Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 100 of 147
Found at i:18328840 original size:12 final size:11
Alignment explanation
Indices: 18328778--18328827 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
18328768 TTATTCTTCC
18328778 TTTCTTTCATTT
1 TTTCTTTC-TTT
18328790 TTTCTTTCTTTT
1 TTTCTTTC-TTT
*
18328802 TTTTTTTCTTT
1 TTTCTTTCTTT
*
18328813 TTGCTTTGCTTT
1 TTTCTTT-CTTT
18328825 TTT
1 TTT
18328828 TTTTTTTGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:18329314 original size:10 final size:10
Alignment explanation
Indices: 18329295--18329329 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
18329285 CATAACCATT
18329295 TTTTTCTTCTC
1 TTTTT-TTCTC
18329306 TTTTTTTCTC
1 TTTTTTTCTC
18329316 TTTTTTT-TC
1 TTTTTTTCTC
18329325 TTTTT
1 TTTTT
18329330 CGTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.29
10 12 0.50
11 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:18330233 original size:23 final size:23
Alignment explanation
Indices: 18330203--18330247 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18330193 AAATTTTTTT
18330203 TTTTTTTTTTTCTTTTTTTGCCC
1 TTTTTTTTTTTCTTTTTTTGCCC
*
18330226 TTTTTTTTTTTTTTTTTTTGCC
1 TTTTTTTTTTTCTTTTTTTGCC
18330248 TTCTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTTTTTTTTTCTTTTTTTGCCC
Found at i:18330249 original size:22 final size:24
Alignment explanation
Indices: 18330202--18330247 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
18330192 CAAATTTTTT
18330202 TTTTTTTTTTTTCTTTTTTTGCCC
1 TTTTTTTTTTTTCTTTTTTTGCCC
18330226 TTTTTTTTTTTT-TTTTTTTGCC
1 TTTTTTTTTTTTCTTTTTTTGCC
18330248 TTCTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTTTTCTTTTTTTGCCC
Found at i:18330259 original size:22 final size:23
Alignment explanation
Indices: 18330210--18330260 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
18330200 TTTTTTTTTT
* **
18330210 TTTTCTTTTTTTGCCCTTTTTTTT
1 TTTT-TTTTTTTGCCCTTCTTTCA
18330234 TTTTTTTTTTTG-CCTTCTTTCA
1 TTTTTTTTTTTGCCCTTCTTTCA
18330256 TTTTT
1 TTTTT
18330261 CCCAAAGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTTTTTTTGCCCTTCTTTCA
Found at i:18330259 original size:23 final size:24
Alignment explanation
Indices: 18330209--18330261 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
18330199 TTTTTTTTTT
*
18330209 TTTTTCTTTTTTTGCCCTTTTT-T
1 TTTTTCTTTTTTTGCCCTTTTTCA
*
18330232 TTTTTTTTTTTTTG-CCTTCTTTCA
1 TTTTTCTTTTTTTGCCCTT-TTTCA
18330256 TTTTTC
1 TTTTTC
18330262 CCAAAGTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTTTTTGCCCTTTTTCA
Found at i:18330260 original size:1 final size:1
Alignment explanation
Indices: 18330196--18330244 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
18330186 AAGACTCAAA
* ****
18330196 TTTTTTTTTTTTTTTTTTCTTTTTTTGCCCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18330245 GCCTTCTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:18331945 original size:4 final size:4
Alignment explanation
Indices: 18331907--18331960 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
18331897 TAGATACATA
* * * * * *
18331907 AATG GATG AATG GATG ACTG TATG AATG GATG AATG AATG ATTG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
18331955 AATG AA
1 AATG AA
18331961 CAAATGACAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (4 bp):
AATG
Found at i:18331947 original size:16 final size:16
Alignment explanation
Indices: 18331907--18331960 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
18331897 TAGATACATA
*
18331907 AATGGATGAATGGATG
1 AATGAATGAATGGATG
* *
18331923 ACTGTATGAATGGATG
1 AATGAATGAATGGATG
* *
18331939 AATGAATGATTGAATG
1 AATGAATGAATGGATG
18331955 AATGAA
1 AATGAA
18331961 CAAATGACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (16 bp):
AATGAATGAATGGATG
Found at i:18333333 original size:14 final size:13
Alignment explanation
Indices: 18333314--18333358 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
18333304 CTATCTTAAA
18333314 TTTTTTTACTCTT
1 TTTTTTTACTCTT
*
18333327 TTTTTTT-CCCTT
1 TTTTTTTACTCTT
*
18333339 TTTTTTCATCTCTT
1 TTTTTTTA-CTCTT
18333353 TTTTTT
1 TTTTTT
18333359 ATCCCAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTACTCTT
Found at i:18333569 original size:19 final size:19
Alignment explanation
Indices: 18333524--18333570 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
18333514 ATGAGAACTC
18333524 TTTTTTTCTTCCTTTTCTCT
1 TTTTTTTCTT-CTTTTCTCT
*
18333544 TCCTTTTTCTT-TTTTCTCCT
1 T-TTTTTTCTTCTTTTCT-CT
18333564 TTTTTTT
1 TTTTTTT
18333571 GTCGATGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 8 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTCTTTTCTCT
Found at i:18335957 original size:17 final size:16
Alignment explanation
Indices: 18335898--18335957 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
18335888 ATGAGATAAA
18335898 AATTAAAACAAGCATGAG
1 AATT-AAACAAGCAT-AG
*
18335916 AATCTAAACAA-CAAAG
1 AAT-TAAACAAGCATAG
18335932 AAATT-AACAATGCATAG
1 -AATTAAACAA-GCATAG
18335949 AATTAAACA
1 AATTAAACA
18335958 TATAATTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.14
16 7 0.20
17 13 0.37
18 9 0.26
19 1 0.03
ACGTcount: A:0.58, C:0.13, G:0.10, T:0.18
Consensus pattern (16 bp):
AATTAAACAAGCATAG
Found at i:18337199 original size:208 final size:206
Alignment explanation
Indices: 18336830--18337251 Score: 451
Period size: 208 Copynumber: 2.0 Consensus size: 206
18336820 AAAAAAAAAT
* * * *
18336830 CAAACACAAAGCATATAAGGAATGTATGATAGAGGAGCAAAAACCCTAAAGCAAAGGAACCAAAA
1 CAAACACAAAGCACATAAGGAATGCATGATAGAGGAGCAAAAACCATAAAGAAAAGGAACCAAAA
* ** * * * * *
18336895 TGGGAGTTTTATGGGGGGCTGAATAGCTATTACCATGGGAGGAAATAGGGGTTGTTCAGCACCTA
66 TGAGAACTTTATGGAGGGCTGAATAGCTACTACCATGGGAGAAAACAGGCGTTGTTCAGCACC-A
* * * *
18336960 AAGAAAATACTAAAAGTGCAGCCAAAAAATGAAA-AAAGAAACAAAGTAAGTA-ATGTTTGGAAC
130 AAGAAAATACTAAAAGTGCAACCAAAAAATGAAACAAAG--ACAAAGCAAATAGA-GCTTGGAAC
18337023 TTTATTAACAAACAC
192 TTTATTAACAAACAC
* * * * *
18337038 CAAACACAAAGCACCTAAGGAATGCATGATGGGGGAG-AAAGAACCATGAAGAAAAGGAACTAAA
1 CAAACACAAAGCACATAAGGAATGCATGATAGAGGAGCAAA-AACCATAAAGAAAAGGAACCAAA
* * *
18337102 ATGAGAACTTTATGGAGGGCTGAATAGCTACTATCATGGGTGAAAACAGGCGTTGTTCGGCAGTC
65 ATGAGAACTTTATGGAGGGCTGAATAGCTACTACCATGGGAGAAAACAGGCGTTGTTCAGCA--C
* * * *
18337167 C-AAGAAAATGA-T-GAAGTTTCAACCACAAAATGAAAGCAAAGATAAAGCAAATAGAGCTTGGA
128 CAAAGAAAAT-ACTAAAAG-TGCAACCAAAAAATGAAA-CAAAGACAAAGCAAATAGAGCTTGGA
*
18337229 ACTTTATTAACACACAC
190 ACTTTATTAACAAACAC
18337246 CAAACA
1 CAAACA
18337252 TCAATCATGC
Statistics
Matches: 177, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
207 6 0.03
208 163 0.92
209 2 0.01
210 6 0.03
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (206 bp):
CAAACACAAAGCACATAAGGAATGCATGATAGAGGAGCAAAAACCATAAAGAAAAGGAACCAAAA
TGAGAACTTTATGGAGGGCTGAATAGCTACTACCATGGGAGAAAACAGGCGTTGTTCAGCACCAA
AGAAAATACTAAAAGTGCAACCAAAAAATGAAACAAAGACAAAGCAAATAGAGCTTGGAACTTTA
TTAACAAACAC
Found at i:18343436 original size:65 final size:65
Alignment explanation
Indices: 18343329--18343459 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
18343319 AGCTAATAAC
*
18343329 TTTGAAATAAAGCCTTCAATCATTCAGATGGTCTAAATTTCTTTTCAATTTGGAGGGTTACCAAG
1 TTTGAAATAAAGCCTTCAATCATTCAGATGGTCTAAACTTCTTTTCAATTTGGAGGGTTACCAAG
*
18343394 TTTGAAATAAAGCCTTCAATCATTTAGATGGTCTAAACTTCTTTTCAATTTGGAGGGTTACCAAG
1 TTTGAAATAAAGCCTTCAATCATTCAGATGGTCTAAACTTCTTTTCAATTTGGAGGGTTACCAAG
18343459 T
1 T
18343460 GATGATCCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (65 bp):
TTTGAAATAAAGCCTTCAATCATTCAGATGGTCTAAACTTCTTTTCAATTTGGAGGGTTACCAAG
Found at i:18347188 original size:29 final size:30
Alignment explanation
Indices: 18347133--18347198 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
18347123 TTGTCCCATT
* *
18347133 GTCAAACTTGATCAAATCTTGTTAAAA-AA
1 GTCAAACTTGATCAAATCTGGTCAAAATAA
* *
18347162 GTCAAACTTTATCAAAAT-TGGTCAAAATCA
1 GTCAAACTTGATC-AAATCTGGTCAAAATAA
18347192 GTCAAAC
1 GTCAAAC
18347199 CATATTGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (30 bp):
GTCAAACTTGATCAAATCTGGTCAAAATAA
Found at i:18350330 original size:12 final size:12
Alignment explanation
Indices: 18350299--18350374 Score: 62
Period size: 12 Copynumber: 6.1 Consensus size: 12
18350289 CAACCGAACG
18350299 CTAAACCCTAAA
1 CTAAACCCTAAA
*
18350311 CTTAAACCGTAAA
1 C-TAAACCCTAAA
*
18350324 CTAAACCCTCAA
1 CTAAACCCTAAA
* *
18350336 CAAAATCCTAAA
1 CTAAACCCTAAA
* *
18350348 CCATAAGCCCTAAC
1 -C-TAAACCCTAAA
*
18350362 CAAAACCCTAAA
1 CTAAACCCTAAA
18350374 C
1 C
18350375 CAATCCCCAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 28 0.58
13 13 0.27
14 7 0.15
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (12 bp):
CTAAACCCTAAA
Found at i:18356154 original size:22 final size:22
Alignment explanation
Indices: 18356113--18356155 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18356103 TTTAGTTTTC
* *
18356113 AATTAATTCAATTTTCAAACCT
1 AATTAATTCAAATTTAAAACCT
*
18356135 AATTAATTGAAATTTAAAACC
1 AATTAATTCAAATTTAAAACC
18356156 AAATATAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAATTCAAATTTAAAACCT
Found at i:18356662 original size:43 final size:42
Alignment explanation
Indices: 18356614--18356698 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 42
18356604 TCCAAGGGAT
*
18356614 ATGTCAGCCATCCTTTAGCTAAAGTCAATAATCCATCAGGAAC
1 ATGTCAGCCATCCTTTAGCTAAAATCAATAATCCATC-GGAAC
* *
18356657 ATGTCAGCTATCCTTTGGCTAAAATCAATAATCCATCGGAAC
1 ATGTCAGCCATCCTTTAGCTAAAATCAATAATCCATCGGAAC
18356699 GATATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
ATGTCAGCCATCCTTTAGCTAAAATCAATAATCCATCGGAAC
Found at i:18357201 original size:18 final size:19
Alignment explanation
Indices: 18357169--18357217 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
18357159 ATATTCATAT
18357169 TATTAAATCAATATTA-TTA
1 TATTAAAT-AATATTACTTA
18357188 TATTAAATAATATTACTTA
1 TATTAAATAATATTACTTA
