247314--12247374 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
12247304 AAATTATATG
*
12247314 TTAAATGAATAAAGAATTTATATGTTAAATTA
1 TTAAATAAATAAAGAATTTATATGTTAAATTA
12247346 TTAAATAAATAACA-AA-TTATATGTTAAAT
1 TTAAATAAATAA-AGAATTTATATGTTAAAT
12247375 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.48
32 13 0.48
33 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (32 bp):
TTAAATAAATAAAGAATTTATATGTTAAATTA
Found at i:12247967 original size:25 final size:25
Alignment explanation
Indices: 12247908--12247967 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
12247898 AAATATTTAT
* *
12247908 TATTATCTATTAAAATTTAAACGAA
1 TATTATATATTAAAATTTAAACAAA
*
12247933 T-TTAGATATTAAATATTTAAA-AAA
1 TATTATATATTAAA-ATTTAAACAAA
*
12247957 TATTATTTATT
1 TATTATATATT
12247968 TTCACTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TATTATATATTAAAATTTAAACAAA
Found at i:12248570 original size:28 final size:28
Alignment explanation
Indices: 12248534--12248600 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
12248524 AATAAATAAA
12248534 TTATTTATTTATGTAACCTATG-AA-TTAT
1 TTATTTATTTATGTAA-C-ATGTAATTTAT
* *
12248562 TTATGTATTTATTTAACATGTAATTTAT
1 TTATTTATTTATGTAACATGTAATTTAT
12248590 TTATTTATTTA
1 TTATTTATTTA
12248601 ACATATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.09
27 3 0.09
28 28 0.82
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (28 bp):
TTATTTATTTATGTAACATGTAATTTAT
Found at i:12248624 original size:24 final size:23
Alignment explanation
Indices: 12248593--12248647 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
12248583 AATTTATTTA
12248593 TTTA-TTTAACATATAAAAATAAT
1 TTTATTTTAACATATAAAAAT-AT
*** *
12248616 TTTATTTTATTGTATAAAAATTT
1 TTTATTTTAACATATAAAAATAT
12248639 TTTATTTTA
1 TTTATTTTA
12248648 TAAATGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTATTTTAACATATAAAAATAT
Found at i:12249607 original size:12 final size:12
Alignment explanation
Indices: 12249592--12249654 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
12249582 ATTTTTAATA
12249592 TAAATATAAAAT
1 TAAATATAAAAT
*
12249604 TAAATAT-ATAT
1 TAAATATAAAAT
*
12249615 AAAATATATAAA-
1 TAAATATA-AAAT
*
12249627 TAATTATAAAAT
1 TAAATATAAAAT
12249639 TAAATA-AATAAT
1 TAAATATAA-AAT
12249651 TAAA
1 TAAA
12249655 AAAATTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 14 0.34
12 25 0.61
13 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:12249616 original size:16 final size:17
Alignment explanation
Indices: 12249588--12249648 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 17
12249578 TATTATTTTT
12249588 AATATAAATATAAAATTA
1 AATAT-AATATAAAATTA
12249606 AATAT-ATATAAAATATA
1 AATATAATATAAAAT-TA
12249623 TAA-ATAATTATAAAATTA
1 -AATATAA-TATAAAATTA
12249641 AATA-AATA
1 AATATAATA
12249649 ATTAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 11 0.29
17 8 0.21
18 11 0.29
19 8 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATAATATAAAATTA
Found at i:12249647 original size:20 final size:20
Alignment explanation
Indices: 12249591--12249656 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
12249581 TATTTTTAAT
*
