Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 190 of 204
Found at i:56474326 original size:29 final size:29
Alignment explanation
Indices: 56474292--56474348 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
56474282 TTTGATTCTT
*
56474292 CTTAATAATATAAAGGCTAAATTGATCCA
1 CTTAATAATAGAAAGGCTAAATTGATCCA
* *
56474321 CTTAATAATGGAATGGCTAAATTGATCC
1 CTTAATAATAGAAAGGCTAAATTGATCC
56474349 CATCCCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (29 bp):
CTTAATAATAGAAAGGCTAAATTGATCCA
Found at i:56475703 original size:50 final size:50
Alignment explanation
Indices: 56475628--56475727 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
56475618 AAGTCGAATC
56475628 GAAATTTTAAGATTAAAAATCCGAACCCGACTCATTTTTCAACTTTAAAA
1 GAAATTTTAAGATTAAAAATCCGAACCCGACTCATTTTTCAACTTTAAAA
56475678 GAAATTTTAAGATTAAAAATCCGAACCCGACTCATTTTTCAACTTTAAAA
1 GAAATTTTAAGATTAAAAATCCGAACCCGACTCATTTTTCAACTTTAAAA
56475728 TATACTTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (50 bp):
GAAATTTTAAGATTAAAAATCCGAACCCGACTCATTTTTCAACTTTAAAA
Found at i:56476131 original size:3 final size:3
Alignment explanation
Indices: 56476123--56476159 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
56476113 TTTCTTTACC
56476123 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56476160 TTACTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56478561 original size:6 final size:6
Alignment explanation
Indices: 56478527--56478558 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
56478517 ATCTTCCTCC
*
56478527 CCTTCA CCTTCA CCTTCA CCTTCA CCATCA CC
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CC
56478559 ATCGACGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.53, G:0.00, T:0.28
Consensus pattern (6 bp):
CCTTCA
Found at i:56482715 original size:31 final size:31
Alignment explanation
Indices: 56482680--56482738 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
56482670 CGCTACAATA
56482680 ACTTAAAT-AAACACTTT-AGAATAGTTCAGTG
1 ACTTAAATGAAA-ACTTTCA-AATAGTTCAGTG
*
56482711 ACTTAAGTGAAAACTTTCAAATAGTTCA
1 ACTTAAATGAAAACTTTCAAATAGTTCA
56482739 ATAACCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAGTTCAGTG
Found at i:56483526 original size:25 final size:25
Alignment explanation
Indices: 56483471--56483527 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
56483461 TTTACATTTT
*
56483471 TATATTACATATACAAATAATTATA
1 TATATTACATATAAAAATAATTATA
*
56483496 TTTATTGAC-TATAAAAATAAATTA-A
1 TATATT-ACATATAAAAAT-AATTATA
56483521 TATATTA
1 TATATTA
56483528 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 7 0.26
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATTACATATAAAAATAATTATA
Found at i:56483759 original size:11 final size:11
Alignment explanation
Indices: 56483743--56483769 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
56483733 TTTTTTATCG
56483743 AAATAATATAA
1 AAATAATATAA
56483754 AAATAATATAA
1 AAATAATATAA
56483765 AAATA
1 AAATA
56483770 GGAAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAATATAA
Found at i:56503456 original size:6 final size:6
Alignment explanation
Indices: 56503445--56503470 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56503435 GGTACTGAGA
56503445 CACATG CACATG CACATG CACATG CA
1 CACATG CACATG CACATG CACATG CA
56503471 AAGGGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
CACATG
Found at i:56507659 original size:19 final size:19
Alignment explanation
Indices: 56507635--56507671 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56507625 TTAATATTTT
*
56507635 ATAAAATTTTAATTTAATA
1 ATAAAATTATAATTTAATA
*
56507654 ATAAAATTATATTTTAAT
1 ATAAAATTATAATTTAAT
56507672 CTCTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAAATTATAATTTAATA
Found at i:56507698 original size:29 final size:29
Alignment explanation
Indices: 56507650--56507723 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
56507640 ATTTTAATTT
* *
56507650 AATAATAAAATTATATTTTAATCTCTT-AA
1 AATAATAAAATTA-AATTTAATATCTTAAA
*
56507679 AATAATAAAATCTAAATTTAATATTTTAAA
1 AATAATAAAAT-TAAATTTAATATCTTAAA
56507709 AATAA-AAAATATAAA
1 AATAATAAAAT-TAAA
56507724 CTATGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 30 0.77
30 9 0.23
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAATAAAATTAAATTTAATATCTTAAA
Found at i:56508939 original size:3 final size:3
Alignment explanation
Indices: 56508931--56508955 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56508921 TGCAAAACGT
56508931 TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG T
56508956 AAATGACAAT
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:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:56516367 original size:20 final size:20
Alignment explanation
Indices: 56516325--56516367 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
56516315 ATGGACCAAA
*
56516325 AAATAAACATATAAAAATTT
1 AAATAAACATATAAAAATCT
56516345 AAATAAA-ATATAAAATATCT
1 AAATAAACATATAAAA-ATCT
56516365 AAA
1 AAA
56516368 AATCAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAACATATAAAAATCT
Found at i:56516400 original size:31 final size:32
Alignment explanation
Indices: 56516340--56516399 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
56516330 AACATATAAA
56516340 AATTTAAATAAAATATAAAATATCTAAAAATC
1 AATTTAAATAAAATATAAAATATCTAAAAATC
*
56516372 AATTTAATTAACAAT-T-AAATAT-TAAAAA
1 AATTTAAATAA-AATATAAAATATCTAAAAA
56516400 AATTTATTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 6 0.23
32 11 0.42
33 3 0.12
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (32 bp):
AATTTAAATAAAATATAAAATATCTAAAAATC
Found at i:56517532 original size:21 final size:21
Alignment explanation
Indices: 56517491--56517539 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56517481 TTTTATTATT
* *
56517491 TAAAATATTATTATTTTTTTA
1 TAAAATATTATTATATATTTA
56517512 TAAAATA-TATATATATATTTA
1 TAAAATATTAT-TATATATTTA
*
56517533 AAAAATA
1 TAAAATA
56517540 GACTTACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATATTATTATATATTTA
Found at i:56534828 original size:12 final size:14
Alignment explanation
Indices: 56534811--56534843 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
56534801 TTTATCGTAT
56534811 ATAAAAATA-AAA-
1 ATAAAAATAGAAAC
56534823 ATAAAAATAGAAAC
1 ATAAAAATAGAAAC
56534837 ATAAAAA
1 ATAAAAA
56534844 AACTCTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (14 bp):
ATAAAAATAGAAAC
Found at i:56537333 original size:18 final size:19
Alignment explanation
Indices: 56537296--56537333 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
56537286 AAAATGACTC
* *
56537296 AAAATTCAAAAAATTCATA
1 AAAATTAAAAAAAATCATA
56537315 AAAATTAAAAAAAAT-ATA
1 AAAATTAAAAAAAATCATA
56537333 A
1 A
56537334 CATTTTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTAAAAAAAATCATA
Found at i:56543008 original size:28 final size:28
Alignment explanation
Indices: 56542908--56543006 Score: 164
Period size: 28 Copynumber: 3.5 Consensus size: 28
56542898 AAAAATAAAA
*
56542908 ATTTATCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
56542937 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
56542965 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
56542993 ATTTACCAAAATAT
1 ATTTACCAAAATAT
56543007 ATCAAAAAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
28 47 0.69
29 21 0.31
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:56543602 original size:19 final size:18
Alignment explanation
Indices: 56543578--56543638 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
56543568 TCTAATTAAG
56543578 TAATAATTCTATTTTAATT
1 TAATAA-TCTATTTTAATT
* * *
56543597 TAATAAACTATTCTCATT
1 TAATAATCTATTTTAATT
* *
56543615 TAATAACTATATTTTAAAT
1 TAATAA-TCTATTTTAATT
56543634 TAATA
1 TAATA
56543639 GAAATATCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATCTATTTTAATT
Found at i:56543607 original size:18 final size:18
Alignment explanation
Indices: 56543586--56543638 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
56543576 AGTAATAATT
56543586 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* *
56543604 CTATTCTCATTTAAT-AA
1 CTATTTTAATTTAATAAA
*
56543621 CTATATTTTAAATTAATA
1 C--TATTTTAATTTAATA
56543639 GAAATATCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:56544164 original size:27 final size:26
Alignment explanation
Indices: 56544128--56544184 Score: 105
Period size: 27 Copynumber: 2.2 Consensus size: 26
56544118 TTTTAGTCCT
56544128 TTGGCACATTGGTGCCGCCAATGGCA
1 TTGGCACATTGGTGCCGCCAATGGCA
56544154 TTGGCACCATTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCGCCAATGGCA
56544181 TTGG
1 TTGG
56544185 GGTGATCAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (26 bp):
TTGGCACATTGGTGCCGCCAATGGCA
Found at i:56544301 original size:29 final size:28
Alignment explanation
Indices: 56544227--56544325 Score: 164
Period size: 28 Copynumber: 3.5 Consensus size: 28
56544217 TTTTTTTGAT
56544227 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
56544254 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
56544283 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAAT-AAAAAAAAGTTGTA
*
56544312 ATATTTTGATAAAT
1 ATATTTTGGTAAAT
56544326 TTTAATTTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
28 39 0.57
29 29 0.43
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:56547812 original size:14 final size:14
Alignment explanation
Indices: 56547793--56547822 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56547783 AAGATACTGC
56547793 TTCCAGTAAAGGAG
1 TTCCAGTAAAGGAG
*
56547807 TTCCAGTAATGGAG
1 TTCCAGTAAAGGAG
56547821 TT
1 TT
56547823 AACCAAGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (14 bp):
TTCCAGTAAAGGAG
Found at i:56552789 original size:6 final size:6