*
18357207 T-TAAAATAATA
1 TATTAAATAATA
18357218 AAAAAGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTAAATAATATTACTTA
Found at i:18366211 original size:23 final size:25
Alignment explanation
Indices: 18366158--18366211 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
18366148 TTACTCTAAA
* *
18366158 ATATTTATTATATTATTAAATTAGT
1 ATATTTAATATATTATTAAATTAAT
*
18366183 CT-TTTAAT-TATTATTAAA-TAAT
1 ATATTTAATATATTATTAAATTAAT
18366205 ATATTTA
1 ATATTTA
18366212 TTAACATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 5 0.21
25 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATTTAATATATTATTAAATTAAT
Found at i:18366222 original size:17 final size:16
Alignment explanation
Indices: 18366193--18366224 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
18366183 CTTTTAATTA
18366193 TTATTAAATAATATAT
1 TTATTAAATAATATAT
18366209 TTATTAACATAATATA
1 TTATTAA-ATAATATA
18366225 AATATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATTAAATAATATAT
Found at i:18366442 original size:1 final size:1
Alignment explanation
Indices: 18366436--18366461 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18366426 AAATACAATG
18366436 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
18366462 ACTTTTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18366622 original size:22 final size:22
Alignment explanation
Indices: 18366579--18366632 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
18366569 GTTTGATTCA
** *
18366579 AAATATTATTTTATTTTTTATT
1 AAATATTATTTTATAATATATT
*
18366601 AAATTTTATTTTATAATATATTT
1 AAATATTATTTTATAATATA-TT
18366624 AAA-ATTATT
1 AAATATTATT
18366633 CAAATATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATTATTTTATAATATATT
Found at i:18366623 original size:17 final size:17
Alignment explanation
Indices: 18366580--18366623 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
18366570 TTTGATTCAA
*
18366580 AATATTATTTTATTTTTT
1 AATA-TATTTTATTTTAT
* *
18366598 ATTAAATTTTATTTTAT
1 AATATATTTTATTTTAT
18366615 AATATATTT
1 AATATATTT
18366624 AAAATTATTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATATATTTTATTTTAT
Found at i:18367554 original size:30 final size:30
Alignment explanation
Indices: 18367518--18367578 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
18367508 ATTATATATT
* *
18367518 ATGTTAAGGGTTTGTTTATATATAAATTAA
1 ATGTTAAGGGTTTATTTAGATATAAATTAA
* *
18367548 ATGTTAAGTGTTTATTTGGATATAAATTAA
1 ATGTTAAGGGTTTATTTAGATATAAATTAA
18367578 A
1 A
18367579 AATTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (30 bp):
ATGTTAAGGGTTTATTTAGATATAAATTAA
Found at i:18373515 original size:81 final size:81
Alignment explanation
Indices: 18373414--18373572 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 81
18373404 TGCTTTGGAT
*
18373414 GAACTAAAAGAAAGAGAGCTTGTAAAAATTGTAAAGAAACTTGTATTGAAATTGCTTAACAAAAC
1 GAACTAAAAGAAAGAAAGCTTGTAAAAATTGTAAAGAAACTTGTATTGAAATTGCTTAACAAAAC
*
18373479 ACAATGTATGCTACAC
66 ACAATGTAGGCTACAC
* *
18373495 GAACTAAAAGTAAGAAAGCTTGTAAAAATTGTAAAGAAACTTGTATTGAAATTGCTTAAGAAAAC
1 GAACTAAAAGAAAGAAAGCTTGTAAAAATTGTAAAGAAACTTGTATTGAAATTGCTTAACAAAAC
*
18373560 ATAATGTAGGCTA
66 ACAATGTAGGCTA
18373573 AATTGTCACT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (81 bp):
GAACTAAAAGAAAGAAAGCTTGTAAAAATTGTAAAGAAACTTGTATTGAAATTGCTTAACAAAAC
ACAATGTAGGCTACAC
Found at i:18374424 original size:18 final size:18
Alignment explanation
Indices: 18374368--18374428 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
18374358 ATATATGATG
*
18374368 AATGCATGACAATTAAAT
1 AATGCATGATAATTAAAT
*
18374386 -ATGAATGATAA--AATAT
1 AATGCATGATAATTAA-AT
18374402 AAATGCATGATAATTAAAT
1 -AATGCATGATAATTAAAT
18374421 AATGCATG
1 AATGCATG
18374429 TGACAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 9 0.26
18 18 0.51
19 2 0.06
20 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.30
Consensus pattern (18 bp):
AATGCATGATAATTAAAT
Found at i:18374590 original size:13 final size:13
Alignment explanation
Indices: 18374581--18374608 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18374571 AGGTTTAGAT
18374581 TTAGGGTTTAAGG
1 TTAGGGTTTAAGG
18374594 TTAGGGTTTAAGG
1 TTAGGGTTTAAGG
18374607 TT
1 TT
18374609 TAAGGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (13 bp):
TTAGGGTTTAAGG
Found at i:18374595 original size:7 final size:7
Alignment explanation
Indices: 18374570--18374616 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
18374560 TTTGGAGTTC
18374570 AAGGTTT
1 AAGGTTT
*
18374577 -AGATTT
1 AAGGTTT
*
18374583 AGGGTTT
1 AAGGTTT
18374590 AAGG-TT
1 AAGGTTT
*
18374596 AGGGTTT
1 AAGGTTT
18374603 AAGGTTT
1 AAGGTTT
18374610 AAGGTTT
1 AAGGTTT
18374617 GGTTTTAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 10 0.31
7 22 0.69
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.43
Consensus pattern (7 bp):
AAGGTTT
Found at i:18374623 original size:20 final size:20
Alignment explanation
Indices: 18374570--18374623 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
18374560 TTTGGAGTTC
* *
18374570 AAGGTTTAGATTTAGGGTTT
1 AAGGTTTGGATTTAAGGTTT
* *
18374590 AAGGTTAGGGTTTAAGGTTT
1 AAGGTTTGGATTTAAGGTTT
*
18374610 AAGGTTTGGTTTTA
1 AAGGTTTGGATTTA
18374624 GGATATAGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (20 bp):
AAGGTTTGGATTTAAGGTTT
Found at i:18376083 original size:143 final size:143
Alignment explanation
Indices: 18375669--18376089 Score: 357
Period size: 143 Copynumber: 2.9 Consensus size: 143
18375659 GTTTATGCAA
* * * ** * * ** *
18375669 TTTTAAAGCACCAAAAATCTTAAAATAATATTAAATTATGATCT-AAAAGTTTTCGTGAAAAACC
1 TTTTAAAGCACCAAAAATCATGAAATAATATAAAACCATGATCTGAAATG-TTGCAAGAAAAACT
* * * * * * *
18375733 AA-CTTCAAGAATATCAAATTACAAAATTATCTTTTAAGGGTATTTTAGTAATTTCACACATTTT
65 AACCTTGAA-AAGATCAAATTATAAAAATA-CTCTTAAGGGTATTTTAGTAATTTTACACATTTC
* * **
18375797 GAGGTACGTTCAAGGT
128 AAAGTACAATCAAGGT
* * *** * *
18375813 TTTTAATGCACCAAAAATCATGAAATAATGTAAAATTGTGATTTGAAATGTTTCAAGAAAAACTA
1 TTTTAAAGCACCAAAAATCATGAAATAATATAAAACCATGATCTGAAATGTTGCAAGAAAAACTA
* * * * * *
18375878 ACCTTGACAAGATCAAATTATGAAAATACCCTTAAGGGTATTTTGGTAATTCTCCATC-TTTCAA
66 ACCTTGAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTAATTTTACA-CATTTCAA
*
18375942 AGTGCAATCAAGGT
130 AGTACAATCAAGGT
* * * * * *
18375956 TTTTAAAGTATCAAAAATTATGAAATAGTATAAAACCATGATCTGGAATGTTGCATGAAAAA-TC
1 TTTTAAAGCACCAAAAATCATGAAATAATATAAAACCATGATCTGAAATGTTGCAAGAAAAACT-
* *
18376020 GACCTTAGAAAAG-TCAAATTATAAAAATACTCTTAAGCGTATTTTAGTAATTTTACACATTTCA
65 AACCTT-GAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTAATTTTACACATTTCA
*
18376084 AGGTAC
129 AAGTAC
18376090 GATAAAAGTT
Statistics
Matches: 219, Mismatches: 52, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
142 2 0.01
143 137 0.63
144 72 0.33
145 8 0.04
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (143 bp):
TTTTAAAGCACCAAAAATCATGAAATAATATAAAACCATGATCTGAAATGTTGCAAGAAAAACTA
ACCTTGAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTAATTTTACACATTTCAAA
GTACAATCAAGGT
Found at i:18376139 original size:143 final size:143
Alignment explanation
Indices: 18375719--18376159 Score: 406
Period size: 143 Copynumber: 3.1 Consensus size: 143
18375709 ATCTAAAAGT
* * * * * * *
18375719 TTTCGTGAAAAACCAA-CTTCAAGAATATCAAATTACAAAATTATCTTTTAAGGGTATTTTAGTA
1 TTTCATGAAAAACTAACCTTGAA-AAGATCAAATTATAAAAATA-CTCTTAAGGGTATTTTAGTA
* ** * * *
18375783 ATTTCACACATTTTGAGGTACGTTCAAGGTTTTTAATGCACCAAAAATCATGAAATAATGTAAAA
64 ATTTTACACATTTCAAGGTACGATCAAGGTTTTTAATGTATCAAAAATCATGAAATAATGTAAAA
** * *
18375848 TTGTGATTTGAAATG
129 TCATGATCTGGAATG
* * * * *
18375863 TTTCAAGAAAAACTAACCTTGACAAGATCAAATTATGAAAATACCCTTAAGGGTATTTTGGTAAT
1 TTTCATGAAAAACTAACCTTGAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTAAT
* * * * * * * * * *
18375928 TCTCCATC-TTTCAAAGTGCAATCAAGGTTTTTAAAGTATCAAAAATTATGAAATAGTATAAAAC
66 TTTACA-CATTTCAAGGTACGATCAAGGTTTTTAATGTATCAAAAATCATGAAATAATGTAAAAT
18375992 CATGATCTGGAATG
130 CATGATCTGGAATG
* * *
18376006 TTGCATGAAAAA-TCGACCTTAGAAAAG-TCAAATTATAAAAATACTCTTAAGCGTATTTTAGTA
1 TTTCATGAAAAACT-AACCTT-GAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTA
* * * * * **
18376069 ATTTTACACATTTCAAGGTACGATAAAAGTTTTCAATGTATAAAAAATCATAAAATAATGTTTAA
64 ATTTTACACATTTCAAGGTACGATCAAGGTTTTTAATGTATCAAAAATCATGAAATAATGTAAAA
*
18376134 TCATGATCTAGAA-G
129 TCATGATCTGGAATG
18376148 TTTTCATGAAAA
1 -TTTCATGAAAA
18376160 TTTGATTTCA
Statistics
Matches: 232, Mismatches: 59, Indels: 13
0.76 0.19 0.04
Matches are distributed among these distances:
142 3 0.01
143 190 0.82
144 35 0.15
145 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (143 bp):
TTTCATGAAAAACTAACCTTGAAAAGATCAAATTATAAAAATACTCTTAAGGGTATTTTAGTAAT
TTTACACATTTCAAGGTACGATCAAGGTTTTTAATGTATCAAAAATCATGAAATAATGTAAAATC
ATGATCTGGAATG
Found at i:18376888 original size:21 final size:21
Alignment explanation
Indices: 18376862--18376901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18376852 AAAATCTAAT
*
18376862 GTTTTACCCGGAGGCCTTAAG
1 GTTTTACCCAGAGGCCTTAAG
*
18376883 GTTTTACCTAGAGGCCTTA
1 GTTTTACCCAGAGGCCTTA
18376902 GGAATCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (21 bp):
GTTTTACCCAGAGGCCTTAAG
Found at i:18376935 original size:61 final size:61
Alignment explanation
Indices: 18376812--18376941 Score: 158
Period size: 61 Copynumber: 2.1 Consensus size: 61
18376802 TTTTGCACGA
* * *
18376812 AGGCCCTAAAGTTTTACTCAGAGGCCTTGGAAATCATTCAAAAATCTAATGTTTTACCCGG
1 AGGCCTTAAAGTTTTACTCAGAGGCCTTGGAAATCATTCAAAAATCTAATGTTCTAACCGG
* * *
18376873 AGGCCTTAAGGTTTTAC-CTAGAGGCCTTAGG-AATCATTTAAAAATCTGAA-GTTCTAATCGG
1 AGGCCTTAAAGTTTTACTC-AGAGGCCTT-GGAAATCATTCAAAAATCT-AATGTTCTAACCGG
18376934 AGGCCTTA
1 AGGCCTTA
18376942 GGATTTTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
60 1 0.02
61 55 0.92
62 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (61 bp):
