Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold113
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: 3764034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 4009 characters in sequence are not A, C, G, or T
File 9 of 23
Found at i:1331998 original size:20 final size:20
Alignment explanation
Indices: 1331972--1332067 Score: 140
Period size: 20 Copynumber: 4.8 Consensus size: 20
1331962 GTTTACCCAG
*
1331972 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTTACA
* *
1331992 TTGTATCAATACATTTCT-CA
1 ATGTATCGATACATTT-TACA
*
1332012 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
1332032 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
1332052 ATGTATCGATACATTT
1 ATGTATCGATACATTT
1332068 AGGCATTTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.01
20 68 0.97
21 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:1334430 original size:51 final size:50
Alignment explanation
Indices: 1334366--1334533 Score: 169
Period size: 51 Copynumber: 3.3 Consensus size: 50
1334356 ATTTTTCATC
* * * *
1334366 TCGGGGATACTCCAATCAC-AGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAATC-CGA-TTTTATTTCCAAAACACCAATTTTCCATAA
* * *
1334417 TCGGGGATGCTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAA-TCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * * *
1334468 TCGGGGATACTCCAACTCTGATTTTATTTCCAAAACACTAACTTTT-TACAA
1 TCGGGGATACTCCAA-TCCGATTTTATTTCCAAAACACCAA-TTTTCCATAA
*
1334519 TCAGGGATACTCCAA
1 TCGGGGATACTCCAA
1334534 CCCTGTTATT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
51 92 0.93
52 7 0.07
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (50 bp):
TCGGGGATACTCCAATCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:1334562 original size:79 final size:78
Alignment explanation
Indices: 1334470--1334951 Score: 531
Period size: 79 Copynumber: 6.2 Consensus size: 78
1334460 TTCCATAATC
* * *
1334470 GGGGATACTCCAACTCTGATTTTATTTCCAAAACA-CTAACTTTTTACAATCAGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACATC-AA-TTTTTACAATCGGGGATACTCCAA
*
1334534 CCCTGTTATTTTTGA
64 CCCTGTTATTTTCGA
* *
1334549 GGGGACACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTT-C-ATCGAGGATACTCCAAAC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTTACAATCGGGGATACTCC-AAC
1334612 CC-GTTATTTTCGA
65 CCTGTTATTTTCGA
*
1334625 GGGGATA-TCCCAAC-CCTGGTTTTATTTCTAAAACATCAATTTTT-C-ATCGGGGATACTCCAA
1 GGGGATACT-CCAACTCC-GATTTTATTTCTAAAACATCAATTTTTACAATCGGGGATACTCCAA
1334686 CCCTGTTATTTTCGA
64 CCCTGTTATTTTCGA
* ** * * * *
1334701 GGGGATACCCCAAC-CCTGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCC-GATTTTATTTCTAAAACATCAATTT-TTACAATCGGGGATACTCCAA
*
1334765 -CCTCGTTATTTCCGA
64 CCCT-GTTATTTTCGA
* * * *
1334780 GGGGATACTCCAAC-CCCAGTTTTATTTCTAAAATATCAAATTTT-CATAGTCAGGGATACTCCA
1 GGGGATACTCCAACTCCGA-TTTTATTTCTAAAACATCAATTTTTACA-A-TCGGGGATACTCCA
** *
1334843 ACCCCCTTATTTCCGA
63 ACCCTGTTATTTTCGA
* * *
1334859 GGGGATACTCCAA-TCCCGATTTTATTTCTAAATCATCGATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACT-CCGATTTTATTTCTAAAACATCAATTTTT-ACAATCGGGGATACTCCAA
1334923 CCCTGTTATTTTCGA
64 CCCTGTTATTTTCGA
1334938 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1334952 CCCATTATTA
Statistics
Matches: 347, Mismatches: 37, Indels: 37
0.82 0.09 0.09
Matches are distributed among these distances:
75 8 0.02
76 121 0.35
77 8 0.02
78 10 0.03
79 192 0.55
80 7 0.02
81 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTTACAATCGGGGATACTCCAACC
CTGTTATTTTCGA
Found at i:1340072 original size:12 final size:14
Alignment explanation
Indices: 1340048--1340081 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1340038 TTATTCTGAA
1340048 ATAAAAATAAATTT
1 ATAAAAATAAATTT
1340062 -TAAAAAT-AATTT
1 ATAAAAATAAATTT
1340074 ATAAAAAT
1 ATAAAAAT
1340082 GATGGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAAAATAAATTT
Found at i:1344915 original size:13 final size:13
Alignment explanation
Indices: 1344897--1344922 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1344887 CATTATGCTC
1344897 TGTATCGATACAT
1 TGTATCGATACAT
1344910 TGTATCGATACAT
1 TGTATCGATACAT
1344923 GTTCATTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1345297 original size:26 final size:30
Alignment explanation
Indices: 1345271--1345326 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
1345261 CAAAGCATTC
*
1345271 AAAG-TTTA-ATTTATT-TTTTTATTTTCA
1 AAAGCTTTACATTCATTGTTTTTATTTTCA
1345298 AAAGCTTTTACATTCATTGTTTTTATTTT
1 AAAGC-TTTACATTCATTGTTTTTATTTT
1345327 TTGAAAGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
29 4 0.17
30 6 0.25
31 10 0.42
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (30 bp):
AAAGCTTTACATTCATTGTTTTTATTTTCA
Found at i:1352353 original size:15 final size:15
Alignment explanation
Indices: 1352330--1352372 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1352320 GTTTTATTTT
* *
1352330 TAATTATATTTTATA
1 TAATAATATTATATA
1352345 TAATAATATTATATA
1 TAATAATATTATATA
*
1352360 -AATAAAATTATAT
1 TAATAATATTATAT
1352373 TTTTGTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATAATATTATATA
Found at i:1352374 original size:34 final size:34
Alignment explanation
Indices: 1352330--1352428 Score: 100
Period size: 34 Copynumber: 2.9 Consensus size: 34
1352320 GTTTTATTTT
1352330 TAATTATATTTTATATAATAATATTATATAAATA-A
1 TAATTATATTTTATATAATAATATTA-A-AAATATA
*
1352365 -AATTATATTTT-TGTAATAAT-TTAAAAATATA
1 TAATTATATTTTATATAATAATATTAAAAATATA
* *
1352396 TAA-TATATCATTTATATTATAATAATAAAAATA
1 TAATTATAT--TTTATATAATAATATTAAAAATA
1352429 ATTTATGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
30 5 0.09
31 7 0.13
32 5 0.09
33 11 0.20
34 18 0.33
35 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (34 bp):
TAATTATATTTTATATAATAATATTAAAAATATA
Found at i:1357042 original size:17 final size:19
Alignment explanation
Indices: 1357020--1357059 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
1357010 TAGCTTTAAG
1357020 TTTTTTAGTTTT-TT-TTT
1 TTTTTTAGTTTTCTTATTT
1357037 TTTTTTAGTTTTCTTATTT
1 TTTTTTAGTTTTCTTATTT
1357056 TTTT
1 TTTT
1357060 CCATTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.07, C:0.03, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTTTTAGTTTTCTTATTT
Found at i:1359273 original size:12 final size:12
Alignment explanation
Indices: 1359256--1359303 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1359246 ACTTAAGAAA
1359256 AAGAAGAAAAAG
1 AAGAAGAAAAAG
*
1359268 AAGAAGAAGAAG
1 AAGAAGAAAAAG
*
1359280 AAGAA-AAATGAG
1 AAGAAGAAA-AAG
*
1359292 AAGAAAAAAAAG
1 AAGAAGAAAAAG
1359304 GAAAATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.83
13 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:1359275 original size:21 final size:21
Alignment explanation
Indices: 1359250--1359309 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1359240 GCATAAACTT
1359250 AAGAAAAAGAAGAAAAA-GAAG
1 AAGAAAAAGAAGAAAAATG-AG
*
1359271 AAGAAGAAGAAGAAAAATGAG
1 AAGAAAAAGAAGAAAAATGAG
* *
1359292 AAGAAAAAAAAGGAAAAT
1 AAGAAAAAGAAGAAAAAT
1359310 CATATTATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (21 bp):
AAGAAAAAGAAGAAAAATGAG
Found at i:1359296 original size:3 final size:3
Alignment explanation
Indices: 1359250--1359284 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1359240 GCATAAACTT
* *
1359250 AAG AAA AAG AAG AAA AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1359285 AAATGAGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1360530 original size:51 final size:51
Alignment explanation
Indices: 1360469--1360585 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
1360459 AAAATAACGG
* *
1360469 GGTTAGAGTATCCCTAATGGTGAAAAATTGATATTTTAGAAATAAAAATGA
1 GGTTAGAGTATCCCTAATGGTGAAAAATCGATATTTGAGAAATAAAAATGA
* * * * * *
1360520 GGTTGGAGTATCTCC-GATGGTGAAAAGTCGATATTTGGGAAATAAAATTGG
1 GGTTAGAGTATC-CCTAATGGTGAAAAATCGATATTTGAGAAATAAAAATGA
1360571 GGTTAGAGTATCCCT
1 GGTTAGAGTATCCCT
1360586 TAAAAATAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 2 0.04
51 51 0.93
52 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTAGAGTATCCCTAATGGTGAAAAATCGATATTTGAGAAATAAAAATGA
Found at i:1360717 original size:79 final size:79
Alignment explanation
Indices: 1360629--1361111 Score: 407
Period size: 79 Copynumber: 6.1 Consensus size: 79
1360619 GAAAACGGGA
* * * *
1360629 TTGGAGTATCCCCTCGAAAATAATGGGGTTATAGTACCCCCAATGGCT-AAAAATCAATGTTTTA
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGG-TGAAAAATCAATGTTTTA
1360693 GAAATAAAACCGAGG
65 GAAATAAAACCGAGG
* * * * * * *
1360708 TTGGAGTATCTCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTATTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
* * *
1360773 AAATAAAATCAAGA
66 AAATAAAACCGAGG
* * * * * * **
1360787 TTGGAGTAGCCCCT-TAGAAATAACGGGGTTGGGGTATCTCCGGTGGT-AGAAAATCGGTGTTTT
1 TTGGAGTATCCCCTCGA-AAATAACGGGGTTAGAGTATCCCCGATGGTGA-AAAATCAATGTTTT
* *
1360850 AGAAATAAAATCGGGG
64 AGAAATAAAACCGAGG
* * * * * ** * *
1360866 TTGAAGTATCCCTTCGGATATAACGGGGATAGAGTATCCTTGATGGTGGAAAATCAATATTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
* *
1360931 AAATAAAATCGGGG
66 AAATAAAACCGAGG
* * **** * *
1360945 TTGAAGTATCCCCTCGAAAATAACGGTGTTAGAGTATCTTTAAAGGTGAAAAATCGATGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
* * *
1361010 AAATAGAACTGGGG
66 AAATAAAACCGAGG
* * * * ** **
1361024 TTGGAGTATCCCCTCAAAAATAATGAGGTTGGAGTATCCCCGACAGTGAAAAATCGGTGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
1361089 AAATAAAACC-AGGG
66 AAATAAAACCGA-GG
*
1361103 TTAGAGTAT
1 TTGGAGTAT
1361112 TTTCGATAGT
Statistics
Matches: 323, Mismatches: 75, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
78 3 0.01
79 320 0.99
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
AAATAAAACCGAGG
Found at i:1361104 original size:158 final size:155
Alignment explanation
Indices: 1360633--1361104 Score: 460
Period size: 158 Copynumber: 3.0 Consensus size: 155
1360623 ACGGGATTGG
* * * * *
1360633 AGTATCCCCTCGAAAATAATGGGGTTATAGTACCCCCAATGGCTAAAAATCAATGTTTTAGAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTAGAGTATCTCCAATGG-TAAAAATCGATGTTTTAGAAAT
* * * * *
1360698 AAAACCGAGGTTGGAGTATCTCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATT
65 -AAACTGGGGTTGGAGTATCCCCTCAAAAATAAGA-GGTTGGAGTATCCCCGATGGTGAAAAATC
* * *
1360763 AGTATTTTAGAAATAAAATCAAGATTGG
128 AGTATTTTAGAAATAAAATCAGGGTTGA
* * * * ** *
1360791 AGTAGCCCCT-TAGAAATAACGGGGTTGGGGTATCTCCGGTGGTAGAAAATCGGTGTTTTAGAAA