Alignment explanation
Indices: 56552771--56552833 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
56552761 ATATGTAAGT
* * *
56552771 ATAATA A-ATATA ATAATA ATAGTA ATAATA AAAATA AAAATA ATAACT-
1 ATAATA ATA-ATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAA-TA
*
56552819 ATATTA ATAA-A ATAA
1 ATAATA ATAATA ATAA
56552834 ACTAAAAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
5 7 0.15
6 38 0.81
7 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (6 bp):
ATAATA
Found at i:56552814 original size:30 final size:30
Alignment explanation
Indices: 56552773--56552841 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
56552763 ATGTAAGTAT
*
56552773 AATAAATATAATAA-TAATAGTAATAATAA-A
1 AATAAAAATAATAACT-ATAGTAATAA-AATA
*
56552803 AATAAAAATAATAACTATATTAATAAAATA
1 AATAAAAATAATAACTATAGTAATAAAATA
56552833 AACTAAAAA
1 AA-TAAAAA
56552842 CTTAAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 25 0.74
31 7 0.21
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (30 bp):
AATAAAAATAATAACTATAGTAATAAAATA
Found at i:56555043 original size:4 final size:4
Alignment explanation
Indices: 56555034--56555058 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56555024 TTGATTTAAG
56555034 TCCA TCCA TCCA TCCA TCCA TCCA T
1 TCCA TCCA TCCA TCCA TCCA TCCA T
56555059 AAACAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCA
Found at i:56562336 original size:4 final size:4
Alignment explanation
Indices: 56562309--56562372 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
56562299 CAATTAAGTA
* * *
56562309 ACAT AAAT ACAT ATAT AGAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
56562357 ACAT ATAT GCAT ACAT
1 ACAT ACAT ACAT ACAT
56562373 TCATTCATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:56563350 original size:20 final size:21
Alignment explanation
Indices: 56563313--56563352 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56563303 GTCCCTTTAT
*
56563313 TTATTCTAAAATTTACAATTA
1 TTATACTAAAATTTACAATTA
56563334 TTATACTAAAA-TTACAATT
1 TTATACTAAAATTTACAATT
56563353 TAATCCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATACTAAAATTTACAATTA
Found at i:56565826 original size:18 final size:18
Alignment explanation
Indices: 56565805--56565873 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
56565795 AAATTTTATT
56565805 TTTTAAAAAATTATAAAA
1 TTTTAAAAAATTATAAAA
**
56565823 TTTTAAAACGTTATTAAAA
1 TTTTAAAAAATTA-TAAAA
*
56565842 TTTATAAAAATATTAAATAAA
1 TTT-TAAAAA-ATTATA-AAA
*
56565863 TTTCAAAAAAT
1 TTTTAAAAAAT
56565874 AAAAATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.27
19 10 0.24
20 11 0.27
21 9 0.22
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
TTTTAAAAAATTATAAAA
Found at i:56578749 original size:42 final size:42
Alignment explanation
Indices: 56578684--56578842 Score: 273
Period size: 42 Copynumber: 3.8 Consensus size: 42
56578674 CCAAAGTGCT
*
56578684 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATGAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
* *
56578726 TTTTGTTTTCTCCAAAACATGTTAAGTTGAATTAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
* *
56578768 TTTTGTTTTCTACGAAACGTGTTAATTTGAATTAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
56578810 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATT
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATT
56578843 CAAAGAAAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
Found at i:56581863 original size:24 final size:24
Alignment explanation
Indices: 56581818--56581864 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
56581808 AGTTTTAAAT
* **
56581818 TTTTTTTTAAATTTATAGATTTAA
1 TTTTTTTAAAATGAATAGATTTAA
*
56581842 TTTTTTTAAAATGAATATATTTA
1 TTTTTTTAAAATGAATAGATTTA
56581865 TTATAGGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTTTTAAAATGAATAGATTTAA
Found at i:56587448 original size:22 final size:23
Alignment explanation
Indices: 56587403--56587448 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56587393 TTGTCTTAAC
* *
56587403 AAAACATTGTTCTTCTTCGTCTA
1 AAAACATTGTTCTGCTTCGGCTA
*
56587426 AAAACATTGTTCTGGTT-GGCTA
1 AAAACATTGTTCTGCTTCGGCTA
56587448 A
1 A
56587449 GATTGTATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (23 bp):
AAAACATTGTTCTGCTTCGGCTA
Found at i:56589272 original size:18 final size:18
Alignment explanation
Indices: 56589244--56589311 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 18
56589234 TTTTCTATTG
56589244 TTTATAGATTTTAATTCAA
1 TTTATA-ATTTTAATTCAA
** *
56589263 TTTATAATTTTTTTTGCAG
1 TTTATAATTTTAATT-CAA
56589282 TTTATAAATTTTAATTCAA
1 TTTAT-AATTTTAATTCAA
56589301 TTTATAATTTT
1 TTTATAATTTT
56589312 TAATATGTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 13 0.32
19 20 0.49
20 8 0.20
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTATAATTTTAATTCAA
Found at i:56589312 original size:19 final size:19
Alignment explanation
Indices: 56589252--56589315 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
56589242 TGTTTATAGA
56589252 TTTTAATTCAATTTATAAT
1 TTTTAATTCAATTTATAAT
* * *
56589271 TTTT-TTTGCAGTTTATAAA
1 TTTTAATT-CAATTTATAAT
56589290 TTTTAATTCAATTTATAAT
1 TTTTAATTCAATTTATAAT
56589309 TTTTAAT
1 TTTTAAT
56589316 ATGTGCTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 2 0.05
19 33 0.89
20 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAATTCAATTTATAAT
Found at i:56589460 original size:71 final size:71
Alignment explanation
Indices: 56589342--56589475 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 71
56589332 AATTTAAATT
* * *
56589342 AATAGTTGATAATAATTAAATTATTTATTAAATATTTTTAATCAATATTTCTTATATGGTATGAT
1 AATAGTTGATAATAACTAAATTATTTATTAAATATATTTAATCAATATTTCGTATATGGTATGAT
56589407 TAATAG
66 TAATAG
* * * * * *
56589413 AATAGTTGATAATGACTAAATTCTTTATTTAATGA-ATTTATTTAATATTTGGTATATGGTATG
1 AATAGTTGATAATAACTAAATTATTTATTAAAT-ATATTTAATCAATATTTCGTATATGGTATG
56589476 GTTTAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 52 0.98
72 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (71 bp):
AATAGTTGATAATAACTAAATTATTTATTAAATATATTTAATCAATATTTCGTATATGGTATGAT
TAATAG
Found at i:56591271 original size:16 final size:16
Alignment explanation
Indices: 56591250--56591282 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56591240 TAGGGAATGC
56591250 CACACACATATATATA
1 CACACACATATATATA
*
56591266 CACACACATGTATATA
1 CACACACATATATATA
56591282 C
1 C
56591283 GTATATGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.24
Consensus pattern (16 bp):
CACACACATATATATA
Found at i:56596425 original size:21 final size:23
Alignment explanation
Indices: 56596397--56596447 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
56596387 CTATTTAAAA
56596397 ATAA-TAATATATATAAC-TTTT
1 ATAATTAATATATATAACTTTTT
*
56596418 AT-ATTAATATCTATAACTTTTT
1 ATAATTAATATATATAACTTTTT
56596440 ATAATTAA
1 ATAATTAA
56596448 ATTTAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
22 6 0.23
23 5 0.19
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTAATATATATAACTTTTT
Found at i:56599761 original size:31 final size:29
Alignment explanation
Indices: 56599690--56599761 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
56599680 TTTGTTTATA
*
56599690 CTTAT-TATGTACATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
56599718 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
56599747 CTTATATATGTATAT
1 CTTATATATGTATAT
56599762 AGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:56607305 original size:103 final size:104
Alignment explanation
Indices: 56606953--56607320 Score: 625
Period size: 104 Copynumber: 3.5 Consensus size: 104
56606943 TGTATATAAA
** *
56606953 GGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
56607018 AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
66 AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
* *
56607057 GGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
56607122 AAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
66 AAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
56607162 GGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCTTT
56607225 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGA-
65 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
** *
56607264 GGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
56607321 ATAACGGTTA
Statistics
Matches: 253, Mismatches: 7, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
102 24 0.09
103 59 0.23
104 113 0.45
105 57 0.23
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (104 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
Found at i:56615307 original size:46 final size:44
Alignment explanation
Indices: 56615240--56615521 Score: 210
Period size: 46 Copynumber: 6.5 Consensus size: 44
56615230 ATTATACAGG
*
56615240 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
56615286 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
56615330 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
56615369 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
56615410 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
56615456 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
56615500 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
56615522 CGAAGCAGAT
Statistics
Matches: 187, Mismatches: 34, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 23 0.12
40 1 0.01
41 28 0.15
42 3 0.02
43 2 0.01
44 57 0.30
45 1 0.01
46 70 0.37
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:56617202 original size:31 final size:29
Alignment explanation
Indices: 56617131--56617202 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
56617121 TTTGTTTATA
*
56617131 CTTAT-TATGTACATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
