Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 76 of 89
Found at i:18153528 original size:20 final size:20
Alignment explanation
Indices: 18153503--18153574 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 20
18153493 TTATGGATCC
18153503 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCA
* *
18153523 TTTCATGCATTTTAGTCATGGCATCC
1 TTTCATGC--CTTA---AT-GCATCA
18153549 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCA
18153569 TTTCAT
1 TTTCAT
18153575 TCATTTTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 19 0.45
21 2 0.05
22 3 0.07
24 3 0.07
25 2 0.05
26 13 0.31
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCA
Found at i:18154210 original size:95 final size:96
Alignment explanation
Indices: 18154010--18154188 Score: 231
Period size: 96 Copynumber: 1.9 Consensus size: 96
18154000 TATTACCATG
* * * * *
18154010 GTATAGATACTTCTATACTATGGTACCGATACCCCCTTTCAGTATCGATACCATTTCTATATTCT
1 GTATAGATACTACTATACTATGGTACCGATACCCACTTTCAGAATCGATACCATTTCGACATTCT
* *
18154075 GTGTTTTCATGGTATCGATACCTTTCTCTCA
66 GTGTATCCATGGTATCGATACCTTTCTCTCA
* * *
18154106 GTATTGATACTACTATACTATGGTATCGATA-CCACTTTCAGAATCGATACGATCTT-GACATTC
1 GTATAGATACTACTATACTATGGTACCGATACCCACTTTCAGAATCGATACCAT-TTCGACATTC
18154169 TG-G-ATCCATGGTATCGATAC
65 TGTGTATCCATGGTATCGATAC
18154189 TTCCGTTTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
93 15 0.21
94 1 0.01
95 26 0.36
96 30 0.42
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (96 bp):
GTATAGATACTACTATACTATGGTACCGATACCCACTTTCAGAATCGATACCATTTCGACATTCT
GTGTATCCATGGTATCGATACCTTTCTCTCA
Found at i:18194622 original size:59 final size:59
Alignment explanation
Indices: 18194525--18194636 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
18194515 ATATGGCAGT
** *
18194525 TGGCAGTGGTCTTAAATCATTAGCAAGGGTAGGGGTTCACGTGAGGTGCATTGGATAAC
1 TGGCAGTGGTCCCAAATCATTAGCAAGGGTAGGCGTTCACGTGAGGTGCATTGGATAAC
* *
18194584 TGGCAGTGGTCCCAAATCATTAGCAGGGGTAGGCGTTCATGTGAGGTGCATTG
1 TGGCAGTGGTCCCAAATCATTAGCAAGGGTAGGCGTTCACGTGAGGTGCATTG
18194637 AACACTTGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (59 bp):
TGGCAGTGGTCCCAAATCATTAGCAAGGGTAGGCGTTCACGTGAGGTGCATTGGATAAC
Found at i:18195382 original size:23 final size:25
Alignment explanation
Indices: 18195356--18195405 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
18195346 CTATTTGATA
*
18195356 AATA-TAAACACTATTTT-TATATT
1 AATAGTAAACAATATTTTATATATT
*
18195379 AATAGTTAAACAATGTTTTATATATT
1 AATAG-TAAACAATATTTTATATATT
18195405 A
1 A
18195406 TATTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
25 11 0.50
26 7 0.32
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
AATAGTAAACAATATTTTATATATT
Found at i:18200669 original size:20 final size:21
Alignment explanation
Indices: 18200629--18200669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18200619 AAATTCATCA
*
18200629 ATTTCAGGTTATTTCTCAATT
1 ATTTCAGGTTAGTTCTCAATT
*
18200650 ATTTCAGTTTAGTT-TCAATT
1 ATTTCAGGTTAGTTCTCAATT
18200670 CATAATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (21 bp):
ATTTCAGGTTAGTTCTCAATT
Found at i:18227810 original size:13 final size:13
Alignment explanation
Indices: 18227747--18227802 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
18227737 CCATAAATCG
18227747 ATGACGCGCATTT
1 ATGACGCGCATTT
* *
18227760 ATGACACACATTT
1 ATGACGCGCATTT
* *
18227773 ATGACTCACATTT
1 ATGACGCGCATTT
18227786 ATGACGCGCATTT
1 ATGACGCGCATTT
18227799 ATGA
1 ATGA
18227803 TGTGCATTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGACGCGCATTT
Found at i:18227847 original size:83 final size:84
Alignment explanation
Indices: 18227760--18227939 Score: 213
Period size: 85 Copynumber: 2.1 Consensus size: 84
18227750 ACGCGCATTT
* * * *
18227760 ATGACACACATTTATG-ACTC-ACATTTATGACGCGCATTTATGA-TGTGCATTGAGCGTCATCG
1 ATGACACACATTTATGTAC-CAAAATTTATGACACGCATGTATGACT-TACATTGAGCGTCATCG
*
18227822 AAGCCCCCGTCATAAATTAAG
64 AAGCCCCCGTCATAAATGAAG
* * * * * *
18227843 ATGACACACATTTGTGTGCCATAAATTTATGACATGCATGTATGACTTACATTGCGTGTCATTGA
1 ATGACACACATTTATGTACCA-AAATTTATGACACGCATGTATGACTTACATTGAGCGTCATCGA
18227908 AGCCCCCGTCATAAATGAAG
65 AGCCCCCGTCATAAATGAAG
18227928 ATGACACACATT
1 ATGACACACATT
18227940 GTGTGTCAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 16 0.20
84 1 0.01
85 64 0.78
86 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (84 bp):
ATGACACACATTTATGTACCAAAATTTATGACACGCATGTATGACTTACATTGAGCGTCATCGAA
GCCCCCGTCATAAATGAAG
Found at i:18233340 original size:26 final size:27
Alignment explanation
Indices: 18233284--18233345 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
18233274 AGTATAACTA
* *
18233284 CATGTGAATAAATTGCACATATAGTTC
1 CATGTGAATAAATTGCACACATAGGTC
** *
18233311 CATGTGAATTTATTGCAC-CATAGGTG
1 CATGTGAATAAATTGCACACATAGGTC
*
18233337 CATGCGAAT
1 CATGTGAAT
18233346 GTACATGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (27 bp):
CATGTGAATAAATTGCACACATAGGTC
Found at i:18254982 original size:20 final size:20
Alignment explanation
Indices: 18254953--18254991 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18254943 AGAGCTCATG
*
18254953 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
18254973 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
18254992 GTGATGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:18255327 original size:30 final size:30
Alignment explanation
Indices: 18255270--18255328 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
18255260 CCACGCAATG
* *
18255270 CTACAGATGATTCTACTGGACCGCGACCTC
1 CTACAGATGATTATACTGGACCACGACCTC
* * *
18255300 CTACAGCTGATTATGCTGGACTACGACCT
1 CTACAGATGATTATACTGGACCACGACCT
18255329 GCTGCAGCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (30 bp):
CTACAGATGATTATACTGGACCACGACCTC
Found at i:18257355 original size:121 final size:121
Alignment explanation
Indices: 18257141--18257382 Score: 484
Period size: 121 Copynumber: 2.0 Consensus size: 121
18257131 ATGTGAAAAT
18257141 CCAAGAGAGAGAATTAGATGTGTGCAAAGAAAAACTTGTAAACTACTTATGCGGATTAATGTGAT
1 CCAAGAGAGAGAATTAGATGTGTGCAAAGAAAAACTTGTAAACTACTTATGCGGATTAATGTGAT
18257206 GTGTCTTTATAAGCTTTAATAGAAGTTTTTTTTTTGCTGGAACTAATTTCTTGTCA
66 GTGTCTTTATAAGCTTTAATAGAAGTTTTTTTTTTGCTGGAACTAATTTCTTGTCA
18257262 CCAAGAGAGAGAATTAGATGTGTGCAAAGAAAAACTTGTAAACTACTTATGCGGATTAATGTGAT
1 CCAAGAGAGAGAATTAGATGTGTGCAAAGAAAAACTTGTAAACTACTTATGCGGATTAATGTGAT
18257327 GTGTCTTTATAAGCTTTAATAGAAGTTTTTTTTTTGCTGGAACTAATTTCTTGTCA
66 GTGTCTTTATAAGCTTTAATAGAAGTTTTTTTTTTGCTGGAACTAATTTCTTGTCA
18257383 TCTTGAAATC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (121 bp):
CCAAGAGAGAGAATTAGATGTGTGCAAAGAAAAACTTGTAAACTACTTATGCGGATTAATGTGAT
GTGTCTTTATAAGCTTTAATAGAAGTTTTTTTTTTGCTGGAACTAATTTCTTGTCA
Found at i:18278408 original size:3 final size:3
Alignment explanation
Indices: 18278400--18278424 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18278390 GAATTGGGTT
18278400 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
18278425 AATAATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:18303238 original size:59 final size:62
Alignment explanation
Indices: 18303098--18303241 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 62
18303088 TATTTATATT
* * * *
18303098 ATTTTTGGTATGAATTACCCAATACAAATTTATATGGTATTTTACTAAATTATTTATCAATA
1 ATTTTGGGTATGAAATACCCAATACAAATTTATATGATATTTTACTAAATTAGTTATCAATA
* * * * * *
18303160 ATTTTGGGTATTAAATACCCAATAC-ATTTTATATGATATTTT-TTAAA-TGGTTATGAATG
1 ATTTTGGGTATGAAATACCCAATACAAATTTATATGATATTTTACTAAATTAGTTATCAATA
*
18303219 ATTTTGGGTATGAACTACCCAAT
1 ATTTTGGGTATGAAATACCCAAT
18303242 GCACTGATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 29 0.41
60 4 0.06
61 15 0.21
62 22 0.31
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (62 bp):
ATTTTGGGTATGAAATACCCAATACAAATTTATATGATATTTTACTAAATTAGTTATCAATA
Found at i:18308305 original size:81 final size:81
Alignment explanation
Indices: 18308200--18308769 Score: 766
Period size: 81 Copynumber: 7.0 Consensus size: 81
18308190 GTATAATGTT
** *
18308200 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAATTGTGTCAACTATGCCAGTTAGATGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
18308265 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
* * * * *
18308281 AAAGATTAATGGCCTAGTTATGCATTTGGAAGAAAGGTGTCAATTATGTCAGTTAGTTGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
**
18308346 TAAATAAATTTGAGTA
66 TAAATACCTTTGAGTA
* * * *
18308362 AAAGAATAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCAAGTTAGATGGAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* *
18308427 TAAATACTTTTGTGTA
66 TAAATACCTTTGAGTA
* ** * * * *
18308443 AAATATTAATGGCCTAGCTAAGCTTTTGGCATG-AATGTGTCAATTTTGTCAGTTAGATGAAAGG
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCA-GAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
*
18308507 TTAAGTA-CTCTTGAGTA
65 TTAAATACCT-TTGAGTA
*
18308524 AAAGATTAATGGCCTAGCTGTTCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
*
18308589 TAAATACCTTAGAGTA
66 TAAATACCTTTGAGTA
* * *
18308605 AAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
18308670 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
* * * * * * *
18308686 AAAGATTAATGGCCTAACTATGCATTTGGTAGAAAAGTGTCAATCATGCAAGTTAGATGAAAGGC
1 AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* *
18308751 TAAATGCCTTTGGGTA
66 TAAATACCTTTGAGTA
18308767 AAA
1 AAA
18308770 TACTAAAGGA
Statistics
Matches: 426, Mismatches: 59, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
80 2 0.00
81 421 0.99
82 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (81 bp):
AAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTA
Found at i:18311624 original size:81 final size:81
Alignment explanation
Indices: 18311418--18312848 Score: 1902
Period size: 81 Copynumber: 17.7 Consensus size: 81
18311408 ATAATGGATT
* * * * * *