1 AGTATCCCCTCGA-AAATAACGGGGTTAGAGTATCTCCAATGGTA-AAAATCGATGTTTTAGAAA
* * * ** * * * * ** *
1360855 TAAAATCGGGGTTGAAGTATCCCTTCGGATATAACGGGGATAGAGTATCCTTGATGGTGGAAAAT
64 TAAACT-GGGGTTGGAGTATCCCCTCAAAAATAA-GAGGTTGGAGTATCCCCGATGGTGAAAAAT
* *
1360920 CAATATTTTAGAAATAAAATCGGGGTTGA
127 CAGTATTTTAGAAATAAAATCAGGGTTGA
* ** *
1360949 AGTATCCCCTCGAAAATAACGGTGTTAGAGTATCTTTAAAGGTGAAAAATCGATGTTTTAGAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTAGAGTATCTCCAATGGT-AAAAATCGATGTTTTAGAAAT
**
1361014 AGAACTGGGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGAGTATCCCCGACAGTGAAAAATC
65 A-AACTGGGGTTGGAGTATCCCCTCAAAAATAA-GAGGTTGGAGTATCCCCGATGGTGAAAAATC
* * *
1361079 GGTGTTTTAGAAATAAAACCAGGGTT
128 AGTATTTTAGAAATAAAATCAGGGTT
1361105 AGAGTATTTT
Statistics
Matches: 242, Mismatches: 65, Indels: 14
0.75 0.20 0.04
Matches are distributed among these distances:
157 6 0.02
158 231 0.95
159 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (155 bp):
AGTATCCCCTCGAAAATAACGGGGTTAGAGTATCTCCAATGGTAAAAATCGATGTTTTAGAAATA
AACTGGGGTTGGAGTATCCCCTCAAAAATAAGAGGTTGGAGTATCCCCGATGGTGAAAAATCAGT
ATTTTAGAAATAAAATCAGGGTTGA
Found at i:1363305 original size:20 final size:20
Alignment explanation
Indices: 1363280--1363330 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1363270 GAAGTTTGTC
*
1363280 TCGATATATTTACTTATATA
1 TCGATACATTTACTTATATA
* *
1363300 TCGATACATTTACTTATTTG
1 TCGATACATTTACTTATATA
1363320 TCGATACATTT
1 TCGATACATTT
1363331 CCTTGGCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (20 bp):
TCGATACATTTACTTATATA
Found at i:1364181 original size:119 final size:119
Alignment explanation
Indices: 1363960--1364608 Score: 739
Period size: 119 Copynumber: 5.4 Consensus size: 119
1363950 GAGAGAGGCA
* * * *
1363960 TCCTACTCTTTGAGGACTAGAAGGTGTCACCAGGCTTGTGTAGGCTTTAAAAGAAAAAAAAAGTG
1 TCCTACTCTTTGAGGACTAGAAGGTGCCACCA-ACTTGTGTGGGCTTTAAAAG----AAAAAGCG
** *
1364025 TCCAGCTCTTTGAGAACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAGAAGGTG
61 TCTTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAGAAGAAGGTG
* * *
1364084 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAACGTCTTG
1 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCTTG
* *
1364149 CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTGTAGGCTTT-AGAAAGAAGGTG
66 CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAG-AAGAAGGTG
* * * *
1364203 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGAAAAAGCATCATG
1 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCTTG
* * * * * * *
1364268 CTTTTTAAGTACTAAAAGATGCCACCAACTAGTTTGGGCTTTAA-AAGGAATGTG
66 CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAGAA-GAAGGTG
* * * *
1364322 TCCTACTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTTT
1 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCTTG
* * * *
1364387 CTTTTTGAGGACTAAAAGATGCCACCAACTTATATGGGCTTTAA-AAGAAAGGTG
66 CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAGAAG-AAGGTG
* * * * * * * *
1364441 TCCTACTCTTTAAGAACTAGAAGGTACCACTAACTTGTATGGGCTTTAAAAGCAAAGGCATCTTG
1 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCTTG
* * * * *
1364506 CTCTTTGAGTACTGAAAGGTGCCACTAACTTATATGGGCTTTAAGAGGAGAAGGCG
66 CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAGA--AGAAGGTG
* * **
1364562 TCCTGCTCTTTAAGGACT-GAAAGGTGCCGTCAACTTGTGTGGGCTTT
1 TCCTACTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTT
1364609 GAGGATGAAA
Statistics
Matches: 457, Mismatches: 60, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
118 5 0.01
119 357 0.78
120 3 0.01
121 43 0.09
122 2 0.00
123 17 0.04
124 30 0.07
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (119 bp):
TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCTTG
CTCTTTGAGAACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAGAAGAAGGTG
Found at i:1364631 original size:35 final size:36
Alignment explanation
Indices: 1364569--1364644 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
1364559 GCGTCCTGCT
* ** *
1364569 CTTTAAGGACTGAAAGGTGCCGTCAACTTGTGTGGG
1 CTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGG
*
1364605 CTTTGAGGA-TGAAATGTGCCACCAACTTGTATGGG
1 CTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGG
1364640 CTTTG
1 CTTTG
1364645 TAAAGAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 27 0.77
36 8 0.23
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (36 bp):
CTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGG
Found at i:1364632 original size:96 final size:97
Alignment explanation
Indices: 1364508--1364706 Score: 237
Period size: 96 Copynumber: 2.1 Consensus size: 97
1364498 GCATCTTGCT
* * * *
1364508 CTTTGAGTACTGAAAGGTGCCACTAACTTATATGGGC-TT-TAAGAGGAGAAGGCGTCCTGCTCT
1 CTTTGAGGACTGAAAGGTGCCACCAACTTATATGGGCTTTGTAA-A-GAAAAGGCGTCCTACTCT
* * *
1364571 TT-AAGGACTGAAAGGTGCCGTC-AACTTGTGTGGG
64 TTGAA-GACTAAAAGGTG-CGACTAACTTATGTGGG
* * *
1364605 CTTTGAGGA-TGAAATGTGCCACCAACTTGTATGGGCTTTGTAAAGAAAAGGCGTCTTACTCTTT
1 CTTTGAGGACTGAAAGGTGCCACCAACTTATATGGGCTTTGTAAAGAAAAGGCGTCCTACTCTTT
1364669 GAAGACTAAAAGGTGCGACTAACTTATGTGGG
66 GAAGACTAAAAGGTGCGACTAACTTATGTGGG
1364701 CTTTGA
1 CTTTGA
1364707 AAGAAAAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
95 3 0.03
96 69 0.78
97 13 0.15
98 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (97 bp):
CTTTGAGGACTGAAAGGTGCCACCAACTTATATGGGCTTTGTAAAGAAAAGGCGTCCTACTCTTT
GAAGACTAAAAGGTGCGACTAACTTATGTGGG
Found at i:1364804 original size:60 final size:60
Alignment explanation
Indices: 1364605--1364840 Score: 240
Period size: 60 Copynumber: 3.8 Consensus size: 60
1364595 CTTGTGTGGG
* * * ** * * *
1364605 CTTTGAGGA-TGAAATGTGCCACCAACTTGTATGGGCTTTGTAAAGAAAAGGCGTCTTACT
1 CTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA-GTGTCCTGCT
* * * *
1364665 CTTTGAAGACTAAAAGGTGCGACTAACTTATGTGGGCTTTGAAAGAAAAAAGAAAAGTGTCCTGC
1 CTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT------AAAAAGAAAAGTGTCCTGC
1364730 T
60 T
* *
1364731 TTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAGTGTCCTGCT
1 CTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGTGTCCTGCT
* * * *
1364791 CTTTGAGGGCTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAA
1 CTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1364841 AGCATCCTGC
Statistics
Matches: 145, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
60 71 0.49
61 24 0.17
66 42 0.29
67 8 0.06
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (60 bp):
CTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGTGTCCTGCT
Found at i:1364830 original size:283 final size:275
Alignment explanation
Indices: 1364330--1364862 Score: 642
Period size: 283 Copynumber: 1.9 Consensus size: 275
1364320 TGTCCTACTT
* * *
1364330 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTTTCTTTTTGA
1 TTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAGGCGTCTTACTCTTTGA
* *
1364395 GGACTAAAAGATGCCACCAACTTATATGGGCTTTAAAAGAAAGGTGTCCTACTCTTTAAGAACTA
66 AGACTAAAAGATGCCACCAACTTATATGGGCTTTAAAAGAAAAGTGTCCTACTCTTTAAGAACTA
* * *
1364460 GAAGGTACCACTAACTTGTATGGGCTTTAAAAGCAAAGGCATCTTGCTCTTTGAGTACTGAAAGG
131 GAAGGTACCACCAACTTGTATGGGCTTTAAAAGCAAAGG-ATCCTGCTCTTTGAGGACTGAAAGG
* * * * * *
1364525 TGCCACTAACTTATATGGGCTTTAAGAGGAGAAGGCGTCCTGCTCTTTAAGGACTGAAAGGTGCC
195 TGCCACCAACCTATATGGGCTTTAAAAGGAAAAAGCATCCTGCTCTTTAAGGACTGAAAGGTGCC
1364590 GTCAACTTGTGTGGGC
260 GTCAACTTGTGTGGGC
* * *
1364606 TTTGAGGA-TGAAATGTGCCACCAACTTGTATGGGCTTTGTAAAGAAAAGGCGTCTTACTCTTTG
1 TTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTT-AAAAGAAAAGGCGTCTTACTCTTTG
* * * * * *
1364670 AAGACTAAAAGGTGCGACTAACTTATGTGGGCTTTGAAAGAAAAAAGAAAAGTGTCCTGCTTTTT
65 AAGACTAAAAGATGCCACCAACTTATATGGGCTTT-------AAAAGAAAAGTGTCCTACTCTTT
* * *
1364735 GAAG-ACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAGTG-TCCTGCTCTTTGA
123 -AAGAACTAG-AAGGTACCACCAACTTGTATGGGCTTT-AAAAGCAAAG-GATCCTGCTCTTTGA
* * * * *
1364797 GGGCTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAGCATCCTGCTTTTTGAGGAC
184 GGACTGAAAGGTGCCACCAACCTATATGGGCTTTAAAAGGAAAAAGCATCCTGCTCTTTAAGGAC
1364862 T
249 T
1364863 AAAAAGATAA
Statistics
Matches: 214, Mismatches: 31, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
275 27 0.13
276 60 0.28
282 1 0.00
283 113 0.53
284 12 0.06
285 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (275 bp):
TTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAGGCGTCTTACTCTTTGA
AGACTAAAAGATGCCACCAACTTATATGGGCTTTAAAAGAAAAGTGTCCTACTCTTTAAGAACTA
GAAGGTACCACCAACTTGTATGGGCTTTAAAAGCAAAGGATCCTGCTCTTTGAGGACTGAAAGGT
GCCACCAACCTATATGGGCTTTAAAAGGAAAAAGCATCCTGCTCTTTAAGGACTGAAAGGTGCCG
TCAACTTGTGTGGGC
Found at i:1364841 original size:126 final size:126
Alignment explanation
Indices: 1364606--1364842 Score: 296
Period size: 126 Copynumber: 1.9 Consensus size: 126
1364596 TTGTGTGGGC
* * ** *
1364606 TTTGAGGATGAAATGTGCCACCAACTTGTATGGGCTTTGTAAAGAAAAGGCGTCTTACTCTTTGA
1 TTTGAAGATGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCGTCCTACTCTTTGA
* * * *
1364671 AGACTAAAAGGTGCGACTAACTTATGTGGGCTTTGAAAGAAAAAAGAAAAGTGTCCTGCTT
66 AGACTAAAAGGTGCCACCAACCTATGTGGGCTTTAAAAGAAAAAAGAAAAGTGTCCTGCTT
* * * *
1364732 TTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAA-GTGTCCTGCTCTTTG
1 TTTGAAGA-TGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCGTCCTACTCTTTG
* * * * *
1364796 AGGGCTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAG
65 AAGACTAAAAGGTGCCACCAACCTATGTGGGCTTTAAAAGAAAAAAG
1364843 CATCCTGCTT
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
126 57 0.62
127 35 0.38
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (126 bp):
TTTGAAGATGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCGTCCTACTCTTTGA
AGACTAAAAGGTGCCACCAACCTATGTGGGCTTTAAAAGAAAAAAGAAAAGTGTCCTGCTT
Found at i:1379829 original size:22 final size:20
Alignment explanation
Indices: 1379776--1379831 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1379766 CAAAACCTGG
1379776 AATGTATCGATACAATGATA
1 AATGTATCGATACAATGATA
*
1379796 AATGTATCGATACAATTATA
1 AATGTATCGATACAATGATA
*
1379816 AGTATGTATAGATACA
1 A--ATGTATCGATACA
1379832 TTTACTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 20 0.62
22 12 0.38
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATGATA
Found at i:1379843 original size:20 final size:20
Alignment explanation
Indices: 1379818--1379859 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1379808 CAATTATAAG
1379818 TATGTATAGATACATTTACT
1 TATGTATAGATACATTTACT
* *
1379838 TATGTATCGATACATTTCCT