56617159 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
56617188 CTTATATATGTATAT
1 CTTATATATGTATAT
56617203 AGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:56620797 original size:192 final size:191
Alignment explanation
Indices: 56620265--56621029 Score: 1404
Period size: 191 Copynumber: 4.0 Consensus size: 191
56620255 AAATATGTCA
* * * * *
56620265 TTTTCAAGAAAAATGCTCTTACACTTTTTTTAAACTAAGTGATATTCAAGTTGTTCATGTAAAAA
1 TTTTAAAG-AAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAA
*
56620330 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATGCTACATGTCATATTACTTTTAATGA
65 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGA
*
56620395 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCA
130 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
*
56620457 TTTTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGTTGTTAATGCAAAAAG
1 TTTTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAG
56620522 TGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGAT
66 TGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGAT
*
56620587 GGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCTATGCAATTAATCCG
131 GGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
56620648 TTTTAAAGAAAATGCTCTTACACTTTTTTTAAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAA
1 TTTTAAAGAAAATGCTCTTACACTTTTTTT-AAACTAAGTGAGATTCAAGCTGTTAATGCAAAAA
56620713 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGA
65 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGA
*
56620778 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCTG
130 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
56620840 TTTTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAG
1 TTTTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAG
* *
56620905 TGTACACGTATTTATAATTTGATCACAAGCTTTAATATGCTACATGTCATATTACTTTTAATGAT
66 TGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGAT
56620970 GGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCC
131 GGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCC
56621030 AAAGTAATGA
Statistics
Matches: 559, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
191 364 0.65
192 195 0.35
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (191 bp):
TTTTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAG
TGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGAT
GGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
Found at i:56620977 original size:383 final size:383
Alignment explanation
Indices: 56620265--56621029 Score: 1406
Period size: 383 Copynumber: 2.0 Consensus size: 383
56620255 AAATATGTCA
* * * * *
56620265 TTTTCAAGAAAAATGCTCTTACACTTTTTTTAAACTAAGTGATATTCAAGTTGTTCATGTAAAAA
1 TTTTAAAGAAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAA
*
56620330 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATGCTACATGTCATATTACTTTTAATGA
66 GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGA
56620395 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCATTT
131 TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCATTT
*
56620460 TAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGTTGTTAATGCAAAAAGTGT
196 TAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAGTGT
*
56620525 ACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGATGGA
261 ACACGTATTTATAATTTGATCACAAGCTTTAATATACTACATGTCATATTACTTTTAATGATGGA
*
56620590 ATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCTATGCAATTAATCCG
326 ATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
56620648 TTTTAAAG-AAAATGCTCTTACACTTTTTTTAAAACTAAGTGAGATTCAAGCTGTTAATGCAAAA
1 TTTTAAAGAAAAATGCTCTTACACTTTTTTT-AAACTAAGTGAGATTCAAGCTGTTAATGCAAAA
56620712 AGTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATG
65 AGTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATG
**
56620777 ATGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCTGTT
130 ATGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCATT
56620842 TTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAGTG
195 TTAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAGTG
*
56620907 TACACGTATTTATAATTTGATCACAAGCTTTAATATGCTACATGTCATATTACTTTTAATGATGG
260 TACACGTATTTATAATTTGATCACAAGCTTTAATATACTACATGTCATATTACTTTTAATGATGG
56620972 AATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCC
325 AATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCC
56621030 AAAGTAATGA
Statistics
Matches: 369, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
382 22 0.06
383 347 0.94
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (383 bp):
TTTTAAAGAAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAA
GTGTACACGTATTTATAATTTGATCACAGGCTTTAATATACTACATGTCATATTACTTTTAATGA
TGGAATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCATTT
TAAAGAAAATGCTCTTACACTTTTTTTAAACTAAGTGAGATTCAAGCTGTTAATGCAAAAAGTGT
ACACGTATTTATAATTTGATCACAAGCTTTAATATACTACATGTCATATTACTTTTAATGATGGA
ATCTAAGGACCAATTTAAAATTTAAACAAAGTTGAGGACTTTCAATGCAATTAATCCG
Found at i:56621469 original size:151 final size:153
Alignment explanation
Indices: 56621296--56622232 Score: 1238
Period size: 151 Copynumber: 6.2 Consensus size: 153
56621286 TTTTTTATTG
* * *
56621296 AAAGTAATAAAACTCGA--TAAAAAATACGAACAAAGGGCCAAAATAA-G-TTTTTTTAAATTTA
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTA
*
56621357 TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
66 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
*
56621422 ATTAGAAAATATTATATTTTTTA
131 ATTAGAAAATAGTATATTTTTTA
*
56621445 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAATGG-TTTGTTTAAAATT
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGATTT-TTTTAAATT
* *
56621509 TATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATA
64 TATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
56621574 AAA-TACGAAAATAATATATTTTATTG
129 AAATTA-GAAAATAGTATATTTT-TTA
* * *
56621600 AAAGTAATAAAA-TC--TG-AAAAAATACGAATAAATGGCCGAAATAAGGATTTTTTTTAAATTT
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGA-TTTTTTTAAATTT
*
56621661 ATTT-AAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
65 ATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
*
56621725 ATTTAGAAAATAGTAT-TTTTTT-
130 AATTAGAAAATAGTATATTTTTTA
* * * *
56621747 AAAGTAATAAAATTCAAGG-AAAAAATATGAACAAATGGCCGAAATAATGATTTTTTTAAAATTT
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTT-AAATTT
* *
56621811 ATTTTAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
65 ATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
*
56621876 AATTA-AAAATAGTATATTTTTTT
130 AATTAGAAAATAGTATATTTTTTA
* * * * *
56621899 AAAGTAAT-AAACTCTGGGGAAAACAATACGAACAAAGGGTCGAAATAAAGG-TTTTTTTTAATT
1 AAAGTAATAAAATTC-GAGGAAAAAAATACGAACAAAGGGCCGAAAT-AAGGATTTTTTTAAATT
* *
56621962 TATTTAAAAAA-ACACTAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATA
64 TATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
56622026 AAATTAGAAAATAGTATATTTTTATTG
129 AAATTAGAAAATAGTATA-TTTT-TTA
* * * * *
56622053 AAAGTAATAAAATTTG-GGGAAAAAATATGAACAAAGGACCGAAATAAAGATTTTTTT-AATTTA
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTA
* * *
56622116 TTTAAAAAACACACTAAATTAATACATTTAAAATATAATGTACTAAAATAATTTAAAATTAA-AA
66 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA-TAATAA
* *
56622180 AATTAAAAAATATTATATTTTTTA
130 AATTAGAAAATAGTATATTTTTTA
*
56622204 AAAGTAATAAAATT-TA--AAAAAAATACGAA
1 AAAGTAATAAAATTCGAGGAAAAAAATACGAA
56622233 TAAAAAACCA
Statistics
Matches: 702, Mismatches: 58, Indels: 56
0.86 0.07 0.07
Matches are distributed among these distances:
147 12 0.02
148 4 0.01
149 38 0.05
150 119 0.17
151 213 0.30
152 61 0.09
153 130 0.19
154 107 0.15
155 18 0.03
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (153 bp):
AAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTA
TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
ATTAGAAAATAGTATATTTTTTA
Found at i:56621865 original size:455 final size:450
Alignment explanation
Indices: 56621287--56622232 Score: 1352
Period size: 455 Copynumber: 2.1 Consensus size: 450
56621277 TTTAGTGTGT
* * * *
56621287 TTTTTATTGAAAGTAATAAAACTCGATAAAAAATACGAACAAAGGGCCAAAATAAGTTTTTTTAA
1 TTTTT-TTAAAAGTAATAAAATTCAAGAAAAAATACGAACAAAGGGCCAAAATAAGTTTTTTTAA
56621352 ATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
65 ATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
* *
56621417 ATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAAT-TCGAGGAAAAAAATACGAACAAA
130 ATAAAATTA-AAAATAGTATATTTTTTAAAAGTAATAAACTCT-GAGGAAAAAAATACGAACAAA
* *
56621481 GGGCCGAAATAATGGTTTGTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACA
193 GGGCCGAAATAAAGGTTT-TTTAAAATTTATTTAAAAAA-ACACTAAATTAATACATTTCAAACA
56621546 TAATGTACTAAAATAATATAAAATAATAAAA-TACGAAAATAATATA-TTTTATTGAAAGTAATA
256 TAATGTACTAAAATAATATAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATA
* *
56621609 AAATCT-GAAAAAATACGAATAAATGG-CCGAAATAAGGATTTTTTTTAAATTTATTT-AAAAAC
320 AAATCTGGAAAAAATACGAACAAA-GGACCGAAATAAAGA-TTTTTTT-AATTTATTTAAAAAAC
* * *
56621671 ACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA-TAATAAATTTAGAAAA
382 ACACTAAATGAATACATTTAAAACATAATGTACTAAAATAATGTAAAATTAA-AAAATTAAAAAA
56621735 TAGTA
446 TAGTA
* * *
56621740 TTTTTTT-AAAGTAATAAAATTCAAGGAAAAAATATGAACAAATGGCCGAAATAATGATTTTTTT
1 TTTTTTTAAAAGTAATAAAATTCAA-GAAAAAATACGAACAAAGGGCCAAAATAA-G-TTTTTTT
* * *
56621804 AAAATTTATTTTAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
63 -AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* * *
56621869 ATAATAAAATTAAAAATAGTATATTTTTTTAAAGTAATAAACTCTGGGGAAAACAATACGAACAA
127 ATAATAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAACTCTGAGGAAAAAAATACGAACAA
* ** *