18311418 GAAAGGTCTCAATTATGCCAGCTAGATGAATGGTTAAATACCTTTGAGAAAAAGAATAATTGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* *
18311483 AGTTGTGCATTTGGTA
66 AGCTGTGCATTTGGCA
* *
18311499 GAAAAGGTGTCAATTATGCCAGTTAGATAAAAGGTTAAACACCTTTGAGTAAAAGATTAATGGCC
1 G-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCC
*
18311564 TAGCTGTGCATTTGGAA
65 TAGCTGTGCATTTGGCA
* *
18311581 GAAAGGTGTCAATTATGCCAATTAGATCAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18311646 AGCTGTGCATTTGGTA
66 AGCTGTGCATTTGGCA
*
18311662 GAAAGGT-TCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT-AAAGATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
18311725 AGCTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * * *
18311741 -AAATGATCTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTAAGTAAAAGATTAATGACC
1 GAAA-GGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCC
*
18311805 TAGATGTGCATTTGGCA
65 TAGCTGTGCATTTGGCA
* * *
18311822 GAAATGTGTCAATTATGCCAGTTAGATAAAAGGTTAAATACCTTTGAGTAAAAGATTAA-AGCAC
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGC-C
* *
18311886 TAGTTGTGCATTTGGAA
65 TAGCTGTGCATTTGGCA
* * *
18311903 GAAATGTGTTAATTAT-CCTAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCC
1 GAAAGGTGTCAATTATGCC-AGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCC
* *
18311967 TACCTGCGCATTTGGCA
65 TAGCTGTGCATTTGGCA
* * * *
18311984 GAAATGTGTCAATTATGTCATTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312049 AGCTGTGCATTTGGTA
66 AGCTGTGCATTTGGCA
* * *
18312065 GAAATGTGTCAAATATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312130 AGTTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * * * * * * * *
18312146 TATAGCTATTAATTATGCCAGTTAGATAAAAGGTTAGATACCTTTGAGTAAAAGATTAAAGGACT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312211 AGCTGTGCATTTGGAA
66 AGCTGTGCATTTGGCA
* * * *
18312227 GAAATGTGTTAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * *
18312292 AGATGTGTATTTGGTA
66 AGCTGTGCATTTGGCA
* * * *
18312308 GAAAGGTGTCAATTATGTCAGTTAGATCAAATGTTAAATACCTTTGAGTAAAAGATTATTGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* *
18312373 AGTTGTGCATTTGGTA
66 AGCTGTGCATTTGGCA
* *
18312389 GAAAGGTGTCAATTATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312454 AGCTGTGTATTTGGCA
66 AGCTGTGCATTTGGCA
* * * ** * * * *
18312470 TAAAAGTGTCAATCATGAAAGTTAGATAAAAGGTTAAATGCCTTTGGGTAAAAGACTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* *
18312535 AGTTATGCATTTGGCA
66 AGCTGTGCATTTGGCA
* *
18312551 GAAATGTGTCAATTATGCCAGTTAGATAAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312616 AACTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * *
18312632 GAAAGGTGTCAATTATGCCAGTTA-AAGAAAATGTTAAATACCTTTGAGTAAAAGATTAATTGCC
1 GAAAGGTGTCAATTATGCCAGTTAGATG-AAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCC
* * *
18312696 TAGTTGTGCATGTAGCA
65 TAGCTGTGCATTTGGCA
18312713 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
18312778 AGCTGTGTATTTGGCA
66 AGCTGTGCATTTGGCA
* ** * * * * * * * *
18312794 TAAAATTGTGAATAATGCAACTTAGATGAAAGGCTAAGTGCCTTTGGGTAAAAGA
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
18312849 CTAAAGGATT
Statistics
Matches: 1185, Mismatches: 154, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
78 3 0.00
79 31 0.03
80 83 0.07
81 989 0.83
82 79 0.07
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
AGCTGTGCATTTGGCA
Found at i:18331360 original size:49 final size:49
Alignment explanation
Indices: 18331283--18331381 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
18331273 GCATAAAAGA
18331283 GTTACTCACAAATATGTAATGTCGAAACATAACTTATTGTAACTTAGGT
1 GTTACTCACAAATATGTAATGTCGAAACATAACTTATTGTAACTTAGGT
* * *
18331332 GTTAGTCACAAATATGTAATGTCGAAACATGACTTCTTGTAACTTAGGT
1 GTTACTCACAAATATGTAATGTCGAAACATAACTTATTGTAACTTAGGT
18331381 G
1 G
18331382 ACTGATACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (49 bp):
GTTACTCACAAATATGTAATGTCGAAACATAACTTATTGTAACTTAGGT
Found at i:18332164 original size:31 final size:30
Alignment explanation
Indices: 18332048--18332153 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
18332038 GGTTGTATTT
* *
18332048 AGATAATGCACAGTAGTCAGGTTTCCATTA
1 AGATAATGCACAGTAGTCAGGTTTGCATTC
* *
18332078 AGATAATTCACAATATGTCAGGTTTGCATTC
1 AGATAATGCACAGTA-GTCAGGTTTGCATTC
* ** *
18332109 ATATGGTGCACAGTAGTTAGGTTTGCATTC
1 AGATAATGCACAGTAGTCAGGTTTGCATTC
*
18332139 AGATAATGCATAGTA
1 AGATAATGCACAGTA
18332154 TGATAGGTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 38 0.62
31 23 0.38
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (30 bp):
AGATAATGCACAGTAGTCAGGTTTGCATTC
Found at i:18332183 original size:61 final size:59
Alignment explanation
Indices: 18332035--18332190 Score: 150
Period size: 61 Copynumber: 2.5 Consensus size: 59
18332025 GGATACTAGT
* * *
18332035 TAGGGTTGTATTTAGATAATGCACAGTAGTCAGGTTTCCATTAAGATAATTCACAATATG
1 TAGGTTTGTA-TTAGATGATGCACAGTAGTCAGGTTTCCATTAAGATAATGCACAATATG
* * * * * * * *
18332095 TCAGGTTTGCATTCATATGGTGCACAGTAGTTAGGTTTGCATTCAGATAATGCATAGTATG
1 T-AGGTTTGTATT-AGATGATGCACAGTAGTCAGGTTTCCATTAAGATAATGCACAATATG
*
18332156 ATAGGTTTGTATTAGGATGATGTACAGTATGTCAG
1 -TAGGTTTGTATTA-GATGATGCACAGTA-GTCAG
18332191 TTTTGGATTT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
60 4 0.05
61 66 0.88
62 5 0.07
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (59 bp):
TAGGTTTGTATTAGATGATGCACAGTAGTCAGGTTTCCATTAAGATAATGCACAATATG
Found at i:18343261 original size:13 final size:13
Alignment explanation
Indices: 18343243--18343267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18343233 TTTCCTCTCC
18343243 ATCTTCTTCATTT
1 ATCTTCTTCATTT
18343256 ATCTTCTTCATT
1 ATCTTCTTCATT
18343268 CATTCCTTCT
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (13 bp):
ATCTTCTTCATTT
Found at i:18360901 original size:15 final size:16
Alignment explanation
Indices: 18360860--18360901 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
18360850 TTTAGGGTTT
18360860 TTAATTCTAAA-TTAA
1 TTAATTCTAAATTTAA
*
18360875 TTAAATCTAAATTTAA
1 TTAATTCTAAATTTAA
18360891 TTAATTC-AAAT
1 TTAATTCTAAAT
18360902 AAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTCTAAATTTAA
Found at i:18360906 original size:20 final size:20
Alignment explanation
Indices: 18360869--18360907 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18360859 TTTAATTCTA
*
18360869 AATTAATTAAATCTAAATTT
1 AATTAATTAAATCAAAATTT
18360889 AATTAATTCAAAT-AAAATT
1 AATTAATT-AAATCAAAATT
18360908 ATTTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAATTAAATCAAAATTT
Found at i:18361002 original size:2 final size:2
Alignment explanation
Indices: 18360995--18361063 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
18360985 AATTAAAATT
18360995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18361037 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 T
18361064 CTTCTTCATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18364869 original size:39 final size:39
Alignment explanation
Indices: 18364811--18365004 Score: 239
Period size: 39 Copynumber: 5.0 Consensus size: 39
18364801 CCAGTCAAAT
*
18364811 ATATGCACC-ATAGTGCTTACACATAAGGTCATGCCCACC
1 ATATGCACCGA-AGTGCTTACACATAAGGTCATACCCACC
* *
18364850 ATATGCACCGAAGTTCTTACACATAAGGTCATGCCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCATACCCACC
** * * **
18364889 ATATGCATTGAAGTTCTTACACCTAAGGTTGTACCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCATACCCACC
* *
18364928 ATATGCACTGAAGTGCTTACACATAAGGT-AGTACACACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCA-TACCCACC
* *
18364967 ATATGCATCGAAGTGCTTACACATAAGGTCGTACCCAC
1 ATATGCACCGAAGTGCTTACACATAAGGTCATACCCAC
18365005 TGTAGTAACC
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 135 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (39 bp):
ATATGCACCGAAGTGCTTACACATAAGGTCATACCCACC
Found at i:18367010 original size:3 final size:3
Alignment explanation
Indices: 18367002--18367080 Score: 108
Period size: 3 Copynumber: 27.0 Consensus size: 3
18366992 ATTTATCATT
* * * *
18367002 TAA TAA TAA TAA TAA -AA TAA TAA TAT TAA TAA TAA TCA T-A TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18367048 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18367081 ATGGGATAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.06
3 66 0.94
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:18367425 original size:123 final size:123
Alignment explanation
Indices: 18367201--18367889 Score: 796
Period size: 123 Copynumber: 5.6 Consensus size: 123
18367191 GATTAAGATG
* * ** *
18367201 AAAATGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
18367266 ACGAACTCCTTCTGGAAACGTTGATGTTGCTCTATCTCCTTCTACGATAAAGTCAAGC
66 ACGAACTCCTTCTGGAAACGTTGATGTTGCTCTATCTCCTTCTACGATAAAGTCAAGC
* * * *
18367324 AAAAGGTTGAATACGTTCTTCAGATTATGACCTTCTTCTTCATCTTCAAATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * *
18367389 ACGAACTCCTTTTAGAAACGTTGATGCTGCTCTATCTCATTATACGATAGAA-TCGAGC
66 ACGAACTCCTTCTGGAAACGTTGATGTTGCTCTATCTCCTTCTACGATA-AAGTCAAGC
** * * *
18367447 AAAATATTGAATATGCTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * *
18367512 ACAAACTCCTTCTGGAAATGTTGATGTTGTTATATCTCCTTCAACGATATAA-TCAAGC
66 ACGAACTCCTTCTGGAAACGTTGATGTTGCTCTATCTCCTTCTACGATA-AAGTCAAGC
* * * * * * **
18367570 AAAAGGTTGAATATGTTATTCATATTATGAATTTCTTCCTCCTCTTCAGACGAGTTCTTCAGATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * * * * *
18367635 ATGAACTCATGTTTCGAAA--TGGCTCTATTCTCTATCTCCTTCTGCGATAAAGTCAAGC
66 ACGAACTCCT-TCTGGAAACGTTGATGT-TGCTCTATCTCCTTCTACGATAAAGTCAAGC
* * * * * **
18367693 AAAAGGCTGAATAAGTTCTTCAGACTATGAACTTCTTCTTCCTGTTCAAAGGAGTTCTTCAGATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* *
18367758 ATGAACTCCTATCTGGAAATGGCTT--TGTTGCTCTATCTCCTTCTACGATAAAGTCAAGC
66 ACGAACTCCT-TCTGGAAA-CG-TTGATGTTGCTCTATCTCCTTCTACGATAAAGTCAAGC
* *
18367817 AAAAGGTTGAATAAGTTCTTTAGAATATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