1 TATGTATAGATACATTTACT
1379858 TA
1 TA
1379860 GCAGATGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (20 bp):
TATGTATAGATACATTTACT
Found at i:1385856 original size:60 final size:59
Alignment explanation
Indices: 1385776--1385973 Score: 197
Period size: 60 Copynumber: 3.3 Consensus size: 59
1385766 GTCTTCTACA
* * *
1385776 TAACCAACTAAAGTGGACTTAATGAAAAACTAAAAATGCTAACAT-TATTGGTTTTACATT
1 TAACCAACTAGAGTGGACTTAATGAAAAACTAAAAATGCTAAC-TCTATCGGTTTT-CAAT
* * * * * *
1385836 TAACCAACTAGAGTGAACTTAATGGAAATCT-AAAATACTAACTCTATCAGTTTTCTAAG
1 TAACCAACTAGAGTGGACTTAATGAAAAACTAAAAATGCTAACTCTATCGGTTTTC-AAT
* * * *
1385895 TAACCAACTAGAGTGGACTTACT-AAGAAACTAAAAATGCCAACTCTACCGGTTTTTCACT
1 TAACCAACTAGAGTGGACTTAATGAA-AAACTAAAAATGCTAACTCTATCGG-TTTTCAAT
*
1385955 TAACCAACTATA-TGGACTT
1 TAACCAACTAGAGTGGACTT
1385974 TCTCTCTTTA
Statistics
Matches: 113, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
58 3 0.03
59 51 0.45
60 54 0.48
61 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (59 bp):
TAACCAACTAGAGTGGACTTAATGAAAAACTAAAAATGCTAACTCTATCGGTTTTCAAT
Found at i:1385928 original size:59 final size:59
Alignment explanation
Indices: 1385776--1385929 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 59
1385766 GTCTTCTACA
* * ** **
1385776 TAACCAACTAAAGTGGACTTAATGAA-AAACTAAAAATGCTAACATTATTGGTTTTACATT
1 TAACCAACTAGAGTGGACTTAAT-AAGAAACT-AAAATACTAACATTATCAGTTTTACAAG
* *
1385836 TAACCAACTAGAGTGAACTTAAT-GGAAATCTAAAATACTAAC-TCTATCAGTTTT-CTAAG
1 TAACCAACTAGAGTGGACTTAATAAGAAA-CTAAAATACTAACAT-TATCAGTTTTAC-AAG
*
1385895 TAACCAACTAGAGTGGACTTACTAAGAAACTAAAA
1 TAACCAACTAGAGTGGACTTAATAAGAAACTAAAA
1385930 ATGCCAACTC
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.03
59 49 0.63
60 27 0.35
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (59 bp):
TAACCAACTAGAGTGGACTTAATAAGAAACTAAAATACTAACATTATCAGTTTTACAAG
Found at i:1386099 original size:2 final size:2
Alignment explanation
Indices: 1386092--1386129 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1386082 TTGAGTATCG
1386092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1386130 GAAAATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1387373 original size:13 final size:13
Alignment explanation
Indices: 1387355--1387380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1387345 CAATTTTTTG
1387355 TGTATCGATACAT
1 TGTATCGATACAT
1387368 TGTATCGATACAT
1 TGTATCGATACAT
1387381 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1389946 original size:13 final size:13
Alignment explanation
Indices: 1389928--1389966 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1389918 ATAATCACCC
1389928 TGTATCGATACAA
1 TGTATCGATACAA
1389941 TGTATCGATACAA
1 TGTATCGATACAA
1389954 TGTATCGATACAA
1 TGTATCGATACAA
1389967 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1392063 original size:15 final size:15
Alignment explanation
Indices: 1392043--1392073 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1392033 ATTTCGTTTG
*
1392043 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1392058 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1392073 G
1 G
1392074 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1393857 original size:21 final size:21
Alignment explanation
Indices: 1393828--1393872 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1393818 AAGTTTTCAT
*
1393828 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1393848 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1393870 TTT
1 TTT
1393873 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1396110 original size:13 final size:13
Alignment explanation
Indices: 1396092--1396117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1396082 CAATTTTTTG
1396092 TGTATCGATACAT
1 TGTATCGATACAT
1396105 TGTATCGATACAT
1 TGTATCGATACAT
1396118 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1396166 original size:33 final size:29
Alignment explanation
Indices: 1396124--1396196 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 29
1396114 ACATACTTGC
1396124 TGTATCGATACAAGTTTGGCTACTGCCAAGAAA
1 TGTATCGATACAA---T-GCTACTGCCAAGAAA
1396157 TGTATCGATAC-ATGCTACTGCCAAGAAA
1 TGTATCGATACAATGCTACTGCCAAGAAA
1396185 TGTATCGATACA
1 TGTATCGATACA
1396197 TCTTTTTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
28 26 0.67
29 1 0.03
32 1 0.03
33 11 0.28
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (29 bp):
TGTATCGATACAATGCTACTGCCAAGAAA
Found at i:1396182 original size:28 final size:28
Alignment explanation
Indices: 1396142--1396197 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1396132 TACAAGTTTG
1396142 GCTACTGCCAAGAAATGTATCGATACAT
1 GCTACTGCCAAGAAATGTATCGATACAT
1396170 GCTACTGCCAAGAAATGTATCGATACAT
1 GCTACTGCCAAGAAATGTATCGATACAT
1396198 CTTTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (28 bp):
GCTACTGCCAAGAAATGTATCGATACAT
Found at i:1410737 original size:20 final size:20
Alignment explanation
Indices: 1410677--1410742 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1410667 TACACATTTA
1410677 ATTGTATCGATACATGTTGC
1 ATTGTATCGATACATGTTGC
**
1410697 ACAGTATCGATACA--TT--
1 ATTGTATCGATACATGTTGC
1410713 A---TATCGATACATGTTGC
1 ATTGTATCGATACATGTTGC
1410730 ATTGTATCGATAC
1 ATTGTATCGATAC
1410743 TTGAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 21 0.57
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGTTGC
Found at i:1410833 original size:13 final size:13
Alignment explanation
Indices: 1410815--1410840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1410805 TACACACAGT
1410815 ATGTATCGATACA
1 ATGTATCGATACA
1410828 ATGTATCGATACA
1 ATGTATCGATACA
1410841 GCATAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1417157 original size:20 final size:20
Alignment explanation
Indices: 1417122--1417162 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1417112 CAAATTTCTT
1417122 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1417144 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1417163 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1419540 original size:19 final size:19
Alignment explanation
Indices: 1419516--1419585 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
1419506 TAGCTAAACT
1419516 TGTATCGATACACATAGTA
1 TGTATCGATACACATAGTA
*
1419535 TGTATCGATACACACAGTA
1 TGTATCGATACACATAGTA
**
1419554 TGTATCGATACACCATAAAA
1 TGTATCGATACA-CATAGTA
1419574 TGTATCGATACA
1 TGTATCGATACA
1419586 TTGGCTTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 30 0.65
20 16 0.35
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACATAGTA
Found at i:1422937 original size:61 final size:60
Alignment explanation
Indices: 1422607--1424616 Score: 2032
Period size: 61 Copynumber: 33.9 Consensus size: 60
1422597 GAGCAAGACA
* *
1422607 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACG-----
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
1422662 CCTTTCAAAGCCCACACGAGTCGGTGGCA-TTTTCTAGTCCTCAAAGAGTAGGACACCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCC--TTT
** * * * *
1422724 TTTTTAAAAAAAAGCCCACATAAGTTGCTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC--T
1 CCTTT----CAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1422786 -C-TT-AAAGCCCACACATGTTGGTGGCA-TTTTCCAATCCTCAAAAAGCAGGACG-----
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
* * ** *
1422838 CCTTTAAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAATAGGACGCATTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCCTT-T
* * * *
1422899 CCTTTTAAAGCCCACAAAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1422959 CCTTTGCAAAGCCCACACAAGTTCGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCCTTCT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTT-T
* * * * *
1423021 CCTTTTAAAGCCCACAAAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGATGCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1423081 CCTTTGCAAAGCCCACACAAGTTCGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCATTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
1423142 CCTTTGCAAAGCCCACACAAGTTCGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1423203 CCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAAAGCAGGACGTCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
1423264 CCCTTTCAAAGCCCACAAAAGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGATGCTTTTT
1 -CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGC-CTTT
* * *
1423326 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCC-TTT
* * *
1423387 CTTTTTAAAAAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC--T
1 C-CTTT---CAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
* *
1423449 -C-TT-AAAGCCCACACATGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG-----
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
*
1423501 CCTTTAAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCCTT-T
* * * * *
1423562 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAAAGCAGGACGTCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * * *
1423622 CCTTTGCGAAGGCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAAGATGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
1423683 CCTTTGCAAAGCCCACAAAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* *
1423744 CCTTTGCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAAAGCAGGACGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
1423805 CCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAA-AGTAGGACGCCTTT
1 -CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
1423865 CCTTTGCAAAGCCCACAAAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGTAGGATGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* *
1423926 CCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCCTTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * ***
1423987 CCCTTTTAAAGCCCACACAAGTTGGTGGCACCTCT-AGTCCTCAAAAAGCAGGACATATTTT
1 -CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GCCTTT
* * * * * *
1424048 CTTTTTAAAGCCCACACGAGTTTGTGGCACCTTT-AGTCCTCAAAGAGCAGGACACATTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-CTTT
* * *
1424108 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAAAAGC-GAGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAG-GACGCC-TTT
* * **
1424168 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTTGTCCTCAAAGAGCAGGACG-----
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
1424223 CCTTTCAAAGCCCATACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGAACACCTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTT-T