AGGCCTTAAAGTTTTACTCAGAGGCCTTGGAAATCATTCAAAAATCTAATGTTCTAACCGG
Found at i:18376992 original size:40 final size:40
Alignment explanation
Indices: 18376948--18377044 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
18376938 CTTAGGATTT
*
18376948 TTCAAAATTTTAAGGTTTTGC-CTGAAGAACTTAGAAATGA
1 TTCAAAATTTTAAGGTTTTGCTC-GAAGAACTTAGAAATCA
* * **
18376988 TTC-AAATGTTTGAGGTTTTGCTCGGAGGCCTTAGAAATCA
1 TTCAAAAT-TTTAAGGTTTTGCTCGAAGAACTTAGAAATCA
*
18377028 TTCAAAAGTTTAAGGTT
1 TTCAAAATTTTAAGGTT
18377045 GCCCGAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.09
40 39 0.83
41 4 0.09
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (40 bp):
TTCAAAATTTTAAGGTTTTGCTCGAAGAACTTAGAAATCA
Found at i:18377312 original size:112 final size:112
Alignment explanation
Indices: 18377190--18377395 Score: 265
Period size: 112 Copynumber: 1.8 Consensus size: 112
18377180 CTTTCAAAAA
* * * * * *
18377190 TTTAAGGTTTTGCCCGA-AGGCTTTGAAAATCATTTAAAATTTTAAAATTTCA-TTCGGAGGTCT
1 TTTAAGGTTTTG-CCGAGAGACTTTGAAAATCATTCAAAAATTTAAAATTTCACCT-GAAAGTCT
*
18377253 TGAAAACTTTTCCAAAA-TTTAAAACTTTGCCCAAAGGTCTTGGAATATT
64 TGAAAAATTTT-CAAAATTTTAAAACTTTGCCCAAAGGTCTTGGAATATT
** * *
18377302 TTTAAGGTTTTGCTTAGAGACTTTGGAAATCATTCAAAAATTTAAAATTTCACCTGAAAGTTTTG
1 TTTAAGGTTTTGCCGAGAGACTTTGAAAATCATTCAAAAATTTAAAATTTCACCTGAAAGTCTTG
18377367 AAAAATTTTCAAAATTTTAAAACTTTGCC
66 AAAAATTTTCAAAATTTTAAAACTTTGCC
18377396 TGGAGGTCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
111 7 0.09
112 72 0.90
113 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (112 bp):
TTTAAGGTTTTGCCGAGAGACTTTGAAAATCATTCAAAAATTTAAAATTTCACCTGAAAGTCTTG
AAAAATTTTCAAAATTTTAAAACTTTGCCCAAAGGTCTTGGAATATT
Found at i:18377475 original size:7 final size:8
Alignment explanation
Indices: 18377455--18377483 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18377445 TAGAGTTAAA
18377455 ATTTTTTC
1 ATTTTTTC
18377463 ATTTTTTC
1 ATTTTTTC
18377471 ATTTTTTC
1 ATTTTTTC
18377479 ATTTT
1 ATTTT
18377484 CACCTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:18377788 original size:28 final size:29
Alignment explanation
Indices: 18377755--18377817 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 29
18377745 TAAATGCTTT
18377755 ATGCAAATATGCAAATGCCTTTTTCC-TA
1 ATGCAAATATGCAAATGCCTTTTTCCTTA
* * *
18377783 ATGC-AA-ATGCACATGTCTTTTTCCTTG
1 ATGCAAATATGCAAATGCCTTTTTCCTTA
18377810 ATGCAAAT
1 ATGCAAAT
18377818 GTTTTATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 16 0.55
27 7 0.24
28 6 0.21
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (29 bp):
ATGCAAATATGCAAATGCCTTTTTCCTTA
Found at i:18382970 original size:18 final size:17
Alignment explanation
Indices: 18382909--18383008 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 17
18382899 AATCATCCAT
*
18382909 TTTTTTTCTTTTCCTTATA
1 TTTTTTTCTTTT--TTATC
*
18382928 TATTTTTTGTTTTTTATC
1 T-TTTTTTCTTTTTTATC
*
18382946 TTCTTTTTCTTTTTTCCTC
1 TT-TTTTTCTTTTTT-ATC
*
18382965 TTTTTTTACCCTTTTT-TC
1 TTTTTTT--CTTTTTTATC
*
18382983 TTTTCTT-TTTTTT-TC
1 TTTTTTTCTTTTTTATC
*
18382998 TTTATTTCTTT
1 TTTTTTTCTTT
18383009 CTCTTTTCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
15 12 0.18
16 3 0.05
17 1 0.02
18 29 0.44
19 5 0.08
20 16 0.24
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTTTTATC
Found at i:18382994 original size:15 final size:15
Alignment explanation
Indices: 18382976--18383020 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
18382966 TTTTTTACCC
18382976 TTTTTTCTTTTCTTT
1 TTTTTTCTTTTCTTT
*
18382991 TTTTTTC-TTTATTT
1 TTTTTTCTTTTCTTT
* *
18383005 CTTTCTCTTTTCTTT
1 TTTTTTCTTTTCTTT
18383020 T
1 T
18383021 GTTAGATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:18383511 original size:11 final size:11
Alignment explanation
Indices: 18383464--18383507 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
18383454 ATCAAACAAT
18383464 TTTTTTCATTTC
1 TTTTTTC-TTTC
* *
18383476 TTTCTTCTTTA
1 TTTTTTCTTTC
18383487 TTTTTTCTTTC
1 TTTTTTCTTTC
18383498 TTTTTT-TTTC
1 TTTTTTCTTTC
18383508 CTTTGCATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 4 0.14
11 18 0.64
12 6 0.21
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:18383511 original size:15 final size:15
Alignment explanation
Indices: 18383471--18383507 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
18383461 AATTTTTTTC
18383471 ATTTCTTTC-TTCTTT
1 ATTT-TTTCTTTCTTT
18383486 ATTTTTTCTTTCTTT
1 ATTTTTTCTTTCTTT
18383501 -TTTTTTC
1 ATTTTTTC
18383508 CTTTGCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (15 bp):
ATTTTTTCTTTCTTT
Found at i:18386508 original size:34 final size:35
Alignment explanation
Indices: 18386437--18386540 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 35
18386427 TTATTTTTAT
*
18386437 TCTAAATAAGCATATTTGAATAAAAAATATGATTG
1 TCTAAATAAGCATATTTGAACAAAAAATATGATTG
* *
18386472 TCTGAATAAGCATATTTGAACCAAAAA-ATGATTG
1 TCTAAATAAGCATATTTGAACAAAAAATATGATTG
* * *
18386506 TCTAAAAAAACTTATTTGAACAGAAAAATATGATT
1 TCTAAATAAGCATATTTGAACA-AAAAATATGATT
18386541 ACATAGATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
34 24 0.41
35 29 0.49
36 6 0.10
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.32
Consensus pattern (35 bp):
TCTAAATAAGCATATTTGAACAAAAAATATGATTG
Found at i:18389626 original size:13 final size:13
Alignment explanation
Indices: 18389595--18389633 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
18389585 ATCTGATAAA
*
18389595 AAAATTCATCGAT
1 AAAATCCATCGAT
18389608 --AATCCATCGAT
1 AAAATCCATCGAT
18389619 AAAATCCATCGAT
1 AAAATCCATCGAT
18389632 AA
1 AA
18389634 TTGATTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 10 0.43
13 13 0.57
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (13 bp):
AAAATCCATCGAT
Found at i:18391603 original size:22 final size:23
Alignment explanation
Indices: 18391578--18391624 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
18391568 AAATCTCAAC
* *
18391578 AATACTTAAC-ATATAAAAAAAA
1 AATACTCAACAATACAAAAAAAA
*
18391600 AATACTCCACAATACAAAAAAAA
1 AATACTCAACAATACAAAAAAAA
18391623 AA
1 AA
18391625 AAACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (23 bp):
AATACTCAACAATACAAAAAAAA
Found at i:18393530 original size:23 final size:23
Alignment explanation
Indices: 18393494--18393548 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
18393484 ATAGATTTAT
* * *
18393494 ATTAAAGATTTATTAATATAAAA
1 ATTAAAAATGTATTAAGATAAAA
* *
18393517 ATTAAAAATGTATTTAGATAAAT
1 ATTAAAAATGTATTAAGATAAAA
18393540 ATTAAAAAT
1 ATTAAAAAT
18393549 CAACAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
ATTAAAAATGTATTAAGATAAAA
Found at i:18393801 original size:14 final size:14
Alignment explanation
Indices: 18393782--18393808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18393772 GCTAGTACAA
18393782 ATAATAATAATAAT
1 ATAATAATAATAAT
18393796 ATAATAATAATAA
1 ATAATAATAATAA
18393809 AAGATACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:18395213 original size:16 final size:16
Alignment explanation
Indices: 18395184--18395217 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18395174 TAAACATTTC
*
18395184 AAAAATTTTAAAAATA
1 AAAAAGTTTAAAAATA
*
18395200 AAAAAGTTTGAAAATA
1 AAAAAGTTTAAAAATA
18395216 AA
1 AA
18395218 TTTCTTCTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAAAGTTTAAAAATA
Found at i:18397369 original size:66 final size:62
Alignment explanation
Indices: 18397181--18397371 Score: 220
Period size: 62 Copynumber: 3.0 Consensus size: 62
18397171 TAATAATAAG
* * * *
18397181 TAAAAAAAGTTATTTAGCACAATAAATTTTATGATTTCCCACTTAATTCTATTCTATCATAT
1 TAAAAAAAGTTATTTAGCACAATAAATCTTATAATTTCCCACATGATTCTATTCTATCATAT
* ** * *
18397243 TAAAAAAAGTTATTTTGCACAATGTATCTCATAATTTCCCACATGATTCTAGTCTATCATAT
1 TAAAAAAAGTTATTTAGCACAATAAATCTTATAATTTCCCACATGATTCTATTCTATCATAT
* * * * *
18397305 TAAAAAAAAAAAGTTATTTAGCAAAATAAATCTTATAATTTCCCACACGATTTTATTTTGTCATA
1 T----AAAAAAAGTTATTTAGCACAATAAATCTTATAATTTCCCACATGATTCTATTCTATCATA
18397370 T
62 T
18397371 T
1 T
18397372 CAAAGGTGAG
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
62 54 0.51
66 52 0.49
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (62 bp):
TAAAAAAAGTTATTTAGCACAATAAATCTTATAATTTCCCACATGATTCTATTCTATCATAT
Found at i:18408509 original size:22 final size:20
Alignment explanation
Indices: 18408477--18408517 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
18408467 AACATAATAA
18408477 ATGAATGAATGCATGAATGAC
1 ATGAATGAATGCAT-AATGAC
18408498 ATGATATGAATGCATAATGA
1 ATGA-ATGAATGCATAATGA
18408518 TTCAAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGAATGAATGCATAATGAC
Found at i:18408627 original size:29 final size:29
Alignment explanation
Indices: 18408593--18408650 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
18408583 AGGGTTTAGA
*
18408593 GTTTAAGATTTTAAATTTGGGGTTTCATG
1 GTTTAAGATTTCAAATTTGGGGTTTCATG
*
18408622 GTTTAAGGTTTCAAATTTGGGGTTTCATG
1 GTTTAAGATTTCAAATTTGGGGTTTCATG
18408651 AAATTTGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (29 bp):
GTTTAAGATTTCAAATTTGGGGTTTCATG
Found at i:18408656 original size:17 final size:17
Alignment explanation
Indices: 18408634--18408672 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18408624 TTAAGGTTTC
* *
18408634 AAATTTGGGGTTTCATG
1 AAATTTGGGATTTCATA
18408651 AAATTTGGGATTTCATA
1 AAATTTGGGATTTCATA
18408668 AAATT
1 AAATT
18408673 GTGCATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (17 bp):
AAATTTGGGATTTCATA
Found at i:18410722 original size:16 final size:16
Alignment explanation
Indices: 18410697--18410737 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
18410687 AACTGTTTTG
*
18410697 TTTGATTTTGACCAAT
1 TTTGACTTTGACCAAT
18410713 TTTGACTTTGACCAAT
1 TTTGACTTTGACCAAT
18410729 TTTGACTTT
1 TTTGACTTT
18410738 ATTTAACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (16 bp):
TTTGACTTTGACCAAT