56621934 AGGGTCGAAATAAAGGTTTTTTTTAATTTATTTAAAAAAACACTAAATTAATACATTTCAAACTT
192 AGGGCCGAAATAAAGGTTTTTTAAAATTTATTTAAAAAAACACTAAATTAATACATTTCAAACAT
* * *
56621999 GATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTATTGAAAGTAATAAA
257 AATGTACTAAAATAATATAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAA
* *
56622064 ATTTGGGGAAAAAATATGAACAAAGGACCGAAATAAAGATTTTTTTAATTTATTTAAAAAACACA
322 ATCT--GGAAAAAATACGAACAAAGGACCGAAATAAAGATTTTTTTAATTTATTTAAAAAACACA
* * * *
56622129 CTAAATTAATACATTTAAAATATAATGTACTAAAATAATTTAAAATTAAAAAATTAAAAAATATT
385 CTAAATGAATACATTTAAAACATAATGTACTAAAATAATGTAAAATTAAAAAATTAAAAAATAGT
56622194 A
450 A
*
56622195 TATTTTTTAAAAGTAATAAAATTTAA-AAAAAATACGAA
1 T-TTTTTTAAAAGTAATAAAATTCAAGAAAAAATACGAA
56622233 TAAAAAACCA
Statistics
Matches: 442, Mismatches: 36, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
451 15 0.03
452 90 0.20
453 48 0.11
454 79 0.18
455 159 0.36
456 35 0.08
457 16 0.04
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (450 bp):
TTTTTTTAAAAGTAATAAAATTCAAGAAAAAATACGAACAAAGGGCCAAAATAAGTTTTTTTAAA
TTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAACTCTGAGGAAAAAAATACGAACAAAGGG
CCGAAATAAAGGTTTTTTAAAATTTATTTAAAAAAACACTAAATTAATACATTTCAAACATAATG
TACTAAAATAATATAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCT
GGAAAAAATACGAACAAAGGACCGAAATAAAGATTTTTTTAATTTATTTAAAAAACACACTAAAT
GAATACATTTAAAACATAATGTACTAAAATAATGTAAAATTAAAAAATTAAAAAATAGTA
Found at i:56622012 original size:302 final size:297
Alignment explanation
Indices: 56621296--56622232 Score: 1312
Period size: 304 Copynumber: 3.1 Consensus size: 297
56621286 TTTTTTATTG
* *
56621296 AAAGTAATAAAA-CTCGATAAAAAATACGAACAAAGGGCCAAAATAA-GTTTTTTTAAATTTATT
1 AAAGTAATAAAATCT-G--AAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAATTTATT
56621359 TAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
63 TAAAAAA-ACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
* *
56621424 TAGAAAATATTATATTTTTTAAAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAGGGCCGAA
127 TAGAAAATAGTAT-TTTTTTAAAAGTAATAAAATTCGAGG-AAAAAATATGAACAAA-GGCCGAA
* *
56621489 ATAATGGTTTGTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTAC
189 ATAATGATTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTAC
*
56621554 TAAAATAATATAAAATAATAAAA-TACGAAAATAATATATTTTATTG
254 TAAAATAATATAAAATAATAAAATTA--AAAATAATATATTTT-TTA
* *
56621600 AAAGTAATAAAATCTGAAAAAATACGAATAAATGGCCGAAATAAGGATTTTTTTTAAATTTATTT
1 AAAGTAATAAAATCTGAAAAAATACGAACAAAGGGCCGAAATAAGG-TTTTTTTT-AATTTATTT
* *
56621665 AAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAATTTA
64 AAAAAAACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA
*
56621730 GAAAATAGTATTTTTTT-AAAGTAATAAAATTCAAGGAAAAAATATGAACAAATGGCCGAAATAA
129 GAAAATAGTATTTTTTTAAAAGTAATAAAATTCGAGGAAAAAATATGAACAAA-GGCCGAAATAA
*
56621794 TGATTTTTTTAAAATTTATTTTAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAA
193 TGATTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAA
* * *
56621859 ATAATGTAAAATAATAAAATTAAAAATAGTATATTTTTTT
258 ATAATATAAAATAATAAAATTAAAAATAATATATTTTTTA
* *
56621899 AAAGTAATAAACTCTGGGGAAAACAATACGAACAAAGGGTCGAAATAAAGGTTTTTTTTAATTTA
1 AAAGTAATAAAATCT---GAAAA-AATACGAACAAAGGGCCGAAAT-AAGGTTTTTTTTAATTTA
* * *
56621964 TTTAAAAAAACACTAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATAAAA
61 TTTAAAAAAACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
* * *
56622029 TTAGAAAATAGTATATTTTTATTGAAAGTAATAAAATTTGGGGAAAAAATATGAACAAAGGACCG
126 TTAGAAAATAG--TATTTTT-TTAAAAGTAATAAAATTCGAGGAAAAAATATGAACAAAGG-CCG
* * * *
56622094 AAATAAAGATTTTTTT--AATTTATTTAAAAAACACACTAAATTAATACATTTAAAATATAATGT
187 AAATAATGATTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGT
* *
56622157 ACTAAAATAATTTAAAATTAA-AAAATTAAAAAATATTATATTTTTTA
252 ACTAAAATAATATAAAA-TAATAAAATT-AAAAATAATATATTTTTTA
* *
56622204 AAAGTAATAAAATTTAAAAAAAATACGAA
1 AAAGTAATAAAATCT-GAAAAAATACGAA
56622233 TAAAAAACCA
Statistics
Matches: 576, Mismatches: 40, Indels: 36
0.88 0.06 0.06
Matches are distributed among these distances:
299 16 0.03
300 14 0.02
301 106 0.18
302 135 0.23
303 38 0.07
304 164 0.28
305 53 0.09
306 50 0.09
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (297 bp):
AAAGTAATAAAATCTGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAATTTATTTAA
AAAAACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGA
AAATAGTATTTTTTTAAAAGTAATAAAATTCGAGGAAAAAATATGAACAAAGGCCGAAATAATGA
TTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATA
ATATAAAATAATAAAATTAAAAATAATATATTTTTTA
Found at i:56623188 original size:18 final size:17
Alignment explanation
Indices: 56623152--56623191 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
56623142 TAATAAAAAT
56623152 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
56623169 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
56623184 ATAATTTT
1 ATAATTTT
56623192 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:56623620 original size:7 final size:8
Alignment explanation
Indices: 56623591--56623618 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
56623581 CTAATATAAT
56623591 TTTTTAAG
1 TTTTTAAG
56623599 TTTTTAAG
1 TTTTTAAG
56623607 TTTTTAAG
1 TTTTTAAG
56623615 TTTT
1 TTTT
56623619 AAATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (8 bp):
TTTTTAAG
Found at i:56631233 original size:17 final size:17
Alignment explanation
Indices: 56631211--56631248 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
56631201 AATCGGGTAT
56631211 TTAACCGAACTTAATAA
1 TTAACCGAACTTAATAA
56631228 TTAACCGAACTTAATAA
1 TTAACCGAACTTAATAA
56631245 TTAA
1 TTAA
56631249 TAATACAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (17 bp):
TTAACCGAACTTAATAA
Found at i:56632163 original size:94 final size:94
Alignment explanation
Indices: 56631913--56632194 Score: 359
Period size: 94 Copynumber: 3.0 Consensus size: 94
56631903 AATCATGTCA
** * *
56631913 AATAAAAATATAAAAAGATTAAATCTTAGTTTTGAGTTTAGTAGAGGGACCAAAACTGTAATTTT
1 AATAAAAATAT--AAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTT
56631978 ACCATTATAATTGAAATGGCAAACAAAAGCTG
64 ACCATTATAATTGAAATGGCAAA-AAAAGCTG
* * * *
56632010 AAGTAAAAATTTAAAGATTAAATCTTAAATTTGAGTTTAACAAAGGGACCAAAACTGAAATTTTT
1 AA-TAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTA
*
56632075 CCATTATAATTGAAATGGCAAAAAGAG-TGG
65 CCATTATAATTGAAATGGCAAAAAAAGCT-G
* * * * *
56632105 CATAAAAATATAACGATTAAATCTTAAAATTGAGTTTAATAGAGGGATCAAAAATGAAATTTTAC
1 AATAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTAC
* * *
56632170 CAGTATAATTAAAAGGGCAAAAAAA
66 CATTATAATTGAAATGGCAAAAAAA
56632195 AAAAAGTGTG
Statistics
Matches: 161, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
94 77 0.48
95 6 0.04
96 68 0.42
97 2 0.01
98 8 0.05
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.29
Consensus pattern (94 bp):
AATAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTAC
CATTATAATTGAAATGGCAAAAAAAGCTG
Found at i:56634796 original size:23 final size:23
Alignment explanation
Indices: 56634769--56634813 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
56634759 CGAAAATATT
56634769 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
56634792 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
56634814 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:56635019 original size:16 final size:16
Alignment explanation
Indices: 56634998--56635039 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
56634988 AATAATTTGA
*
56634998 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
56635014 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
56635030 TAGTTTTAAT
1 TAATTTTAAT
56635040 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:56635023 original size:22 final size:23
Alignment explanation
Indices: 56635013--56635068 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
56635003 TTACTAACAA
* * *
56635013 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
56635035 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
56635058 TTAATTTTAAT
1 TTAATTTTAAT
56635069 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:56636982 original size:29 final size:30
Alignment explanation
Indices: 56636929--56636986 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
56636919 AATTGAATCC
*
56636929 AATCAAAATTACATTTATAAAATTACATAA
1 AATCAAAATTACATATATAAAATTACATAA
*
56636959 AATCAAAATT-TATATATAAAATTACATA
1 AATCAAAATTACATATATAAAATTACATA
56636987 TTAGACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (30 bp):
AATCAAAATTACATATATAAAATTACATAA
Found at i:56637000 original size:31 final size:29
Alignment explanation
Indices: 56636944--56637008 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
56636934 AAATTACATT
*
56636944 TATAAAATTACATAAAATCAAAATTTATA
1 TATAAAATTACATAAAACCAAAATTTATA
* *
56636973 TATAAAATTACATATTAGACCAAAATTTATG
1 TATAAAATTACATA--AAACCAAAATTTATA
56637004 TATAA
1 TATAA
56637009 TTTTGAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
TATAAAATTACATAAAACCAAAATTTATA
Found at i:56640669 original size:11 final size:11
Alignment explanation
Indices: 56640636--56640671 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
56640626 AATCAATTTC
*
56640636 TATCAATTTAA
1 TATCAATTCAA
*
56640647 AATCAATTCAA
1 TATCAATTCAA
56640658 TATCAATTCAA
1 TATCAATTCAA
56640669 TAT
1 TAT
56640672 TAAAATGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (11 bp):
TATCAATTCAA
Found at i:56642727 original size:6 final size:6
Alignment explanation
Indices: 56642667--56642753 Score: 54
Period size: 6 Copynumber: 14.3 Consensus size: 6
56642657 TTATCTTGAT
* * * * *
56642667 TATATG TATATACG TATGTG TATGTG CATA-G -ATATG TACATG TACATG
1 TATATG TATAT--G TATATG TATATG TATATG TATATG TATATG TATATG
* *