12249591 ATAAATATAAAATTAAAT--
1 ATAATTATAAAATTAAATAA
*
12249609 AT-A-TATAAAA-TATATAA
1 ATAATTATAAAATTAAATAA
12249626 ATAATTATAAAATTAAATAA
1 ATAATTATAAAATTAAATAA
12249646 ATAATTA-AAAA
1 ATAATTATAAAA
12249657 AATTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.10
16 7 0.17
17 3 0.07
18 3 0.07
19 11 0.27
20 13 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATTATAAAATTAAATAA
Found at i:12249660 original size:29 final size:34
Alignment explanation
Indices: 12249596--12249662 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
12249586 TTAATATAAA
*
12249596 TATAAAATTAAATATATATAAAATATATAAATAAT
1 TATAAAATTAAATATATAT-AAATATATAAAAAAT
12249631 TATAAAATTAAATA-A-AT-AAT-TA-AAAAAAT
1 TATAAAATTAAATATATATAAATATATAAAAAAT
12249660 TAT
1 TAT
12249663 TTTTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 9 0.29
30 2 0.06
31 3 0.10
33 2 0.06
34 1 0.03
35 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
TATAAAATTAAATATATATAAATATATAAAAAAT
Found at i:12252034 original size:30 final size:29
Alignment explanation
Indices: 12251998--12252082 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 29
12251988 TATCTAAAAA
12251998 TTTTAAAATTAAAAACTCATATTTTTTATT
1 TTTTAAAATTAAAAACT-ATATTTTTTATT
*
12252028 TTTTAAAATTAAAAACT-TATTGTTTATT
1 TTTTAAAATTAAAAACTATATTTTTTATT
12252056 TTTT-AAA-TAAAAA-TATATTTTTATATT
1 TTTTAAAATTAAAAACTATATTTTT-TATT
12252083 ATATGTTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.02
26 12 0.24
27 7 0.14
28 14 0.27
30 17 0.33
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTTAAAATTAAAAACTATATTTTTTATT
Found at i:12252854 original size:61 final size:61
Alignment explanation
Indices: 12252697--12252872 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 61
12252687 TGTAAAAAGC
* * *
12252697 TTAATTATTACGTTTTTTTAAAA-TAAATATAATAATTGATTATTA--TAATTTATTTTAAATAA
1 TTAATTATTACGTTTATTTAAAATTAAATATAGTAATTG-TT-TTATGTAA-TT-TTTAAAATAA
* * **
12252759 TTAAATATTACATTTA-AAAAAATTAAATATAGTAATTGTTTTATGTAATTTTTAAAATAA
1 TTAATTATTACGTTTATTTAAAATTAAATATAGTAATTGTTTTATGTAATTTTTAAAATAA
* * *
12252819 TTAATTAGTACGTTTATTTAAAATTAAATACAGTAATTG-TATATTGTAATTTTT
1 TTAATTATTACGTTTATTTAAAATTAAATATAGTAATTGTTTTA-TGTAATTTTT
12252873 TTAAAACGTA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
60 28 0.29
61 37 0.39
62 30 0.32
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
TTAATTATTACGTTTATTTAAAATTAAATATAGTAATTGTTTTATGTAATTTTTAAAATAA
Found at i:12253004 original size:196 final size:195
Alignment explanation
Indices: 12252660--12253077 Score: 486
Period size: 196 Copynumber: 2.1 Consensus size: 195
12252650 AAAAATAATT
* * * * *
12252660 ATTATTTATTATAATTTTTTAAAAATATGTAAAAAGCTTAATTATTACGTTTTTTTAAAATAAAT
1 ATTATATATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTCTTTAAAATAAAT
* *
12252725 ATAATAATTGATTATTATAATTTATTTTAAATAATTAAATATTACATTTAAAAAAATTAAATATA
66 ATAATAATTGATTATTATAATTTATTTAAAATAATTAAATATTACATTTAAAAAAATTAAATACA
* * * * *
12252790 GTAATTGTTTTATGTAA-TTTTT-AAAATAATTAATTAGTACGTTTATTTAAAATTAAATA-CAG
131 ATAATTATTATATGTAATTTTTTCAAAATAATCAATTAGTACATTT-TTTAAAATTAAA-AGCAG
12252852 TA
194 TA
* * * * *