*
1424284 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAAG-AGGACG-----
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG-AGCAGGACGCCTTT
* * * *
1424339 CCTTTCAAAG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-CTTT
* *
1424399 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA---C--A
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
1424454 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAGGAGCAGGACACC--T
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
*
1424512 -C-TT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCC--T
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1424567 --TTT-AAAGCCCACACGAGTTGATGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
1424617 TGCACTTTAT
Statistics
Matches: 1705, Mismatches: 170, Indels: 160
0.84 0.08 0.08
Matches are distributed among these distances:
53 4 0.00
54 48 0.03
55 416 0.24
56 6 0.00
57 1 0.00
58 1 0.00
59 8 0.00
60 237 0.14
61 851 0.50
62 40 0.02
65 48 0.03
66 44 0.03
67 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (60 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:1425462 original size:19 final size:18
Alignment explanation
Indices: 1425438--1425500 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1425428 AAGCAGAAAA
1425438 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1425457 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
1425470 TGTATCGAAACATAAGTTT
1 TGTATCGATACATAAG-TT
1425489 TGTATCGATACA
1 TGTATCGATACA
1425501 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1425477 original size:32 final size:32
Alignment explanation
Indices: 1425436--1425508 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
1425426 ACAAGCAGAA
*
1425436 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGAAACATAAGTGTTGTATCGATAC
*
1425468 AATGTATCGAAACATAAGTTTTGTATCGATAC
1 AATGTATCGAAACATAAGTGTTGTATCGATAC
1425500 AATGTATCG
1 AATGTATCG
1425509 CTACGAAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
AATGTATCGAAACATAAGTGTTGTATCGATAC
Found at i:1425550 original size:13 final size:13
Alignment explanation
Indices: 1425532--1425557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1425522 GCCAAGGAAA
1425532 TGTATCGATACAT
1 TGTATCGATACAT
1425545 TGTATCGATACAT
1 TGTATCGATACAT
1425558 CGATCTTTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1425633 original size:19 final size:20
Alignment explanation
Indices: 1425595--1425668 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
1425585 GTTTACCCAG
*
1425595 ATGTATTGATACATTTTACA
1 ATGTATCGATACATTTTACA
1425615 ATGTATCGATACA-TTTACA
1 ATGTATCGATACATTTTACA
1425634 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
1425654 ATGTATCGATACATT
1 ATGTATCGATACATT
1425669 CAGGCATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 19 0.37
20 33 0.63
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:1428020 original size:52 final size:51
Alignment explanation
Indices: 1427953--1428351 Score: 249
Period size: 51 Copynumber: 7.6 Consensus size: 51
1427943 TCAAGTTTCT
1427953 CAATTGTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * * * *
1428004 CAATTTTCCTTTAATCGGGGATACTCGAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
* * * * * *
1428057 CAATTTTTCACAATCGAGGATACTCCAACCTC-G--TTATTTCATCAGGGATACTC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTT--TCA---AAACAC
* ** * * * * * * * *
1428110 TAA--CCCCGTTACCTCCGAGGGGATACTCCAAGCCTGGCTTTATTTCCAAAATAT
1 CAATTTTCC-ATA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * *
1428164 TAA-TTTCTCATAATCGGGGATACTCAAACCCTGGTTTTA-TTTCTAAAACAC
1 CAATTTTC-CATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
* * * *
1428215 TAATTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCGAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * * *
1428266 CAA-TTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTTC--AAAACAC
* * *
1428319 CAATTTTTCACAACCGGGGATACTCCAACCCCG
1 CAATTTTCCATAATCGGGGATACTCCAACCCCG
1428352 TTATTTTCAA
Statistics
Matches: 263, Mismatches: 60, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
49 6 0.02
50 11 0.04
51 101 0.38
52 56 0.21
53 52 0.20
54 11 0.04
55 3 0.01
56 14 0.05
57 3 0.01
59 6 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
Found at i:1432621 original size:106 final size:106
Alignment explanation
Indices: 1432339--1433050 Score: 569
Period size: 106 Copynumber: 6.7 Consensus size: 106
1432329 TCTCGAAAAG
* * * * * * * *
1432339 GTGGGGTTGGAGTATCCCCAAAGAT-AAAATTAT-GAAAATATTTAGGAATAAAGATAAAACTTG
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTTA
** * * * * *
1432402 AGTAGATTAGTGAAAAACGAGGTTGGATTATCTCCTTGGAGTT
66 AGT-TTTTA-TGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
** ** * * * * *
1432445 GTGGGGTTAAAGTTTCCCTGAAG-TCAAGA-ATTATGAAAACATTGAAGAACAAAGAGAAAATTT
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTA-GAAAATATTTAGGAACAAAGAGAAAATTT
* * * * *
1432508 AATTTTTTATGAAGAACGAGGCTAGAGTATCCCCTCAAAGTA
65 AAGTTTTTATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
*
1432550 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAACTTA
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTTA
** * * ** *
1432615 AGTTTTTAAAAAAGGACGGGGTTGGAGTATCCATTTGGAGTA
66 AGTTTTT-ATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
** ** * **
1432657 GTGGAATTAAAGTTTTCCCAAA-TTCGAAGATTTTAGAAAATATTTAAAAACAAAGAGAAAATTT
1 GTGGGGTTGGAGTTTCCCCAAAGTT-GAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTT
* * * * * * *
1432721 GATTTTTTATGAAGAACGAAGTTAGAGTATTCCTTTAGAGTG
65 AAGTTTTTATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
** * ** *
1432763 GTGGGGTTGGAGTTTCCCCAAAGTCAAAAATCAT-GAAAATATTTAGGAATAAAGAGAAAATTTA
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTTA
* * *
1432827 AGTTTTTTATGAAGAACAAGGTTGGGGCATCCCCTTAGAGTA
66 AG-TTTTTATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
* * * * * *
1432869 ATGGGCTTGGAGTTT-TCGAAAGTTGAAGATCTTAGAAAA-ATTTAGGAACATAGAGAAAATTTG
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTT-
** * * * * *
1432932 ATTTTTTTATGAAGAATGAGGCTGAAGTATTCCCTTAAAGTA
65 AAGTTTTTATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
* ** * * * *
1432974 GTGGGGTTGGAGTTTCCCTAAAGTCAAATATTTTATAAAATACTTAGGAACAAAGAGAAAATTTG
1 GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTTA
1433039 A-TTTTGTATGAA
66 AGTTTT-TATGAA
1433051 AAATGAGATT
Statistics
Matches: 467, Mismatches: 125, Indels: 28
0.75 0.20 0.05
Matches are distributed among these distances:
105 153 0.33
106 182 0.39
107 132 0.28
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (106 bp):
GTGGGGTTGGAGTTTCCCCAAAGTTGAAGATTTTAGAAAATATTTAGGAACAAAGAGAAAATTTA
AGTTTTTATGAAGAACGAGGTTGGAGTATCCCCTTAGAGTA
Found at i:1435782 original size:13 final size:13
Alignment explanation
Indices: 1435764--1435788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1435754 ATTATGCTTC
1435764 GTATCGATACATT
1 GTATCGATACATT
1435777 GTATCGATACAT
1 GTATCGATACAT
1435789 GTTCATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1444871 original size:20 final size:20
Alignment explanation
Indices: 1444843--1444892 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1444833 TCTAAAATGT
1444843 ATCGATACATTGAATGATGC
1 ATCGATACATTGAATGATGC
*
1444863 ATTGATACATTGAATGATGC
1 ATCGATACATTGAATGATGC
1444883 ATCGATACAT
1 ATCGATACAT
1444893 CTGGAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
ATCGATACATTGAATGATGC
Found at i:1447471 original size:13 final size:13
Alignment explanation
Indices: 1447453--1447479 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1447443 CATGGGATAA
1447453 TGTATCGATACAT
1 TGTATCGATACAT
1447466 TGTATCGATACAT
1 TGTATCGATACAT
1447479 T
1 T
1447480 ATGCCCAACG
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1448952 original size:73 final size:71
Alignment explanation
Indices: 1448875--1449111 Score: 184
Period size: 73 Copynumber: 3.3 Consensus size: 71
1448865 ATAACCAAGC
*
1448875 GCCACTAGCTTATATGGGCTTTAAAGTAGGTAAGAAAAAGTATCCTGCTCTTTGAGGACTAGAAT
1 GCCACTAGCTTGTATGGGCTTT-AAGTAGGTAAGAAAAAG-ATCCTGCTCTTTGAGGACTAGAAT
1448940 AGATAGGT
64 AGATAGGT
* * ** **
1448948 GCCACTAGCTTGTGTGAGCTTTGGGATAAATAAGGAAATAAG-T-CTAGCTCTTT-ATGGACTCA
1 GCCACTAGCTTGTATGGGCTTTAAG-TAGGTAA-GAAA-AAGATCCT-GCTCTTTGA-GGACT-A
* * *
1449010 G-GTGGCTAGGT
60 GAATAGATAGGT
* * *
1449021 GCCATTAGCTTGTGTGGGCTTTGACGTAGGTAAG--AAA-ATCCTGCTCTTTGAGGACTA-AAGT
1 GCCACTAGCTTGTATGGGCTTT-AAGTAGGTAAGAAAAAGATCCTGCTCTTTGAGGACTAGAA-T
1449082 AGATAGGT
64 AGATAGGT
* * *
1449090 GCCACCAGCTTCTATAGGCTTT
1 GCCACTAGCTTGTATGGGCTTT
1449112 GGGATAGGTG
Statistics
Matches: 128, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
68 1 0.01
69 39 0.30
70 4 0.03
72 5 0.04
73 69 0.54
74 7 0.05
75 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (71 bp):
GCCACTAGCTTGTATGGGCTTTAAGTAGGTAAGAAAAAGATCCTGCTCTTTGAGGACTAGAATAG
ATAGGT
Found at i:1449113 original size:142 final size:140
Alignment explanation
Indices: 1448831--1449284 Score: 432
Period size: 142 Copynumber: 3.2 Consensus size: 140
1448821 ATTGAGATCG
* * * ** * * *
1448831 GTAAGAAAATGAGTCTAGCTCTTTATGGACAT-AGATAACCAAGCGCCACTAGCTTATATGGGCT
1 GTAAGAAAATAAGTCTAGCTCTTTACGGAC-TCAGGTGGCCAAGTGCCATTAGCTTGTATGGGCT
*
1448895 TTAAAGTAGGTAAGAAAAAGTATCCTGCTCTTTGAGGACTAGAA-TAGATAGGTGCCACTAGCTT
65 TT-AAGTAGGTAAG--AAA--ATCCTGCTCTTTGAGGACTA-AAGTAGATAGGTGCCACCAGCTT
*
1448959 GTGTGAGCTTTGGGATAA
124 -TATGAGCTTTGGGATAA
* * * * * *
1448977 ATAAGGAAATAAGTCTAGCTCTTTATGGACTCAGGTGGCTAGGTGCCATTAGCTTGTGTGGGCTT
1 GTAAGAAAATAAGTCTAGCTCTTTACGGACTCAGGTGGCCAAGTGCCATTAGCTTGTATGGGCTT
*
1449042 TGACGTAGGTAAGAAAATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACCAGCTTCTAT-A
66 T-AAGTAGGTAAGAAAATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACCAGCTT-TATGA
*
1449106 GGCTTTGGGATAG
129 -GCTTTGGGATAA
* * * * * **
1449119 GTGAGAAAATGAGTCTAGCTCTTTGCGGACTCAGGTGGCCAAGTGCCATCAACTTGTATAAGCTT
1 GTAAGAAAATAAGTCTAGCTCTTTACGGACTCAGGTGGCCAAGTGCCATTAGCTTGTATGGGCTT
* ** ** * *
1449184 TAAGTAGGTAAAAAAAATGTTATGCTCTTTGAGGACTGGAGCAG-TAGGTGCCACCAAC-TTATG
66 TAAGTAGGT-AAGAAAA--TCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACCAGCTTTATG
*
1449247 CGACTTTGGGATAA
128 AG-CTTTGGGATAA
*
1449261 GTAAAAAAATAAGTCTAGCTCTTT
1 GTAAGAAAATAAGTCTAGCTCTTT
1449285 GTGTAGGCTT
Statistics
Matches: 256, Mismatches: 44, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