56642715 TAATATG TGTATG TGA-GTG TATATG TATATG TATATG TA
1 T-ATATG TATATG T-ATATG TATATG TATATG TATATG TA
56642754 CGTGGAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.05
5 3 0.05
6 49 0.75
7 5 0.08
8 5 0.08
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (6 bp):
TATATG
Found at i:56645848 original size:6 final size:6
Alignment explanation
Indices: 56645832--56645867 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
56645822 ATTTGTCTCT
56645832 CTTTACC CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
1 CTTT-CC CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
56645868 GTTGTTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTTCC
Found at i:56646250 original size:21 final size:21
Alignment explanation
Indices: 56646199--56646258 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 21
56646189 AATATTGAAT
**
56646199 AATTATTAAATGTTATAAAAA
1 AATTATTAAAAATTATAAAAA
* *
56646220 TATT-TT-AAAATTGTAAAAA
1 AATTATTAAAAATTATAAAAA
*
56646239 AATTATTAAAAATAATAAAA
1 AATTATTAAAAATTATAAAA
56646259 TATTAATTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
AATTATTAAAAATTATAAAAA
Found at i:56646505 original size:22 final size:21
Alignment explanation
Indices: 56646467--56646539 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 21
56646457 ATGCCATCGG
**
56646467 TTCAC-AATTTTCAAATATATT
1 TTCACAAATTTTTTAATA-ATT
* *
56646488 TTTACAATTTTTTTAATAATT
1 TTCACAAATTTTTTAATAATT
56646509 TTCACAAA--TTTTAATAATT
1 TTCACAAATTTTTTAATAATT
* *
56646528 TTAATAAATTTT
1 TTCACAAATTTT
56646540 AAATAAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCACAAATTTTTTAATAATT
Found at i:56646510 original size:10 final size:9
Alignment explanation
Indices: 56646498--56646541 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
56646488 TTTACAATTT
56646498 TTTTAATAA
1 TTTTAATAA
56646507 TTTTCACA-AA
1 TTTT-A-ATAA
56646517 TTTTAATAA
1 TTTTAATAA
56646526 TTTTAATAAA
1 TTTTAAT-AA
56646536 TTTTAA
1 TTTTAA
56646542 ATAAAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 14 0.45
10 15 0.48
11 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTTAATAA
Found at i:56646522 original size:19 final size:19
Alignment explanation
Indices: 56646498--56646541 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
56646488 TTTACAATTT
*
56646498 TTTTAATAATTTTCACAAA
1 TTTTAATAATTTTAACAAA
*
56646517 TTTTAATAATTTTAATAAA
1 TTTTAATAATTTTAACAAA
56646536 TTTTAA
1 TTTTAA
56646542 ATAAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTAACAAA
Found at i:56651152 original size:14 final size:14
Alignment explanation
Indices: 56651133--56651160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56651123 TTTGCAATCC
56651133 GGGGCTCGGTTTAG
1 GGGGCTCGGTTTAG
56651147 GGGGCTCGGTTTAG
1 GGGGCTCGGTTTAG
56651161 TGTGCTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.50, T:0.29
Consensus pattern (14 bp):
GGGGCTCGGTTTAG
Found at i:56656654 original size:20 final size:20
Alignment explanation
Indices: 56656629--56656710 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 20
56656619 ATACTATTTA
56656629 AAAAATAGTTTAAAAATTAT
1 AAAAATAGTTTAAAAATTAT
* *
56656649 AAAAATATTTTTAAAA--AT
1 AAAAATAGTTTAAAAATTAT
*
56656667 AAAAAT-G-TTCAAAATTA-
1 AAAAATAGTTTAAAAATTAT
* *
56656684 AAAAA-AGTATATAAAGTTCAT
1 AAAAATAGTTTA-AAAATT-AT
56656705 AAAAAT
1 AAAAAT
56656711 TCAAAGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
16 6 0.13
17 6 0.13
18 10 0.21
19 5 0.11
20 15 0.32
21 5 0.11
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAAATAGTTTAAAAATTAT
Found at i:56661492 original size:11 final size:13
Alignment explanation
Indices: 56661462--56661493 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56661452 TTAATGTACA
56661462 ACACAATGGCAAT
1 ACACAATGGCAAT
56661475 ACACAATGGC-AT
1 ACACAATGGCAAT
56661487 -CACAATG
1 ACACAATG
56661494 TACGAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 2 0.11
13 10 0.53
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.16
Consensus pattern (13 bp):
ACACAATGGCAAT
Found at i:56663369 original size:69 final size:69
Alignment explanation
Indices: 56663254--56663445 Score: 197
Period size: 69 Copynumber: 2.8 Consensus size: 69
56663244 TCATAAAATA
** ** * * *
56663254 AGATATATCTCCAAAAAGTTTATTGGAACCGAGATCTAAATACTCGAGCGACT-TTAAATTTTTA
1 AGATATATCTCCAAAAAAATTATTGGAAGAGATATCTAAATACTCGAG-GAATGTTAAATTCTTA
* *
56663318 AGCAT
65 AACAC
* * * * *
56663323 AGATATATCTCCAAAAAAACTGTTGGAAGAGATATCTAAATTCTCGAGTAATGTTAGATTCTTAA
1 AGATATATCTCCAAAAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGTTAAATTCTTAA
*
56663388 ATAC
66 ACAC
* * * *
56663392 ATATATATTTCCAAAAAAATTATTGGAAGAGATATCTAAATACTTGAGGGATGT
1 AGATATATCTCCAAAAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGT
56663446 GAGTTCAGAG
Statistics
Matches: 99, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
68 2 0.02
69 97 0.98
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (69 bp):
AGATATATCTCCAAAAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGTTAAATTCTTAA
ACAC
Found at i:56667957 original size:22 final size:22
Alignment explanation
Indices: 56667932--56667974 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56667922 TATTCAAATA
56667932 ATAATA-TCAAAATAGTAGCAAC
1 ATAATAGT-AAAATAGTAGCAAC
*
56667954 ATAATAGTAAAATGGTAGCAA
1 ATAATAGTAAAATAGTAGCAA
56667975 AATAGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (22 bp):
ATAATAGTAAAATAGTAGCAAC
Found at i:56667987 original size:22 final size:22
Alignment explanation
Indices: 56667940--56667989 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
56667930 TAATAATATC
* *
56667940 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
*
56667962 AAAATGGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
56667984 AAAATA
1 AAAATA
56667990 ACAATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:56668446 original size:38 final size:36
Alignment explanation
Indices: 56668371--56668446 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
56668361 TAGTACTTTC
* *
56668371 CTGCAAATCTTTCTTTGTGGAAATACGGTCAATTTT
1 CTGCAAATCTTTCTTTGTGGAAATACAGTCAAATTT
*
56668407 CTGCAAGTCTTTCTTTGTGGAAAAATACAGTCAAATTT
1 CTGCAAATCTTTCTTTGTGG--AAATACAGTCAAATTT
56668445 CT
1 CT
56668447 TAGTACTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 19 0.54
38 16 0.46
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (36 bp):
CTGCAAATCTTTCTTTGTGGAAATACAGTCAAATTT
Found at i:56668716 original size:16 final size:16
Alignment explanation
Indices: 56668676--56668709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56668666 TTTTTTTCTT
*
56668676 AAATACAAATACAAATA
1 AAATA-AAATAAAAATA
56668693 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
56668709 A
1 A
56668710 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:56671194 original size:15 final size:16
Alignment explanation
Indices: 56671169--56671201 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56671159 TCAAATCTTG
*
56671169 TTGATTCTTGAAGGCT
1 TTGATTCTTGAAGCCT
56671185 TTGA-TCTTGAAGCCT
1 TTGATTCTTGAAGCCT
56671200 TT
1 TT
56671202 TTTCTTGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (16 bp):
TTGATTCTTGAAGCCT
Found at i:56673263 original size:41 final size:41
Alignment explanation
Indices: 56673217--56673331 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
56673207 ACCGGCTTTT
* *
56673217 AGCCTGCTAGACTTATAGTCCG-A-AATGTATCACCGACATTA
1 AGCCTGCTAGACGTATAGTCCGAATAAT-T-TCACCGACATAA
* *
56673258 AGCCTGCTAGACGTATAGTCTGAATAATTTCACCGGCATAA
1 AGCCTGCTAGACGTATAGTCCGAATAATTTCACCGACATAA
* * * *
56673299 AGCCTGCTAGACATAAAGTCTGAATTATTTCAC
1 AGCCTGCTAGACGTATAGTCCGAATAATTTCAC
56673332 TGGCAATAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 60 0.92
42 2 0.03
43 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACGTATAGTCCGAATAATTTCACCGACATAA
Found at i:56674976 original size:25 final size:25
Alignment explanation
Indices: 56674931--56674979 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
56674921 TATTTGTTTA
*
56674931 ATTATAATATTATAATATAATATAT
1 ATTATAACATTATAATATAATATAT
56674956 ATTATAACATTTATAAT-TAATATA
1 ATTATAACA-TTATAATATAATATA
56674980 AAAACTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATAACATTATAATATAATATAT
Found at i:56679451 original size:20 final size:20
Alignment explanation
Indices: 56679426--56679475 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
56679416 TGGCTTAAAA
56679426 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
56679446 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
56679463 GTGGTAGTGGATT
1 TTGGTAGTGGATT
56679476 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:56684089 original size:20 final size:20
Alignment explanation
Indices: 56684064--56684113 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
56684054 TGGCTTAAAA
56684064 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
56684084 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
56684101 GTGGTAGTGGATT
1 TTGGTAGTGGATT
56684114 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:56685717 original size:24 final size:24
Alignment explanation
Indices: 56685690--56685741 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56685680 TTAGTAAGTC
*
56685690 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
56685714 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
56685738 AAAT
1 AAAT
56685742 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:56687686 original size:24 final size:24
Alignment explanation
Indices: 56687659--56687710 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56687649 TTAGTAAGTC
*
56687659 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