Found at i:18410929 original size:19 final size:18
Alignment explanation
Indices: 18410905--18411016 Score: 82
Period size: 19 Copynumber: 6.0 Consensus size: 18
18410895 TAGGTATATA
18410905 CACCCATGAAAACCTAAAC
1 CACCCAT-AAAACCTAAAC
*
18410924 CACCCATCAAACCCTAAAC
1 CACCCAT-AAAACCTAAAC
*
18410943 CAACCATAAAACCTTAAAC
1 CACCCATAAAACC-TAAAC
** * *
18410962 CACCTTTCAAATCTAAA-
1 CACCCATAAAACCTAAAC
* *
18410979 CACCCTCTAAACCCTAAAC
1 CACCC-ATAAAACCTAAAC
* *
18410998 CACCTATGAAACCCTAAAC
1 CACCCAT-AAAACCTAAAC
18411017 TAAACCTCAA
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
17 4 0.05
18 18 0.25
19 51 0.70
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.16
Consensus pattern (18 bp):
CACCCATAAAACCTAAAC
Found at i:18411047 original size:7 final size:7
Alignment explanation
Indices: 18411037--18411107 Score: 55
Period size: 7 Copynumber: 10.9 Consensus size: 7
18411027 ACCATGACCT
*
18411037 TAAACTC
1 TAAACCC
*
18411044 TAAACTC
1 TAAACCC
18411051 TAAACCC
1 TAAACCC
18411058 TAAACCC
1 TAAACCC
18411065 T-AACCC
1 TAAACCC
18411071 GT-AA-CC
1 -TAAACCC
*
18411077 TAAA-CT
1 TAAACCC
18411083 TAAA-CC
1 TAAACCC
18411089 -AAACCC
1 TAAACCC
*
18411095 TAAACTC
1 TAAACCC
18411102 TAAACC
1 TAAACC
18411108 AAGCCTTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
5 4 0.07
6 17 0.31
7 34 0.62
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:18411230 original size:19 final size:19
Alignment explanation
Indices: 18411203--18411245 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
18411193 CTTAAACCTT
*
18411203 AAACTCTAACCTTGACCCC
1 AAACCCTAACCTTGACCCC
18411222 AAACCCTAACCTTGACCCC
1 AAACCCTAACCTTGACCCC
18411241 AAACC
1 AAACC
18411246 AATCCTAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.44, G:0.05, T:0.16
Consensus pattern (19 bp):
AAACCCTAACCTTGACCCC
Found at i:18411267 original size:12 final size:12
Alignment explanation
Indices: 18411250--18411274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18411240 CAAACCAATC
18411250 CTAAGCCCTAAA
1 CTAAGCCCTAAA
18411262 CTAAGCCCTAAA
1 CTAAGCCCTAAA
18411274 C
1 C
18411275 CCTAACATAG
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:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTAAGCCCTAAA
Found at i:18411279 original size:49 final size:49
Alignment explanation
Indices: 18411217--18411336 Score: 145
Period size: 49 Copynumber: 2.5 Consensus size: 49
18411207 TCTAACCTTG
* * * * *
18411217 ACCCCAAACCCTAACCTTGACCCCAAACCAATCCTAAGCCCTAAACT-AA
1 ACCCTAAACCCTAACCTAGACCCCAAACCAA-CCCAAACCCTAAAATCAA
* * *
18411266 GCCCTAAACCCTAACATAGACCCCAAATCAACCCAAACCCTAAAATCAA
1 ACCCTAAACCCTAACCTAGACCCCAAACCAACCCAAACCCTAAAATCAA
18411315 ACCCTAAA-CCTAACCTAGACCC
1 ACCCTAAACCCTAACCTAGACCC
18411337 TTAACCTACC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 25 0.42
49 35 0.58
ACGTcount: A:0.41, C:0.42, G:0.04, T:0.13
Consensus pattern (49 bp):
ACCCTAAACCCTAACCTAGACCCCAAACCAACCCAAACCCTAAAATCAA
Found at i:18411389 original size:25 final size:25
Alignment explanation
Indices: 18411339--18411389 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
18411329 CTAGACCCTT
* * *
18411339 AACCTACCCCAAACCTTAAACCTCA
1 AACCAACCCCAAACCCTAAACATCA
18411364 AACCAACCCTCAAACCCTAAA-ATCA
1 AACCAACCC-CAAACCCTAAACATCA
18411389 A
1 A
18411390 CTTTTAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (25 bp):
AACCAACCCCAAACCCTAAACATCA
Found at i:18429279 original size:10 final size:10
Alignment explanation
Indices: 18429219--18429265 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
18429209 GAAAATAATG
* *
18429219 AATCTTGTTA
1 AATCTTGATC
*
18429229 AATCTTGA-A
1 AATCTTGATC
18429238 AATTCTTGATC
1 AA-TCTTGATC
18429249 AATCTTGATC
1 AATCTTGATC
18429259 AATCTTG
1 AATCTTG
18429266 GATGATTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 3 0.09
10 28 0.85
11 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (10 bp):
AATCTTGATC
Found at i:18429595 original size:25 final size:25
Alignment explanation
Indices: 18429567--18429626 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
18429557 GTCTATTTAG
18429567 TATTCCTACTT-AGATTTGG-ATTTCC
1 TATTCCTA-TTAAGATTTGGTA-TTCC
**
18429592 TATTTATATTAAGATTTGGTATTCC
1 TATTCCTATTAAGATTTGGTATTCC
18429617 TATTCCTATT
1 TATTCCTATT
18429627 TGGAGTAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 26 0.90
26 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (25 bp):
TATTCCTATTAAGATTTGGTATTCC
Found at i:18435381 original size:2 final size:2
Alignment explanation
Indices: 18435374--18435402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18435364 AATTAAGTCT
18435374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18435403 TATGTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18435626 original size:10 final size:10
Alignment explanation
Indices: 18435611--18435658 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
18435601 AAAGCCAACT
18435611 TTAGTCAAAC
1 TTAGTCAAAC
18435621 TTAGTC-AAC
1 TTAGTCAAAC
** *
18435630 AAAGTCAAAA
1 TTAGTCAAAC
18435640 TTAGTCAAAC
1 TTAGTCAAAC
*
18435650 TAAGTCAAA
1 TTAGTCAAA
18435659 ATTGATAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (10 bp):
TTAGTCAAAC
Found at i:18435637 original size:19 final size:20
Alignment explanation
Indices: 18435613--18435661 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
18435603 AGCCAACTTT
*
18435613 AGTCAAACTTAGTC-AACAA
1 AGTCAAAATTAGTCAAACAA
*
18435632 AGTCAAAATTAGTCAAACTA
1 AGTCAAAATTAGTCAAACAA
18435652 AGTCAAAATT
1 AGTCAAAATT
18435662 GATAAAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (20 bp):
AGTCAAAATTAGTCAAACAA
Found at i:18438484 original size:16 final size:16
Alignment explanation
Indices: 18438463--18438495 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18438453 TAAGTCTAAC
18438463 GTTAGTAAAGAAAGAT
1 GTTAGTAAAGAAAGAT
18438479 GTTAGTAAAGAAAGAT
1 GTTAGTAAAGAAAGAT
18438495 G
1 G
18438496 GGTACAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.24
Consensus pattern (16 bp):
GTTAGTAAAGAAAGAT
Found at i:18439297 original size:13 final size:14
Alignment explanation
Indices: 18439275--18439303 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
18439265 AGTAAAAAAA
18439275 AATTTATAAAATAT
1 AATTTATAAAATAT
18439289 AATTT-TAAAATAT
1 AATTTATAAAATAT
18439302 AA
1 AA
18439304 AATTGTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATAAAATAT
Found at i:18439307 original size:15 final size:15
Alignment explanation
Indices: 18439273--18439313 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
18439263 AAAGTAAAAA
18439273 AAAATTTATAAAATAT
1 AAAATTT-TAAAATAT
18439289 --AATTTTAAAATAT
1 AAAATTTTAAAATAT
*
18439302 AAAATTGTAAAA
1 AAAATTTTAAAA
18439314 GTTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAATTTTAAAATAT
Found at i:18444841 original size:27 final size:27
Alignment explanation
Indices: 18444770--18444834 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
18444760 TTAGTTGCTT
18444770 GCATTACTAA-TTA-GTGGTATTGATTG
1 GCATTAC-AATTTATGTGGTATTGATTG
18444796 GCATTACAATTTATGTGGTATTGATTG
1 GCATTACAATTTATGTGGTATTGATTG
18444823 GCATTACAATTT
1 GCATTACAATTT
18444835 TTTTGGTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
25 2 0.05
26 10 0.27
27 25 0.68
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (27 bp):
GCATTACAATTTATGTGGTATTGATTG
Found at i:18450820 original size:16 final size:17
Alignment explanation
Indices: 18450790--18450839 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
18450780 TTGAATTTAC
*
18450790 TATTTAGGCCTTGAATT
1 TATTTAGGTCTTGAATT
18450807 TATTT-GGTCTTGAACTT
1 TATTTAGGTCTTGAA-TT
* *
18450824 TGTTTAGGTCCTGAAT
1 TATTTAGGTCTTGAAT
18450840 CCAAATCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.29
17 12 0.43
18 8 0.29
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (17 bp):
TATTTAGGTCTTGAATT
Found at i:18455532 original size:22 final size:22
Alignment explanation
Indices: 18455492--18455535 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
18455482 CTTTTCTTTT
*
18455492 TTTTTCTTTATTTTCTTTTTCC
1 TTTTTCTTTATCTTCTTTTTCC
*
18455514 TTTTTCTTTAATCTTTTTTTTC
1 TTTTTCTTT-ATCTTCTTTTTC
18455536 TCTATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTATCTTCTTTTTCC
Found at i:18457981 original size:34 final size:35
Alignment explanation
Indices: 18457943--18458009 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
18457933 TTAATTTTCA
* *
18457943 TTTAGGGTTTCACCTAGGG-TTTTGGGTTTTACAG
1 TTTAGGGTTTCACCTAGGGCATTTAGGTTTTACAG
*
18457977 TTTAGGGTTTTACCTAGGGCATTTAGGTTTTAC
1 TTTAGGGTTTCACCTAGGGCATTTAGGTTTTAC
18458010 CTAGGGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.45
Consensus pattern (35 bp):
TTTAGGGTTTCACCTAGGGCATTTAGGTTTTACAG
Found at i:18458007 original size:20 final size:21
Alignment explanation
Indices: 18457977--18458015 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
18457967 GGTTTTACAG
18457977 TTTAGGGTTTTACCTAGGGCA
1 TTTAGGGTTTTACCTAGGGCA
18457998 TTTA-GGTTTTACCTAGGG
1 TTTAGGGTTTTACCTAGGG
18458016 TTTTGATTTT
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:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (21 bp):
TTTAGGGTTTTACCTAGGGCA
Found at i:18458105 original size:40 final size:41
Alignment explanation
Indices: 18458048--18458142 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
18458038 CAGTTTTTAC
* *
18458048 TTAGGGTTTTTAA-TTTA-GGATTTGGGATT-GGGGTTTCAT
1 TTAGGG-TTTTAATTTTAGGGATTTGGGATTAAGGGTTTCAG
* **
18458087 TCTAGGGTTTTAATTTTAGGGCTTTGGTTTTAAGGGTTTCAG
1 T-TAGGGTTTTAATTTTAGGGATTTGGGATTAAGGGTTTCAG
18458129 TTAGGGTTTTAATT
1 TTAGGGTTTTAATT
18458143 CTTTATGAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
39 7 0.15
40 9 0.19
41 22 0.47
42 9 0.19
ACGTcount: A:0.18, C:0.04, G:0.28, T:0.49
Consensus pattern (41 bp):
TTAGGGTTTTAATTTTAGGGATTTGGGATTAAGGGTTTCAG