141 14 0.05
142 143 0.56
143 13 0.05
144 23 0.09
145 1 0.00
146 62 0.24
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (140 bp):
GTAAGAAAATAAGTCTAGCTCTTTACGGACTCAGGTGGCCAAGTGCCATTAGCTTGTATGGGCTT
TAAGTAGGTAAGAAAATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACCAGCTTTATGAGC
TTTGGGATAA
Found at i:1449120 original size:69 final size:68
Alignment explanation
Indices: 1448916--1449128 Score: 191
Period size: 69 Copynumber: 3.0 Consensus size: 68
1448906 AAGAAAAAGT
**
1448916 ATCCTGCTCTTTGAGGACTAGAA-TAGATAGGTGCCACTAGCTTGTGTGAGCTTTGGGATAAATA
1 ATCCTGCTCTTTGAGGACTA-AAGTAGATAGGTGCCACTAGCTTGTGTG-GCTTTGGGATAGGTA
1448980 AGGAAATA
64 A-G-AA-A
* * * * * *
1448988 AGT-CTAGCTCTTT-ATGGACTCAGGTGGCTAGGTGCCATTAGCTTGTGTGGGCTTTGACG-TAG
1 A-TCCT-GCTCTTTGA-GGACTAAAGTAGATAGGTGCCACTAGCTTGTGT-GGCTTTG-GGATAG
1449050 GTAAGAAA
61 GTAAGAAA
* * * *
1449058 ATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACCAGCTTCTATAGGCTTTGGGATAGGTGA
1 ATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACTAGCTTGTGT-GGCTTTGGGATAGGTAA
1449123 GAAA
65 GAAA
1449127 AT
1 AT
1449129 GAGTCTAGCT
Statistics
Matches: 113, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
68 1 0.01
69 52 0.46
70 5 0.04
71 2 0.02
72 6 0.05
73 45 0.40
74 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (68 bp):
ATCCTGCTCTTTGAGGACTAAAGTAGATAGGTGCCACTAGCTTGTGTGGCTTTGGGATAGGTAAG
AAA
Found at i:1449542 original size:75 final size:73
Alignment explanation
Indices: 1449301--1449542 Score: 243
Period size: 72 Copynumber: 3.3 Consensus size: 73
1449291 GCTTTGAAAC
* * ** * * * *
1449301 AAGAAAAAGTATCATGCCCTTCAAGGACTGGAGTAGATAGGTGTCACTAGCTTGTGTGGGCTTTA
1 AAGAAAAAGCATCATGCTCTTTGAGGACTAGAGTAAATAGGTGCCACTAGTTTGTGTGGGCTTTA
1449366 TGGTAGGT
66 TGGTAGGT
* * * * * * *
1449374 AA-AAAAAGCGTCATGCTCCTTGAGGACTAGAGTAGATAGATGCCACCAATTTGTGTGGGCTTTG
1 AAGAAAAAGCATCATGCTCTTTGAGGACTAGAGTAAATAGGTGCCACTAGTTTGTGTGGGCTTTA
* *
1449438 TGGCAAGT
66 TGGTAGGT
* * * *
1449446 AAGAAAAAACATCTTGTTCTTTGAGGACTAGTTGATAAATAGGTGCCACTAGTTTGTGTGGGCTT
1 AAGAAAAAGCATCATGCTCTTTGAGGACTAG-AG-TAAATAGGTGCCACTAGTTTGTGTGGGCTT
**
1449511 TACAGTAGGT
64 TATGGTAGGT
*
1449521 AAGAAAAAGCATCATACTCTTT
1 AAGAAAAAGCATCATGCTCTTT
1449543 AAAAACTAAA
Statistics
Matches: 132, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
72 57 0.43
73 25 0.19
74 1 0.01
75 49 0.37
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (73 bp):
AAGAAAAAGCATCATGCTCTTTGAGGACTAGAGTAAATAGGTGCCACTAGTTTGTGTGGGCTTTA
TGGTAGGT
Found at i:1452149 original size:20 final size:20
Alignment explanation
Indices: 1452122--1452176 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1452112 CTGCCAATTT
*
1452122 CATGTATCGATACAATTTAA
1 CATGTATCGATACAATTGAA
** * *
1452142 GGTGTATCAATACTA-TGAA
1 CATGTATCGATACAATTGAA
1452161 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1452177 GTATCAATAC
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1452185 original size:32 final size:33
Alignment explanation
Indices: 1452144--1452207 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1452134 CAATTTAAGG
*
1452144 TGTATCAATACTATG-AACATGTATCGATACAA
1 TGTATCAATACTAAGCAACATGTATCGATACAA
*
1452176 TGTATCAATACTAAGCAATATGTATCGATACA
1 TGTATCAATACTAAGCAACATGTATCGATACA
1452208 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (33 bp):
TGTATCAATACTAAGCAACATGTATCGATACAA
Found at i:1452615 original size:32 final size:32
Alignment explanation
Indices: 1452579--1452680 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 32
1452569 TCAACATATG
1452579 CATTTTCGAAAAGCGTTTATAACCTTACCAAT
1 CATTTTCGAAAAGCGTTTATAACCTTACCAAT
* * *
1452611 CA-TTTC---AAGC-TTGTGTGCAATCATTAACATAT
1 CATTTTCGAAAAGCGTT-TAT--AA-CCTTACCA-AT
1452643 GCATTTTCGAAAAGCGTTTATAACCTTACCAAT
1 -CATTTTCGAAAAGCGTTTATAACCTTACCAAT
1452676 CATTT
1 CATTT
1452681 CAAGCTTGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 22
0.65 0.07 0.27
Matches are distributed among these distances:
27 2 0.04
28 6 0.11
30 2 0.04
31 10 0.19
32 9 0.17
33 4 0.08
34 10 0.19
35 2 0.04
37 6 0.11
38 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (32 bp):
CATTTTCGAAAAGCGTTTATAACCTTACCAAT
Found at i:1452675 original size:65 final size:65
Alignment explanation
Indices: 1452571--1452700 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
1452561 TATAAATTTC
1452571 AACATATGCATTTTCGAAAAGCGTTTATAACCTTACCAATCATTTCAAGCTTGTGTGCAATCATT
1 AACATATGCATTTTCGAAAAGCGTTTATAACCTTACCAATCATTTCAAGCTTGTGTGCAATCATT
1452636 AACATATGCATTTTCGAAAAGCGTTTATAACCTTACCAATCATTTCAAGCTTGTGTGCAATCATT
1 AACATATGCATTTTCGAAAAGCGTTTATAACCTTACCAATCATTTCAAGCTTGTGTGCAATCATT
1452701 CTCTTCGTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (65 bp):
AACATATGCATTTTCGAAAAGCGTTTATAACCTTACCAATCATTTCAAGCTTGTGTGCAATCATT
Found at i:1452948 original size:25 final size:25
Alignment explanation
Indices: 1452914--1452961 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1452904 GTAATTTTCA
*
1452914 ATTTAGTACTCCCCCTTAACAAAAT
1 ATTTAATACTCCCCCTTAACAAAAT
*
1452939 ATTTAATACTCTCCCTTAACAAA
1 ATTTAATACTCCCCCTTAACAAA
1452962 TTATCCCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTTAATACTCCCCCTTAACAAAAT
Found at i:1453095 original size:43 final size:43
Alignment explanation
Indices: 1453031--1453112 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
1453021 AGTTCTAAAA
* *
1453031 CAAATTTATTGCAAAATTACTTCTTCCTCTTTTTATTATCCCC
1 CAAATTTATTACAAAATTACTTCTTCCCCTTTTTATTATCCCC
*
1453074 CAAATTTATTTACAAAA-TACTTCTTCCCCTTTTTGTTAT
1 CAAATTTA-TTACAAAATTACTTCTTCCCCTTTTTATTAT
1453113 TGCAAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
43 28 0.80
44 7 0.20
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (43 bp):
CAAATTTATTACAAAATTACTTCTTCCCCTTTTTATTATCCCC
Found at i:1454506 original size:10 final size:10
Alignment explanation
Indices: 1454491--1454530 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
1454481 GGATAGCCGG
*
1454491 TTGTGACCAA
1 TTGTGACCGA
1454501 TTGTGACCGA
1 TTGTGACCGA
1454511 TTGTGACCGA
1 TTGTGACCGA
*
1454521 GTGTGACCGA
1 TTGTGACCGA
1454531 GCAAGCTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (10 bp):
TTGTGACCGA
Found at i:1454980 original size:13 final size:13
Alignment explanation
Indices: 1454961--1455000 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1454951 AATAGTACCC
1454961 ATGTATCGATACT
1 ATGTATCGATACT
* * *
1454974 CTGTATCAATACA
1 ATGTATCGATACT
1454987 ATGTATCGATACT
1 ATGTATCGATACT
1455000 A
1 A
1455001 AGAACTTTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACT
Found at i:1463522 original size:236 final size:236
Alignment explanation
Indices: 1463103--1463571 Score: 875
Period size: 236 Copynumber: 2.0 Consensus size: 236
1463093 GTTTGATTTT
1463103 GAGGATTTTCAAGATGAAGCACCTTGAGTGCGTCTTTGAGCGGGCAATTTCATTCGAGGAGCCAT
1 GAGGATTTTCAAGATGAAGCACCTTGAGTGCGTCTTTGAGCGGGCAATTTCATTCGAGGAGCCAT
* *
1463168 CGGATTGGTTGAAAAGTGTTTCAGTGTAAGATGGGACAGTTTCAAATGGTCTAGGCAGTAGGTGT
66 CGGATTGGTTGAAAAGTGTTTCAGTGTAAGATGGGACAGTTTCAAATGGTCTAGGCAGTAGATGC
1463233 GGGAGCTGCCCGATTGTGACCTGGGAGTGTCGATCGTGACCTGGAGATGGCTGCCTAGGCGTATT
131 GGGAGCTGCCCGATTGTGACCTGGGAGTGTCGATCGTGACCTGGAGATGGCTGCCTAGGCGTATT
*
1463298 TTGTTTAGGCTTTTCACCAAACAGGTGGTGGTCACTACCTG
196 TGGTTTAGGCTTTTCACCAAACAGGTGGTGGTCACTACCTG
*
1463339 GAGGATTTTCAAGATGAAGCACCTTGAGTGCGTCTTTGAGCGGGCAATTTCATTTGAGGAGCCAT
1 GAGGATTTTCAAGATGAAGCACCTTGAGTGCGTCTTTGAGCGGGCAATTTCATTCGAGGAGCCAT
*
1463404 CGGATTGTTTGAAAAGTGTTTCAGTGTAAGATGGGACAGTTTCAAATGGTCTAGGCAGTAGATGC
66 CGGATTGGTTGAAAAGTGTTTCAGTGTAAGATGGGACAGTTTCAAATGGTCTAGGCAGTAGATGC
* *
1463469 GGGAGCTGCCCGGTTGTGACCTGGGAGTGTCGATCGTGACCTGGAGGTGGCTGCCTAGGCGTATT
131 GGGAGCTGCCCGATTGTGACCTGGGAGTGTCGATCGTGACCTGGAGATGGCTGCCTAGGCGTATT
1463534 TGGTTTAGGCTTTTCACCAAACAGGTGGTGGTCACTAC
196 TGGTTTAGGCTTTTCACCAAACAGGTGGTGGTCACTAC
1463572 TTTGGGAGCT
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 226 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (236 bp):
GAGGATTTTCAAGATGAAGCACCTTGAGTGCGTCTTTGAGCGGGCAATTTCATTCGAGGAGCCAT
CGGATTGGTTGAAAAGTGTTTCAGTGTAAGATGGGACAGTTTCAAATGGTCTAGGCAGTAGATGC
GGGAGCTGCCCGATTGTGACCTGGGAGTGTCGATCGTGACCTGGAGATGGCTGCCTAGGCGTATT
TGGTTTAGGCTTTTCACCAAACAGGTGGTGGTCACTACCTG
Found at i:1470157 original size:13 final size:13
Alignment explanation
Indices: 1470116--1470168 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1470106 CCGTTTAAAG
1470116 CAATGTATCGATA
1 CAATGTATCGATA
1470129 CAA--T-TC-AT-
1 CAATGTATCGATA
1470137 C-ATGTATCGATA
1 CAATGTATCGATA
*
1470149 CATTGTATCGATA
1 CAATGTATCGATA
1470162 CAATGTA
1 CAATGTA
1470169 CCATGTATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1470161 original size:33 final size:33
Alignment explanation
Indices: 1470119--1470183 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1470109 TTTAAAGCAA
*
1470119 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
*
1470152 TGTATCGATACAATGTACCATGTATGGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
1470184 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:1470266 original size:13 final size:13
Alignment explanation
Indices: 1470248--1470274 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1470238 TACAATGAAC
1470248 ATGTATCGATACA
1 ATGTATCGATACA
1470261 ATGTATCGATACA
1 ATGTATCGATACA
1470274 A
1 A
1470275 ATCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1471070 original size:10 final size:10
Alignment explanation
Indices: 1471040--1471073 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1471030 ATTGCTTGGA
*
1471040 TTTCTTGTTG
1 TTTCTTGTTC
*
1471050 ATTCTTGTTC
1 TTTCTTGTTC
1471060 TTTCTTGTTC
1 TTTCTTGTTC
1471070 TTTC
1 TTTC
1471074 CTATTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.03, C:0.18, G:0.12, T:0.68
Consensus pattern (10 bp):
TTTCTTGTTC
Found at i:1482492 original size:20 final size:19
Alignment explanation
Indices: 1482466--1482521 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1482456 CGACCAGTTT
1482466 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
1482486 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
1482505 CATATATCGATATAATG
1 CATGTATCGATACAATG
1482522 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:1485071 original size:13 final size:13
Alignment explanation
Indices: 1485049--1485084 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1485039 ATAGTAACCC
1485049 TGTATCGATATAA
1 TGTATCGATATAA
*
1485062 TGTATTGATATAA