18367882 ACGAACTC
66 ACGAACTC
18367890 TATAAATCAA
Statistics
Matches: 473, Mismatches: 85, Indels: 15
0.83 0.15 0.03
Matches are distributed among these distances:
122 6 0.01
123 363 0.77
124 101 0.21
125 2 0.00
127 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (123 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
ACGAACTCCTTCTGGAAACGTTGATGTTGCTCTATCTCCTTCTACGATAAAGTCAAGC
Found at i:18368207 original size:177 final size:177
Alignment explanation
Indices: 18367893--18368428 Score: 858
Period size: 177 Copynumber: 3.0 Consensus size: 177
18367883 CGAACTCTAT
*
18367893 AAATCAAGAAACCCCCGAAGGATTAGTTTCTTAGTTGTCAAAT-AACCCCTTTGTTAGGCTTAGC
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTC-AATGAACCCCTTTGTTAGGCTTAGC
** * * *
18367957 TTCCTTTAACAACTCTTTTGAGATAATTAGTAAACCCCTAAAGGCTTTGTTTTTAAAATTTCATT
65 TTCCTTTAACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATT
* *
18368022 TAAAAACATCCTGCACTGAAGGTCTTATGAATGGCCCGTAGGACTTAC
130 TGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTAC
*
18368070 AAATCAAGAAACCCCTGAAGGCTTAGTTTCTTAGTTGTCAATGAACCCCTTTGTTAGGCTTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAATGAACCCCTTTGTTAGGCTTAGCT
** * * *
18368135 TCCTTTAACAGGTCATTTGAGATAATTAGTAAACCCCCGAAGGCTTGGCTTCTAAAATCTCATCT
66 TCCTTTAACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
*
18368200 GAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGATTTAC
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTAC
* * * * *
18368247 AAATCTAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGATCCCCTTTGTTGGGATTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAATGAACCCCTTTGTTAGGCTTAGCT
* *
18368312 TCCTTTAACATCTCTTTTGAGATAATGAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
66 TCCTTTAACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
18368377 GAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTAC
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTAC
18368424 AAATC
1 AAATC
18368429 TGGGAAATAG
Statistics
Matches: 330, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
176 3 0.01
177 327 0.99
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (177 bp):
AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAATGAACCCCTTTGTTAGGCTTAGCT
TCCTTTAACAACTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
GAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTAC
Found at i:18369605 original size:54 final size:54
Alignment explanation
Indices: 18369496--18369658 Score: 245
Period size: 54 Copynumber: 3.0 Consensus size: 54
18369486 TAATCACTGG
* * * * **
18369496 TTCGAAAAATATTTAACAACACATTCATCATTTCCTGTGGCTTCTGTACAAATT
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAAATT
* *
18369550 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTTTGCCCATATT
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAAATT
*
18369604 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATT
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAAATT
18369658 T
1 T
18369659 CTTGTCAGTA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (54 bp):
TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAAATT
Found at i:18371698 original size:7 final size:7
Alignment explanation
Indices: 18371686--18371786 Score: 96
Period size: 7 Copynumber: 13.7 Consensus size: 7
18371676 CTTGATTCAA
18371686 TTTCTTT
1 TTTCTTT
18371693 TTTCTTCT
1 TTTCTT-T
18371701 TTTCTTT
1 TTTCTTT
*
18371708 TCTCTTT
1 TTTCTTT
*
18371715 TCTCTTT
1 TTTCTTT
*
18371722 TCTCTTT
1 TTTCTTT
18371729 TTGTCTTCT
1 TT-TCTT-T
18371738 TTTCTTT
1 TTTCTTT
18371745 TTT-TTT
1 TTTCTTT
*
18371751 CATTCTTT
1 -TTTCTTT
*
18371759 TCTCTTT
1 TTTCTTT
18371766 TTTCTTTT
1 TTTC-TTT
18371774 TTTCCTTT
1 TTT-CTTT
18371782 TTTCT
1 TTTCT
18371787 CTATGATGGA
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
6 3 0.04
7 44 0.54
8 30 0.37
9 4 0.05
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTCTTT
Found at i:18371738 original size:37 final size:35
Alignment explanation
Indices: 18371688--18371784 Score: 133
Period size: 37 Copynumber: 2.7 Consensus size: 35
18371678 TGATTCAATT
18371688 TCTTTTTTCTTCTTTTCTTTTCTCTTTTC-TCTTTTC
1 TCTTTTTTCTTCTTTTCTTTT-T-TTTTCATCTTTTC
18371724 TCTTTTTGTCTTCTTTTCTTTTTTTTTCATTCTTTTC
1 TCTTTTT-TCTTCTTTTCTTTTTTTTTCA-TCTTTTC
* *
18371761 TCTTTTTTCTTTTTTTCCTTTTTT
1 TCTTTTTTCTTCTTTTCTTTTTTT
18371785 CTCTATGATG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
35 5 0.09
36 23 0.41
37 28 0.50
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (35 bp):
TCTTTTTTCTTCTTTTCTTTTTTTTTCATCTTTTC
Found at i:18371785 original size:44 final size:41
Alignment explanation
Indices: 18371692--18371786 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 41
18371682 TCAATTTCTT
18371692 TTTTCTTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTTGTC
1 TTTT-TTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTTGTC
* * *
18371734 TTCTTTTCTTTTTTTTTCATTCTTTTCTCTTTTTTCTTTTTTTCC
1 TT-TTTTCTTTTCTTTTC--TCTTTTCTCTTTTCTCTTTTTGT-C
18371779 TTTTTTCT
1 TTTTTTCT
18371787 CTATGATGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 14 0.30
43 2 0.04
44 27 0.59
45 3 0.07
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (41 bp):
TTTTTTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTTGTC
Found at i:18374602 original size:33 final size:33
Alignment explanation
Indices: 18374565--18374629 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
18374555 CAATTGTTCT
* *
18374565 TTTGAATCATATTGGAATTTTTTTGCTTGATCA
1 TTTGAATCATACTGGAACTTTTTTGCTTGATCA
* *
18374598 TTTGAATCGTCCTGGAACTTTTTTGCTTGATC
1 TTTGAATCATACTGGAACTTTTTTGCTTGATC
18374630 GATCATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTGAATCATACTGGAACTTTTTTGCTTGATCA
Found at i:18377328 original size:11 final size:12
Alignment explanation
Indices: 18377312--18377340 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18377302 ATATACAGAT
18377312 ATAAAAT-AAAA
1 ATAAAATAAAAA
18377323 ATAAAATAAAAA
1 ATAAAATAAAAA
18377335 ATAAAA
1 ATAAAA
18377341 ATTGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:18379429 original size:3 final size:3
Alignment explanation
Indices: 18379421--18379490 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
18379411 ATTTATCATT
* * * *
18379421 TAA TAA TAA TAA TAA -AA TAA TAT TAT TAT TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18379468 T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
18379491 ATGGGACAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:18379455 original size:20 final size:20
Alignment explanation
Indices: 18379421--18379489 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
18379411 ATTTATCATT
18379421 TAATAATAATAATAA-AATAA
1 TAATAAT-ATAATAATAATAA
* * *
18379441 TATTATTATTAATAATATTAA
1 TAATAATA-TAATAATAATAA
18379462 TAATAATATAATAATAATAA
1 TAATAATATAATAATAATAA
18379482 TAATAATA
1 TAATAATA
18379490 AATGGGACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 30 0.73
21 10 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATAATATAATAATAATAA
Found at i:18379463 original size:32 final size:32
Alignment explanation
Indices: 18379421--18379490 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
18379411 ATTTATCATT
* * *
18379421 TAATAATAATAATAAAATAATATTATTATTAA
1 TAATAATAATAATAAAATAATAATAATAATAA
* *
18379453 TAATATTAATAATAATATAATAATAATAATAA
1 TAATAATAATAATAAAATAATAATAATAATAA
18379485 TAATAA
1 TAATAA
18379491 ATGGGACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
TAATAATAATAATAAAATAATAATAATAATAA
Found at i:18379489 original size:35 final size:35
Alignment explanation
Indices: 18379424--18379490 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
18379414 TATCATTTAA
* * *
18379424 TAATAATAATAAAATAATATTATTATTAATAATAT
1 TAATAATAATAAAATAATAATAATAATAATAATAT
*
18379459 TAATAATAATATAATAATAATAATAATAATAA
1 TAATAATAATAAAATAATAATAATAATAATAA
18379491 ATGGGACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (35 bp):
TAATAATAATAAAATAATAATAATAATAATAATAT
Found at i:18379700 original size:22 final size:23
Alignment explanation
Indices: 18379670--18379716 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
18379660 CATACCCAAA
* *
18379670 ATATCATTCATGTTAAATATCAT
1 ATATCATTCATGATAAACATCAT
18379693 ATAT-ATTCATGATAAACATCAT
1 ATATCATTCATGATAAACATCAT
18379715 AT
1 AT
18379717 GTAATGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATCATTCATGATAAACATCAT
Found at i:18395765 original size:22 final size:22
Alignment explanation
Indices: 18395739--18395788 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
18395729 TGTCTAGCAT
18395739 GTTGAAGCCAACTTTTCTAAAG
1 GTTGAAGCCAACTTTTCTAAAG
* *
18395761 GTTGAAGCCAACTTTTCTGAGG
1 GTTGAAGCCAACTTTTCTAAAG
18395783 GTTGAA
1 GTTGAA
18395789 ACTCAATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (22 bp):
GTTGAAGCCAACTTTTCTAAAG
Found at i:18397969 original size:24 final size:24
Alignment explanation
Indices: 18397927--18397976 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
18397917 TATCAATCGA
*
18397927 TCATGTTTAGTGCATTTGTTGCAC
1 TCATGTTTAGTGCACTTGTTGCAC
*
18397951 TCATGTTTTAGTGC-CTTGTTTCAC
1 TCATG-TTTAGTGCACTTGTTGCAC
18397975 TC
1 TC
18397977 CAGCAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (24 bp):
TCATGTTTAGTGCACTTGTTGCAC
Found at i:18398010 original size:24 final size:24
Alignment explanation
Indices: 18397983--18398058 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
18397973 ACTCCAGCAA
*
18397983 TAGTGCATTCATGCACTCTTATAT
1 TAGTGCATTCATGCACTCCTATAT
* * * *
18398007 TAGTACCTAT-ATGTACTCCTGTAT
1 TAGTGCAT-TCATGCACTCCTATAT
* *
18398031 AAGTGCATACATGCACTCCTATAT
1 TAGTGCATTCATGCACTCCTATAT
18398055 TAGT
1 TAGT
18398059 ACTTTTGGGT
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (24 bp):
TAGTGCATTCATGCACTCCTATAT
Found at i:18401262 original size:13 final size:13