Found at i:18459838 original size:18 final size:18
Alignment explanation
Indices: 18459812--18459846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18459802 GACCTTAAAA
18459812 TTTTGTTCTTTTCTTTTT
1 TTTTGTTCTTTTCTTTTT
* *
18459830 TTTTTTTCTTTTGTTTT
1 TTTTGTTCTTTTCTTTT
18459847 GGCCTTTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTGTTCTTTTCTTTTT
Found at i:18460035 original size:26 final size:28
Alignment explanation
Indices: 18459993--18460055 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 28
18459983 TTTGATTACT
*
18459993 TTTTAATTTTTTGATTTTA-A-GTTTATA
1 TTTT-ATTTTTTAATTTTATATGTTTATA
*
18460020 TTTTATTTTTTAATTTTATATGTTTGTA
1 TTTTATTTTTTAATTTTATATGTTTATA
18460048 TTATTATT
1 TT-TTATT
18460056 ATTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 13 0.42
27 5 0.16
28 8 0.26
29 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (28 bp):
TTTTATTTTTTAATTTTATATGTTTATA
Found at i:18460054 original size:3 final size:3
Alignment explanation
Indices: 18460046--18460075 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
18460036 TATATGTTTG
18460046 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18460076 GACCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18466328 original size:22 final size:21
Alignment explanation
Indices: 18466293--18466333 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18466283 TCATTTGGAA
**
18466293 GTTAAGAGTTAGTTAAGTTTTG
1 GTTAAGAGGAAGTT-AGTTTTG
18466315 GTTAAGAGGAAGTTAGTTT
1 GTTAAGAGGAAGTTAGTTT
18466334 CAGTTATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (21 bp):
GTTAAGAGGAAGTTAGTTTTG
Found at i:18467429 original size:97 final size:97
Alignment explanation
Indices: 18467263--18467455 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
18467253 GGCTTTTATA
* *
18467263 GCTTCATCACACTCAATTTTAAGATTATTAAAGTTTATTTGCCTTGTTCGACCCTTGTAAAATCA
1 GCTTCATCACACTCAATTTTAAGATTATTAAAATTTATTTGCCTTGTTCGACCCTTGGAAAATCA
18467328 TTGGCTTCACTGTTGCCATTTGTTCCCCATTG
66 TTGGCTTCACTGTTGCCATTTGTTCCCCATTG
* * *
18467360 GCTTCATTACTCTCAGTTTTAAGATTATTAAAATTTATTTGCCTTGTTC-AGCCCTTGGAAAATC
1 GCTTCATCACACTCAATTTTAAGATTATTAAAATTTATTTGCCTTGTTCGA-CCCTTGGAAAATC
*
18467424 ATTGGCTTCATTGTTGCCATTTGTTCCCCATT
65 ATTGGCTTCACTGTTGCCATTTGTTCCCCATT
18467456 TGGCCTACAA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
96 1 0.01
97 88 0.99
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (97 bp):
GCTTCATCACACTCAATTTTAAGATTATTAAAATTTATTTGCCTTGTTCGACCCTTGGAAAATCA
TTGGCTTCACTGTTGCCATTTGTTCCCCATTG
Found at i:18470333 original size:21 final size:20
Alignment explanation
Indices: 18470303--18470342 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18470293 TTTATAATAT
*
18470303 AAGGGCTATTATTCAATCTTA
1 AAGGGATATTATTC-ATCTTA
*
18470324 AAGGGATATTTTTCATCTT
1 AAGGGATATTATTCATCTT
18470343 TTTCTTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
AAGGGATATTATTCATCTTA
Found at i:18470433 original size:19 final size:20
Alignment explanation
Indices: 18470399--18470436 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
18470389 GAGATGGGTG
18470399 GAAACAAAAGAGAAAAAAAT
1 GAAACAAAAGAGAAAAAAAT
*
18470419 GAAAGAAAA-AGAAAAAAA
1 GAAACAAAAGAGAAAAAAA
18470437 AAAGAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (20 bp):
GAAACAAAAGAGAAAAAAAT
Found at i:18471701 original size:746 final size:724
Alignment explanation
Indices: 18470269--18471988 Score: 2057
Period size: 746 Copynumber: 2.4 Consensus size: 724
18470259 AAAAATAAGG
* * *
18470269 GAGTATTTTGGACCATTCGATGCATTTATAATATAAGGGCTATTATTCAATCTTAAAGGGATATT
1 GAGTATTTTGGACCATTGGATGCATTTATAATCTAAGGGCTACT-TTCAATCTTAAAGGGATATT
* * * *
18470334 TTTCATCTTTTTCTTAG-GAAAGTTTAA-TGTTGAAGAATAGAGGAGAAAAGAAGAAGAGATGGG
65 TTTCATCTTTTTCTTAGAG-GAGATTAACT-TTGAAGAATAGAGGAGAAGAG-AGAAAAGATGGG
18470397 TG-GAAACAAAAGAGAAAAAAATGAAAG---A-AAAAG----AAAAAAA-A--AAGAATTGAAGA
127 TGTGAAAC-AAAGAGAAAAAAATGAAAGAAAAGAAAAGAAAAAAAAAAAGAGGAAGAATTGAAGA
* * *
18470450 AAGCTTAGATA-AGGTAGAAATATTTTTTC---CTTTTTTGCATTCTT-ATTAAATTCTCATCAT
191 AAGCTT-GA-AGAGGTAG-AATATTTTTTCTTTTTTTTTTGCATT-TTCATTACATTCTCATCAC
**
18470510 ATTTTCCATATCACTTTCATATTGATTTTTTACTTTTTTCTATTTTTTTTGAAAGATTATAGGTT
252 ATTTTCCATATCACTTTCATATTGA-TTTTTAC---TTAATATTTTTTTTGAAAGATTATAGGTT
* * * *
18470575 TTTTTATATTTAATCTTGATTCAAAGTTCATCCAATTAAACTATAGTTGTGATTGAAATTAAATG
313 TTTTTATATTCAATCTTGATTCAAAGTTCATCCAACTAAACTATAGTTATGATTGAAATTAAAGG
18470640 AATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAGAAGGTTCAGCCAAGCAACTTCAC
378 AATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAGAAGGTTCAGCCAAGCAACTTCAC
** * *
18470705 CACTACCAAACCTCTTTTTAGTTCTTTTTAAATGTTTTCATTGCTCTTTTTGTCAATTATGGATG
443 CACTACCAAACCTCTTTTTAGTTCTCCTTAAATGTTTTCATAGCTCTTTATGTCAATTATGGATG
* *
18470770 ATTTAGTTGCTAGTTTACTTGAATTTTGATTGGTTTGTTAGTGAATGTTTGGTTATTTGACTAAT
508 ATTTAGTTGCTAGTTTACTTAAATTTTGATTGGTTTGTTAGTGAATGCTTGGTTATTTGACTAAT
* * *
18470835 GTTCTTGCTTTCATGATTTCCATGCTAACTAGCTCATTACATGTTTGATAAAGTTTTTCTCATGG
573 GTTATTGCTTTCATGATTTCCATGCTAACTAGCTCATCACATGTTTGATAAAGTTTTTCTCATGA
* * *
18470900 TATAACTCCCTTCATATGGTGACTGGATAAGTGATTGACGCTTGATTTTCCTTAGTAAATCATTG
638 TATAAATCCCTTCATATGGTGACTGGATAAGTGATTGACGCATGATTTGCCTTAGTAAATCATTG
* *
18470965 TATGATTTGGGAATAGCCAATGATGCATTTGAACAAAA
703 TAGGA-TT-----TAG-----GA---ATAT--ACAAAA
18471003 GAGTATTTTGGACCATTGGATGCATTTATAATCTAAGGGCTAGCTTTCAATCTTAAAGGGATATT
1 GAGTATTTTGGACCATTGGATGCATTTATAATCTAAGGGCTA-CTTTCAATCTTAAAGGGATATT
* * * *
18471068 TTTCATCTTCTTCTTAGAGGAGATTAACTTTGAAGAATAGAGGACAAGAGAGGAAAAGCTAGGTG
65 TTTCATCTTTTTCTTAGAGGAGATTAACTTTGAAGAATAGAGGAGAAGAGA-GAAAAGATGGGTG
18471133 TGAAACAAATGAGAAAAAAATGAAAGAAAAAGAAAAGTAAAAAAAAAAAAGAGGAAGAATTGAAG
129 TGAAACAAA-GAGAAAAAAATGAAAG-AAAAGAAAAG--AAAAAAAAAAAGAGGAAGAATTGAAG
* *
18471198 AAAGCTTGAAGGAGGTAGAATTTTTTTCCTTCTTTTTTTTTTGAATTTTCATTACATTCTCATCA
190 AAAGCTTGAA-GAGGTAGAA-TATTTT--TTCTTTTTTTTTTGCATTTTCATTACATTCTCATCA
* *
18471263 CATTTTCCATAAT-ATTTTCATATTG-TTTTT-C-TAAT-TTTTTTTTGAAAGATTATAGTTTTT
251 CATTTTCCAT-ATCACTTTCATATTGATTTTTACTTAATATTTTTTTTGAAAGATTATAGGTTTT
* * * *
18471323 TTTTTATTCAATCTTGATTTAAAGTTTATCCAACTAAACTGTAGTTATGATTGAAATTAAAGGAA
315 TTTATATTCAATCTTGATTCAAAGTTCATCCAACTAAACTATAGTTATGATTGAAATTAAAGGAA
* * ** *
18471388 TCATGTAACAAAGAATATATCCACTATTGAAACCAATTAGGAGGTTTGGCCAAGCAGCTTCACCA
380 TCATGTAACAAAGAATATATCCACCATTGAAACCAATTAGAAGGTTCAGCCAAGCAACTTCACCA
*** * * **
18471453 C-AGTTGAACCGTC-TTTTGGTTCTCCTTAAATGTTTTCCTAGCTCTTTATGTTGATTATGGATG
445 CTA-CCAAACC-TCTTTTTAGTTCTCCTTAAATGTTTTCATAGCTCTTTATGTCAATTATGGATG
*
18471516 ATTTAGTTGCTAGTTTACTTAAATTTTGATTGGTTTGTTAGTGAATGCTTGGTTGTTTGACTAAT
508 ATTTAGTTGCTAGTTTACTTAAATTTTGATTGGTTTGTTAGTGAATGCTTGGTTATTTGACTAAT
* *
18471581 GTTATTGCTTTCATGATTTCTATTCTAACTAGCTCATCACATGTTTGATAAAGTTTTTCTCATGA
573 GTTATTGCTTTCATGATTTCCATGCTAACTAGCTCATCACATGTTTGATAAAGTTTTTCTCATGA
* * ** *
18471646 TATAAATCCCTTCATATGGTGATTGGATAAGTGCTTGGTGCATGATTTGCCTTAGTAAATGATTG
638 TATAAATCCCTTCATATGGTGACTGGATAAGTGATTGACGCATGATTTGCCTTAGTAAATCATTG
**
18471711 TAGGATTTAGGAATATACAAGG
703 TAGGATTTAGGAATATACAAAA
* * *
18471733 GAGTATTTTGGACCATGGGATTCATTTATAATCTAAGGGCTAACATTCAATCTTAAAGGGATATT
1 GAGTATTTTGGACCATTGGATGCATTTATAATCTAAGGGCT-ACTTTCAATCTTAAAGGGATATT
* * * * *
18471798 TTGT-ATCTTTTTCTTAAAGGAGATTAACTTTGAAGAACAAAGGAGAAGAGATAAAGAGTTGGGT
65 TT-TCATCTTTTTCTTAGAGGAGATTAACTTTGAAGAATAGAGGAGAAGAGAGAAA-AGATGGGT
* * * *
18471862 GTGAAATAGAGGAGAAAAAAA-G---TAAAAGACAAAGAAAAGAAAAAAAGTGGAAGAATTGAAG
128 GTGAAACA-AAGAGAAAAAAATGAAAGAAAAGA-AAAGAAAA-AAAAAAAGAGGAAGAATTGAAG
* * *
18471923 AAAGCATGGAAGAGGTAGAA-ATTTTTT-TTTTTTTTTTGCATTTTCATTACATTTTCAACACAT
190 AAAGC-TTGAAGAGGTAGAATATTTTTTCTTTTTTTTTTGCATTTTCATTACATTCTCATCACAT
18471986 TTT
254 TTT
18471989 TTGACATCAG
Statistics
Matches: 863, Mismatches: 84, Indels: 92
0.83 0.08 0.09
Matches are distributed among these distances:
720 36 0.04
721 2 0.00
723 4 0.00
724 4 0.00
725 41 0.05
726 8 0.01
729 4 0.00
730 131 0.15
731 3 0.00
732 3 0.00
733 1 0.00
734 114 0.13
735 26 0.03
739 1 0.00
740 8 0.01
745 3 0.00
746 378 0.44
747 6 0.01
748 4 0.00
749 29 0.03
751 4 0.00
752 5 0.01
753 2 0.00
754 44 0.05
755 2 0.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (724 bp):
GAGTATTTTGGACCATTGGATGCATTTATAATCTAAGGGCTACTTTCAATCTTAAAGGGATATTT
TTCATCTTTTTCTTAGAGGAGATTAACTTTGAAGAATAGAGGAGAAGAGAGAAAAGATGGGTGTG
AAACAAAGAGAAAAAAATGAAAGAAAAGAAAAGAAAAAAAAAAAGAGGAAGAATTGAAGAAAGCT
TGAAGAGGTAGAATATTTTTTCTTTTTTTTTTGCATTTTCATTACATTCTCATCACATTTTCCAT
ATCACTTTCATATTGATTTTTACTTAATATTTTTTTTGAAAGATTATAGGTTTTTTTATATTCAA
TCTTGATTCAAAGTTCATCCAACTAAACTATAGTTATGATTGAAATTAAAGGAATCATGTAACAA
AGAATATATCCACCATTGAAACCAATTAGAAGGTTCAGCCAAGCAACTTCACCACTACCAAACCT
CTTTTTAGTTCTCCTTAAATGTTTTCATAGCTCTTTATGTCAATTATGGATGATTTAGTTGCTAG
TTTACTTAAATTTTGATTGGTTTGTTAGTGAATGCTTGGTTATTTGACTAATGTTATTGCTTTCA
TGATTTCCATGCTAACTAGCTCATCACATGTTTGATAAAGTTTTTCTCATGATATAAATCCCTTC
ATATGGTGACTGGATAAGTGATTGACGCATGATTTGCCTTAGTAAATCATTGTAGGATTTAGGAA
TATACAAAA
Found at i:18478348 original size:24 final size:24
Alignment explanation
Indices: 18478313--18478368 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
18478303 TTTCAATGCA
*
18478313 TTTTCTATAACATTTTCATAATGG
1 TTTTCTACAACATTTTCATAATGG
18478337 TTTTCTACAACATTTTCATAATGG
1 TTTTCTACAACATTTTCATAATGG
18478361 TTTTCTAC
1 TTTTCTAC
18478369 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (24 bp):
TTTTCTACAACATTTTCATAATGG
Found at i:18479395 original size:23 final size:22
Alignment explanation
Indices: 18479350--18479396 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
18479340 CTAGTTTACT
*
18479350 TGAATTTTGGTTGATTTGTTAA
1 TGAATTTTGGTTGATTTGCTAA
18479372 TGAATGTTTGGTTG-TTTGACTAA
1 TGAAT-TTTGGTTGATTTG-CTAA
18479395 TG
1 TG
18479397 TTATGGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (22 bp):
TGAATTTTGGTTGATTTGCTAA