1 TGTATCGATATAA
1485075 TGTATCGATA
1 TGTATCGATA
1485085 CTTAGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:1485147 original size:20 final size:21
Alignment explanation
Indices: 1485117--1485155 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1485107 TCTGGGTCTT
1485117 TTCAGATGTATCGATACATCA
1 TTCAGATGTATCGATACATCA
1485138 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
1485156 TCCGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:1486973 original size:160 final size:155
Alignment explanation
Indices: 1486765--1487278 Score: 613
Period size: 155 Copynumber: 3.3 Consensus size: 155
1486755 TTTATCACCA
* * * * *
1486765 GGTCTGCTTTTATGCTAAAGGTAGATATTTAGGATAGGTTCATCTCATCTATTATCCCCTCTAAG
1 GGTCTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATCTCATCTATTATCCTCTTTAAG
* * *
1486830 TCCTTTAGGGGTACGGGGTACTTCTACGTCGAAAGTATCCCCTAGGGGCATTTTCATAATTTTTT
66 TCCTTTAGGGGTACAGAGTACTTCTACGTCGAAAGTATCCCCTAGGGGCATTTTCGTAATTTTTT
*
1486895 AGAACCGATTCGTAGGTTAGGTTGTCATTG
131 AGAACCAATTC-----TTAGGTTGTCATTG
*
1486925 GGTTTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATCTCATCTATTATCCTCTTTAAG
1 GGTCTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATCTCATCTATTATCCTCTTTAAG
* * *
1486990 TCCTTTTA-GGGTACAGAGTACTTCTACGTCGAAAATATCCCCTAGAGACATTTTCGTAATTTTT
66 TCC-TTTAGGGGTACAGAGTACTTCTACGTCGAAAGTATCCCCTAGGGGCATTTTCGTAATTTTT
* *
1487054 AAAAACCAATTCTTAGGTTGTCATTG
130 TAGAACCAATTCTTAGGTTGTCATTG
* * * * *
1487080 GGTCCGCTTTTATGTTGAAGGTAGACATATAAGAGAGGTTCATCTCAACTATTATCCTCTTTAAG
1 GGTCTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATCTCATCTATTATCCTCTTTAAG
* * * *
1487145 TCCTTTAGGGGTACCA-AGTACTTTTACGTC-AAAGGTATCCCCTAAGGGTATTTTTGTAATTTT
66 TCCTTTAGGGGTA-CAGAGTACTTCTACGTCGAAA-GTATCCCCTAGGGGCATTTTCGTAA-TTT
* * **
1487208 TTTAGAACCAAGTCCTAGGTTGTCACCG
128 TTTAGAACCAATTCTTAGGTTGTCATTG
* *** * *
1487236 AGTCTGCTTTTATGCCAAAGGT-GGCAGTTAGGATAGGTTCATC
1 GGTCTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATC
1487279 CCATTTCAAA
Statistics
Matches: 305, Mismatches: 44, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
154 7 0.02
155 129 0.42
156 44 0.14
160 121 0.40
161 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (155 bp):
GGTCTGCTTTTATGTTGAAGGTAGACATTTAGGATAGGTTCATCTCATCTATTATCCTCTTTAAG
TCCTTTAGGGGTACAGAGTACTTCTACGTCGAAAGTATCCCCTAGGGGCATTTTCGTAATTTTTT
AGAACCAATTCTTAGGTTGTCATTG
Found at i:1489478 original size:17 final size:17
Alignment explanation
Indices: 1489456--1489491 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1489446 ACATAAGAAT
1489456 AATTTGAGTTTGAATGG
1 AATTTGAGTTTGAATGG
1489473 AATTTGAGTTTGAATGG
1 AATTTGAGTTTGAATGG
1489490 AA
1 AA
1489492 CGTAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (17 bp):
AATTTGAGTTTGAATGG
Found at i:1492601 original size:2 final size:2
Alignment explanation
Indices: 1492594--1492629 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1492584 AACATTATGT
1492594 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1492630 CCTCATAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1496455 original size:21 final size:23
Alignment explanation
Indices: 1496439--1496486 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
1496429 TCAAATTATA
1496439 TTAAAAAA-AATTAAAATAAAAT
1 TTAAAAAATAATTAAAATAAAAT
1496461 TTAAAAAATAATT--AATAAAA-
1 TTAAAAAATAATTAAAATAAAAT
1496481 TTAAAA
1 TTAAAA
1496487 TATGATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.24
21 7 0.28
22 8 0.32
23 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
TTAAAAAATAATTAAAATAAAAT
Found at i:1496461 original size:11 final size:11
Alignment explanation
Indices: 1496438--1496488 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1496428 TTCAAATTAT
1496438 ATTAAAA-AAA
1 ATTAAAATAAA
1496448 ATTAAAATAAA
1 ATTAAAATAAA
1496459 ATTTAAAA-AATA
1 A-TTAAAATAA-A
1496471 ATT--AATAAA
1 ATTAAAATAAA
1496480 ATTAAAATA
1 ATTAAAATA
1496489 TGATATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
9 6 0.17
10 9 0.26
11 12 0.34
12 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATTAAAATAAA
Found at i:1496464 original size:12 final size:10
Alignment explanation
Indices: 1496438--1496486 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
1496428 TTCAAATTAT
1496438 ATTAAAAAAA
1 ATTAAAAAAA
1496448 ATTAAAATAAA
1 ATTAAAA-AAA
1496459 ATTTAAAAAATA
1 A-TTAAAAAA-A
*
1496471 ATT-AATAAA
1 ATTAAAAAAA
1496480 ATTAAAA
1 ATTAAAA
1496487 TATGATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 4 0.12
10 13 0.39
11 8 0.24
12 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:1498057 original size:33 final size:33
Alignment explanation
Indices: 1498019--1498085 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1498009 GTTACAAGTT
*
1498019 ATGTATCGATACATT-TCTTCATATATCGATACA
1 ATGTATCGATACATTGT-ATCATATATCGATACA
*
1498052 ATGTATCGATACATTGTATCATGTATCGATACA
1 ATGTATCGATACATTGTATCATATATCGATACA
1498085 A
1 A
1498086 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTATCATATATCGATACA
Found at i:1498060 original size:13 final size:13
Alignment explanation
Indices: 1498042--1498071 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1498032 TTTCTTCATA
1498042 TATCGATACAATG
1 TATCGATACAATG
*
1498055 TATCGATACATTG
1 TATCGATACAATG
1498068 TATC
1 TATC
1498072 ATGTATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1498200 original size:33 final size:32
Alignment explanation
Indices: 1498136--1498200 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1498126 TAATTTGTCC
* * *
1498136 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTACCGATACAAAGAACATGTATCAATACA
*
1498168 ATGTACCGATACAAAGCAGCATGTATCAATACA
1 ATGTACCGATACAAAG-AACATGTATCAATACA
1498201 TTTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (32 bp):
ATGTACCGATACAAAGAACATGTATCAATACA
Found at i:1498769 original size:19 final size:19
Alignment explanation
Indices: 1498747--1498804 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
1498737 TTCTCCCCCT
1498747 TAAACGATTATCTCCTTTA
1 TAAACGATTATCTCCTTTA
** *
1498766 TAAAAAATTCTCTCC--T-
1 TAAACGATTATCTCCTTTA
1498782 TAAACGATTATCTCCTTTA
1 TAAACGATTATCTCCTTTA
1498801 TAAA
1 TAAA
1498805 AAATTCTCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 12 0.40
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAACGATTATCTCCTTTA
Found at i:1498771 original size:36 final size:36
Alignment explanation
Indices: 1498731--1498830 Score: 175
Period size: 35 Copynumber: 2.8 Consensus size: 36
1498721 TCTCCCCTTA
1498731 AAAAAATTCTCCCCCTTAAACGATTATCTCCTTTAT
1 AAAAAATTCTCCCCCTTAAACGATTATCTCCTTTAT
*
1498767 AAAAAATTCT-CTCCTTAAACGATTATCTCCTTTAT
1 AAAAAATTCTCCCCCTTAAACGATTATCTCCTTTAT
*
1498802 AAAAAATTCTCCCCCTTAAACAATTATCT
1 AAAAAATTCTCCCCCTTAAACGATTATCT
1498831 TCTCTCCCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 34 0.57
36 26 0.43
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (36 bp):
AAAAAATTCTCCCCCTTAAACGATTATCTCCTTTAT
Found at i:1498795 original size:16 final size:16
Alignment explanation
Indices: 1498744--1498798 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1498734 AAATTCTCCC
1498744 CCTTAAACGATTATCT
1 CCTTAAACGATTATCT
** *
1498760 CCTTTATAAAAAATTCTCT
1 CC--T-TAAACGATTATCT
1498779 CCTTAAACGATTATCT
1 CCTTAAACGATTATCT
1498795 CCTT
1 CCTT
1498799 TATAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 16 0.53
17 1 0.03
18 1 0.03
19 12 0.40
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (16 bp):
CCTTAAACGATTATCT
Found at i:1500702 original size:12 final size:12
Alignment explanation
Indices: 1500685--1500709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1500675 AATAGTACCA
1500685 ATGTATCGATAC
1 ATGTATCGATAC
1500697 ATGTATCGATAC
1 ATGTATCGATAC
1500709 A
1 A
1500710 AGGAATGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1505156 original size:16 final size:17
Alignment explanation
Indices: 1505135--1505168 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1505125 TAGCATATAA
*
1505135 TTTGCTC-ATTGTCCTT
1 TTTGCTCGATTCTCCTT
1505151 TTTGCTCGATTCTCCTT
1 TTTGCTCGATTCTCCTT
1505168 T
1 T
1505169 GAGCATAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.06, C:0.26, G:0.12, T:0.56
Consensus pattern (17 bp):
TTTGCTCGATTCTCCTT
Found at i:1506888 original size:20 final size:20
Alignment explanation
Indices: 1506861--1506915 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1506851 CCGTTACAAG
1506861 CTATGTATCGATACATT-T-
1 CTATGTATCGATACATTGTA
1506879 CTTCATGTATCGATACATTGTA
1 C-T-ATGTATCGATACATTGTA
1506901 CTATGTATCGATACA
1 CTATGTATCGATACA
1506916 AATAGTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.85
21 2 0.06
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (20 bp):
CTATGTATCGATACATTGTA
Found at i:1506983 original size:13 final size:13
Alignment explanation
Indices: 1506965--1507024 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
1506955 TACAATGAAC
1506965 ATGTATCGATACA
1 ATGTATCGATACA
1506978 ATGTATCGATACA
1 ATGTATCGATACA
* *
1506991 A---AGC-A-GC-
1 ATGTATCGATACA
1506998 ATGTATCGATACA
1 ATGTATCGATACA
1507011 ATGTATCGATACA
1 ATGTATCGATACA
1507024 A
1 A
1507025 AGCAGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 1 0.03
10 4 0.11
11 1 0.03
12 1 0.03
13 28 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1507003 original size:20 final size:20
Alignment explanation
Indices: 1506978--1507043 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1506968 TATCGATACA
1506978 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
1506998 ATGTATCGAT----A-CA--
1 ATGTATCGATACAAAGCAGC
1507011 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
1507031 ATGTATCGATACA
1 ATGTATCGATACA
1507044 TCTGGGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 23 0.59
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAGC
Found at i:1507006 original size:33 final size:33
Alignment explanation
Indices: 1506946--1507043 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
1506936 TGCTAGTTTC
* *
1506946 ATGTATCGATACAATG-AACATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
1506978 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
1507011 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
1507044 TCTGGGTGTA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 15 0.24
33 48 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAGCATGTATCGATACA
Found at i:1510798 original size:10 final size:11
Alignment explanation