Alignment explanation
Indices: 18401244--18401268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18401234 AAAAATAGTG
18401244 GTGAATATCAATT
1 GTGAATATCAATT
18401257 GTGAATATCAAT
1 GTGAATATCAAT
18401269 GCATATCATT
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
GTGAATATCAATT
Found at i:18406017 original size:16 final size:16
Alignment explanation
Indices: 18405996--18406026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18405986 TGGTTAGGGT
18405996 TAGGGTTAAGGTTAGC
1 TAGGGTTAAGGTTAGC
*
18406012 TAGGGTTTAGGTTAG
1 TAGGGTTAAGGTTAG
18406027 GTTGTGGGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.39, T:0.35
Consensus pattern (16 bp):
TAGGGTTAAGGTTAGC
Found at i:18406087 original size:15 final size:15
Alignment explanation
Indices: 18406063--18406099 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
18406053 TTGGGTTTTC
18406063 AAAA-AAAATAATAA
1 AAAATAAAATAATAA
18406077 AAAATAAAATAATAA
1 AAAATAAAATAATAA
18406092 AAAATAAA
1 AAAATAAA
18406100 CCCAGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAAATAATAA
Found at i:18406989 original size:191 final size:191
Alignment explanation
Indices: 18406709--18407078 Score: 476
Period size: 191 Copynumber: 1.9 Consensus size: 191
18406699 TGAATAAATG
* * ** *
18406709 TGCATCTGAAGACAACATTGTTTCTTCTTGTTGAGGAAATATGATTGTCTAGAGAAAATGTGATG
1 TGCATCTGAAAACAACACTGTTTCTTCTTGTTGAGGAAATATGATTACCTAGAGAAAATATGATG
*
18406774 TTGGAAACAACACTGCTCGTTCATGTTGAAGAGAATCTGGCCGCCTTTGCGATGATTTACTCGAT
66 TTGGAAACAACACTGCTCGTTCATGTTGAAAAGAATCTGGCCGCCTTTGCGATGATTTACTCGAT
* *
18406839 GTCAAATCTGGTACTGACATTGC-TCATTCACATTGAGGAGGTATAGTCACATTTCAATGAC
131 GTCAAATCTGATACTGACATTACTTC-TTCACATTGAGGAGGTATAGTCACATTTCAATGAC
* * *
18406900 TGCATCTGAAAACAACACT-TTTCATTCTTGTTGAGGAAATCTGATTACCTGGAGATAATATGAT
1 TGCATCTGAAAACAACACTGTTTC-TTCTTGTTGAGGAAATATGATTACCTAGAGAAAATATGAT
* * * * * * * *
18406964 GTTGGAAACGACACTGC-CGGTTCATGTTGAAAAGAATTTGGTCGTCTTTGGGGTTATTTGCTCG
65 GTTGGAAACAACACTGCTC-GTTCATGTTGAAAAGAATCTGGCCGCCTTTGCGATGATTTACTCG
* ** * *
18407028 ATGTCAAATTTGATGTTGACATTACTTCTTCACGTTGAGGAGGTCTAGTCA
129 ATGTCAAATCTGATACTGACATTACTTCTTCACATTGAGGAGGTATAGTCA
18407079 ATGGATGACT
Statistics
Matches: 152, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
190 5 0.03
191 145 0.95
192 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (191 bp):
TGCATCTGAAAACAACACTGTTTCTTCTTGTTGAGGAAATATGATTACCTAGAGAAAATATGATG
TTGGAAACAACACTGCTCGTTCATGTTGAAAAGAATCTGGCCGCCTTTGCGATGATTTACTCGAT
GTCAAATCTGATACTGACATTACTTCTTCACATTGAGGAGGTATAGTCACATTTCAATGAC
Found at i:18407939 original size:22 final size:22
Alignment explanation
Indices: 18407914--18407956 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18407904 ATAAAAGAAT
18407914 TTTTAAAAAATGTTTGATGAAG
1 TTTTAAAAAATGTTTGATGAAG
* *
18407936 TTTTGAAAAATGTTTTATGAA
1 TTTTAAAAAATGTTTGATGAA
18407957 AGAATTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (22 bp):
TTTTAAAAAATGTTTGATGAAG
Found at i:18407972 original size:24 final size:25
Alignment explanation
Indices: 18407882--18408048 Score: 130
Period size: 25 Copynumber: 6.8 Consensus size: 25
18407872 AAGATCAATG
* * * *
18407882 AAGAAGTTTCGAAAAGTGTTCGATAA
1 AAGAA-TTTTGAAAAATGTTTGATGA
*
18407908 AAGAATTTTTAAAAAATGTTTGATG-
1 AAGAA-TTTTGAAAAATGTTTGATGA
*
18407933 AAG--TTTTGAAAAATGTTTTATGA
1 AAGAATTTTGAAAAATGTTTGATGA
* *
18407956 AAGAATTTTG-CAAATGTTTGATTA
1 AAGAATTTTGAAAAATGTTTGATGA
* **
18407980 AAGAGTTTTGAAAAATGTTT-AACA
1 AAGAATTTTGAAAAATGTTTGATGA
*
18408004 AAG-ATGGTTTGAAAAATGATTGATGA
1 AAGAAT--TTTGAAAAATGTTTGATGA
* *
18408030 AAGAAGTTTGAAATATGTT
1 AAGAATTTTGAAAAATGTT
18408049 AGGGTTCACA
Statistics
Matches: 111, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
22 17 0.15
23 4 0.04
24 25 0.23
25 40 0.36
26 24 0.22
27 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (25 bp):
AAGAATTTTGAAAAATGTTTGATGA
Found at i:18408871 original size:30 final size:31
Alignment explanation
Indices: 18408807--18408889 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 31
18408797 AAGTACTTGA
*
18408807 TATATTTTATTTCTTTTTTTATTGCTTATCTTTT
1 TATA-TTT-TTTCTTTCTTT-TTGCTTATCTTTT
*
18408841 T-TGATTTTTTCTTTCTTTTTG-TTTTCTTTT
1 TAT-ATTTTTTCTTTCTTTTTGCTTATCTTTT
*
18408871 TATATTTTTT-TCTCTTTTT
1 TATATTTTTTCTTTCTTTTT
18408890 TCTTTTTTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 8 0.18
30 16 0.36
31 4 0.09
32 10 0.23
33 4 0.09
34 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.77
Consensus pattern (31 bp):
TATATTTTTTCTTTCTTTTTGCTTATCTTTT
Found at i:18408889 original size:47 final size:47
Alignment explanation
Indices: 18408816--18408910 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 47
18408806 ATATATTTTA
* * *
18408816 TTTCTTTTTTTATTGCTTATCTTTTTTGATTTTTTCTTTCTTTTTGT
1 TTTCTTTTTATATTGCTTATCTTTTTTGATTTTTTCTCTCTCTTTGT
* * **
18408863 TTTCTTTTTATATT-TTTTTCTCTTTTTTCTTTTTTCTCTCTCTTTGT
1 TTTCTTTTTATATTGCTTATCT-TTTTTGATTTTTTCTCTCTCTTTGT
18408910 T
1 T
18408911 ATCGACTTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 5 0.12
47 35 0.88
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (47 bp):
TTTCTTTTTATATTGCTTATCTTTTTTGATTTTTTCTCTCTCTTTGT
Found at i:18408896 original size:18 final size:18
Alignment explanation
Indices: 18408852--18408903 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
18408842 TGATTTTTTC
18408852 TTTCTTTTTGTTT-TCTTT
1 TTTCTTTTT-TTTCTCTTT
*
18408870 TTAT-ATTTTTTTCTCTTT
1 TT-TCTTTTTTTTCTCTTT
*
18408888 TTTCTTTTTTCTCTCT
1 TTTCTTTTTTTTCTCT
18408904 CTTTGTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 23 0.82
19 1 0.04
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTTTCTCTTT
Found at i:18412576 original size:64 final size:64
Alignment explanation
Indices: 18412501--18412670 Score: 193
Period size: 64 Copynumber: 2.6 Consensus size: 64
18412491 TGACCGTTGG
* * *
18412501 AGCCTTAGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AAA
1 AGCCTGAGTGCATCGATGCA-TAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAA
*** *
18412564 TAGCCTGAGTGCATCGATGCATGACTTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA
1 -AGCCTGAGTGCATCGATGCAT-AAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAA
18412629 A
64 A
* *
18412630 ACCCTGAGTGCATCGATGCAT-GGTATGTGCATCGATGCATG
1 AGCCTGAGTGCATCGATGCATAAG-A-GTGCATCGATGCATG
18412671 GATTGGTGCA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 46 0.52
65 39 0.44
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
AGCCTGAGTGCATCGATGCATAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAA
Found at i:18412659 original size:65 final size:64
Alignment explanation
Indices: 18412527--18412669 Score: 209
Period size: 65 Copynumber: 2.2 Consensus size: 64
18412517 TGCACTAAGA
* * *
18412527 GTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGACTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGACTT
*
18412591 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATG-GT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATACCCTGAGTGCATCGATGCATGACT
18412654 AT
64 -T
18412656 GTGCATCGATGCAT
1 GTGCATCGATGCAT
18412670 GGATTGGTGC
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
64 28 0.39
65 41 0.57
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGACTT
Found at i:18420338 original size:64 final size:65
Alignment explanation
Indices: 18420252--18420390 Score: 185
Period size: 65 Copynumber: 2.2 Consensus size: 65
18420242 TGCACTAAGA
* * * **
18420252 GTGCACCGATGCATGAAGTGCATTCGATG-TTTCA-AAATAGTCTGAGTGCATCGATGCATGACT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATG-CT
18420315 -T
64 AT
*
18420316 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGCTAT
18420381 GTGCATCGAT
1 GTGCATCGAT
18420391 ACATGGATTG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 27 0.41
65 36 0.55
66 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGCTAT
Found at i:18421632 original size:19 final size:19
Alignment explanation
Indices: 18421608--18421656 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
18421598 AGCCTGAGTA
18421608 CATCGATGCATGACTTGTG
1 CATCGATGCATGACTTGTG
18421627 CATCGATGCATGACTTGTG
1 CATCGATGCATGACTTGTG
*
18421646 CATTGATGCAT
1 CATCGATGCAT
18421657 AAAATGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (19 bp):
CATCGATGCATGACTTGTG
Found at i:18421653 original size:83 final size:85
Alignment explanation
Indices: 18421560--18421716 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 85
18421550 TGCACTAAGA
* * *
18421560 GTGCATTGATGCATGAAGTGCATTCGATG-TTTCA-AAATAGCCTGAGTACATCGATGCAT-GAC
1 GTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAA-AACCTGAGTACATCGATGCATGGA-
18421622 TT-GTGCATCGATGCATGACTT
64 TTGGTGCATCGATGCATGACTT
*
18421643 GTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGATT
1 GTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTACATCGATGCATGGATT
18421708 GGTGCATCG
66 GGTGCATCG
18421717 GTACACTCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 27 0.41
84 26 0.39
85 13 0.20
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (85 bp):
GTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTACATCGATGCATGGATT
GGTGCATCGATGCATGACTT
Found at i:18429658 original size:18 final size:19
Alignment explanation
Indices: 18429624--18429659 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18429614 TCAAATATAA
18429624 AACAACTTAATAACATTAT
1 AACAACTTAATAACATTAT
*
18429643 AACAATTTAA-AACATTA
1 AACAACTTAATAACATTA
18429660 AGCTTGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (19 bp):
AACAACTTAATAACATTAT
Found at i:18433997 original size:25 final size:25
Alignment explanation
Indices: 18433963--18434019 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
18433953 CTAAAGTTTT
18433963 GAAATTTATATTTTGGTCACTAACC
1 GAAATTTATATTTTGGTCACTAACC
18433988 GAAATTTATATTTTGGTCACTAACC
1 GAAATTTATATTTTGGTCACTAACC
*
