Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 131 of 145
Found at i:43905391 original size:22 final size:22
Alignment explanation
Indices: 43905306--43905388 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 22
43905296 TATGCATCTT
*
43905306 AGATATGATATGCAAT-TT--T
1 AGATATGATATGCAATATTAGA
* *
43905325 AGATATGATATGTAATCTTAG-
1 AGATATGATATGCAATATTAGA
*
43905346 A--TATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
43905366 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
43905389 GATTTAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
19 32 0.62
20 3 0.06
21 1 0.02
22 5 0.10
23 11 0.21
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.40
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:43905616 original size:23 final size:23
Alignment explanation
Indices: 43905572--43905616 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
43905562 TCTTATTTTG
* *
43905572 TTGATTTGTGTATACTTTATTTA
1 TTGATTTGTATATACTTGATTTA
**
43905595 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATACTTGATTT
43905617 CAAATCTCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATACTTGATTTA
Found at i:43910550 original size:7 final size:7
Alignment explanation
Indices: 43910538--43910563 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43910528 TTTTAAACTT
43910538 ACATCAC
1 ACATCAC
43910545 ACATCAC
1 ACATCAC
43910552 ACATCAC
1 ACATCAC
43910559 ACATC
1 ACATC
43910564 TACCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (7 bp):
ACATCAC
Found at i:43914049 original size:21 final size:21
Alignment explanation
Indices: 43914024--43914087 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
43914014 ATGTTATGTC
43914024 AATGTATGAATTGTATGATTT
1 AATGTATGAATTGTATGATTT
* * *
43914045 AATGT-TCAAATTCTAT-A-GT
1 AATGTAT-GAATTGTATGATTT
43914064 AA--TATGAATTGTATGATTT
1 AATGTATGAATTGTATGATTT
43914083 AATGT
1 AATGT
43914088 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 8 0.26
18 2 0.06
19 6 0.19
20 2 0.06
21 13 0.42
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (21 bp):
AATGTATGAATTGTATGATTT
Found at i:43914079 original size:38 final size:38
Alignment explanation
Indices: 43914028--43914105 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
43914018 TATGTCAATG
43914028 TATGAATTGTATGATTTAATGTTCAAATTCTATAGTAA
1 TATGAATTGTATGATTTAATGTTCAAATTCTATAGTAA
*
43914066 TATGAATTGTATGATTTAATGTTCAAATTGTATAGTAA
1 TATGAATTGTATGATTTAATGTTCAAATTCTATAGTAA
43914104 TA
1 TA
43914106 CTCCGTAACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (38 bp):
TATGAATTGTATGATTTAATGTTCAAATTCTATAGTAA
Found at i:43914094 original size:21 final size:21
Alignment explanation
Indices: 43914032--43914098 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
43914022 TCAATGTATG
43914032 AATTGTATGATTTAATGTTCA
1 AATTGTATGATTTAATGTTCA
* * * *
43914053 AATTCTAT-A-GTAAT-AT-G
1 AATTGTATGATTTAATGTTCA
43914070 AATTGTATGATTTAATGTTCA
1 AATTGTATGATTTAATGTTCA
43914091 AATTGTAT
1 AATTGTAT
43914099 AGTAATACTC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
17 7 0.21
18 2 0.06
19 8 0.24
20 2 0.06
21 15 0.44
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.46
Consensus pattern (21 bp):
AATTGTATGATTTAATGTTCA
Found at i:43914104 original size:19 final size:19
Alignment explanation
Indices: 43914044--43914104 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
43914034 TTGTATGATT
*
43914044 TAATGTTCAAATTCTATAG
1 TAATGTTCAAATTGTATAG
* * *
43914063 TAAT-AT-GAATTGTATGATT
1 TAATGTTCAAATTGTAT-A-G
43914082 TAATGTTCAAATTGTATAG
1 TAATGTTCAAATTGTATAG
43914101 TAAT
1 TAAT
43914105 ACTCCGTAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
19 12 0.39
20 2 0.06
21 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (19 bp):
TAATGTTCAAATTGTATAG
Found at i:43914188 original size:24 final size:24
Alignment explanation
Indices: 43914152--43914203 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43914142 GGGTGTTACA
*
43914152 TTTTTGACATTTTCATTGATATCC
1 TTTTCGACATTTTCATTGATATCC
* * *
43914176 TTTTCGACCTTTTCTTTTATATCC
1 TTTTCGACATTTTCATTGATATCC
43914200 TTTT
1 TTTT