Indices: 1510755--1510812 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
1510745 CCTTTTTTAC
*
1510755 AATATAA-TAT
1 AATATAATTTT
*
1510765 AATATAACTTTC
1 AATATAA-TTTT
* *
1510777 GATATGATTTT
1 AATATAATTTT
1510788 AATA-AATTTT
1 AATATAATTTT
1510798 AATATAATTTT
1 AATATAATTTT
1510809 AATA
1 AATA
1510813 GCTTGTGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 16 0.42
11 16 0.42
12 6 0.16
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
AATATAATTTT
Found at i:1510802 original size:21 final size:21
Alignment explanation
Indices: 1510768--1510909 Score: 124
Period size: 21 Copynumber: 6.8 Consensus size: 21
1510758 ATAATATAAT
** *
1510768 ATAACTTTCGATATGATTTTA
1 ATAACTTTTAATATAATTTTA
*
1510789 ATAAATTTTAATATAATTTTA
1 ATAACTTTTAATATAATTTTA
* * * ** *
1510810 ATAGCTTGTGATATGGTATTA
1 ATAACTTTTAATATAATTTTA
* * *
1510831 ATAAC-CTTGATAAAATTTTA
1 ATAACTTTTAATATAATTTTA
*
1510851 ATAACTTTTAATATAATTTTG
1 ATAACTTTTAATATAATTTTA
*
1510872 ATAACTTTTAATATAATCTTA
1 ATAACTTTTAATATAATTTTA
* *
1510893 GTAACTTTTTATATAAT
1 ATAACTTTTAATATAAT
1510910 ATCATTGAAA
Statistics
Matches: 94, Mismatches: 26, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 14 0.15
21 80 0.85
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAACTTTTAATATAATTTTA
Found at i:1510861 original size:10 final size:10
Alignment explanation
Indices: 1510846--1510884 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1510836 CTTGATAAAA
1510846 TTTTAATAAC
1 TTTTAATAAC
*
1510856 TTTTAATATAA
1 TTTTAATA-AC
*
1510867 TTTTGATAAC
1 TTTTAATAAC
1510877 TTTTAATA
1 TTTTAATA
1510885 TAATCTTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (10 bp):
TTTTAATAAC
Found at i:1511777 original size:20 final size:20
Alignment explanation
Indices: 1511752--1511801 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1511742 CAGTTTCATA
* *
1511752 TATCGATACAATTGTACATG
1 TATCGATACAAGTGAACATG
1511772 TATCGATAC-AGTGAACATG
1 TATCGATACAAGTGAACATG
1511791 TATCGATACAA
1 TATCGATACAA
1511802 AACATAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACAAGTGAACATG
Found at i:1512230 original size:32 final size:30
Alignment explanation
Indices: 1512180--1512252 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
1512170 AGTTTTGGCA
1512180 AACTTTTGATATTTTGATA-AATTTCTATATT
1 AACTTTTGATATTTTGATATAATTT-TATA-T
*
1512211 AA-TTTTGATAGGTTTTGATATAATTTTTTAT
1 AACTTTTGATA--TTTTGATATAATTTTATAT
1512242 AACTTTTGATA
1 AACTTTTGATA
1512253 AGATTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 8 0.22
31 5 0.14
32 19 0.51
33 5 0.14
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.55
Consensus pattern (30 bp):
AACTTTTGATATTTTGATATAATTTTATAT
Found at i:1512467 original size:15 final size:16
Alignment explanation
Indices: 1512437--1512469 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1512427 ATATAACCAT
1512437 ATGATATTAGACATAA
1 ATGATATTAGACATAA
*
1512453 ATGATTTTA-ACATAA
1 ATGATATTAGACATAA
1512468 AT
1 AT
1512470 ATAACAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (16 bp):
ATGATATTAGACATAA
Found at i:1512579 original size:21 final size:20
Alignment explanation
Indices: 1512538--1512656 Score: 87
Period size: 21 Copynumber: 5.8 Consensus size: 20
1512528 ATTTGGTTGT
* *
1512538 CTTTAATATGATTTTAATAA
1 CTTTAATATAATTTTAGTAA
* *
1512558 CTTTAAACATAATTTTGGTAA
1 CTTT-AATATAATTTTAGTAA
*
1512579 CTTTTAATATCATTTTAGTAA
1 C-TTTAATATAATTTTAGTAA
*
1512600 TCTTTAATATAA-TTTCGTAA
1 -CTTTAATATAATTTTAGTAA
* * *
1512620 TCTTTAATGTAGTTTTTGTAA
1 -CTTTAATATAATTTTAGTAA
* *
1512641 CATTTGATACAATTTT
1 C-TTTAATATAATTTT
1512657 GATAATTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
20 22 0.28
21 52 0.67
22 4 0.05
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (20 bp):
CTTTAATATAATTTTAGTAA
Found at i:1512621 original size:20 final size:21
Alignment explanation
Indices: 1512581--1512627 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1512571 TTTGGTAACT
*
1512581 TTTAATATCATTTTAGTAATC
1 TTTAATATCAATTTAGTAATC
*
1512602 TTTAATAT-AATTTCGTAATC
1 TTTAATATCAATTTAGTAATC
1512622 TTTAAT
1 TTTAAT
1512628 GTAGTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTAATATCAATTTAGTAATC
Found at i:1512752 original size:21 final size:21
Alignment explanation
Indices: 1512678--1512755 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1512668 ACGCAGTTTC
*
1512678 GATAACCATTT-ATATAATTTT
1 GATAACC-TTTGATATGATTTT
* * * *
1512699 GGTAAGCTTTAATATAGGTTTT
1 GATAACCTTTGATAT-GATTTT
1512721 GATAACCTTTGATATGATTTT
1 GATAACCTTTGATATGATTTT
* *
1512742 GTTAATCTTTGATA
1 GATAACCTTTGATA
1512756 ACATTTACAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 26 0.58
22 16 0.36
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (21 bp):
GATAACCTTTGATATGATTTT
Found at i:1512761 original size:21 final size:21
Alignment explanation
Indices: 1512717--1512761 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1512707 TTAATATAGG
**
1512717 TTTTGATAACCTTTGATATGA
1 TTTTGATAACCTTTGATAACA
* *
1512738 TTTTGTTAATCTTTGATAACA
1 TTTTGATAACCTTTGATAACA
1512759 TTT
1 TTT
1512762 ACATTTTGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (21 bp):
TTTTGATAACCTTTGATAACA
Found at i:1512854 original size:41 final size:40
Alignment explanation
Indices: 1512809--1512971 Score: 152
Period size: 41 Copynumber: 4.0 Consensus size: 40
1512799 TTTATAGTTT
* *
1512809 TTTATATAATTTTGGTAACTTTTGAAATAATTTTAGTGACC
1 TTTATATAATTTTGGTAACTTTTGAAATAATTTTA-TAAAC
*
1512850 TTTATATAATTTTGGTAAC--TTCAATATTAA-TTTATAAAC
1 TTTATATAATTTTGGTAACTTTTGAA-A-TAATTTTATAAAC
* *
1512889 TTTGATATAATTTTGATAACTTTTGATATAATTTTAATAAAC
1 TTT-ATATAATTTTGGTAACTTTTGAAATAATTTT-ATAAAC
* * * *
1512931 TTAGATATAATTTTGTTAAACTTTAGAAATGATTTTGATAA
1 TT-TATATAATTTTGGT-AACTTTTGAAATAATTTT-ATAA
1512972 TTGTTGATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
39 10 0.10
40 23 0.23
41 26 0.26
42 23 0.23
43 19 0.19
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (40 bp):
TTTATATAATTTTGGTAACTTTTGAAATAATTTTATAAAC
Found at i:1512909 original size:40 final size:42
Alignment explanation
Indices: 1512812--1513162 Score: 154
Period size: 42 Copynumber: 8.4 Consensus size: 42
1512802 ATAGTTTTTT
* * * * *
1512812 ATATAATTTTGGTAACTTTTGAA-ATAATTTTAGTGACCTTT-
1 ATATAATTTTGATAAC-TTTCAATATAATTTTAATAAACTTTG
*
1512853 ATATAATTTTGGTAAC-TTCAATATTAA-TTT-ATAAACTTTG
1 ATATAATTTTGATAACTTTCAATA-TAATTTTAATAAACTTTG
** *
1512893 ATATAATTTTGATAACTTTTGATATAATTTTAATAAACTTAG
1 ATATAATTTTGATAACTTTCAATATAATTTTAATAAACTTTG
* * * * *
1512935 ATATAATTTTGTTAAACTTT-AGAAATGATTTTGAT-AATTGTTG
1 ATATAATTTTGAT-AACTTTCA-ATATAATTTTAATAAACT-TTG
* * *
1512978 ATATGATTTTGACAACCTTTC-ATATAATTTTGAT-AACTTTGG
1 ATATAATTTTGATAA-CTTTCAATATAATTTTAATAAACTTT-G
* * * * *
1513020 AT-TTATTATTGGTGATCTTTGAA-ATAATTTTAAT-AACATTTT
1 ATATAATT-TTGAT-AACTTTCAATATAATTTTAATAAAC-TTTG
* * * * * *
1513062 ATATTATTTTGATAACCTTT-GATATTATTTTGATTGCAA-TTTA
1 ATATAATTTTGATAA-CTTTCAATATAATTTT-AAT-AAACTTTG
* * *** * * *
1513105 ATGTGATTTTTCCAACTTTCAATGTAATTTTAGTAATCTTTG
1 ATATAATTTTGATAACTTTCAATATAATTTTAATAAACTTTG
*
1513147 ATACAATTTTGATAAC
1 ATATAATTTTGATAAC
1513163 ATCTATTATA
Statistics
Matches: 234, Mismatches: 52, Indels: 47
0.70 0.16 0.14
Matches are distributed among these distances:
39 10 0.04
40 22 0.09
41 36 0.15
42 99 0.42
43 65 0.28
45 2 0.01
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (42 bp):
ATATAATTTTGATAACTTTCAATATAATTTTAATAAACTTTG
Found at i:1512914 original size:10 final size:11
Alignment explanation
Indices: 1512889--1513012 Score: 71
Period size: 11 Copynumber: 11.6 Consensus size: 11
1512879 ATTTATAAAC
1512889 TTTGATATAAT
1 TTTGATATAAT
*
1512900 TTTGATA-ACT
1 TTTGATATAAT
1512910 TTTGATATAAT
1 TTTGATATAAT
* *
1512921 TTTAATA-AAC
1 TTTGATATAAT
*
1512931 TTAGATATAAT
1 TTTGATATAAT
*
1512942 TTTGTTA-AACT
1 TTTGATATAA-T
* * *
1512953 TTAGAAATGAT
1 TTTGATATAAT
1512964 TTTG--ATAAT
1 TTTGATATAAT
*
1512973 TGTTGATATGAT
1 T-TTGATATAAT
* **
1512985 TTTGACA-ACC
1 TTTGATATAAT
*
1512995 TTTCATATAAT
1 TTTGATATAAT
1513006 TTTGATA
1 TTTGATA
1513013 ACTTTGGATT
Statistics
Matches: 80, Mismatches: 25, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
9 5 0.06
10 26 0.32
11 43 0.54
12 6 0.08
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (11 bp):
TTTGATATAAT
Found at i:1513003 original size:64 final size:63
Alignment explanation
Indices: 1512812--1513018 Score: 162
Period size: 64 Copynumber: 3.3 Consensus size: 63
1512802 ATAGTTTTTT
* * * ***
1512812 ATATAATTTTGGT-AACTTTTGAAATAATTTT-AGTGACCTTT-ATATAATTTT-GGTAACTT-C
1 ATATAATTTTGATAAAC-TTTGAAATAATTTTGA-TAACTTTTGATATAATTTTAACAAACTTAC
* * *
1512872 AATATTAA-TTT-ATAAACTTTGATATAATTTTGATAACTTTTGATATAATTTTAATAAACTTAG
1 -ATA-TAATTTTGATAAACTTTGAAATAATTTTGATAACTTTTGATATAATTTTAACAAACTTAC
* * * * * *
1512935 ATATAATTTTGTTAAACTTTAGAAATGATTTTGATAA-TTGTTGATATGATTTTGACAACCTTTC
1 ATATAATTTTGATAAACTTT-GAAATAATTTTGATAACTT-TTGATATAATTTTAACAAACTTAC
1512999 ATATAATTTTGAT-AACTTTG
1 ATATAATTTTGATAAACTTTG
1513019 GATTTATTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
60 20 0.17
61 23 0.19
62 15 0.13
63 16 0.14
64 44 0.37
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (63 bp):
ATATAATTTTGATAAACTTTGAAATAATTTTGATAACTTTTGATATAATTTTAACAAACTTAC
Found at i:1513094 original size:21 final size:21
Alignment explanation
Indices: 1512812--1513095 Score: 188
Period size: 21 Copynumber: 13.6 Consensus size: 21
1512802 ATAGTTTTTT
* *
1512812 ATATAATTTTGGTAACTTTTG
1 ATATAATTTTGATAACCTTTG
* *
1512833 AAATAATTTT-AGTGACCTTT-
1 ATATAATTTTGA-TAACCTTTG
* **
1512853 ATATAATTTTGGTAA-CTTCA
1 ATATAATTTTGATAACCTTTG
*
1512873 ATATTAA-TTT-ATAAACTTTG
1 ATA-TAATTTTGATAACCTTTG
*
1512893 ATATAATTTTGATAACTTTTG
1 ATATAATTTTGATAACCTTTG
* * *
1512914 ATATAATTTTAATAAACTTAG
1 ATATAATTTTGATAACCTTTG
* *
1512935 ATATAATTTTGTTAAACTTTAG
1 ATATAATTTTGATAACCTTT-G
* * *
1512957 AAATGATTTTGATAA-TTGTTG
1 ATATAATTTTGATAACCT-TTG
* * *
1512978 ATATGATTTTGACAACCTTTC
1 ATATAATTTTGATAACCTTTG
1512999 ATATAATTTTGATAA-CTTTGG
1 ATATAATTTTGATAACCTTT-G
* * * *
1513020 AT-TTATTATTGGTGATCTTTG
1 ATATAATT-TTGATAACCTTTG
* * * *
1513041 AAATAATTTTAATAACATTTT
1 ATATAATTTTGATAACCTTTG
*
1513062 ATATTATTTTGATAACCTTTG
1 ATATAATTTTGATAACCTTTG
*
1513083 ATATTATTTTGAT
1 ATATAATTTTGAT
1513096 TGCAATTTAA
Statistics
Matches: 202, Mismatches: 47, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
19 9 0.04
20 34 0.17
21 135 0.67
22 24 0.12