18434013 AAAATTT
1 GAAATTT
18434020 GGGGTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (25 bp):
GAAATTTATATTTTGGTCACTAACC
Found at i:18434445 original size:21 final size:19
Alignment explanation
Indices: 18434421--18434476 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
18434411 TCTTTTTTTT
*
18434421 ATAAAATATTATAGAATATAA
1 ATAAAATA--ATAAAATATAA
18434442 ATAATCAATAATAAAATATAA
1 ATAA--AATAATAAAATATAA
18434463 ATAAAATAA-AAAAT
1 ATAAAATAATAAAAT
18434477 GAATATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
21 18 0.56
23 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAATAATAAAATATAA
Found at i:18435599 original size:12 final size:12
Alignment explanation
Indices: 18435565--18435607 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
18435555 AAAACAGAAA
*
18435565 AAATGAAATAAAT
1 AAATAAAAT-AAT
* *
18435578 AATTATAATAAT
1 AAATAAAATAAT
18435590 AAATAAAATAAT
1 AAATAAAATAAT
18435602 AAATAA
1 AAATAA
18435608 TAAACCCGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:18445714 original size:2 final size:2
Alignment explanation
Indices: 18445707--18445781 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
18445697 ACTAACTATC
18445707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18445749 TA TA 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 TA TA T
18445782 TACCTACAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18445839 original size:23 final size:23
Alignment explanation
Indices: 18445809--18445861 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
18445799 ACATATAATC
18445809 TATA-ACAAAATCATTTAAGCAT
1 TATAGACAAAATCATTTAAGCAT
18445831 TATAGACAAAATCATTTAAGCAT
1 TATAGACAAAATCATTTAAGCAT
18445854 TATAGACA
1 TATAGACA
18445862 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (23 bp):
TATAGACAAAATCATTTAAGCAT
Found at i:18446991 original size:17 final size:16
Alignment explanation
Indices: 18446971--18447037 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
18446961 CTTACTTTAC
18446971 TGTTTCGTTTATTGTAT
1 TGTTTC-TTTATTGTAT
* * *
18446988 TGTTTTATTTACTATAT
1 TG-TTTCTTTATTGTAT
*
18447005 TGTTTCTTTATTGTAC
1 TGTTTCTTTATTGTAT
*
18447021 TATATT-TTTATTGTAT
1 TGT-TTCTTTATTGTAT
18447037 T
1 T
18447038 TATACTTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 22 0.56
17 14 0.36
18 3 0.08
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.66
Consensus pattern (16 bp):
TGTTTCTTTATTGTAT
Found at i:18447037 original size:21 final size:20
Alignment explanation
Indices: 18446991--18447039 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
18446981 ATTGTATTGT
*
18446991 TTTATTTACTATATTGTTTC
1 TTTATTTACTATATTGTTTA
18447011 TTTATTGTACTATATT-TTTA
1 TTTATT-TACTATATTGTTTA
18447031 TTGTATTTA
1 TT-TATTTA
18447040 TACTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.65
Consensus pattern (20 bp):
TTTATTTACTATATTGTTTA
Found at i:18447046 original size:17 final size:16
Alignment explanation
Indices: 18447011--18447056 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
18447001 ATATTGTTTC
*
18447011 TTTATTGTACTATATT
1 TTTATTGTACTATACT
*
18447027 TTTATTGTATTTATACT
1 TTTATTGTA-CTATACT
18447044 TTTATTGTACTAT
1 TTTATTGTACTAT
18447057 TTCTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTATTGTACTATACT
Found at i:18447062 original size:17 final size:17
Alignment explanation
Indices: 18447007--18447063 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
18446997 TACTATATTG
18447007 TTTC-TTTATTGTACTA
1 TTTCTTTTATTGTACTA
*
18447023 TAT-TTTTATTGTA-T-
1 TTTCTTTTATTGTACTA
18447037 TTATACTTTTATTGTACTA
1 TT-T-CTTTTATTGTACTA
18447056 TTTCTTTT
1 TTTCTTTT
18447064 TAATTTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 1 0.03
15 2 0.06
16 11 0.33
17 15 0.45
18 2 0.06
19 2 0.06
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTCTTTTATTGTACTA
Found at i:18447382 original size:49 final size:49
Alignment explanation
Indices: 18447172--18447449 Score: 201
Period size: 49 Copynumber: 5.7 Consensus size: 49
18447162 TTTGTAACTA
* * * *
18447172 TATGACACATTTAGTGACCTGTACGTAGTATAAT-A--ACATGTATCTG
1 TATGACACATTTAGTGCCCTGTATGCAGCATAATAACTACATGTATCTG
* * ** * * *
18447218 TATGACACATTTAGTGCCCTATATGAAATATAATAACTCCTTGTATCGG
1 TATGACACATTTAGTGCCCTGTATGCAGCATAATAACTACATGTATCTG
* * * ** *
18447267 TATGGA-ACAATTAGTGCCCTGTATGCAACATAGCTTCCTGTA-ATTTGTAAT-TA
1 TAT-GACACATTTAGTGCCCTGTATGCAGCATA-ATAAC--TACA--TGT-ATCTG
* * *
18447320 TATGACACATTTAGTGACATGTATGCAGCATAATAACTACATGTATTTG
1 TATGACACATTTAGTGCCCTGTATGCAGCATAATAACTACATGTATCTG
* ** * *
18447369 TATGACACATTTAGTGCCCTATATGCAATATAATAACTGCTTGTATCTG
1 TATGACACATTTAGTGCCCTGTATGCAGCATAATAACTACATGTATCTG
*
18447418 TATGGA-ACAATTAGTGCCCTGTATGCAGCATA
1 TAT-GACACATTTAGTGCCCTGTATGCAGCATA
18447450 GCTGCCTGTA
Statistics
Matches: 179, Mismatches: 39, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
46 29 0.16
47 1 0.01
48 2 0.01
49 103 0.58
50 8 0.04
51 1 0.01
52 5 0.03
53 28 0.16
54 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (49 bp):
TATGACACATTTAGTGCCCTGTATGCAGCATAATAACTACATGTATCTG
Found at i:18447426 original size:151 final size:148
Alignment explanation
Indices: 18447152--18447460 Score: 492
Period size: 151 Copynumber: 2.1 Consensus size: 148
18447142 TGAAGTATAA
* * *
18447152 CTGCCTGTAATTTGTAACTATATGACACATTTAGTGACCTGTACGTAGTATAATAACATGTATCT
1 CTGCCTGTAATTTGTAACTATATGACACATTTAGTGACATGTACGCAGCATAATAACATGTATCT
18447217 GTATGACACATTTAGTGCCCTATATGAAATATAATAACTCCTTGTATCGGTATGGAACAATTAGT
66 GTATGACACATTTAGTGCCCTATATGAAATATAATAACTCCTTGTATCGGTATGGAACAATTAGT
18447282 GCCCTGTATGCAACATAG
131 GCCCTGTATGCAACATAG
* * *
18447300 CTTCCTGTAATTTGTAATTATATGACACATTTAGTGACATGTATGCAGCATAATAACTACATGTA
1 CTGCCTGTAATTTGTAACTATATGACACATTTAGTGACATGTACGCAGCATAAT-A--ACATGTA
* * * *
18447365 TTTGTATGACACATTTAGTGCCCTATATGCAATATAATAACTGCTTGTATCTGTATGGAACAATT
63 TCTGTATGACACATTTAGTGCCCTATATGAAATATAATAACTCCTTGTATCGGTATGGAACAATT
*
18447430 AGTGCCCTGTATGCAGCATAG
128 AGTGCCCTGTATGCAACATAG
18447451 CTGCCTGTAA
1 CTGCCTGTAA
18447461 CAATATGGCA
Statistics
Matches: 146, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
148 48 0.33
149 1 0.01
151 97 0.66
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (148 bp):
CTGCCTGTAATTTGTAACTATATGACACATTTAGTGACATGTACGCAGCATAATAACATGTATCT
GTATGACACATTTAGTGCCCTATATGAAATATAATAACTCCTTGTATCGGTATGGAACAATTAGT
GCCCTGTATGCAACATAG
Found at i:18447506 original size:20 final size:20
Alignment explanation
Indices: 18447477--18447515 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18447467 GGCACATTTA
*
18447477 GTGCCCTGTATGCATTATAG
1 GTGCCCTGTATGCAGTATAG
*
18447497 GTGCCTTGTATGCAGTATA
1 GTGCCCTGTATGCAGTATA
18447516 ACTGCTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTGCCCTGTATGCAGTATAG
Found at i:18452817 original size:14 final size:13
Alignment explanation
Indices: 18452783--18452819 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18452773 GCAAATTTTA
*
18452783 AAAACTATGTTTG
1 AAAACAATGTTTG
18452796 AAAACAATGTTTG
1 AAAACAATGTTTG
18452809 AAAATCAATGT
1 AAAA-CAATGT
18452820 GTAGTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (13 bp):
AAAACAATGTTTG
Found at i:18457670 original size:19 final size:20
Alignment explanation
Indices: 18457646--18457686 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
18457636 CCGTTATGGA
18457646 CTAGGGA-TATCGGTACCAT
1 CTAGGGAGTATCGGTACCAT
18457665 CTAGGGATGTATCGGTACCAT
1 CTAGGGA-GTATCGGTACCAT
18457686 C
1 C
18457687 CGAGCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (20 bp):
CTAGGGAGTATCGGTACCAT
Found at i:18459162 original size:7 final size:7
Alignment explanation
Indices: 18459140--18459179 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
18459130 TTTTTTAATC
*
18459140 ATTTTTT
1 ATTTTCT
18459147 ATCTTTCT
1 AT-TTTCT
18459155 ATTTTCT
1 ATTTTCT
18459162 ATTTTCT
1 ATTTTCT
*
18459169 ATTTTTT
1 ATTTTCT
18459176 ATTT
1 ATTT
18459180 CTTTTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTCT
Found at i:18459167 original size:14 final size:14
Alignment explanation
Indices: 18459140--18459179 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
18459130 TTTTTTAATC
18459140 ATTTTTTATCTTTCT
1 ATTTTTTAT-TTTCT
*
18459155 ATTTTCTATTTTCT
1 ATTTTTTATTTTCT
18459169 ATTTTTTATTT
1 ATTTTTTATTT
18459180 CTTTTTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTTTATTTTCT
Found at i:18459662 original size:257 final size:257
Alignment explanation
Indices: 18459199--18459911 Score: 966
Period size: 257 Copynumber: 2.8 Consensus size: 257
18459189 TTTTTAAAAA
* *
18459199 TAAATGAGAAACTTTGAAAACCATTTTCTCATTCTCTT-ACAAATACCATATGAAAACATCTTTC
1 TAAATGAGAAACTTTGAAAAAC-TTTTCTCATT-T-TTCACAAATACCATATGAAAGCATCTTTC
* * * * *
18459263 CCAAAGGTCTTATAGAT-TTCCCGAAGGACTTATCATCTTTCTCAAAAGACTGACATATGAACCG
63 CCAAAGGTCTTATAGATGGT-CCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
* * * * *
18459327 AATGATTTAATCATCATGCTAGAAAGGCTTACTGATCGCCTGAAGGACTTACCAATTTTGGAAAT
127 AAGGATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAAT
* *
18459392 AGTTTACTAGGTAAGAAACTTTTGAAAT-C-GCTTACTTTTCAAAAATTTCATTTTCTAAAAACA
192 AGTTTACTAGGTAAAAAACTTTGGAAATACTGCTTACTTTTCAAAAATTTCATTTTCTAAAAACA
18459455 T
257 T
** * * *
18459456 TAAATGAGAAACTTTGAAAGTTGCTTTTCTCATTTTTCAAAAATATCATATGAAAGCATCTTGCC
1 TAAATGAGAAACTTTGAAA--AACTTTTCTCATTTTTCACAAATACCATATGAAAGCATCTTTCC
* * * *
18459521 CAAAGGTCTTACAGATGGTGCGAAGGACATATCATCTTGCTCGAAAGAATGACAGATGACCCGAA
64 CAAAGGTCTTATAGATGGTCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAA
* * * *
18459586 GGATTTAATCATCAAGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACAAATTTTGGAAACAG
129 GGATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAG
* *
18459651 TTTATTAGGTAAAAAACTTTGGAAATCACTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACAT
194 TTTACTAGGTAAAAAACTTTGGAAAT-ACTGCTTACTTTTCAAAAATTTCATTTTCTAAAAACAT