12252854 ATTGTATATTGTAATTTTTTTAAAACGTATAAAAAGTTTAATTATTATGTTTCTTTAAAGATAAA
1 ATTATATATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTCTTTAAA-AT-AA
* * * * **** *
12252919 ATGTAGTAATTGATTATTATAATTTATTTAAAATATTTAAATATTATATTTTTTTAAGTTAAATA
64 ATATAATAATTGATTATTATAATTTATTTAAAATAATTAAATATTACATTTAAAAAAATTAAATA
* * *
12252984 CAATAATTATTCAT-TGTAATTTTTTCAAAATAATCAATTAGTGCATTTTTTAAAGTTAAAAGTA
129 CAATAATTATT-ATATGTAATTTTTTCAAAATAATCAATTAGTACATTTTTTAAAATTAAAAGCA
12253048 GTA
193 GTA
*
12253051 ATTATTTATTATAA-TTTTTTAAAACAT
1 ATTATATATTATAATTTTTTTAAAACAT
12253078 GTGTATAATC
Statistics
Matches: 185, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
194 49 0.26
195 2 0.01
196 83 0.45
197 32 0.17
198 19 0.10
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (195 bp):
ATTATATATTATAATTTTTTTAAAACATATAAAAAGCTTAATTATTACGTTTCTTTAAAATAAAT
ATAATAATTGATTATTATAATTTATTTAAAATAATTAAATATTACATTTAAAAAAATTAAATACA
ATAATTATTATATGTAATTTTTTCAAAATAATCAATTAGTACATTTTTTAAAATTAAAAGCAGTA
Found at i:12258446 original size:18 final size:18
Alignment explanation
Indices: 12258423--12258465 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12258413 TTTCTCATTT
*
12258423 TTTATTACCTA-TTTTTAA
1 TTTATTAACTAGTTTTT-A
*
12258441 TTTATTAATTAGTTTTTA
1 TTTATTAACTAGTTTTTA
12258459 TTTATTA
1 TTTATTA
12258466 TTTTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTAACTAGTTTTTA
Found at i:12259859 original size:33 final size:33
Alignment explanation
Indices: 12259817--12259884 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
12259807 TTTTTTTGTA
12259817 TTTTATATTTTGTATTTTTATAGT-TT-TATATTT
1 TTTTATATTTTGTATTTTT-T-GTATTCTATATTT
*
12259850 TTTTGTATTTTGTATTTTTTGTATTCTATATTT
1 TTTTATATTTTGTATTTTTTGTATTCTATATTT
12259883 TT
1 TT
12259885 GTTTAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 27 0.84
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (33 bp):
TTTTATATTTTGTATTTTTTGTATTCTATATTT
Found at i:12259860 original size:7 final size:7
Alignment explanation
Indices: 12259810--12259867 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
12259800 TTTTTATTTT
12259810 TTTTGTA
1 TTTTGTA
*
12259817 TTTTATA
1 TTTTGTA
12259824 TTTTGTA
1 TTTTGTA
12259831 TTTT-TA
1 TTTTGTA
12259837 TAGTTT-TA
1 T--TTTGTA
*
12259845 TATT-T-
1 TTTTGTA
12259850 TTTTGTA
1 TTTTGTA
12259857 TTTTGTA
1 TTTTGTA
12259864 TTTT
1 TTTT
12259868 TTGTATTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 3 0.07
6 7 0.16
7 27 0.63
8 6 0.14
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (7 bp):
TTTTGTA
Found at i:12259870 original size:16 final size:16
Alignment explanation
Indices: 12259817--12259884 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
12259807 TTTTTTTGTA
*
12259817 TTTTATATTTTGTA-T
1 TTTTATATTTTATATT
12259832 TTTTATAGTTTTATATTT
1 TTTTATA-TTTTATA-TT
* *
12259850 TTTTGTATTTTGTATT
1 TTTTATATTTTATATT
* *
12259866 TTTTGTATTCTATATT
1 TTTTATATTTTATATT
12259882 TTT
1 TTT
12259885 GTTTAATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.16
16 25 0.56
17 6 0.13
18 7 0.16
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTTATATTTTATATT
Found at i:12263747 original size:24 final size:24