56687683 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
56687707 AAAT
1 AAAT
56687711 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:56689784 original size:16 final size:16
Alignment explanation
Indices: 56689765--56689830 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
56689755 ATTATGTAAG
*
56689765 TTATATAAGTTGTGTA
1 TTATATAAGTTATGTA
*
56689781 TTATGTAAGTTATGTAA
1 TTATATAAGTTATGT-A
***
56689798 GTTGCGTAAGTTATGTA
1 -TTATATAAGTTATGTA
* *
56689815 TAATGTAAGTTATGTA
1 TTATATAAGTTATGTA
56689831 AGTTATGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
16 26 0.63
17 2 0.05
18 13 0.32
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (16 bp):
TTATATAAGTTATGTA
Found at i:56689794 original size:34 final size:34
Alignment explanation
Indices: 56689756--56689966 Score: 228
Period size: 34 Copynumber: 6.5 Consensus size: 34
56689746 AAGTTATATA
* *
56689756 TTATGTAAGTTATATAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
** *
56689790 TTATGTAAGTTGCGTAAGTTATGTATAATGTAAG
1 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
56689824 TTATGTAAG---T-T-A----TGTATAATGTAAG
1 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
56689849 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
1 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
* *
56689883 TTATGTAAGTTATGTAAGTTGCGTAAGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTGTGT-A-TAATGTAAG
* *
56689917 TTATGTAAGTTATGTAAGTTCTGTATTATGTAAG
1 TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
* *
56689951 TTATGGAAGTTGTGTA
1 TTATGTAAGTTATGTA
56689967 TAATGTAATT
Statistics
Matches: 152, Mismatches: 12, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
25 22 0.14
28 1 0.01
29 2 0.01
30 2 0.01
32 6 0.04
33 2 0.01
34 110 0.72
35 2 0.01
36 5 0.03
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTGTGTATAATGTAAG
Found at i:56689801 original size:25 final size:27
Alignment explanation
Indices: 56689744--56689966 Score: 222
Period size: 25 Copynumber: 8.8 Consensus size: 27
56689734 TATTTCACGC
*
56689744 GTAAGTTATAT-A-TTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
* *
56689769 ATAAGTTGTGT-A-TTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
** *
56689794 GTAAGTTGCGTAAGTTATGT-A-TAAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
56689819 GTAAGTTATGTAAGTTATGT-A-TAAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
56689844 GTAAGTTATGTAAGTTATGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
56689871 GT-A-TAATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
**
56689896 GTAAGTTGCGTAAGTTATGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
56689921 GTAAGTTATGTAAGTTCTGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
* *
56689946 GTAAGTTATGGAAGTTGTGTA
1 GTAAGTTATGTAAGTTATGTA
56689967 TAATGTAATT
Statistics
Matches: 171, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
25 143 0.84
26 6 0.04
27 22 0.13
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.44
Consensus pattern (27 bp):
GTAAGTTATGTAAGTTATGTAAGTTAT
Found at i:56689822 original size:59 final size:59
Alignment explanation
Indices: 56689743--56689932 Score: 249
Period size: 59 Copynumber: 3.2 Consensus size: 59
56689733 TTATTTCACG
* * * * *
56689743 CGTAAGTTATATATTATGTAAGTTATATAAGTTGTGTATTATGTAAGTTATGTAAGTTG
1 CGTAAGTTATGTATAATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTA
*
56689802 CGTAAGTTATGTATAATGTAAGTTATGTAAGTTATGTATAATGTAAGTTATGTAAGTTA
1 CGTAAGTTATGTATAATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTA
* * **
56689861 TGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTGCGTAAGTTATGT-A-TTA
1 CGTAAGTTATGTATAATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTA
*
56689920 TGTAAGTTATGTA
1 CGTAAGTTATGTA
56689933 AGTTCTGTAT
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 103 0.88
60 2 0.02
61 12 0.10
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.44
Consensus pattern (59 bp):
CGTAAGTTATGTATAATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTA
Found at i:56690734 original size:11 final size:12
Alignment explanation
Indices: 56690718--56690762 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
56690708 AAATAATAGT
56690718 TATTAAAA-AAA
1 TATTAAAATAAA
56690729 TATTAAAATAAA
1 TATTAAAATAAA
56690741 -A-TAAAATAAA
1 TATTAAAATAAA
56690751 TATTAAAATAAA
1 TATTAAAATAAA
56690763 AGAAGTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.29
11 10 0.32
12 12 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TATTAAAATAAA
Found at i:56690752 original size:22 final size:21
Alignment explanation
Indices: 56690721--56690763 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
56690711 TAATAGTTAT
56690721 TAAAAAAATATTAAAATAAAA
1 TAAAAAAATATTAAAATAAAA
56690742 TAAAATAAATATTAAAATAAAA
1 TAAAA-AAATATTAAAATAAAA
56690764 GAAGTGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAAAATATTAAAATAAAA
Found at i:56690974 original size:18 final size:17
Alignment explanation
Indices: 56690953--56690995 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
56690943 CTACACAAGA
*
56690953 AAAAATGGCTAGAGGAAC
1 AAAAAT-GCTAGAGAAAC
56690971 AAAACATGCTAGAGAAAC
1 AAAA-ATGCTAGAGAAAC
56690989 AGAAAAT
1 A-AAAAT
56690996 AGAAAGCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.56, C:0.12, G:0.21, T:0.12
Consensus pattern (17 bp):
AAAAATGCTAGAGAAAC
Found at i:56691050 original size:19 final size:19
Alignment explanation
Indices: 56691026--56691079 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
56691016 CGGAAAATAG
56691026 AGAAACAAGAAACAGCTAC
1 AGAAACAAGAAACAGCTAC
*
56691045 AGAAAC-A-AAACATGCTAG
1 AGAAACAAGAAACA-GCTAC
56691063 AGAAACAAGAAACAGCT
1 AGAAACAAGAAACAGCT
56691080 TAGAGGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 10 0.32
20 5 0.16
ACGTcount: A:0.57, C:0.19, G:0.17, T:0.07
Consensus pattern (19 bp):
AGAAACAAGAAACAGCTAC
Found at i:56691066 original size:18 final size:17
Alignment explanation
Indices: 56691023--56691084 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 17
56691013 AAACGGAAAA
56691023 TAGAGAAACAAGAAACAGC
1 TAGAGAAAC-A-AAACAGC
*
56691042 TACAGAAACAAAACATGC
1 TAGAGAAACAAAACA-GC
56691060 TAGAGAAACAAGAAACAGC
1 TAGAGAAAC-A-AAACAGC
56691079 TTAGAG
1 -TAGAG
56691085 GTTAACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 5 0.14
18 11 0.30
19 11 0.30
20 10 0.27
ACGTcount: A:0.55, C:0.16, G:0.19, T:0.10
Consensus pattern (17 bp):
TAGAGAAACAAAACAGC
Found at i:56692885 original size:18 final size:18
Alignment explanation
Indices: 56692862--56692936 Score: 132
Period size: 18 Copynumber: 4.2 Consensus size: 18
56692852 TACGACCGTT
56692862 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
56692880 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
56692898 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
56692916 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
56692934 TAC
1 TAC
56692937 AGTAGTTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:56697363 original size:28 final size:29
Alignment explanation
Indices: 56697332--56697409 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
56697322 TATTATTATT
*
56697332 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
56697360 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
56697388 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
56697410 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:56697409 original size:31 final size:28
Alignment explanation
Indices: 56697343--56697410 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
56697333 ATATAAATAT
**
56697343 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
56697371 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
56697402 ATAAATTAA
1 ATAAATTAA
56697411 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:56697577 original size:16 final size:16
Alignment explanation
Indices: 56697558--56697592 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56697548 AAAGAAAAAG
56697558 AAAGAAACAAAACAGA
1 AAAGAAACAAAACAGA
* *
56697574 AAAGAAACAGAATAGA
1 AAAGAAACAAAACAGA
56697590 AAA
1 AAA
56697593 AACAAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAGAAACAAAACAGA
Found at i:56697632 original size:11 final size:11
Alignment explanation
Indices: 56697616--56697641 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56697606 AGAAAGAGAC
56697616 GAAACAGGGGA
1 GAAACAGGGGA
56697627 GAAACAGGGGA
1 GAAACAGGGGA
56697638 GAAA
1 GAAA
56697642 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:56698757 original size:37 final size:39
Alignment explanation
Indices: 56698698--56698793 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
56698688 CGGATAGATT
* * * *
56698698 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
56698735 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
56698774 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
56698794 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:56705105 original size:9 final size:9
Alignment explanation
Indices: 56705075--56705314 Score: 213
Period size: 9 Copynumber: 29.3 Consensus size: 9
56705065 TATTTTATGC
56705075 GTAAGTTAT
1 GTAAGTTAT
*
56705084 GT-A-TTAG
1 GTAAGTTAT
56705091 GTAAGTTAT
1 GTAAGTTAT
*
56705100 GTAAGTTTT
1 GTAAGTTAT
56705109 GT-A-TTAT
1 GTAAGTTAT
*
56705116 GTAAGTTCT
1 GTAAGTTAT
*
56705125 GTAAGTTGT
1 GTAAGTTAT
56705134 GT-A-TTAT
1 GTAAGTTAT
56705141 GTAAGTTAT
1 GTAAGTTAT
*
56705150 GTAAGTTGT
1 GTAAGTTAT
*
56705159 GTAAGTTGT
1 GTAAGTTAT
56705168 GT-A-TTAT
1 GTAAGTTAT
56705175 GTAAGTTAT
1 GTAAGTTAT
*
56705184 GTAAGTTCT
1 GTAAGTTAT
56705193 GT-A-TTAT
1 GTAAGTTAT
*
56705200 ATAAGTTAT
1 GTAAGTTAT
56705209 GT-A---AT
1 GTAAGTTAT
*
56705214 -TAAGTTGT
1 GTAAGTTAT