* **** * * *
18459716 TAAATGTGAAACTTTGAAAAAAAAATCTTATTTTTCACAAACACCATATGAAAGCTTCTTTCCCA
1 TAAATGAGAAACTTTGAAAAACTTTTCTCATTTTTCACAAATACCATATGAAAGCATCTTTCCCA
* * *
18459781 AAGGTCTTATAGATGGCCCGAAGGACTTATTATCTTGCTCGAAAGACTGATAGATGACCCGAAGG
66 AAGGTCTTATAGATGGTCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
*
18459846 ATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAATGACTTACCAATTTTGGAAATAGTT
131 ATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAGTT
18459911 T
196 T
18459912 GCTTTATAAG
Statistics
Matches: 396, Mismatches: 53, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
256 2 0.01
257 176 0.44
258 164 0.41
259 2 0.01
260 52 0.13
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (257 bp):
TAAATGAGAAACTTTGAAAAACTTTTCTCATTTTTCACAAATACCATATGAAAGCATCTTTCCCA
AAGGTCTTATAGATGGTCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
ATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAGTT
TACTAGGTAAAAAACTTTGGAAATACTGCTTACTTTTCAAAAATTTCATTTTCTAAAAACAT
Found at i:18459846 original size:41 final size:42
Alignment explanation
Indices: 18459789--18459867 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
18459779 CAAAGGTCTT
* * *
18459789 ATAGATGGCCCGAAGGACTT-ATTATCTTGCTCGAAAGACTG
1 ATAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGACTG
*
18459830 ATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAG
1 ATAGATGACCCGAAGGACTTAATCATCATGCTCGAAAG
18459868 GCTTACTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
ATAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGACTG
Found at i:18459884 original size:42 final size:41
Alignment explanation
Indices: 18459789--18459892 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
18459779 CAAAGGTCTT
* *
18459789 ATAGATGGCCCGAAGGACTTATTATCTTGCTCGAAAGACTG
1 ATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTG
* * * *
18459830 ATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGGCTT
1 ATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTG
*
18459872 ACT-GATGGCCCGAATGACTTA
1 A-TAGATGGCCCGAAGGACTTA
18459893 CCAATTTTGG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 19 0.37
42 32 0.62
43 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (41 bp):
ATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTG
Found at i:18473466 original size:21 final size:21
Alignment explanation
Indices: 18473441--18473514 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
18473431 ATTATGACTA
*
18473441 TCGCAATACGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* *
18473462 TCGCATTGCGATATTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
18473483 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
18473504 TCGCAATGCGA
1 TCGCAATGCGA
18473515 ATAAGTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 41 0.91
22 4 0.09
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:18473529 original size:20 final size:21
Alignment explanation
Indices: 18473504--18473555 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18473494 TTTTCCCAAT
*
18473504 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
18473524 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
18473545 TCGCAATGCGA
1 TCGCAATGCGA
18473556 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:18473569 original size:20 final size:20
Alignment explanation
Indices: 18473544--18473647 Score: 120
Period size: 20 Copynumber: 5.2 Consensus size: 20
18473534 AATTTGGAAA
*
18473544 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
18473564 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
18473585 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
18473605 TTCGCAACGCGATTCTGCCT
1 ATCGCAACGCGATACTGACT
*
18473625 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
18473645 ATC
1 ATC
18473648 ACAAGGAGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 52 0.73
21 15 0.21
22 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:18473679 original size:41 final size:41
Alignment explanation
Indices: 18473541--18473678 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
18473531 GCGAATTTGG
*
18473541 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* ** *
18473582 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
18473623 -CTATCGCAACGCGATTCTGACTATCACAAGGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
18473663 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
18473679 TTTCAATGTT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 30 0.38
41 48 0.62
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:18474436 original size:24 final size:24
Alignment explanation
Indices: 18474404--18474453 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
18474394 TCGAAATTTC
18474404 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
18474428 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
18474452 AT
1 AT
18474454 GATGTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:18477025 original size:20 final size:20
Alignment explanation
Indices: 18476939--18477008 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
18476929 CAATGGGGAA
18476939 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* **
18476959 ATCACAACAAGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
18476979 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
18476999 ATCGCAACGC
1 ATCGCAACGC
18477009 TAATTTGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:18477069 original size:20 final size:20
Alignment explanation
Indices: 18477032--18477081 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
18477022 GCAATGAGAG
*
18477032 AATCGCAATGC-GAAATGAA
1 AATCGCAATGCAAAAATGAA
*
18477051 AATCGTAATGCAAAAATGAA
1 AATCGCAATGCAAAAATGAA
18477071 AATCGCAATGC
1 AATCGCAATGC
18477082 GAATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAATGCAAAAATGAA
Found at i:18477132 original size:14 final size:14
Alignment explanation
Indices: 18477115--18477169 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
18477105 TGTGTTTCGT
18477115 GTTGCGATTTTCTC
1 GTTGCGATTTTCTC
18477129 GTTGCGATTTTCATTTC
1 GTTGCGATTTTC---TC
*
18477146 GCATTGCGATTCTCTC
1 G--TTGCGATTTTCTC
18477162 GTTGCGAT
1 GTTGCGAT
18477170 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (14 bp):
GTTGCGATTTTCTC
Found at i:18477146 original size:33 final size:34
Alignment explanation
Indices: 18477108--18477189 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
18477098 TGCGATTTGT
* **
18477108 GTTTCGTGTTGCGATTTTCTCGTTGCGATTTTCA
1 GTTTCGTGTTGCGATTCTCTCGTTGCGATAGTCA
**
18477142 -TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 GTTTCGTGTTGCGATTCTCTCGTTGCGATAGTCA
18477175 GTTTCGTGTTGCGAT
1 GTTTCGTGTTGCGAT
18477190 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (34 bp):
GTTTCGTGTTGCGATTCTCTCGTTGCGATAGTCA
Found at i:18477152 original size:19 final size:18
Alignment explanation
Indices: 18477090--18477156 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
18477080 GCGAATTTAG
*
18477090 TTTCGCATTGCGATTTGTG
1 TTTCGCATTGCGATTT-TC
**
18477109 TTTCGTGTTGCGATTTTC
1 TTTCGCATTGCGATTTTC
18477127 --TCG--TTGCGATTTTC
1 TTTCGCATTGCGATTTTC
18477141 ATTTCGCATTGCGATT
1 -TTTCGCATTGCGATT
18477157 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.28
16 3 0.08
17 3 0.08
18 1 0.03
19 22 0.55
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.49
Consensus pattern (18 bp):
TTTCGCATTGCGATTTTC
Found at i:18477315 original size:14 final size:14
Alignment explanation
Indices: 18477296--18477332 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18477286 CATTAATTAA
18477296 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
18477310 ACAAATCATCTTTT
1 ACAAATCAACATTT
18477324 ACAAATCAA
1 ACAAATCAA
18477333 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:18478784 original size:42 final size:42
Alignment explanation
Indices: 18478738--18478830 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
18478728 CCTATTCAAC
* * *
18478738 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGATTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
18478780 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
18478822 GATGACAGG
1 GATGACAGG
18478831 TGAGTCAAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:18478789 original size:21 final size:21
Alignment explanation
Indices: 18478764--18478826 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
18478754 TGAACGGTGG
*
18478764 GAGGGGATTCTTGAGGGATGA
1 GAGGGGACTCTTGAGGGATGA
* * **
18478785 TAGGGGCCTCTTGAACGATTG-
1 GAGGGGACTCTTGAGGGA-TGA
18478806 GAGGGGACTCTTGAGGGATGA
1 GAGGGGACTCTTGAGGGATGA
18478827 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.43, T:0.24
Consensus pattern (21 bp):
GAGGGGACTCTTGAGGGATGA
Found at i:18479204 original size:20 final size:20
Alignment explanation
Indices: 18479181--18479229 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
18479171 GAAACTTAAA
18479181 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
18479201 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
18479221 ATCGTAACG
1 ATCGCAACG
18479230 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:18479302 original size:19 final size:19
Alignment explanation
Indices: 18479234--18479303 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
18479224 GTAACGAGAG
*
18479234 AATCGCAATGCG--ATATGA
1 AATCGCAATGCGAAACAT-A
*
18479252 AACTCGCAACGCGAAACATA
1 AA-TCGCAATGCGAAACATA
18479272 AATCGCAATGCGAAAC-TA
1 AATCGCAATGCGAAACATA
*
18479290 AATTCGCATTGCGA
1 AA-TCGCAATGCGA
18479304 TTTTCATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.14
19 32 0.73
20 3 0.07
21 3 0.07
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (19 bp):
AATCGCAATGCGAAACATA
Found at i:18479321 original size:20 final size:20
Alignment explanation
Indices: 18479292--18479450 Score: 92
Period size: 20 Copynumber: 8.6 Consensus size: 20