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.49
Consensus pattern (21 bp):
ATATAATTTTGATAACCTTTG
Found at i:1513335 original size:21 final size:19
Alignment explanation
Indices: 1513305--1513374 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 19
1513295 ACATAATTTT
1513305 TATGAATTTTGATAATCTTTGA
1 TATG-ATTTT-ATAA-CTTTGA
1513327 TATGATTTTAGTAACTATTGA
1 TATGATTTTA-TAACT-TTGA
* * *
1513348 TATAAATTTCATAACCTTAGA
1 TAT-GATTTTATAA-CTTTGA
1513369 TATGAT
1 TATGAT
1513375 ATGGTTGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 5 0.12
21 24 0.60
22 11 0.28
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (19 bp):
TATGATTTTATAACTTTGA
Found at i:1513441 original size:21 final size:21
Alignment explanation
Indices: 1513385--1513529 Score: 120
Period size: 21 Copynumber: 6.9 Consensus size: 21
1513375 ATGGTTGTCC
*
1513385 TTTAATATAAATTTTGATGACT
1 TTTAATAT-AATTTTGATAACT
* * *
1513407 TCT-ATAATAGTTTTGATAACG
1 TTTAAT-ATAATTTTGATAACT
1513428 TTTAATATAATTTTGATAATCT
1 TTTAATATAATTTTGATAA-CT
*
1513450 TTGTAAT-T-ATTTT-AGTAACC
1 TT-TAATATAATTTTGA-TAACT
*
1513470 TTAAATATAATTTTGATAACTT
1 TTTAATATAATTTTGATAAC-T
* * *
1513492 TTTAA-ATATTTTTGGTAAAT
1 TTTAATATAATTTTGATAACT
1513512 TTTAATATAATTTTGATA
1 TTTAATATAATTTTGATA
1513530 GTCTTGGATA
Statistics
Matches: 97, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.03
20 11 0.11
21 64 0.66
22 15 0.15
23 4 0.04
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (21 bp):
TTTAATATAATTTTGATAACT
Found at i:1513546 original size:84 final size:85
Alignment explanation
Indices: 1513383--1513547 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 85
1513373 ATATGGTTGT
* * *
1513383 CCTTTAATATAAATTTTGATGACTTCTATAATAGTTTTGATAACGTTTAATATAATTTTGATAAT
1 CCTTAAATATAAATTTTGATAACTTCTATAATAGTTTTGATAAAGTTTAATATAATTTTGATAAT
* *
1513448 CTTTGTAATTATTTTAGTAA
66 CTTGGTAATAATTTTAGTAA
* * * * *
1513468 CCTTAAATAT-AATTTTGATAACTT-TTTAAATATTTTTGGTAAATTTTAATATAATTTTGATAG
1 CCTTAAATATAAATTTTGATAACTTCTAT-AATAGTTTTGATAAAGTTTAATATAATTTTGATAA
1513531 TCTTGG-ATATAATTTTA
65 TCTTGGTA-ATAATTTTA
1513548 ATAATCGTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
83 3 0.04
84 56 0.82
85 9 0.13
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (85 bp):
CCTTAAATATAAATTTTGATAACTTCTATAATAGTTTTGATAAAGTTTAATATAATTTTGATAAT
CTTGGTAATAATTTTAGTAA
Found at i:1513561 original size:21 final size:20
Alignment explanation
Indices: 1513429--1513561 Score: 61
Period size: 21 Copynumber: 6.3 Consensus size: 20
1513419 TTGATAACGT
*
1513429 TTAATATAATTTTGATAATC
1 TTAATATAATTTTAATAATC
** * * *
1513449 TTTGTAATTATTTTAGTAACC
1 TTAAT-ATAATTTTAATAATC
* *
1513470 TTAAATATAATTTTGATAACTTT
1 TT-AATATAATTTTAATAA--TC
* ** *
1513493 TTAA-ATATTTTTGGTAAATT
1 TTAATATAATTTTAAT-AATC
* *
1513513 TTAATATAATTTTGATAGTC
1 TTAATATAATTTTAATAATC
*
1513533 TTGGATATAATTTTAATAATC
1 TT-AATATAATTTTAATAATC
1513554 GTTAATAT
1 -TTAATAT
1513562 TAGCTTGTCA
Statistics
Matches: 82, Mismatches: 23, Indels: 15
0.68 0.19 0.12
Matches are distributed among these distances:
20 13 0.16
21 60 0.73
22 7 0.09
23 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TTAATATAATTTTAATAATC
Found at i:1513649 original size:21 final size:22
Alignment explanation
Indices: 1513625--1513667 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1513615 AATCTTGTAT
*
1513625 TTACTTTTGGTAAAC-TTTGAA
1 TTACTTTTAGTAAACATTTGAA
1513646 TTACTTTTAGTAAACATTTGAA
1 TTACTTTTAGTAAACATTTGAA
1513668 ATAATTCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (22 bp):
TTACTTTTAGTAAACATTTGAA
Found at i:1513678 original size:22 final size:21
Alignment explanation
Indices: 1513634--1513704 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1513624 TTTACTTTTG
* * *
1513634 GTAAACTTTGAATTACTTTTA
1 GTAAACTTTGAAATAATTCTA
1513655 GTAAACATTTGAAATAATTCTA
1 GTAAAC-TTTGAAATAATTCTA
* *
1513677 GT-AACTTTTAATATGATTCTA
1 GTAAACTTTGAA-ATAATTCTA
*
1513698 ATAAACT
1 GTAAACT
1513705 CTGATATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 5 0.12
21 18 0.44
22 18 0.44
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (21 bp):
GTAAACTTTGAAATAATTCTA
Found at i:1513786 original size:21 final size:20
Alignment explanation
Indices: 1513753--1513799 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
1513743 CATTGGTGTA
1513753 ATTTT-ATTAACCTTTTATATG
1 ATTTTGATTAACC-TTT-TATG
1513774 ATTTTGATT-ACCTTTTATG
1 ATTTTGATTAACCTTTTATG
1513793 ATTTTGA
1 ATTTTGA
1513800 AGTTGATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.44
20 3 0.12
21 8 0.32
22 3 0.12
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTTGATTAACCTTTTATG
Found at i:1514389 original size:3 final size:3
Alignment explanation
Indices: 1514381--1514422 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1514371 GAGAGAGAGT
*
1514381 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAC AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1514423 GAAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1514524 original size:18 final size:19
Alignment explanation
Indices: 1514501--1514539 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
1514491 TTTATAATTA
1514501 AAAAGAAAAAATA-AAAAT
1 AAAAGAAAAAATATAAAAT
1514519 AAAAGAAAAAATATAAAAT
1 AAAAGAAAAAATATAAAAT
1514538 AA
1 AA
1514540 TTGATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAAGAAAAAATATAAAAT
Found at i:1515458 original size:34 final size:35
Alignment explanation
Indices: 1515420--1515486 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1515410 CCTTACAACA
1515420 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1515454 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1515487 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1518844 original size:84 final size:84
Alignment explanation
Indices: 1518754--1518918 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1518744 CATTTTCCAC
* * * *
1518754 TTGCAACTCATTTC-TTTTCTCCTCTAATTCATTTATTTTCTCTTTAAAAGAAT-T-ATTTTCTA
1 TTGCAACTC-TTTCATATTCTCCTCTAATTCACTTAATTTCT-TTT-AAAGAATATCATTCTCTA
1518816 AACTCATTGATTTACTTTCATT
63 AACTCATTGATTTACTTTCATT
* * *
1518838 TTGCAACTCTTTCATATTCTTCTCTAATTCACTTAATTTCTTTTCAAGAATATCATTCTCTACAC
1 TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTCTCTAAAC
* *
1518903 TTATTGATTTATTTTC
66 TCATTGATTTACTTTC
1518919 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 8 0.12
84 55 0.80
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1520482 original size:34 final size:35
Alignment explanation
Indices: 1520444--1520510 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1520434 CCTTACAACA
1520444 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1520478 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1520511 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1520987 original size:13 final size:13
Alignment explanation
Indices: 1520969--1520994 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1520959 CAATTTTTTG
1520969 TGTATCGATACAT
1 TGTATCGATACAT
1520982 TGTATCGATACAT
1 TGTATCGATACAT
1520995 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1521470 original size:13 final size:15
Alignment explanation
Indices: 1521440--1521471 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1521430 TTAAGATAGA
1521440 CTTTGTTCAATCTTT
1 CTTTGTTCAATCTTT
1521455 CTTTGTT-AAT-TTT
1 CTTTGTTCAATCTTT
1521468 CTTT
1 CTTT
1521472 AAACAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.66
Consensus pattern (15 bp):
CTTTGTTCAATCTTT
Found at i:1521863 original size:25 final size:23
Alignment explanation
Indices: 1521811--1521866 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
1521801 CACATCCTTG
*
1521811 TATAATTGTTTTATATTTTAGTAG
1 TATAATTGTTTTATATTTTA-TAA
1521835 TATAATTGGTTTTAGTTATTTT-TAA
1 TATAATT-GTTTTA--TATTTTATAA
1521860 TATAATT
1 TATAATT
1521867 TGGTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.25
25 15 0.54
27 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (23 bp):
TATAATTGTTTTATATTTTATAA
Found at i:1521896 original size:21 final size:20
Alignment explanation
Indices: 1521850--1521908 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1521840 TTGGTTTTAG
**
1521850 TTATTTTTAATATAATTTGG
1 TTATTTTTAATATAATTTCA
*
1521870 TAATTTTTAATATAATCTTCA
1 TTATTTTTAATATAAT-TTCA
*
1521891 TTATTTTTTATATAATTT
1 TTATTTTTAATATAATTT
1521909 TGAAAATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTATTTTTAATATAATTTCA
Found at i:1522945 original size:17 final size:17
Alignment explanation
Indices: 1522923--1522955 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1522913 ATATTTTTTA
1522923 AAAAAATCCAAAAAAAT
1 AAAAAATCCAAAAAAAT
*
1522940 AAAAAATTCAAAAAAA
1 AAAAAATCCAAAAAAA
1522956 AATATGTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAATCCAAAAAAAT
Found at i:1522956 original size:18 final size:18
Alignment explanation
Indices: 1522921--1522956 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1522911 AAATATTTTT
*
1522921 TAAAAAAATCCAAAAAAA
1 TAAAAAAATCAAAAAAAA
*
1522939 TAAAAAATTCAAAAAAAA
1 TAAAAAAATCAAAAAAAA
1522957 ATATGTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (18 bp):
TAAAAAAATCAAAAAAAA
Found at i:1523636 original size:68 final size:67
Alignment explanation
Indices: 1523525--1523806 Score: 366
Period size: 68 Copynumber: 4.1 Consensus size: 67
1523515 GCAGTCCCGT
* * * * * * *
1523525 AGCTCCCACAGCTCCAGCAACAGCCAACGGCAACTCAGTAACCATCGCAATCTCCAGCAACTTCT
1 AGCTCCCACAGCTCCA-CAGCAGCCAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCC
1523590 AGC
65 AGC
* * * * * *
1523593 AGCTCCCATAGCTCCAGCAGTAGCCAATAGCAGCTCAGCAACCACCACAACGTCCAGCAACTTTC
1 AGCTCCCACAGCTCCA-CAGCAGCCAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCC
1523658 AGC
65 AGC
* *
1523661 AGCTCCCACAGCTCCCACAGCAGCCAACAGCTGCTCAACAACCACCGCAACCTCCAGCAACTTCC
1 AGCTCCCACAGCT-CCACAGCAGCCAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCC
1523726 AGC
65 AGC
* *
1523729 AGCTCCCACATCTCCTACAGCAGCTAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCC
1 AGCTCCCACAGCTCC-ACAGCAGCCAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCC
1523794 AGC
65 AGC
*
1523797 AGCTTCCACA
1 AGCTCCCACA
1523807 ACAGTTTCCA
Statistics
Matches: 186, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
67 2 0.01
68 181 0.97
69 3 0.02
ACGTcount: A:0.30, C:0.42, G:0.14, T:0.13
Consensus pattern (67 bp):
AGCTCCCACAGCTCCACAGCAGCCAACAGCAGCTCAGCAACCACCGCAACCTCCAGCAACTTCCA
GC
Done.