43914204 TGGATAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTCGACATTTTCATTGATATCC
Found at i:43914259 original size:41 final size:39
Alignment explanation
Indices: 43914172--43914273 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 39
43914162 TTTCATTGAT
* * * *
43914172 ATCCTTTTCGACCTTTTC-TTTTATATCCTTTTTGGATA
1 ATCCTTTTCAACCTTTTCATTTGATATCCTTTTAGGAGA
43914210 ATACCCTTTTCAACCTTTTCATTTGATATCCTTTTCAGGAGA
1 AT--CCTTTTCAACCTTTTCATTTGATATCCTTTT-AGGAGA
*
43914252 CATCCTTTTCAACCTATTCATT
1 -ATCCTTTTCAACCTTTTCATT
43914274 GATTTGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
38 2 0.04
40 15 0.28
41 31 0.57
42 4 0.07
43 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.48
Consensus pattern (39 bp):
ATCCTTTTCAACCTTTTCATTTGATATCCTTTTAGGAGA
Found at i:43919900 original size:13 final size:13
Alignment explanation
Indices: 43919861--43919908 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
43919851 ACAAAATTAT
43919861 AAAAGTTATGGAA
1 AAAAGTTATGGAA
43919874 AAAA-TTAT----
1 AAAAGTTATGGAA
43919882 AAAAGTTATGGAA
1 AAAAGTTATGGAA
43919895 AAAAGTTATGGAA
1 AAAAGTTATGGAA
43919908 A
1 A
43919909 TTTGTTGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
12 4 0.13
13 18 0.60
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (13 bp):
AAAAGTTATGGAA
Found at i:43919903 original size:22 final size:21
Alignment explanation
Indices: 43919853--43919903 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
43919843 ACAAAGAGAC
43919853 AAAATTATAAAAGTTATGGAA
1 AAAATTATAAAAGTTATGGAA
43919874 AAAATTATAAAAGTTATGGAA
1 AAAATTATAAAAGTTATGGAA
43919895 AAAAGTTAT
1 AAAA-TTAT
43919904 GGAAATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (21 bp):
AAAATTATAAAAGTTATGGAA
Found at i:43921741 original size:20 final size:21
Alignment explanation
Indices: 43921696--43921742 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
43921686 CTTATACAAA
43921696 TTATAAACAAATTACTAAAAC
1 TTATAAACAAATTACTAAAAC
* *
43921717 CTATAAA-AAATTA-TAATAAT
1 TTATAAACAAATTACTAA-AAC
43921737 TTATAA
1 TTATAA
43921743 TATTTATCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (21 bp):
TTATAAACAAATTACTAAAAC
Found at i:43921743 original size:10 final size:10
Alignment explanation
Indices: 43921727--43921785 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
43921717 CTATAAAAAA
43921727 TTATAATAAT
1 TTATAATAAT
43921737 TTATAAT-AT
1 TTATAATAAT
*
43921746 TTATCAGT-AT
1 TTAT-AATAAT
43921756 TTATAA-AAT
1 TTATAATAAT
*
43921765 TTATAAAAAT
1 TTATAATAAT
* *
43921775 TCATAAAAAT
1 TTATAATAAT
43921785 T
1 T
43921786 CAAAATTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 15 0.35
10 28 0.65
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (10 bp):
TTATAATAAT
Found at i:43930737 original size:25 final size:25
Alignment explanation
Indices: 43930696--43930745 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
43930686 AGCATGTCAG
* *
43930696 TTTTTAAAGCTCGATTTTACTGCAA
1 TTTTTAAACCTCAATTTTACTGCAA
43930721 TTTTTAAACCTCAATTTTACTGCAA
1 TTTTTAAACCTCAATTTTACTGCAA
43930746 GCGTACATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTTAAACCTCAATTTTACTGCAA
Found at i:43932562 original size:28 final size:31
Alignment explanation
Indices: 43932504--43932574 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 31
43932494 ACCAAAAATT
43932504 TATTTTAAAAATTAAAACAAAAATTAAAAAAAG
1 TATTTT-AAAATT-AAACAAAAATTAAAAAAAG
43932537 TATTTTAAAATT-AA-AAAAATT-AAAAAAG
1 TATTTTAAAATTAAACAAAAATTAAAAAAAG
43932565 TATTTTAAAA
1 TATTTTAAAA
43932575 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 17 0.45
29 7 0.18
30 2 0.05
32 6 0.16
33 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (31 bp):
TATTTTAAAATTAAACAAAAATTAAAAAAAG
Found at i:43932575 original size:40 final size:39
Alignment explanation
Indices: 43932531--43932633 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
43932521 CAAAAATTAA
43932531 AAAAAGTATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
1 AAAAAGTATTTTAAAATTAAAAAAATTAAAAAA-TATTTT
** **
43932571 AAAAA--AAATTAAAATTTTAAAAATTTTAAAAAATATTTT
1 AAAAAGTATTTTAAAA--TTAAAAAAATTAAAAAATATTTT