Found at i:18479905 original size:755 final size:736
Alignment explanation
Indices: 18477567--18480047 Score: 2838
Period size: 763 Copynumber: 3.3 Consensus size: 736
18477557 TTTTCGGTAT
* * * * * *
18477567 CATTTTCTATAACATTTTT-ATAATGGTTTTCTAATTTTTTTCTATTTTTTTTGAAAAATTATAG
1 CATTTTCCATAATATTTTTCACACTGGTTTTCT-ACTTTTTTCTA-TTTTTTTGAAATATTATA-
* *
18477631 TTTATTTTTTATTCAATCTTGATTCAAGGTTCATACAACTAAACCATAGTTGTGA-TTACAATTA
63 TTT-TTTTTTATTCAATCTTGATTCAAAGTTCATCCAACTAAACCATAGTTGTGATTTA-AATTA
* *
18477695 AAGGAACCATGTAACAAAGAATATATCCATCATTGAAACCAATTAAGAGGTTCAACCAACTAACT
126 AAGGAATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCAACCAAC-AACT
* * *
18477760 CCACCATGGAC-AAACCT-CTTCTTAGTTCTCTTTAAATGTTTTCCTTGCTCTTTGTGTTGATTA
190 CCACCATGG-CTAAACCTCCTT-TTGGTT-TCCTTAAATGTTTTCCTTACTCTTTGTGTTGATTA
* * * *
18477823 TGGATGATTTATTTGCCAGTTTACTTGAATTTTGATAGGCTTGTTAGTGAATGTTTGGTTATTTG
252 TGGATGATTTAGTTGCTAGTTTACTTGAATTTTGATTGGTTTGTTAGTGAATGTTTGGTTATTTG
* * *
18477888 GCAAATGTTCTTACTTCCATGATTTCCATTCTAACTAGTTCATCACATGTTTGATAAAGTTTTTC
317 GCTAATGTTCTTGCTTTCATGATTTCCATTCTAACTAGTTCATCACATGTTTGATAAAGTTTTTC
* * *
18477953 TCATGGTATAAATCCCTTTAAATGGTGATTGGATAAGTGATTGCTGCATGATTTGCCTTAGTAAA
382 TCATGGTATAAATCCCTTCATATGGTGATTGGATAAGTGATTGATGCATGATTTGCCTTAGTAAA
* * * *
18478018 TGATTGTATGATTTAGGAATAGCCAATGAAA-CATTTGGCCTATGGAGTATTTTGCACCACTGCA
447 TGATTGTATGATTTAGGAATAGCCAATGAAAGCATTTGGCCAAAGGAGTATTTTG-ACCATTGGA
* * *
18478082 TGC-------ATT-AGGCTAGCATTCTATCTTAAATGGATATTTTGCATCTTTTTCTTGGAGGAG
511 TGCATTTATAATTAAGGCTAGCATTCAATCTTAAA-GGATATTTTGCATCTTCTTCTTGGGGGAG
* * * ** *
18478139 ATTAACTTTAAAGAATAGAGGAGAATAGAGGAAAAGCTAGGCATGAAATAGAAGAGAAAAAAGTG
575 ATTAACTTTGAAGAATAGAGGAGAATAGAGGAAGAGCTGGGTGTGAAATAG-AG-GAGAAAA---
* *
18478204 AAAGAAATAGAAAAAAGAAAAAAAGAAAAAAAGTGGAAGAATTGAAGAAAGCTTGGGGGAGGTAG
635 AAATAAA-AG-AAAAAG---AAAAGAAAAAAAGTGGAAGAATTGAAGAAAGCTT-GGAGAGGTAG
** * * * * *
18478269 AATTTTTTTTTCAACTTTTGCATATTCATTACATTTTCAATGCATTTTCTATAA
694 AA-AATTTTTTC--C-TTT---T-TT--TTGCATTTTCATTACATTATC-ATCA
* *
18478323 CATTTT-CATAATGGTTTTCTACAACATTTTCATAATGGTTTTCTAC--TTTT-TATTTTTTTAA
1 CATTTTCCATAAT-ATTTT-T-C-ACA----C----TGGTTTTCTACTTTTTTCTATTTTTTTGA
* * *
18478384 AAGATTATAGTTTTTTTTTTATTTAATCTTGATTCAAAGTTCATCCAATTAAACCATAGTTGTGA
54 AATATTATA--TTTTTTTTTATTCAATCTTGATTCAAAGTTCATCCAACTAAACCATAGTTGTGA
** * * * * *
18478449 TTGCAATTAAAGGAATCATGTAACAAAGAATACATCGACCACTAAAACCAATTAAGAGGTTCGAC
117 TTTAAATTAAAGGAATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCAAC
* ** * ** *
18478514 CAAGCAATTCCACCATCACCAAACCTTTTTTTGGTTCTCCTTAAATGTTTTCCTTACTCTTTGTA
182 CAA-CAACTCCACCATGGCTAAACCTCCTTTTGGTT-TCCTTAAATGTTTTCCTTACTCTTTGTG
* * *
18478579 TTGATTATGGATTATTTAGTTGATAGTTTACATGAATTTTGATTGGTTTGTTAGTGAATGTTTGG
245 TTGATTATGGATGATTTAGTTGCTAGTTTACTTGAATTTTGATTGGTTTGTTAGTGAATGTTTGG
*
18478644 TTATTTGGCTAATGTTCTTGCTTTCATGATTTTCATTCTAACTAGTTCATCACATGTTTGATAAA
310 TTATTTGGCTAATGTTCTTGCTTTCATGATTTCCATTCTAACTAGTTCATCACATGTTTGATAAA
* * *
18478709 GTTTTTCTCATGGTATAAATCCCTTCATATGGTGATTAGATAAGTGACTGATGCATGATTGGCCT
375 GTTTTTCTCATGGTATAAATCCCTTCATATGGTGATTGGATAAGTGATTGATGCATGATTTGCCT
* *
18478774 TAGTAAATGATTGTATGATTTGGGAATAGCTAATG-AAGCATTTGGCCAAAGGAGTATTTTGGAC
440 TAGTAAATGATTGTATGATTTAGGAATAGCCAATGAAAGCATTTGGCCAAAGGAGTATTTT-GAC
* * * *
18478838 CATTGGATGCATTTATAATATAAAGGCTAGCTTTCAATCTTGAAGGCATATTTTCCATGTTCTTC
504 CATTGGATGCATTTATAAT-T-AAGGCTAGCATTCAATCTTAAAGG-ATATTTTGCATCTTCTTC
* * * *
18478903 -TGGGGGAGATTAACTTTGAAGGATAGAGGAGAAGAGAGGAAGAGCTGGGTGTGAAATATATGAG
566 TTGGGGGAGATTAACTTTGAAGAATAGAGGAGAATAGAGGAAGAGCTGGGTGTGAAATAGAGGAG
* * * *
18478967 AAAAAAGTGAAAGAAAAAGAAAAGAAAAAGAA--GAAAGAATTGAAGAAAGCTTGGATGAGGTAA
631 AAAAAAATAAAAGAAAAAGAAAAGAAAAA-AAGTGGAAGAATTGAAGAAAGCTTGGA-GAGGTAG
*
18479030 AAAATTTTTT--TTTTTATTGCATTTTCATTACATTATCATCA
694 AAAATTTTTTCCTTTTTTTTGCATTTTCATTACATTATCATCA
* * * * ** **
18479071 TATTTTTCATAATA-TTTTCATATTGGTTTTCTACTTTTTAATGGTTTTTTGAAATATTATAGTT
1 CATTTTCCATAATATTTTTCACACTGGTTTTCTACTTTTTTCTATTTTTTTGAAATATTATA---
*
18479135 TCTTTTTTTTATTCAATCTTGATTCAAAGTCCATCCAACTAAACCATAGTTGTGATTTAAATTAA
63 T-TTTTTTTTATTCAATCTTGATTCAAAGTTCATCCAACTAAACCATAGTTGTGATTTAAATTAA
**
18479200 AGGAATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCGGCCAACAACTCC
127 AGGAATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCAACCAACAACTCC
* * *
18479265 AACATGGCTGAACCTCCTTTTGGTTTCCTCTAAA-GTTTTCCTTTCTCTTTGTGTTGATTATGGA
192 ACCATGGCTAAACCTCCTTTTGGTTTCCT-TAAATGTTTTCCTTACTCTTTGTGTTGATTATGGA
* * * * *
18479329 TGATTTAGTTGCTAGTTTACTTGAATTTTGGTTGATTTGTTAATGAATGTTTGGTTGTTTGACTA
256 TGATTTAGTTGCTAGTTTACTTGAATTTTGATTGGTTTGTTAGTGAATGTTTGGTTATTTGGCTA
* * *
18479394 ATGTTATGGCTTTCATGATTTCCATTCTAACTAGCTCATCACATGTTTGATAAAGTTTTTCTCAT
321 ATGTTCTTGCTTTCATGATTTCCATTCTAACTAGTTCATCACATGTTTGATAAAGTTTTTCTCAT
18479459 GGTATAACTTTATTATGTTATAAATCCCTTCATATGGTGATTGGATAAGTGATTGATGCATGATT
386 -G--------------G-TATAAATCCCTTCATATGGTGATTGGATAAGTGATTGATGCATGATT
* * * *
18479524 TGCCTTAGTAAATGATTGTACGATTTTGGAATAACCAA-GAAAGCATTTGGCCAAGGGAGTATTT
435 TGCCTTAGTAAATGATTGTATGATTTAGGAATAGCCAATGAAAGCATTTGGCCAAAGGAGTATTT
*
18479588 TAGACCATTGGATGCATTTATAATCTAAGGTCTAGCACTCAATCTTAAAGCGATATTTTGCATCT
500 T-GACCATTGGATGCATTTATAAT-TAAGG-CTAGCATTCAATCTTAAAG-GATATTTTGCATCT
* *
18479653 TCTTCTTGGGGGAGATTAACTTTGAAGAATATAGGAGAATAGATGAAGAGCTGGGTGTGAAATAG
561 TCTTCTTGGGGGAGATTAACTTTGAAGAATAGAGGAGAATAGAGGAAGAGCTGGGTGTGAAATAG
*
18479718 AGGAGAAAAAAATTAAAGAAAAAGAAAAGAAAAAAAGTGGAAGAATTGAAGAAAGCTTGGAGAAG
626 AGGAGAAAAAAATAAAAGAAAAAGAAAAGAAAAAAAGTGGAAGAATTGAAGAAAGCTTGGAG-AG
*
18479783 GTAGAAAATTTTTTCCTTTTTTTTGCATTTTCATTACATTCTCATCA
690 GTAGAAAATTTTTTCCTTTTTTTTGCATTTTCATTACATTATCATCA
*
18479830 CATTTTCCATAATATTTTTCACACTGGTTTTCTACTTTTTTCTATTTTTTTGAAATATTATA-AT
1 CATTTTCCATAATATTTTTCACACTGGTTTTCTACTTTTTTCTATTTTTTTGAAATATTATATTT
* * * *
18479894 TTTTTTATTCAATCTTGATTTAAATTTCATCCACCTAAACCATAGTTCTGATTTAAATTAAAGGA
66 TTTTTTATTCAATCTTGATTCAAAGTTCATCCAACTAAACCATAGTTGTGATTTAAATTAAAGGA
*** * * * ** *
18479959 ATCATGTAACAAAGAATATATCCAGTTTTGAAACCAATTAGGAGGTTCAGCCAGCAACTTTAGCA
131 ATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCAACCAACAACTCCACCA
* *
18480024 TGGCTGAACCTCCTAATTGGTTTC
196 TGGCTAAACCTCCT-TTTGGTTTC
18480048 AAAAGTGGAT
Statistics
Matches: 1481, Mismatches: 177, Indels: 134
0.83 0.10 0.07
Matches are distributed among these distances:
736 11 0.01
738 3 0.00
739 166 0.11
740 31 0.02
741 111 0.07
744 2 0.00
745 1 0.00
746 1 0.00
747 3 0.00
748 8 0.01
749 23 0.02
751 1 0.00
752 1 0.00
754 6 0.00
755 297 0.20
756 105 0.07
757 38 0.03
759 41 0.03
760 51 0.03
761 27 0.02
762 13 0.01
763 410 0.28
764 10 0.01
765 10 0.01
766 2 0.00
767 5 0.00
768 9 0.01
770 8 0.01
771 2 0.00
772 52 0.04
773 33 0.02
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (736 bp):
CATTTTCCATAATATTTTTCACACTGGTTTTCTACTTTTTTCTATTTTTTTGAAATATTATATTT
TTTTTTATTCAATCTTGATTCAAAGTTCATCCAACTAAACCATAGTTGTGATTTAAATTAAAGGA
ATCATGTAACAAAGAATATATCCACCATTGAAACCAATTAAGAGGTTCAACCAACAACTCCACCA
TGGCTAAACCTCCTTTTGGTTTCCTTAAATGTTTTCCTTACTCTTTGTGTTGATTATGGATGATT
TAGTTGCTAGTTTACTTGAATTTTGATTGGTTTGTTAGTGAATGTTTGGTTATTTGGCTAATGTT
CTTGCTTTCATGATTTCCATTCTAACTAGTTCATCACATGTTTGATAAAGTTTTTCTCATGGTAT
AAATCCCTTCATATGGTGATTGGATAAGTGATTGATGCATGATTTGCCTTAGTAAATGATTGTAT
GATTTAGGAATAGCCAATGAAAGCATTTGGCCAAAGGAGTATTTTGACCATTGGATGCATTTATA
ATTAAGGCTAGCATTCAATCTTAAAGGATATTTTGCATCTTCTTCTTGGGGGAGATTAACTTTGA
AGAATAGAGGAGAATAGAGGAAGAGCTGGGTGTGAAATAGAGGAGAAAAAAATAAAAGAAAAAGA
AAAGAAAAAAAGTGGAAGAATTGAAGAAAGCTTGGAGAGGTAGAAAATTTTTTCCTTTTTTTTGC
ATTTTCATTACATTATCATCA
Found at i:18480929 original size:7 final size:7
Alignment explanation
Indices: 18480837--18480910 Score: 62
Period size: 7 Copynumber: 10.4 Consensus size: 7
18480827 CCCAAATTTG
18480837 AAACCCT
1 AAACCCT
*
18480844 AAACTCT
1 AAACCCT
18480851 AAATCCCT
1 AAA-CCCT
18480859 AAACCCCT
1 AAA-CCCT
*
18480867 AAACCTT
1 AAACCCT
18480874 AAACCCT
1 AAACCCT
*
18480881 -AA-TCT
1 AAACCCT
* *
18480886 AAAATCAT
1 -AAACCCT
18480894 AAACCCT
1 AAACCCT
18480901 AAACCCT
1 AAACCCT
18480908 AAA
1 AAA
18480911 ACATACCTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
7 35 0.66
8 14 0.26
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:18480941 original size:20 final size:19
Alignment explanation
Indices: 18480895--18480941 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
18480885 TAAAATCATA
18480895 AACCC-TAAACCCTAAAAC
1 AACCCTTAAACCCTAAAAC
*
18480913 ATA-CCTTAAATCCTAAAACC
1 A-ACCCTTAAACCCTAAAA-C
18480933 AACCCTTAA
1 AACCCTTAA
18480942 CCCCATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 13 0.54
20 8 0.33
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (19 bp):
AACCCTTAAACCCTAAAAC
Found at i:18481356 original size:23 final size:23
Alignment explanation
Indices: 18481330--18481400 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 23
18481320 ATTGTTTCAC
18481330 TTTTCAAAAAAAAATAAAAATGT
1 TTTTCAAAAAAAAATAAAAATGT
18481353 TTTTCTTTAAAAAAAAGA-AAAAAT-T
1 TTTTC---AAAAAAAA-ATAAAAATGT
18481378 TTTT-AAAATAAAAATAAAGAATG
1 TTTTCAAAA-AAAAATAAA-AATG
18481401 AAAGATGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
21 5 0.12
22 7 0.17
23 8 0.20
25 5 0.12
26 14 0.35
27 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (23 bp):
TTTTCAAAAAAAAATAAAAATGT
Found at i:18483079 original size:26 final size:24
Alignment explanation
Indices: 18483022--18483080 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
18483012 AAAAGAAAAT
*
18483022 TATTGAAAAGGAGAAAGGAAGAAGC
1 TATTG-AAAGGAGAAAGAAAGAAGC
**
18483047 TGCTGAAAGCGAGAAAGAAAAGAAGC
1 TATTGAAAG-GAGAAAG-AAAGAAGC
18483073 TATTGAAA
1 TATTGAAA
18483081 AAAAGAAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.15
25 10 0.37
26 13 0.48
ACGTcount: A:0.51, C:0.07, G:0.29, T:0.14
Consensus pattern (24 bp):