Alignment explanation
Indices: 12263719--12263779 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 24
12263709 TTCTGGGTAT
*
12263719 AATCTTTAAGAATTTTTAAATGAG
1 AATCTTTAAGAATTTTTAAATAAG
12263743 AATCTTTAAG---TTTTAAATAAG
1 AATCTTTAAGAATTTTTAAATAAG
*
12263764 AATCTTGAA-AATTTTT
1 AATCTTTAAGAATTTTT
12263780 TGATGTGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 18 0.56
23 4 0.12
24 10 0.31
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (24 bp):
AATCTTTAAGAATTTTTAAATAAG
Found at i:12263941 original size:47 final size:45
Alignment explanation
Indices: 12263794--12263945 Score: 112
Period size: 47 Copynumber: 3.3 Consensus size: 45
12263784 GTGAACCCCC
* * * * *
12263794 AAAG-TTTTTGAATAAGAATA-TTGAAATAGTGGAA-GTGAAACACT
1 AAAGTTTTTTGAATGACAATATTTGAAATAAT-AAATGTGAATC-CT
** ***
12263838 AAAGTTTTTTTGAATGACAATATTTGAAATCTTGGTTGTGAATCCTT
1 AAAG-TTTTTTGAATGACAATATTTGAAATAATAAATGTGAATCC-T
* * *
12263885 AGAAGTTTTTCGAATGAGAATATTTGAAATAATAAATGTGAACTGCT
1 A-AAGTTTTTTGAATGACAATATTTGAAATAATAAATGTGAA-TCCT
12263932 AAAGTTTTTTGAAT
1 AAAGTTTTTTGAAT
12263946 AAGATTCTTC
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
44 4 0.05
46 28 0.33
47 48 0.56
48 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (45 bp):
AAAGTTTTTTGAATGACAATATTTGAAATAATAAATGTGAATCCT
Found at i:12264137 original size:35 final size:35
Alignment explanation
Indices: 12264091--12264183 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 35
12264081 AAATTTTTGC
*
12264091 ATTCTTACAAATATGAAAATTCTTACAAATC-TAAA
1 ATTCTTGCAAATAT-AAAATTCTTACAAATCTTAAA
* * * * * *
12264126 ATTTTTTCAAATCTAAAATTTTTGCGAATCTTAAA
1 ATTCTTGCAAATATAAAATTCTTACAAATCTTAAA
*
12264161 ATTCTTGCAAATCTAAAGATTCT
1 ATTCTTGCAAATATAAA-ATTCT
12264184 CGTGAATTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 13 0.28
35 30 0.64
36 4 0.09
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (35 bp):
ATTCTTGCAAATATAAAATTCTTACAAATCTTAAA
Found at i:12264182 original size:18 final size:17
Alignment explanation
Indices: 12264091--12264183 Score: 96
Period size: 17 Copynumber: 5.3 Consensus size: 17
12264081 AAATTTTTGC
*
12264091 ATTCTTACAAATATGAAA
1 ATTCTTACAAATCT-AAA
12264109 ATTCTTACAAATCTAAA
1 ATTCTTACAAATCTAAA
* *
12264126 ATTTTTTCAAATCTAAA
1 ATTCTTACAAATCTAAA
* * *
12264143 ATTTTTGCGAATCTTAAA
1 ATTCTTACAAATC-TAAA
*
12264161 ATTCTTGCAAATCTAAA
1 ATTCTTACAAATCTAAA
12264178 GATTCT
1 -ATTCT
12264184 CGTGAATTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
17 33 0.50
18 33 0.50
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (17 bp):
ATTCTTACAAATCTAAA
Found at i:12264200 original size:18 final size:18
Alignment explanation
Indices: 12264140--12264261 Score: 79
Period size: 18 Copynumber: 6.8 Consensus size: 18
12264130 TTTCAAATCT
* *
12264140 AAAATTTTTGCGAATCTT-
1 AAAATTCTTGTGAAT-TTG
** *
12264158 AAAATTCTTGCAAATCT-
1 AAAATTCTTGTGAATTTG
*
12264175 AAAGATTCTCGTGAATTTG
1 AAA-ATTCTTGTGAATTTG
**
12264194 AAAATTCTTGCAAATTTG
1 AAAATTCTTGTGAATTTG
**
12264212 AAGGTTCTTGTGAATTT-
1 AAAATTCTTGTGAATTTG
* *
12264229 AAAATTTTTTGTTAATTTG
1 AAAA-TTCTTGTGAATTTG
*
12264248 AAAATTATTGTGAA