18479282 CGAAACTAAA
*
18479292 TTCGCATTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
18479312 TTCGCGTTGCGA--TT--TT
1 TTCGCGTTGCGATTTTCATT
*
18479328 GT--CGTTGCGATTTTCA-T
1 TTCGCGTTGCGATTTTCATT
*
18479345 TTCGCATTGCGATTTTC---
1 TTCGCGTTGCGATTTTCATT
***
18479362 -T--CGTTGCGATAGCCATT
1 TTCGCGTTGCGATTTTCATT
* **
18479379 TCCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
**
18479399 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
* * *
18479419 TTCGCGTTGCAATTTTAAGT
1 TTCGCGTTGCGATTTTCATT
*
18479439 TTCGTGTTGCGA
1 TTCGCGTTGCGA
18479451 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 17 0.16
16 6 0.06
17 2 0.02
18 2 0.02
19 12 0.11
20 70 0.64
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:18479355 original size:33 final size:34
Alignment explanation
Indices: 18479298--18479371 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
18479288 TAAATTCGCA
* *
18479298 TTGCGATTTTCATTTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTTTCTCG
18479332 TTGCGATTTTCA-TTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTTTCTCG
18479365 TTGCGAT
1 TTGCGAT
18479372 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.49
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTTTCTCG
Found at i:18479368 original size:14 final size:14
Alignment explanation
Indices: 18479309--18479371 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 14
18479299 TGCGATTTTC
*
18479309 ATTTTCGCGTTGCG
1 ATTTTCTCGTTGCG
*
18479323 ATTTTGTCGTTGCG
1 ATTTTCTCGTTGCG
18479337 ATTTTCATTTCGCATTGCG
1 ATTTTC---TCG--TTGCG
18479356 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
18479370 AT
1 AT
18479372 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
14 24 0.59
16 3 0.07
17 3 0.07
19 11 0.27
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:18479379 original size:33 final size:33
Alignment explanation
Indices: 18479311--18479391 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
18479301 CGATTTTCAT
* ***
18479311 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATAGCCA
*
18479344 TTTCGCATTGCGATTTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATAGCCA
18479377 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
18479392 AGTCATTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 31 0.76
34 10 0.24
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATAGCCA
Found at i:18479442 original size:40 final size:40
Alignment explanation
Indices: 18479358--18479450 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
18479348 GCATTGCGAT
* * * *
18479358 TTTCTCGTTGCGATAGCCATTTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCAATAGTAAG
* * **
18479398 TTTCGCGTTGCGATAGTCATTTTCGCGTTGCAATTTTAAG
1 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCAATAGTAAG
*
18479438 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
18479451 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (40 bp):
TTTCGCGTTGCGATAGCCATTTCCGCGTTGCAATAGTAAG
Found at i:18480018 original size:18 final size:18
Alignment explanation
Indices: 18479995--18480043 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
18479985 CGGGTTGATC
18479995 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
18480013 AGGTGATGGCTCTGTGTG
1 AGGTGATGGCTCTGGGTG
18480031 AGGTGATGGCTCT
1 AGGTGATGGCTCT
18480044 CGAAGTGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.12, G:0.45, T:0.31
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:18481398 original size:20 final size:20
Alignment explanation
Indices: 18481375--18481446 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
18481365 GAAACTTAAA
18481375 ATCGCAACGAGAAAATGACT
1 ATCGCAACGAGAAAATGACT
18481395 ATCGCAAC-ACGAAAATGACT
1 ATCGCAACGA-GAAAATGACT
* * *
18481415 ATCGCAATGCGGAAATGACT
1 ATCGCAACGAGAAAATGACT
18481435 ATCGCAACGAGA
1 ATCGCAACGAGA
18481447 GAATCACAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGACT
Found at i:18481476 original size:32 final size:34
Alignment explanation
Indices: 18481419--18481509 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 34
18481409 ATGACTATCG
** *
18481419 CAATGCGGAAATGACTATCGCAACGAGAGAATCA
1 CAATGCGGAAATGAAAATCGCAACGAGAAAATCA
* * *
18481453 CAATGC-GAATTG-AAATTGCAACGAGAAAATCG
1 CAATGCGGAAATGAAAATCGCAACGAGAAAATCA
18481485 CAATGCGGAAATGAAAATCGCAACG
1 CAATGCGGAAATGAAAATCGCAACG
18481510 TGAATTTGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
32 21 0.45
33 10 0.21
34 16 0.34
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (34 bp):
CAATGCGGAAATGAAAATCGCAACGAGAAAATCA
Found at i:18481536 original size:19 final size:19
Alignment explanation
Indices: 18481514--18481554 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
18481504 GCAACGTGAA
18481514 TTTGGTTTCGCGTTGCGAT
1 TTTGGTTTCGCGTTGCGAT
18481533 TTTGGTTTCGCGTTGCGAT
1 TTTGGTTTCGCGTTGCGAT
18481552 TTT
1 TTT
18481555 AATTCGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.05, C:0.15, G:0.29, T:0.51
Consensus pattern (19 bp):
TTTGGTTTCGCGTTGCGAT
Found at i:18481600 original size:20 final size:19
Alignment explanation
Indices: 18481575--18481662 Score: 95
Period size: 20 Copynumber: 4.5 Consensus size: 19
18481565 ACGATTCTCT
*
18481575 CGTTGCGATAATCATTTCCG
1 CGTTGCGATAGTCATTT-CG
18481595 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
* *
18481615 TGTTGCGATAGTCATTTTG
1 CGTTGCGATAGTCATTTCG
**
18481634 TCGTTGCGATTCTCATTTCG
1 -CGTTGCGATAGTCATTTCG
*
18481654 TGTTGCGAT
1 CGTTGCGAT
18481663 TCTCGGTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
19 12 0.21
20 43 0.74
21 3 0.05
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:18481631 original size:40 final size:39
Alignment explanation
Indices: 18481576--18481662 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
18481566 CGATTCTCTC
*
18481576 GTTGCGATAATCATTTCCG-CGTTGCGATAGTCATTTTCGT
1 GTTGCGATAATCATTT-CGTCGTTGCGATACTCA-TTTCGT
* * *
18481616 GTTGCGATAGTCATTTTGTCGTTGCGATTCTCATTTCGT
1 GTTGCGATAATCATTTCGTCGTTGCGATACTCATTTCGT
18481655 GTTGCGAT
1 GTTGCGAT
18481663 TCTCGGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (39 bp):
GTTGCGATAATCATTTCGTCGTTGCGATACTCATTTCGT
Found at i:18482033 original size:22 final size:22
Alignment explanation
Indices: 18482003--18482059 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
18481993 GATGGAGATA
*
18482003 GACGAATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
18482025 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
18482047 GACGGATGTCGCC
1 GACGGATTTCGCC
18482060 GTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.40, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:18482276 original size:20 final size:20
Alignment explanation
Indices: 18482253--18482319 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
18482243 TATTATCTCG
* * *
18482253 TTGCGATAGGCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
*
18482273 TTGCGAAAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
18482293 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
18482313 TTGCGAT
1 TTGCGAT
18482320 TTTCCAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:18482352 original size:20 final size:21
Alignment explanation
Indices: 18482308--18482355 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18482298 ATAGTCAGTA
*
18482308 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
18482329 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
18482349 TCGCATT
1 TCGCATT
18482356 TCGAATTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:18482401 original size:21 final size:22
Alignment explanation
Indices: 18482349--18482401 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
18482339 ATTTACTTAT
*
18482349 TCGCATTTCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
18482370 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
18482391 TCGCATTGCGA
1 TCGCATTGCGA
18482402 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:18494137 original size:20 final size:21
Alignment explanation
Indices: 18494107--18494146 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
18494097 AGCCATTGGG
18494107 GCCTGATGGTATCGATATTAT
1 GCCTGATGGTATCGATATTAT
18494128 GCCT-ATGGTATCGATATTA
1 GCCTGATGGTATCGATATTA
18494147 CTATACAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (21 bp):
GCCTGATGGTATCGATATTAT
Found at i:18495180 original size:177 final size:178
Alignment explanation
Indices: 18494883--18495237 Score: 703
Period size: 177 Copynumber: 2.0 Consensus size: 178
18494873 TGCAATACCA
18494883 ATTTGAAATTAAGTGCATATGCATAAAGCTTTTTCAAAAATGTTATGCATTTGAAAAATGGATAT
1 ATTTGAAATTAAGTGCATATGCATAAAGCTTTTTCAAAAATGTTATGCATTTGAAAAATGGATAT
18494948 CAATTGTTAGAAAGATATCATTTATAATAAATCACTTGCATAACCATTTAAAATTAAAGTCAAAA
66 CAATTGTTAGAAAGATATCATTTATAATAAATCACTTGCATAACCATTTAAAATTAAAGTCAAAA
18495013 ATTTAAAATTTGTAAACTCAAAGCATTTGAAAAGTTGATATCAATTGT
131 ATTTAAAATTTGTAAACTCAAAGCATTTGAAAAGTTGATATCAATTGT
18495061 ATTTGAAATTAAGTGCATATGCATAAAGCTTTTTCAAAAA-GTTATGCATTTGAAAAATGGATAT
1 ATTTGAAATTAAGTGCATATGCATAAAGCTTTTTCAAAAATGTTATGCATTTGAAAAATGGATAT
18495125 CAATTGTTAGAAAGATATCATTTATAATAAATCACTTGCATAACCATTTAAAATTAAAGTCAAAA
66 CAATTGTTAGAAAGATATCATTTATAATAAATCACTTGCATAACCATTTAAAATTAAAGTCAAAA
18495190 ATTTAAAATTTGTAAACTCAAAGCATTTGAAAAGTTGATATCAATTGT
131 ATTTAAAATTTGTAAACTCAAAGCATTTGAAAAGTTGATATCAATTGT
18495238 TAGAGAGATA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
177 137 0.77
178 40 0.23
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (178 bp):
ATTTGAAATTAAGTGCATATGCATAAAGCTTTTTCAAAAATGTTATGCATTTGAAAAATGGATAT
CAATTGTTAGAAAGATATCATTTATAATAAATCACTTGCATAACCATTTAAAATTAAAGTCAAAA
ATTTAAAATTTGTAAACTCAAAGCATTTGAAAAGTTGATATCAATTGT
Found at i:18498590 original size:23 final size:22
Alignment explanation
Indices: 18498546--18498592 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
18498536 TTGCACTATG