TATTGAAAGGAGAAAGAAAGAAGC
Found at i:18485303 original size:8 final size:9
Alignment explanation
Indices: 18485266--18485312 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
18485256 TATGACAAAC
*
18485266 AAAAAATCA
1 AAAAAATAA
*
18485275 AAAAATTAA
1 AAAAAATAA
*
18485284 AAAAAATGA
1 AAAAAATAA
18485293 AAAAAATAA
1 AAAAAATAA
18485302 AAAAAATAA
1 AAAAAATAA
18485311 AA
1 AA
18485313 TTCAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:18487834 original size:12 final size:12
Alignment explanation
Indices: 18487817--18487841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18487807 ATAAGATAAT
18487817 AAAGAATTGAAA
1 AAAGAATTGAAA
18487829 AAAGAATTGAAA
1 AAAGAATTGAAA
18487841 A
1 A
18487842 GTGAAAAGAA
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAGAATTGAAA
Found at i:18492306 original size:21 final size:20
Alignment explanation
Indices: 18492264--18492306 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
18492254 TCTTTTTACA
* *
18492264 ATTTTTATTCATGCCCATAT
1 ATTTTTATTCATGCCAAAAT
*
18492284 ATTTTTCATTCTTGCCAAAAT
1 ATTTTT-ATTCATGCCAAAAT
18492305 AT
1 AT
18492307 CTACCTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTTATTCATGCCAAAAT
Found at i:18498749 original size:16 final size:16
Alignment explanation
Indices: 18498728--18498761 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18498718 CCTCAAATTT
18498728 AAAACCTTAAACCCTA
1 AAAACCTTAAACCCTA
*
18498744 AAAACCTTAAGCCCTA
1 AAAACCTTAAACCCTA
18498760 AA
1 AA
18498762 CCCCAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAACCTTAAACCCTA
Found at i:18498783 original size:14 final size:14
Alignment explanation
Indices: 18498766--18498840 Score: 64
Period size: 14 Copynumber: 5.2 Consensus size: 14
18498756 CCTAAACCCC
18498766 AAATCTTAAACCTT
1 AAATCTTAAACCTT
*
18498780 AAAT-TTCAAACCCT
1 AAATCTT-AAACCTT
*
18498794 AAATCCCTAAACCTT
1 AAAT-CTTAAACCTT
* *
18498809 AAAAACCTAAA-CTCT
1 -AAATCTTAAACCT-T
18498824 AAATCTTAAACCTT
1 AAATCTTAAACCTT
18498838 AAA
1 AAA
18498841 ACATACCCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 2 0.04
14 28 0.57
15 15 0.31
16 4 0.08
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATCTTAAACCTT
Found at i:18498818 original size:58 final size:57
Alignment explanation
Indices: 18498715--18498840 Score: 155
Period size: 58 Copynumber: 2.2 Consensus size: 57
18498705 TAATTCCATG
* * **
18498715 AAACCTCAAATTTAAAACCTTAAACCCTAAAAACCTTAAGCCCTAAACCCCAAATCTT
1 AAACCTTAAATTTAAAACCCTAAACCCT-AAAACCTTAAAACCTAAACCCCAAATCTT
* * *
18498773 AAACCTTAAATTTCAAACCCTAAATCCCT-AAACCTTAAAAACCTAAACTCTAAATCTT
1 AAACCTTAAATTTAAAACCCTAAA-CCCTAAAACCTT-AAAACCTAAACCCCAAATCTT
18498831 AAACCTTAAA
1 AAACCTTAAA
18498841 ACATACCCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 7 0.12
58 48 0.81
59 4 0.07
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.25
Consensus pattern (57 bp):
AAACCTTAAATTTAAAACCCTAAACCCTAAAACCTTAAAACCTAAACCCCAAATCTT
Found at i:18498859 original size:7 final size:7
Alignment explanation
Indices: 18498729--18498840 Score: 50
Period size: 7 Copynumber: 15.4 Consensus size: 7
18498719 CTCAAATTTA
18498729 AAACCTT
1 AAACCTT
*
18498736 AAACCCTAA
1 AAA-CCT-T
18498745 AAACCTT
1 AAACCTT
* *
18498752 AAGCCCT
1 AAACCTT
**
18498759 AAACCCC
1 AAACCTT
*
18498766 AAATCTT
1 AAACCTT
18498773 AAACCTT
1 AAACCTT
*
18498780 AAA-TTT
1 AAACCTT
*
18498786 CAAACCCT
1 -AAACCTT
*
18498794 AAATCCCT
1 AAA-CCTT
18498802 AAACCTT
1 AAACCTT
18498809 AAAAACC-T
1 --AAACCTT
18498817 AAA-CTCT
1 AAACCT-T
*
18498824 AAATCTT
1 AAACCTT
18498831 AAACCTT
1 AAACCTT
18498838 AAA
1 AAA
18498841 ACATACCCTA
Statistics
Matches: 80, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
5 1 0.01
6 5 0.06
7 49 0.61
8 17 0.21
9 8 0.10
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (7 bp):
AAACCTT
Found at i:18500712 original size:24 final size:27
Alignment explanation
Indices: 18500681--18500747 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 27
18500671 AAAAAAAGAA
18500681 AAAT-AAAAGAA-GAT-GAATG-AATG
1 AAATGAAAAGAATGATGGAATGAAATG
18500704 AAATGAAAATTGAATGATGGAATGAAATG
1 AAATGAAAA--GAATGATGGAATGAAATG
*
18500733 AAATGAATAGAATGA
1 AAATGAAAAGAATGA
18500748 CATGATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 4 0.11
24 4 0.11
26 3 0.08
27 9 0.24
28 5 0.14
29 12 0.32
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.21
Consensus pattern (27 bp):
AAATGAAAAGAATGATGGAATGAAATG
Found at i:18500745 original size:19 final size:19
Alignment explanation
Indices: 18500693--18500752 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 19
18500683 ATAAAAGAAG
18500693 ATGAAT-GAATGAAATGAAA
1 ATGAATAGAATGAAATG-AA
18500712 ATTGAATGATGGAATGAAATGAA
1 A-TGAAT-A--GAATGAAATGAA
*
18500735 ATGAATAGAATGACATGA
1 ATGAATAGAATGAAATGA
18500753 TAAAAGAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 11 0.31
20 5 0.14
21 1 0.03
22 5 0.14
23 3 0.09
24 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (19 bp):
ATGAATAGAATGAAATGAA
Found at i:18500752 original size:24 final size:24
Alignment explanation
Indices: 18500693--18500752 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
18500683 ATAAAAGAAG
18500693 ATGAATGAATGAAATGAAAATTGA
1 ATGAATGAATGAAATGAAAATTGA
18500717 ATG-ATGGAATGAAATG-AAA-TGA
1 ATGAAT-GAATGAAATGAAAATTGA
18500739 ATAGAATGACATGA
1 AT-GAATGA-ATGA
18500753 TAAAAGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 5 0.16
23 8 0.25
24 19 0.59
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (24 bp):
ATGAATGAATGAAATGAAAATTGA
Found at i:18501495 original size:49 final size:48
Alignment explanation
Indices: 18501438--18501638 Score: 152
Period size: 49 Copynumber: 4.1 Consensus size: 48
18501428 ATAGAAGCTT
* * **
18501438 TTTTCAAATTGAAAATTTTAAAGTTCGTTTTTTATCTTTATAAGAGCCC
1 TTTTCAAATAGAAAATTTTAAAGTTC-ATTCCTATCTTTATAAGAGCCC
* * * * *
18501487 TTTTCAAATTGAGATATTTTTAAAGTTCACTGCCTATCTTCATAAGAGCTC
1 TTTTCAAA-T-AGAAAATTTTAAAGTTCA-TTCCTATCTTTATAAGAGCCC
* * * * * *
18501538 ATTTCAAAAAGAAAGTTTTAAAGATCATTGCTATCTTTATAAGAGCCT
1 TTTTCAAATAGAAAATTTTAAAGTTCATTCCTATCTTTATAAGAGCCC
* ** ** *
18501586 TTTTCAAA-AGAAAGATTGTAAAGTTTGTTGCCTATCTCCATAGGAGCCC
1 TTTTCAAATAGAAA-ATTTTAAAGTTCATT-CCTATCTTTATAAGAGCCC
18501635 TTTT
1 TTTT
18501639 TAAACTAAGA
Statistics
Matches: 117, Mismatches: 30, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
47 5 0.04
48 33 0.28
49 41 0.35
50 1 0.01
51 37 0.32
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (48 bp):
TTTTCAAATAGAAAATTTTAAAGTTCATTCCTATCTTTATAAGAGCCC
Found at i:18501523 original size:100 final size:99
Alignment explanation
Indices: 18501397--18501593 Score: 222
Period size: 100 Copynumber: 2.0 Consensus size: 99
18501387 TTTTCAAGAA
* ** **
18501397 GAGATTTTTTAAATGTCACTTGCCTAT-GTC-TATAGAAGCTTTTTTCAAATTGAAAATTTTAAA
1 GAGATTTTTTAAATGTCACTTGCCTATCTTCATA-AG-AGCTCATTTCAAAAAGAAAATTTTAAA
* * **
18501460 GTTCGTTTTTTATCTTTATAAGAGCCCTTTTCAAATT
64 GATC-ATTGCTATCTTTATAAGAGCCCTTTTCAAATT
*
18501497 GAGATATTTTTAAA-GTTCAC-TGCCTATCTTCATAAGAGCTCATTTCAAAAAGAAAGTTTTAAA
1 GAGAT-TTTTTAAATG-TCACTTGCCTATCTTCATAAGAGCTCATTTCAAAAAGAAAATTTTAAA
*
18501560 GATCATTGCTATCTTTATAAGAGCCTTTTTCAAA
64 GATCATTGCTATCTTTATAAGAGCCCTTTTCAAA
18501594 AGAAAGATTG
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
99 26 0.32
100 38 0.46
101 16 0.20
102 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (99 bp):
GAGATTTTTTAAATGTCACTTGCCTATCTTCATAAGAGCTCATTTCAAAAAGAAAATTTTAAAGA
TCATTGCTATCTTTATAAGAGCCCTTTTCAAATT
Found at i:18501525 original size:51 final size:48
Alignment explanation
Indices: 18501470--18501608 Score: 145
Period size: 48 Copynumber: 2.8 Consensus size: 48
18501460 GTTCGTTTTT
* * * *
18501470 TATCTTTATAAGAGCCCTTTTCAAATTGAGATATTTTTAAAGTTCACTGCC
1 TATCTTTATAAGAGCCCTTTTCAAA--AAGAAAGTTTTAAAGATCACTG-C
* * * *
18501521 TATCTTCATAAGAGCTCATTTCAAAAAGAAAGTTTTAAAGATCATTGC
1 TATCTTTATAAGAGCCCTTTTCAAAAAGAAAGTTTTAAAGATCACTGC
* *
18501569 TATCTTTATAAGAGCCTTTTTC-AAAAGAAAGATTGTAAAG
1 TATCTTTATAAGAGCCCTTTTCAAAAAGAAAG-TTTTAAAG
18501609 TTTGTTGCCT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
47 9 0.12
48 26 0.35
49 17 0.23
51 22 0.30
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (48 bp):
TATCTTTATAAGAGCCCTTTTCAAAAAGAAAGTTTTAAAGATCACTGC
Found at i:18503122 original size:11 final size:11
Alignment explanation
Indices: 18503103--18503145 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
18503093 CCTTTCTTTG
*
18503103 CATTGTCATTA
1 CATTTTCATTA
* *
18503114 CATTCTCATCA
1 CATTTTCATTA
18503125 CATTTTCCATTA
1 CATTTT-CATTA
18503137 CATTTTCAT
1 CATTTTCAT
18503146 ATTCGTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (11 bp):
CATTTTCATTA
Found at i:18504041 original size:14 final size:14
Alignment explanation
Indices: 18504022--18504063 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
18504012 TGTATTTTCC
18504022 TTTGAAACCTTAAA
1 TTTGAAACCTTAAA
18504036 TTTGAAACCTTAAA
1 TTTGAAACCTTAAA
* *
18504050 TCTAAAACCTTAAA
1 TTTGAAACCTTAAA
18504064 GTACTAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (14 bp):
TTTGAAACCTTAAA
Found at i:18510440 original size:27 final size:29
Alignment explanation
Indices: 18510380--18510440 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
18510370 AAAATATTAA
18510380 AATAAATTTAGTGATTTAATATAATAAAT
1 AATAAATTTAGTGATTTAATATAATAAAT
*
18510409 -A-AAATTTA-TTA-TT-ATATAATAAACT
1 AATAAATTTAGTGATTTAATATAATAAA-T
18510434 AATAAAT
1 AATAAAT
18510441 AAATAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 10 0.36
25 3 0.11
26 3 0.11
27 11 0.39
28 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (29 bp):
AATAAATTTAGTGATTTAATATAATAAAT
Found at i:18510453 original size:36 final size:36
Alignment explanation
Indices: 18510396--18510482 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
18510386 TTTAGTGATT