56705222 GT-A-TTAT
1 GTAAGTTAT
*
56705229 GTAAGTTGT
1 GTAAGTTAT
56705238 GTAAGTTAT
1 GTAAGTTAT
56705247 GT-A-TTAT
1 GTAAGTTAT
56705254 GT-AGTTAT
1 GTAAGTTAT
*
56705262 GTAAGTTGT
1 GTAAGTTAT
56705271 GT-A-TTAT
1 GTAAGTTAT
56705278 GTAAGTTAT
1 GTAAGTTAT
56705287 GTAAGTTAT
1 GTAAGTTAT
56705296 GTAAG-T-T
1 GTAAGTTAT
56705303 GTAAGTTAT
1 GTAAGTTAT
56705312 GTA
1 GTA
56705315 TAATGTAATT
Statistics
Matches: 189, Mismatches: 19, Indels: 46
0.74 0.07 0.18
Matches are distributed among these distances:
4 1 0.01
5 3 0.02
7 47 0.25
8 25 0.13
9 113 0.60
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:56705105 original size:25 final size:26
Alignment explanation
Indices: 56705075--56705314 Score: 203
Period size: 25 Copynumber: 9.8 Consensus size: 26
56705065 TATTTTATGC
*
56705075 GTAAGTTATGTA-TTAGGTAAGTTAT
1 GTAAGTTATGTAGTTATGTAAGTTAT
* *
56705100 GTAAGTTTTGTA-TTATGTAAGTTCT
1 GTAAGTTATGTAGTTATGTAAGTTAT
*
56705125 GTAAGTTGTGTA-TTATGTAAGTTAT
1 GTAAGTTATGTAGTTATGTAAGTTAT
* *
56705150 GTAAGTTGTGTAAGTTGTGT-A-TTAT
1 GTAAGTTATGT-AGTTATGTAAGTTAT
*
56705175 GTAAGTTATGTAAGTTCTGT-A-TTAT
1 GTAAGTTATGT-AGTTATGTAAGTTAT
* *
56705200 ATAAGTTATGTA---AT-TAAGTTGT
1 GTAAGTTATGTAGTTATGTAAGTTAT
*
56705222 GT-A-TTATGTAAGTTGTGTAAGTTAT
1 GTAAGTTATGT-AGTTATGTAAGTTAT
*
56705247 GT-A-TTATGTAGTTATGTAAGTTGT
1 GTAAGTTATGTAGTTATGTAAGTTAT
56705271 GT-A-TTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGT-AGTTATGTAAGTTAT
56705296 GTAAG-T-TGTAAGTTATGTA
1 GTAAGTTATGT-AGTTATGTA
56705315 TAATGTAATT
Statistics
Matches: 186, Mismatches: 17, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.04
21 4 0.02
22 4 0.02
24 24 0.13
25 138 0.74
26 4 0.02
27 5 0.03
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (26 bp):
GTAAGTTATGTAGTTATGTAAGTTAT
Found at i:56705131 original size:34 final size:36
Alignment explanation
Indices: 56705075--56705314 Score: 213
Period size: 34 Copynumber: 7.3 Consensus size: 36
56705065 TATTTTATGC
* *
56705075 GTAAGTTATGT-A-TTAGGTAAGTTATGTAAGTTTT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
* *
56705109 GT-A-TTATGTAAGTTCTGTAAGTTGTGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
* *
56705141 GTAAGTTATGTAAGTTGTGTAAGTTGTGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
* *
56705175 GTAAGTTATGTAAGTTCTGT-A-TTATATAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
* *
56705209 GT-A---AT-TAAGTTGTGT-A-TTATGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
*
56705238 GTAAGTTATGT-A-TTATGT-AGTTATGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
56705271 GT-A-TTATGTAAGTTATGTAAGTTATGTAAG-T-T
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
56705303 GTAAGTTATGTA
1 GTAAGTTATGTA
56705315 TAATGTAATT
Statistics
Matches: 177, Mismatches: 12, Indels: 34
0.79 0.05 0.15
Matches are distributed among these distances:
29 23 0.13
30 3 0.02
31 6 0.03
32 26 0.15
33 33 0.19
34 86 0.49
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (36 bp):
GTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
Found at i:56705322 original size:16 final size:16
Alignment explanation
Indices: 56705075--56705302 Score: 160
Period size: 16 Copynumber: 14.4 Consensus size: 16
56705065 TATTTTATGC
*
56705075 GTAAGTTATGTATTAG
1 GTAAGTTATGTATTAT
*
56705091 GTAAGTTATGTAAGTTTT
1 GTAAGTTATGT-A-TTAT
*
56705109 GT-A-TTATGTAAGTTCT
1 GTAAGTTATGT-A-TTAT
*
56705125 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
*
56705141 GTAAGTTATGTAAGTTGT
1 GTAAGTTATGT-A-TTAT
*
56705159 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
56705175 GT-A---A-G--TTAT
1 GTAAGTTATGTATTAT
*
56705184 GTAAGTTCTGTATTAT
1 GTAAGTTATGTATTAT
*
56705200 ATAAGTTATGTA--AT
1 GTAAGTTATGTATTAT
*
56705214 -TAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
*
56705229 GTAAGTTGTGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
56705247 GT-A-TTATGTAGTTAT
1 GTAAGTTATGTA-TTAT
*
56705262 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
56705278 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
56705296 GTAAGTT
1 GTAAGTT
56705303 GTAAGTTATG
Statistics
Matches: 173, Mismatches: 17, Indels: 42
0.75 0.07 0.18
Matches are distributed among these distances:
9 6 0.03
10 1 0.01
11 1 0.01
13 10 0.06
14 3 0.02
15 11 0.06
16 87 0.50
17 15 0.09
18 39 0.23
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.48
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:56706262 original size:21 final size:21
Alignment explanation
Indices: 56706223--56706264 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56706213 TAGAGAAGCA
*
56706223 GAAAATAGAAAACGGAAAACG
1 GAAAATAGAAAACGAAAAACG
*
56706244 GAAAATAGAGAAACAAAAAAC
1 GAAAATAGA-AAACGAAAAAC
56706265 TGCTACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.67, C:0.10, G:0.19, T:0.05
Consensus pattern (21 bp):
GAAAATAGAAAACGAAAAACG
Found at i:56706276 original size:19 final size:20
Alignment explanation
Indices: 56706252--56706295 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
56706242 CGGAAAATAG
56706252 AGAAAC-AAAAAACTGCTAC
1 AGAAACAAAAAAACTGCTAC
56706271 AGAAACAAAAAAACTGCTAC
1 AGAAACAAAAAAACTGCTAC
56706291 AGAAA
1 AGAAA
56706296 TATTTGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.09
Consensus pattern (20 bp):
AGAAACAAAAAAACTGCTAC
Found at i:56710568 original size:69 final size:68
Alignment explanation
Indices: 56710442--56710649 Score: 238
Period size: 69 Copynumber: 3.0 Consensus size: 68
56710432 AAAATGAGAT
* * ** * * *
56710442 ATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAAACAC
1 ATATCTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTCAAGTGACGTTAGATTCTT-AACAC
56710507 ATAA
65 ATAA
* ** *
56710511 ATATTTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTTGAGTGAGGTTAGATTCTTGAACAC
1 ATATCTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTCAAGTGACGTTAGATTCTT-AACAC
* *
56710576 AGAT
65 ATAA
* * * *
56710580 ATATCTCCAGAAAATTTATTGTAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAA-ACA
1 ATATCTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAACACA
56710644 TAA
66 TAA
56710647 ATA
1 ATA
56710650 CATTTTCAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
67 7 0.06
68 2 0.02
69 108 0.92
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (68 bp):
ATATCTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAACACA
TAA
Found at i:56710675 original size:69 final size:68
Alignment explanation
Indices: 56710457--56710695 Score: 232
Period size: 69 Copynumber: 3.5 Consensus size: 68
56710447 TCCAGAAAAC
* * * * *
56710457 TTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAAACACATAAAT-ATTTCCAA
1 TTATTGAAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTT-AA-ACATAAATAATTTCCAA
*
56710521 AAAAA
64 AAATA
** * * * * *
56710526 TTATTGGAAA-AGAGATCTAAATACTTGAGTGAGGTTAGATTCTTGAACACAGATATATCTCCAG
1 TTATT-GAAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAAACATAAATA-ATTTCCA-
56710590 AAAAT-
63 AAAATA
* *
56710595 TTATTGTAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAAACATAAATACATTTTCAAA
1 TTATTGAAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAAACATAAATA-ATTTCCAAA
56710660 AATA
65 AATA
** * *
56710664 CCATTGAAAGAGAGATCTAAATGCTTAAGTGA
1 TTATTGAAAGAGAGATCTAAATACTCAAGTGA
56710696 TATGAGTTCA
Statistics
Matches: 138, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
67 6 0.04
68 9 0.07
69 117 0.85
70 6 0.04
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (68 bp):
TTATTGAAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTTAAACATAAATAATTTCCAAAA
ATA
Found at i:56710695 original size:138 final size:138
Alignment explanation
Indices: 56710438--56710695 Score: 360
Period size: 138 Copynumber: 1.9 Consensus size: 138
56710428 TTCTAAAATG
* *
56710438 AGATATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAA
1 AGATATATCTCCAGAAAACTTATTGGAAGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTAA
** *
56710503 ACACATAAATATTTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTTGAGTGAGGTTAGATTC
66 ACACATAAATATTTCCAAAAAAACCATTGGAAAAGAGATCTAAATACTTAAGTGAGGTTAGATTC
56710568 TTGAACAC
131 TTGAACAC
* * * *
56710576 AGATATATCTCCAGAAAATTTATTGTAAGAGAGATCTAAATACTCAAGTGACGTTAGATTCTT-A
1 AGATATATCTCCAGAAAACTTATTGGAAGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTAA
* * *
56710640 A-ACATAAATACATTTTCAAAAATACCATT-GAAAGAGAGATCTAAATGCTTAAGTGA
66 ACACATAAAT--ATTTCCAAAAAAACCATTGGAAA-AGAGATCTAAATACTTAAGTGA
56710696 TATGAGTTCA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
136 8 0.08
137 6 0.06
138 91 0.87
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (138 bp):
AGATATATCTCCAGAAAACTTATTGGAAGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTAA
ACACATAAATATTTCCAAAAAAACCATTGGAAAAGAGATCTAAATACTTAAGTGAGGTTAGATTC
TTGAACAC
Found at i:56719916 original size:12 final size:12
Alignment explanation
Indices: 56719899--56719923 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56719889 CCCACTCAAA
56719899 TTTCACACTACT
1 TTTCACACTACT
56719911 TTTCACACTACT
1 TTTCACACTACT
56719923 T
1 T
56719924 CCCTACTTTC
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTCACACTACT
Found at i:56720241 original size:10 final size:10
Alignment explanation
Indices: 56720210--56720257 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
56720200 GAAAAGTCTT
56720210 AAATTATAAA
1 AAATTATAAA
*
56720220 AAAGTTACAAA
1 AAA-TTATAAA
56720231 AAATTAT-AA
1 AAATTATAAA
56720240 AAATT-TAAA
1 AAATTATAAA
56720249 AAATATATA
1 AAAT-TATA
56720258 TAATAAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 1 0.03
9 13 0.41
10 7 0.22
11 11 0.34
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AAATTATAAA
Found at i:56720259 original size:21 final size:22