*
18498546 TTATTTCTTTTTTTGTATAAAT
1 TTATTTCTTTTTTTGTACAAAT
* *
18498568 TTATTTGTTATTTTTGTCCAAAT
1 TTATTTCTT-TTTTTGTACAAAT
18498591 TT
1 TT
18498593 TCAGGTGTTG
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:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (22 bp):
TTATTTCTTTTTTTGTACAAAT
Found at i:18506870 original size:21 final size:21
Alignment explanation
Indices: 18506846--18506895 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
18506836 AAATTTGTTA
18506846 CAAAGCCAAGCAACACTTTTG
1 CAAAGCCAAGCAACACTTTTG
*
18506867 CAAAACCAAGCAACACTTTTG
1 CAAAGCCAAGCAACACTTTTG
18506888 CAAAGCCA
1 CAAAGCCA
18506896 TAGTTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.16
Consensus pattern (21 bp):
CAAAGCCAAGCAACACTTTTG
Found at i:18508490 original size:14 final size:14
Alignment explanation
Indices: 18508447--18508492 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
18508437 CGTTCGTGAA
*
18508447 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
*
18508461 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
18508475 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
18508489 CGTT
1 CGTT
18508493 TATGTTCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:18509478 original size:16 final size:16
Alignment explanation
Indices: 18509457--18509496 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
18509447 TATGTTCGTT
18509457 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
18509473 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
18509489 TTTATGTT
1 TTTATGTT
18509497 TGTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:18509588 original size:16 final size:16
Alignment explanation
Indices: 18509567--18509597 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18509557 CAAAAAAAAT
18509567 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
18509583 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
18509598 ATTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:18527001 original size:12 final size:11
Alignment explanation
Indices: 18526982--18527194 Score: 117
Period size: 12 Copynumber: 19.4 Consensus size: 11
18526972 GGAAAGGGAG
18526982 GAGGAGAGAGA
1 GAGGAGAGAGA
*
18526993 GAGGTAGAGAAA
1 GAGG-AGAGAGA
*
18527005 GA-AAGAGAGA
1 GAGGAGAGAGA
18527015 G-GGAGAGGGAGA
1 GAGGAGA--GAGA
* *
18527027 AAGG-GAGGGA
1 GAGGAGAGAGA
* *
18527037 GAGGGAGAAAGG
1 GA-GGAGAGAGA
18527049 GAGG-GAGAGGAA
1 GAGGAGAGA-G-A
18527061 GAGG-GAGAGA
1 GAGGAGAGAGA
18527071 G-GGATGAAGAGA
1 GAGGA-G-AGAGA
*
18527083 GAGG-GAGGGA
1 GAGGAGAGAGA
*
18527093 GAGG-GAGACA
1 GAGGAGAGAGA
* *
18527103 GA-GAGATATA
1 GAGGAGAGAGA
*
18527113 GA-GAGAGGGA
1 GAGGAGAGAGA
18527123 G-GGAGAGAGA
1 GAGGAGAGAGA
*
18527133 GAGG-GAGGGA
1 GAGGAGAGAGA
18527143 GAGAGAGAGAGA
1 GAG-GAGAGAGA
18527155 GAGAGAGAGAGA
1 GAG-GAGAGAGA
18527167 GAGAGAGAGAGA
1 GAG-GAGAGAGA
*
18527179 GAGGGAGAGGGA
1 GA-GGAGAGAGA
18527191 GAGG
1 GAGG
18527195 GAGTGGGAGT
Statistics
Matches: 159, Mismatches: 24, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
9 3 0.02
10 61 0.38
11 17 0.11
12 73 0.46
13 5 0.03
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.02
Consensus pattern (11 bp):
GAGGAGAGAGA
Found at i:18527034 original size:18 final size:18
Alignment explanation
Indices: 18527008--18527236 Score: 168
Period size: 18 Copynumber: 12.8 Consensus size: 18
18526998 AGAGAAAGAA
*
18527008 AGAGAGAGGGAGAGGGAG
1 AGAGGGAGGGAGAGGGAG
*
18527026 AAAGGGAGGGAGAGGGAG
1 AGAGGGAGGGAGAGGGAG
*
18527044 AAAGGGAGGGAGAGGAAGAG
1 AGAGGGAGGGAGAGG--GAG
* * *
18527064 GGAGAGAGGGATGA-AGAG
1 AGAGGGAGGGA-GAGGGAG
18527082 AGAGGGAGGGAGAGGGAG
1 AGAGGGAGGGAGAGGGAG
* * * **
18527100 ACA--GAGAGATATAGAG
1 AGAGGGAGGGAGAGGGAG
18527116 AGAGGGAGGGAGA--GAG
1 AGAGGGAGGGAGAGGGAG
*
18527132 AGAGGGAGGGAGAGAGAG
1 AGAGGGAGGGAGAGGGAG
* * *
18527150 AGAGAGAGAGAGAGAGAG
1 AGAGGGAGGGAGAGGGAG
* *
18527168 AGAGAGAGAGAGAGGGAG
1 AGAGGGAGGGAGAGGGAG
*
18527186 AG-GGAGAGGGAGTGGGAG
1 AGAGG-GAGGGAGAGGGAG
*
18527204 TG-GGAAAGAGGGAGAGGGAG
1 AGAGG---GAGGGAGAGGGAG
18527224 AGAGGG-GGGAGAG
1 AGAGGGAGGGAGAG
18527237 ATAGAGGATG
Statistics
Matches: 173, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
16 27 0.16
17 10 0.06
18 107 0.62
20 25 0.14
21 4 0.02
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.02
Consensus pattern (18 bp):
AGAGGGAGGGAGAGGGAG
Found at i:18527193 original size:24 final size:24
Alignment explanation
Indices: 18526976--18527236 Score: 188
Period size: 24 Copynumber: 11.1 Consensus size: 24
18526966 GAAGAAGGAA
*
18526976 AGGGAG-GAGGAGAGAGAGAGGTAG
1 AGGGAGAGA-GAGAGAGAGAGGGAG
*
18527000 A--GA-A-AGAAAGAGAGAGGGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
* * *
18527020 AGGGAGAAAGGGAGGGAGAGGGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
*
18527044 AAAGGGAGGGAGAG-GA-AGAGGGAG
1 --AGGGAGAGAGAGAGAGAGAGGGAG
*
18527068 AGAGG-GATGAAGAGAGAGGGAGGGAG
1 AG-GGAGA-G-AGAGAGAGAGAGGGAG
* * * *
18527094 AGGGAGACAGAGAGATATAGAGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
18527118 AGGGAG-G-GAGAGAGAGA-GG-G
1 AGGGAGAGAGAGAGAGAGAGGGAG
*
18527138 AGGGAGAGAGAGAGAGAGAGAGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
*
18527162 AGAGAGAGAGAGAGAGAGAGGGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
* * * *
18527186 AGGGAGAGGGAGTGGGAGTGGGAAAG
1 AGGGAGAGAGAGAGAGAGAGGG--AG
* *
18527212 AGGGAGAGGGAGAGAG-GGGGGAG
1 AGGGAGAGAGAGAGAGAGAGGGAG
18527235 AG
1 AG
18527237 ATAGAGGATG
Statistics
Matches: 187, Mismatches: 31, Indels: 39
0.73 0.12 0.15
Matches are distributed among these distances:
20 21 0.11
21 3 0.02
22 25 0.13
23 9 0.05
24 84 0.45
25 9 0.05
26 36 0.19
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.02
Consensus pattern (24 bp):
AGGGAGAGAGAGAGAGAGAGGGAG
Found at i:18527194 original size:6 final size:6
Alignment explanation
Indices: 18527011--18527225 Score: 131
Period size: 6 Copynumber: 35.8 Consensus size: 6
18527001 GAAAGAAAGA
* *
18527011 GAGAGG GAGAGG GAGAAAG G-GAGG GAGAGG GAGAAAG G-GAGG GAGAGG
1 GAGAGG GAGAGG GAG-AGG GAGAGG GAGAGG GAG-AGG GAGAGG GAGAGG
* * ** *
18527059 AAGAGG GAGAGAG G-GATGAA GAGAGAG G-GAGG GAGAGG GAGACA GAGAGA
1 GAGAGG GAGAG-G GAGA-G-G GAGAG-G GAGAGG GAGAGG GAGAGG GAGAGG
* * * * * *
18527109 TATAGA GAGA-G G-GAGG GAGAGA GAGA-G G-GAGG GAGAGA GAGAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
* * * * *
18527153 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGG GAGAGG GAGAGG GAGTGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
*
18527201 GAGTGG GAAAGAGG GAGAGG GAGAG
1 GAGAGG G--AGAGG GAGAGG GAGAG
18527226 AGGGGGGAGA
Statistics
Matches: 173, Mismatches: 22, Indels: 28
0.78 0.10 0.13
Matches are distributed among these distances:
4 4 0.02
5 14 0.08
6 134 0.77
7 14 0.08
8 7 0.04
ACGTcount: A:0.40, C:0.00, G:0.58, T:0.02
Consensus pattern (6 bp):
GAGAGG
Found at i:18527949 original size:2 final size:2
Alignment explanation
Indices: 18527942--18528052 Score: 92
Period size: 2 Copynumber: 57.5 Consensus size: 2
18527932 TGGAAGGTCT
18527942 GA GA GA 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 GA GA GA
* * *
18527984 AA GA G- GC GA -A TGA GA G- GA GA GA G- GTA GA GA GA -A TGG GA
1 GA GA GA GA GA GA -GA GA GA GA GA GA GA G-A GA GA GA GA -GA GA
* * *
18528022 GA GA G- GG GA -A GA GG GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
18528053 GAAGAGGGAG
Statistics
Matches: 89, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
1 7 0.08
2 80 0.90
3 2 0.02
ACGTcount: A:0.46, C:0.01, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:18528057 original size:10 final size:10
Alignment explanation
Indices: 18527942--18528073 Score: 50
Period size: 12 Copynumber: 11.8 Consensus size: 10
18527932 TGGAAGGTCT
18527942 GAGAGA-GAGA
1 GAGAGAGGA-A
18527952 GAGAGAGAGAGA
1 GAGAGAG-GA-A
18527964 GAGAGAGAGAGA
1 GAGAGAG-GA-A
*
18527976 GAGAGAGAAA
1 GAGAGAGGAA
* *
18527986 GAGGCGAATGAGAG
1 GA-GAG-A-G-GAA
*
18528000 GAGAGAGGTA
1 GAGAGAGGAA
*
18528010 GAGAGAATGGGA
1 GAGAG-A-GGAA
*
18528022 GAGAGGGGAA
1 GAGAGAGGAA
18528032 GAGGGAGAGAGAAA
1 GA--GAGAG-G-AA
18528046 GAGAGAGGAA
1 GAGAGAGGAA
*
18528056 GAGGGAGGAA
1 GAGAGAGGAA
*
18528066 GAGGGAGG
1 GAGAGAGG
18528074 GAGGGGGAGG
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
10 39 0.40
11 6 0.06
12 42 0.43
13 4 0.04
14 7 0.07
ACGTcount: A:0.45, C:0.01, G:0.52, T:0.02
Consensus pattern (10 bp):
GAGAGAGGAA
Found at i:18528075 original size:14 final size:14
Alignment explanation
Indices: 18528056--18528104 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
18528046 GAGAGAGGAA
*
18528056 GAGGGAGGAAGAGG
1 GAGGGAGGGAGAGG
*
18528070 GAGGGAGGGGGAGG
1 GAGGGAGGGAGAGG
*
18528084 GAGGGAGGGACAGG
1 GAGGGAGGGAGAGG
18528098 GAGGGAG
1 GAGGGAG
18528105 ACAAGGAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.69, T:0.00
Consensus pattern (14 bp):
GAGGGAGGGAGAGG
Found at i:18528098 original size:10 final size:10
Alignment explanation
Indices: 18528045--18528105 Score: 63
Period size: 10 Copynumber: 6.3 Consensus size: 10
18528035 GGAGAGAGAA
* *
18528045 AGAGAGAGGA
1 AGAGGGAGGG
*
18528055 AGAGGGAGGA
1 AGAGGGAGGG
18528065 AGAGGGAGGG
1 AGAGGGAGGG
*
18528075 AGGGGGA-GG
1 AGAGGGAGGG
18528084 -GAGGGAGGG
1 AGAGGGAGGG
*
18528093 ACAGGGAGGG
1 AGAGGGAGGG
18528103 AGA
1 AGA
18528106 CAAGGAGAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
8 5 0.12
9 4 0.09
10 34 0.79
ACGTcount: A:0.34, C:0.02, G:0.64, T:0.00
Consensus pattern (10 bp):
AGAGGGAGGG
Found at i:18528150 original size:12 final size:12
Alignment explanation
Indices: 18528135--18528167 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
18528125 ACGGAGAGTA
18528135 GGAGAAAGAGAG
1 GGAGAAAGAGAG
18528147 GGAGAAAGAGAG
1 GGAGAAAGAGAG
18528159 GGAGAAAGA
1 GGAGAAAGA
18528168 TGGGGGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
GGAGAAAGAGAG
Done.