18510396 TAATATAATAAATAAAATTTATTATTATATAATAAAC
1 TAATA-AATAAATAAAATTTATTATTATATAATAAAC
* *
18510433 TAATAAATAAATAAATTTTATTATTATATAATAAAT
1 TAATAAATAAATAAAATTTATTATTATATAATAAAC
18510469 TAATAAATAAATAA
1 TAATAAATAAATAA
18510483 TATGTATTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 43 0.90
37 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (36 bp):
TAATAAATAAATAAAATTTATTATTATATAATAAAC
Found at i:18514472 original size:31 final size:28
Alignment explanation
Indices: 18514436--18514513 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 28
18514426 AAAATATATC
*
18514436 TAATAAAAATATAAAATATAAAATAAAGAAA
1 TAATAAAAA-ATAAAAAATAAAA-AAA-AAA
*
18514467 TAATAAAAAATAAAAAATAAAAAGAAAA
1 TAATAAAAAATAAAAAATAAAAAAAAAA
*
18514495 GAATAAAAAAATAAAAAAT
1 TAAT-AAAAAATAAAAAAT
18514514 GAGCTTATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.14
29 16 0.37
30 12 0.28
31 9 0.21
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (28 bp):
TAATAAAAAATAAAAAATAAAAAAAAAA
Found at i:18514476 original size:18 final size:17
Alignment explanation
Indices: 18514450--18514513 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
18514440 AAAAATATAA
*
18514450 AATATAAAATAAAGAAAT
1 AATAAAAAATAAA-AAAT
18514468 AATAAAAAATAAAAAAT
1 AATAAAAAATAAAAAAT
* * *
18514485 AAAAAGAAAAGAATAAAAA
1 AATAA-AAAATAA-AAAAT
18514504 AATAAAAAAT
1 AATAAAAAAT
18514514 GAGCTTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 8 0.21
18 22 0.58
19 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AATAAAAAATAAAAAAT
Found at i:18514477 original size:25 final size:27
Alignment explanation
Indices: 18514443--18514510 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
18514433 ATCTAATAAA
* *
18514443 AATATAAAATATAAAAT-AAAG-AAAT
1 AATAAAAAATATAAAATAAAAGAAAAG
*
18514468 AATAAAAAATAAAAAATAAAAAGAAAAG
1 AATAAAAAATATAAAAT-AAAAGAAAAG
18514496 AATAAAAAA-ATAAAA
1 AATAAAAAATATAAAA
18514511 AATGAGCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.42
27 9 0.25
28 12 0.33
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.16
Consensus pattern (27 bp):
AATAAAAAATATAAAATAAAAGAAAAG
Found at i:18514489 original size:7 final size:7
Alignment explanation
Indices: 18514437--18514513 Score: 68
Period size: 7 Copynumber: 10.4 Consensus size: 7
18514427 AAATATATCT
18514437 AATAAAA
1 AATAAAA
18514444 ATATAAAA
1 A-ATAAAA
*
18514452 TATAAAA
1 AATAAAA
18514459 TAA-AGAAA
1 -AATA-AAA
18514467 TAATAAAA
1 -AATAAAA
18514475 AATAAAA
1 AATAAAA
18514482 AATAAAA
1 AATAAAA
*
18514489 AGA-AAAG
1 A-ATAAAA
18514496 AATAAAAA
1 AAT-AAAA
18514504 AATAAAA
1 AATAAAA
18514511 AAT
1 AAT
18514514 GAGCTTATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 34 0.58
8 23 0.39
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (7 bp):
AATAAAA
Found at i:18524383 original size:79 final size:80
Alignment explanation
Indices: 18524252--18524578 Score: 473
Period size: 79 Copynumber: 4.1 Consensus size: 80
18524242 TTAAATACTG
18524252 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAGTATT-TATGATATTAGGGGGCT
1 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAGTATTGTATGATATTAGGGGGCT
18524316 GAATCGTATGCTGAA
66 GAATCGTATGCTGAA
* * * *
18524331 TGGTTTGCTGAACTTTGCTGTTTGATATTGTTTTGCTTAATAGTATT-TATGATATTGGGGGGCT
1 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAGTATTGTATGATATTAGGGGGCT
18524395 GAATCGTATGCTGAA
66 GAATCGTATGCTGAA
* * *
18524410 TGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGCTGAAT-GATATTGTATGATATTGGGGGGC
1 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAG-TATTGTATGATATTAGGGGGC
* *
18524474 TAAATCATATGCTGAA
65 TGAATCGTATGCTGAA
* * * * *
18524490 TGATTTGCTAAACCTTGTTGTCTGATATTGTTTTG-TTGAATGGTATTGTATGGTATTAGGGGAC
1 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTT-AATAGTATTGTATGATATTAGGGGGC
*
18524554 TGAATCGTATGCTAAA
65 TGAATCGTATGCTGAA
18524570 TGGTTTGCT
1 TGGTTTGCT
18524579 AAATGATGTT
Statistics
Matches: 224, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
78 1 0.00
79 118 0.53
80 104 0.46
81 1 0.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.43
Consensus pattern (80 bp):
TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAGTATTGTATGATATTAGGGGGCT
GAATCGTATGCTGAA
Found at i:18524593 original size:159 final size:158
Alignment explanation
Indices: 18524252--18524581 Score: 439
Period size: 159 Copynumber: 2.1 Consensus size: 158
18524242 TTAAATACTG
* * * * *
18524252 TGGTTTGCTGAACCTTGTTGTCTGATATTGTTTTGCTTAATAGTATTTATGATATTAGGGGGCTG
1 TGGTTTGCTAAACCATGTTGTTTGATATTGTTTTGCTGAATAGTATTTATGATATTAGGGGGCTA
* * * * *
18524317 AATCGTATGCTGAATGGTTTGCTGAACTTTGCTGTTTGATATTGTTTTGCTTAATAGTATTTATG
66 AATCATATGCTGAATGATTTGCTAAACCTTGCTGTCTGATATTGTTTTGCTTAATAGTATTTATG
* * *
18524382 ATATTGGGGGGCTGAATCGTATGCTGAA
131 ATATTAGGGGACTGAATCGTATGCTAAA
* * *
18524410 TGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGCTGAAT-GATATTGTATGATATTGGGGGGC
1 TGGTTTGCTAAACCATGTTGTTTGATATTGTTTTGCTGAATAG-TATT-TATGATATTAGGGGGC
* *
18524474 TAAATCATATGCTGAATGATTTGCTAAACCTTGTTGTCTGATATTGTTTTG-TTGAATGGTATTG
64 TAAATCATATGCTGAATGATTTGCTAAACCTTGCTGTCTGATATTGTTTTGCTT-AATAGTATT-
*
18524538 TATGGTATTAGGGGACTGAATCGTATGCTAAA
127 TATGATATTAGGGGACTGAATCGTATGCTAAA
18524570 TGGTTTGCTAAA
1 TGGTTTGCTAAA
18524582 TGATGTTTTT
Statistics
Matches: 152, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
157 1 0.01
158 45 0.30
159 67 0.44
160 39 0.26
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (158 bp):
TGGTTTGCTAAACCATGTTGTTTGATATTGTTTTGCTGAATAGTATTTATGATATTAGGGGGCTA
AATCATATGCTGAATGATTTGCTAAACCTTGCTGTCTGATATTGTTTTGCTTAATAGTATTTATG
ATATTAGGGGACTGAATCGTATGCTAAA
Found at i:18525580 original size:24 final size:24
Alignment explanation
Indices: 18525548--18525604 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
18525538 ACACTTGTTT
*
18525548 ATACTCATTATTGAATATTTATGA
1 ATACTCATTAATGAATATTTATGA
18525572 ATACTCATTAATGAATATTTATGA
1 ATACTCATTAATGAATATTTATGA
*
18525596 ATATTCATT
1 ATACTCATT
18525605 TCATACATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (24 bp):
ATACTCATTAATGAATATTTATGA
Found at i:18530576 original size:21 final size:21
Alignment explanation
Indices: 18530552--18530602 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
18530542 TGTCTTGCAG
18530552 CATAACAGAA-ATCTTTAAAAC
1 CATAACA-AAGATCTTTAAAAC
* *
18530573 CATAAGAAAGATTTTTAAAAC
1 CATAACAAAGATCTTTAAAAC
*
18530594 C-TAAAAAAG
1 CATAACAAAG
18530603 TATAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.24
Consensus pattern (21 bp):
CATAACAAAGATCTTTAAAAC
Found at i:18534792 original size:22 final size:22
Alignment explanation
Indices: 18534749--18534792 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18534739 TCTTTTCTTA
*
18534749 CTTTTAGTTTTTAGTTTTAGTT
1 CTTTTAGTTTTTAGTTTGAGTT
*
18534771 CTTTTATTTCTTTAG-TTGAGTT
1 CTTTTAGTT-TTTAGTTTGAGTT
18534793 ATTGGATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (22 bp):
CTTTTAGTTTTTAGTTTGAGTT
Found at i:18536096 original size:16 final size:16
Alignment explanation
Indices: 18536075--18536107 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18536065 CACTTCCTCC
18536075 TTTTGATCT-TTTTTTT
1 TTTTGA-CTATTTTTTT
18536091 TTTTGACTATTTTTTT
1 TTTTGACTATTTTTTT
18536107 T
1 T
18536108 AAACTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTGACTATTTTTTT
Found at i:18538574 original size:14 final size:13
Alignment explanation
Indices: 18538543--18538577 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18538533 ACCAACAACT
18538543 AAACTAAACAAAA
1 AAACTAAACAAAA
*
18538556 AAACTAAAGAAAA
1 AAACTAAACAAAA
18538569 AGAACTAAA
1 A-AACTAAA
18538578 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (13 bp):
AAACTAAACAAAA
Found at i:18546500 original size:17 final size:18
Alignment explanation
Indices: 18546465--18546506 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
18546455 TTAAAACAAA
*
18546465 TTATATATTTTTATTAAT
1 TTATATATTTTTATAAAT
18546483 TTATATATTTTTA-AAAT
1 TTATATATTTTTATAAAT
*
18546500 TTGTATA
1 TTATATA
18546507 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATATATTTTTATAAAT
Found at i:18547843 original size:76 final size:76
Alignment explanation
Indices: 18547757--18547909 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
18547747 TAGTCAAATC
18547757 TAAAATAAGTCCTCCACCCTTGTTAGCATGAATTATTGCATATGAAATTATATATCGATTACTTC
1 TAAAATAAGTCCTCCACCCTTGTTAGCATGAATTATTGCATATGAAATTATATATCGATTACTTC
18547822 TTTATTAATTT
66 TTTATTAATTT
18547833 TAAAATAAGTCCTCCACCCTTGTTAGCATGAATTATTGCATATGAAATTATATATCGATTACTTC
1 TAAAATAAGTCCTCCACCCTTGTTAGCATGAATTATTGCATATGAAATTATATATCGATTACTTC
18547898 TTTATTAATTT
66 TTTATTAATTT
18547909 T
1 T
18547910 CTTCTTTTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (76 bp):
TAAAATAAGTCCTCCACCCTTGTTAGCATGAATTATTGCATATGAAATTATATATCGATTACTTC
TTTATTAATTT
Found at i:18550679 original size:16 final size:14
Alignment explanation
Indices: 18550644--18550685 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
18550634 AACTTTGATA
18550644 TATTAAT-TTAAAT
1 TATTAATATTAAAT
18550657 TATTAATATTATAAT
1 TATTAATATTA-AAT
18550672 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
18550686 GATAATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 6 0.23
16 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:18550711 original size:23 final size:23
Alignment explanation
Indices: 18550674--18550737 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
18550664 ATTATAATTG
* *
18550674 ATTAATATAAATGATAATAGT-ATT
1 ATTAAT-TATATGATAATA-TAATA
* *
18550698 ATTATTTATATGATATTATAATA
1 ATTAATTATATGATAATATAATA
18550721 ATTAATTATAT-ATAATA
1 ATTAATTATATGATAATA
18550738 AAAACTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 6 0.18
23 22 0.67
24 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
ATTAATTATATGATAATATAATA
Done.