1 AAAATTCTTGTGAA
12264262 CCTGAAATTC
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
17 6 0.08
18 67 0.84
19 7 0.09
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (18 bp):
AAAATTCTTGTGAATTTG
Found at i:12264203 original size:36 final size:35
Alignment explanation
Indices: 12264122--12264234 Score: 129
Period size: 36 Copynumber: 3.2 Consensus size: 35
12264112 CTTACAAATC
* * * *
12264122 TAAAATTTTTTCAAATCTAAA-ATTTTTGCGAATCT
1 TAAAATTCTTGCAAATCTAAAGATTCTTGTGAAT-T
*
12264157 TAAAATTCTTGCAAATCTAAAGATTCTCGTGAATT
1 TAAAATTCTTGCAAATCTAAAGATTCTTGTGAATT
* * *
12264192 TGAAAATTCTTGCAAATTTGAAGGTTCTTGTGAATT
1 T-AAAATTCTTGCAAATCTAAAGATTCTTGTGAATT
12264228 TAAAATT
1 TAAAATT
12264235 TTTTGTTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 27 0.40
36 40 0.60
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (35 bp):
TAAAATTCTTGCAAATCTAAAGATTCTTGTGAATT
Found at i:12264408 original size:17 final size:17
Alignment explanation
Indices: 12264386--12264433 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12264376 TTTGAATTTG
12264386 AAAATTCTTGTGAACCT
1 AAAATTCTTGTGAACCT
* * *
12264403 AAAATTTTTATGAAGCT
1 AAAATTCTTGTGAACCT
* *
12264420 AAAAGTCATGTGAA
1 AAAATTCTTGTGAA
12264434 TCTTTGGTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (17 bp):
AAAATTCTTGTGAACCT
Found at i:12265087 original size:25 final size:23
Alignment explanation
Indices: 12265040--12265094 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
12265030 CGAAGAGAGT
*
12265040 GAAAAA-CACATAAAAAATCAAA
1 GAAAAATCACATAAAAAACCAAA
12265062 GAAAAATCACATAAAAAAACCAAAA
1 GAAAAATCACAT-AAAAAACC-AAA
12265087 GAATAAAT
1 GAA-AAAT
12265095 GATTACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 6 0.21
23 5 0.18
24 7 0.25
25 6 0.21
26 4 0.14
ACGTcount: A:0.71, C:0.13, G:0.05, T:0.11
Consensus pattern (23 bp):
GAAAAATCACATAAAAAACCAAA
Found at i:12266359 original size:57 final size:56
Alignment explanation
Indices: 12266259--12266403 Score: 157
Period size: 57 Copynumber: 2.6 Consensus size: 56
12266249 TTCCTTTGAA
* * *
12266259 AAAAATTTTCAAAAAAGAGTTTTGAAAAAAATTTAAAGTATTAATTTTTCTTAAAAAT
1 AAAAATTTTCAAAAAAGAGTTTTGAAAAAAAGTTAAAGGATTAA-TTTTCCT-AAAAT
* ** *
12266317 AAAAATTTTCAAAAAA-TGTTTTGAGGAAAAGTTGAAGGATTAATTTTCCTAAAAT
1 AAAAATTTTCAAAAAAGAGTTTTGAAAAAAAGTTAAAGGATTAATTTTCCTAAAAT
* * * *
12266372 AAATATTTTCAAAATAAAAATTTTCAAAAAAA
1 AAAAATTTTCAAAA-AAGAGTTTTGAAAAAAA
12266404 TTCTTTGAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
55 18 0.25
56 8 0.11
57 30 0.42
58 16 0.22
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (56 bp):
AAAAATTTTCAAAAAAGAGTTTTGAAAAAAAGTTAAAGGATTAATTTTCCTAAAAT
Found at i:12266381 original size:17 final size:16
Alignment explanation
Indices: 12266358--12266400 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12266348 TTGAAGGATT
12266358 AATTTTCCTAAAATAAA
1 AATTTTCC-AAAATAAA
*
12266375 TATTTT-CAAAATAAA
1 AATTTTCCAAAATAAA
12266390 AATTTT-CAAAA
1 AATTTTCCAAAA
12266401 AAATTCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.75
16 1 0.04
17 5 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTTCCAAAATAAA
Done.