Alignment explanation
Indices: 56720210--56720260 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
56720200 GAAAAGTCTT
56720210 AAAT-TATA-AAAAAGTTACAA
1 AAATATATATAAAAAGTTACAA
*
56720230 AAA-AT-TATAAAAATTTA-AA
1 AAATATATATAAAAAGTTACAA
56720249 AAATATATATAA
1 AAATATATATAA
56720261 TAAACGGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATATATATAAAAAGTTACAA
Found at i:56725710 original size:12 final size:12
Alignment explanation
Indices: 56725678--56725712 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
56725668 TTCACATAAA
56725678 AAATT-TAATTT
1 AAATTATAATTT
56725689 AAATTTATAATTT
1 AAA-TTATAATTT
56725702 AAATTATAATT
1 AAATTATAATT
56725713 ACCACAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 10 0.45
13 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATTATAATTT
Found at i:56725855 original size:44 final size:44
Alignment explanation
Indices: 56725758--56725856 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
56725748 TCATTAAAGC
* * * *
56725758 AATAAC-TCTATTAAATTGTAATTATTTTTAAATTTATAATTAT
1 AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
* * * *
56725801 CACAATTTCTATCAAATTATAAATCTTTTTAAATGTATAATTAT
1 AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
56725845 AATAACTTCTAT
1 AATAACTTCTAT
56725857 TTTACTTCAA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.47
Consensus pattern (44 bp):
AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
Found at i:56726627 original size:2 final size:2
Alignment explanation
Indices: 56726620--56726647 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56726610 AATAACAGTA
56726620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56726648 GCTATTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:56735697 original size:19 final size:18
Alignment explanation
Indices: 56735662--56735696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56735652 CTTTTTTGAA
*
56735662 AATTTTAATAAAATTTTC
1 AATTTTTATAAAATTTTC
*
56735680 AATTTTTATACAATTTT
1 AATTTTTATAAAATTTT
56735697 TTATTTTTTA
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:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTATAAAATTTTC
Found at i:56741367 original size:108 final size:108
Alignment explanation
Indices: 56741178--56741373 Score: 322
Period size: 108 Copynumber: 1.8 Consensus size: 108
56741168 TTTTGCGCAA
* * * *
56741178 AACACCATATTAAAAAAATAAATTTTAAATCGGTAAGCAATAAATTTAATATCGTGTTTTGAGAA
1 AACACCATATTAAAAAAATAAAATTTAAATCGATAAACAATAAATTTAATATCATGTTTTGAGAA
*
56741243 AAAAATTTATGTACTAAATTGAATATCAAAATCAAACTTAAGT
66 AAAAAATTATGTACTAAATTGAATATCAAAATCAAACTTAAGT
*
56741286 AACACCATATTAAAAAAATAAAATTTAAATC-ATCAAACAATAAATTTAATTTCATGTTTTGAGA
1 AACACCATATTAAAAAAATAAAATTTAAATCGAT-AAACAATAAATTTAATATCATGTTTTGAGA
56741350 AAAAAAATTATGTACTAAATTGAA
65 AAAAAAATTATGTACTAAATTGAA
56741374 CAAATTAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 1 0.01
108 80 0.99
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (108 bp):
AACACCATATTAAAAAAATAAAATTTAAATCGATAAACAATAAATTTAATATCATGTTTTGAGAA
AAAAAATTATGTACTAAATTGAATATCAAAATCAAACTTAAGT
Found at i:56747286 original size:12 final size:13
Alignment explanation
Indices: 56747271--56747299 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
56747261 AATAAAATTT
56747271 TCTTGTATTT-TC
1 TCTTGTATTTCTC
56747283 TCTTGTATTTCTC
1 TCTTGTATTTCTC
56747296 TCTT
1 TCTT
56747300 TTTAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (13 bp):
TCTTGTATTTCTC
Found at i:56749847 original size:7 final size:7
Alignment explanation
Indices: 56749835--56749864 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
56749825 TACCATTTTT
56749835 AAAAATA
1 AAAAATA
56749842 AAAAATA
1 AAAAATA
56749849 AAAAAT-
1 AAAAATA
56749855 AAAAATA
1 AAAAATA
56749862 AAA
1 AAA
56749865 CGAATCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:56749852 original size:13 final size:14
Alignment explanation
Indices: 56749835--56749864 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
56749825 TACCATTTTT
56749835 AAAAATAAAAAATA
1 AAAAATAAAAAATA
56749849 AAAAAT-AAAAATA
1 AAAAATAAAAAATA
56749862 AAA
1 AAA
56749865 CGAATCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:56750571 original size:22 final size:22
Alignment explanation
Indices: 56750509--56750572 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
56750499 AAAGCAATAA
* *
56750509 AAATATTAATTTTGTTAAACATT
1 AAATA-TAATTTTATTAAACACT
* *
56750532 AAATGATCATTTTTTTAAACACT
1 AAAT-ATAATTTTATTAAACACT
*
56750555 GAATATAATTTTATTAAA
1 AAATATAATTTTATTAAA
56750573 ATTTGATCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.35
23 21 0.62
24 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATATAATTTTATTAAACACT
Found at i:56752882 original size:21 final size:22
Alignment explanation
Indices: 56752845--56752889 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
56752835 ATTACATAAA
*
56752845 AAAATTAAAAATATTTATGTTT
1 AAAATTAAAAATATTTAAGTTT
56752867 AAAATTAAAAAT-TTTAAGTTT
1 AAAATTAAAAATATTTAAGTTT
56752888 AA
1 AA
56752890 TCATTGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATTAAAAATATTTAAGTTT
Found at i:56761088 original size:6 final size:6
Alignment explanation
Indices: 56761077--56761101 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56761067 ATCAGCTTTA
56761077 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
56761102 ATTGATACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:56762917 original size:16 final size:17
Alignment explanation
Indices: 56762896--56762929 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
56762886 ATTCCATGTT
56762896 GAATTAAATTG-AATGA
1 GAATTAAATTGAAATGA
*
56762912 GAATTATATTGAAATGA
1 GAATTAAATTGAAATGA
56762929 G
1 G
56762930 TTAAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
GAATTAAATTGAAATGA
Found at i:56763267 original size:24 final size:25
Alignment explanation
Indices: 56763206--56763327 Score: 74
Period size: 24 Copynumber: 5.0 Consensus size: 25
56763196 GTCATTAGAG
* *
56763206 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* *
56763230 TTACCGATACTCAGCT-GTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* * *
56763254 TTACTGTTATTCAGCT--TAGAGAAGT
1 TTACCGTTATTCAGCTCGTA-TG-AGC
** * * *
56763279 TTACTATTATTCAGCTAGGAAGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
*
56763304 TTACCGTT-TACAGCTCGTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
56763328 ATACATGTAC
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
23 2 0.03
24 41 0.53
25 31 0.40
26 2 0.03
27 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
TTACCGTTATTCAGCTCGTATGAGC
Found at i:56763307 original size:25 final size:24
Alignment explanation
Indices: 56763250--56763307 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
56763240 TCAGCTGTAT
*
56763250 GAGCTTACTGTTATTCAGCTTAGA
1 GAGCTTACTATTATTCAGCTTAGA
*
56763274 GAAGTTTACTATTATTCAGC-TAGGAA
1 G-AGCTTACTATTATTCAGCTTA-G-A
56763300 GAGCTTAC
1 GAGCTTAC
56763308 CGTTTACAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.11
25 23 0.82
26 2 0.07
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (24 bp):
GAGCTTACTATTATTCAGCTTAGA
Found at i:56766201 original size:6 final size:6
Alignment explanation
Indices: 56766171--56766211 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
56766161 GGTACCTAAT
* *
56766171 CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGT
1 CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGT
56766212 GTTCAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (6 bp):
CAGTAA
Found at i:56766266 original size:45 final size:45
Alignment explanation
Indices: 56766192--56766434 Score: 272
Period size: 45 Copynumber: 5.6 Consensus size: 45
56766182 AACGGTAGCA
* * * *
56766192 GTAACAGTAACAGTAACAGTGTTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
** * *
56766237 GTAACAGTAACAGTAACTGTATTCGACACACAAAGTACCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
*
56766282 GTAACAGTAACGGTAACAATATTCGACACAC--AGTG-TCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCT-GAATCG
*
56766325 GTAACAGTAACAATAACAATATTCGACACACAAAGTGCTGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
* *
56766370 GTAACAGTAACAG------TATTCAACACACAAAATG-TCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCT-GAATCG
* *
56766409 GTAACAGTAACGGTAACAGTATTCGA
1 GTAACAGTAACAGTAACAATATTCGA
56766435 TTTAACTTTT
Statistics
Matches: 169, Mismatches: 18, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
38 1 0.01
39 34 0.20
43 38 0.22
45 95 0.56
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
Found at i:56766424 original size:127 final size:129
Alignment explanation
Indices: 56766192--56766434 Score: 346
Period size: 127 Copynumber: 1.9 Consensus size: 129
56766182 AACGGTAGCA
* * * *
56766192 GTAACAGTAACAGTAACAGTGTTCAACACACAAAGTGCTGAATCTGTAACAGTAACAGTAACTGT
1 GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCTG----AGTAACAGTAACAGT
* *
56766257 ATTCGACACACAAAGTACCGAATCGGTAACAGTAACGGTAACAATATTCGACACACAGTGTCGAA
62 ATTCAACACACAAAATACCGAATCGGTAACAGTAACGGTAACAATATTCGACACACAGTGTCGAA
56766322 TCG
127 TCG
*
56766325 GTAACAGTAACAATAACAATATTCGACACACAAAGTGCTGAATC-G-GTAACAGTAACAGTATTC
1 GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCTGAGTAACAGTAACAGTATTC
** *
56766388 AACACACAAAATGTCGAATCGGTAACAGTAACGGTAACAGTATTCGA
66 AACACACAAAATACCGAATCGGTAACAGTAACGGTAACAATATTCGA
56766435 TTTAACTTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
127 59 0.59
132 1 0.01
133 40 0.40
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (129 bp):
GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCTGAGTAACAGTAACAGTATTC
AACACACAAAATACCGAATCGGTAACAGTAACGGTAACAATATTCGACACACAGTGTCGAATCG
Done.