43932610 -AAAAGTATTTTAAAA-TAAAAAAAT
1 AAAAAGTATTTTAAAATTAAAAAAAT
43932634 GAGCACCTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
37 7 0.14
38 11 0.22
39 6 0.12
40 27 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAAAAAATATTTT
Found at i:43932584 original size:29 final size:27
Alignment explanation
Indices: 43932517--43932603 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
43932507 TTTAAAAATT
*
43932517 AAAACAAAAATTAAAAAAAGTATTTTAA
1 AAAAAAAAAATT-AAAAAAGTATTTTAA
*
43932545 AATTAAAAAAATTAAAAAAGTATTTTAA
1 AA-AAAAAAAATTAAAAAAGTATTTTAA
**
43932573 AAAAAATTAAAATTTTAAAA--ATTTTAA
1 AAAAAA--AAAATTAAAAAAGTATTTTAA
43932600 AAAA
1 AAAA
43932604 TATTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.27
28 19 0.37
29 18 0.35
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAAAAAATTAAAAAAGTATTTTAA
Found at i:43932613 original size:11 final size:11
Alignment explanation
Indices: 43932584--43932624 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
43932574 AAAAATTAAA
43932584 ATTTTAAAAAT
1 ATTTTAAAAAT
*
43932595 -TTTAAAAAAT
1 ATTTTAAAAAT
*
43932605 ATTTTAAAAGT
1 ATTTTAAAAAT
43932616 ATTTTAAAA
1 ATTTTAAAA
43932625 TAAAAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:43932626 original size:21 final size:20
Alignment explanation
Indices: 43932584--43932624 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
43932574 AAAAATTAAA
43932584 ATTTTAAAAATTTTAAAAAAT
1 ATTTTAAAAATTTT-AAAAAT
43932605 ATTTTAAAAGTATTTTAAAA
1 ATTTTAAAA--ATTTTAAAA
43932625 TAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTTAAAAATTTTAAAAAT
Found at i:43932632 original size:39 final size:40
Alignment explanation
Indices: 43932532--43932633 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 40
43932522 AAAAATTAAA
43932532 AAAAGTATTTTAAAATTAAAAAAA-TTAAAAAAGTATTTT
1 AAAAGTATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
* ** * *
43932571 AAAA-AAAATTAAAATTTTAAAAATTTTAAAAAA-TATTTT
1 AAAAGTATTTTAAAA-TTAAAAAAATTTAAAAAAGTATTTT
43932610 AAAAGTATTTTAAAA-TAAAAAAAT
1 AAAAGTATTTTAAAATTAAAAAAAT
43932634 GAGCACCTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
38 14 0.28
39 21 0.42
40 15 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
AAAAGTATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
Found at i:43935028 original size:89 final size:90
Alignment explanation
Indices: 43934876--43935080 Score: 245
Period size: 89 Copynumber: 2.3 Consensus size: 90
43934866 AGTAAAATCA
** * * *
43934876 CGATGGTTGTCACCATCCCTTTTCATAGTTTGATAGCCAAACCTATCCCTTTTCATAGTTCGATG
1 CGATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAACCTATCCCTTTTCATAGTTCGATA
*
43934941 GTCGTCA-CCATCCCTTTTCAT-TGTT
66 GTCG-AAGCCATCCCTTTTCATAT-TT
* * * *
43934966 -GATGGTCATCACCATCCCTTTTCATAATTCGGTAGCCGAAGCTATCCCTTTTCATATTTCGATA
1 CGATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAACCTATCCCTTTTCATAGTTCGATA
* * *
43935030 TTCGAAGCTATCCCTTTTTATATTT
66 GTCGAAGCCATCCCTTTTCATATTT
*
43935055 CGATGGTCGTCACCATCCCTTTTCAT
1 CGATGGTCATCACCATCCCTTTTCAT
43935081 TATTGACGGT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
88 1 0.01
89 72 0.73
90 25 0.26
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (90 bp):
CGATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAACCTATCCCTTTTCATAGTTCGATA
GTCGAAGCCATCCCTTTTCATATTT
Found at i:43935073 original size:30 final size:30
Alignment explanation
Indices: 43934876--43935109 Score: 178
Period size: 30 Copynumber: 7.9 Consensus size: 30
43934866 AGTAAAATCA
*
43934876 CGATGGTTGTCACCATCCCTTTTCATAGTTT
1 CGATGGTCGTCACCATCCCTTTTCATA-TTT
* *** *
43934907 -GATAG-CCAAACCTATCCCTTTTCATAGTT
1 CGATGGTCGTCACC-ATCCCTTTTCATATTT
43934936 CGATGGTCGTCACCATCCCTTTTCAT-TGTT
1 CGATGGTCGTCACCATCCCTTTTCATAT-TT
* *
43934966 -GATGGTCATCACCATCCCTTTTCATAATT
1 CGATGGTCGTCACCATCCCTTTTCATATTT
* * * * *
43934995 CGGTAGCCG-AAGCTATCCCTTTTCATATTT
1 CGATGGTCGTCA-CCATCCCTTTTCATATTT
** * * *
43935025 CGATATTCG-AAGCTATCCCTTTTTATATTT
1 CGATGGTCGTCA-CCATCCCTTTTCATATTT
43935055 CGATGGTCGTCACCATCCCTTTTCAT-TATT
1 CGATGGTCGTCACCATCCCTTTTCATAT-TT
* *
43935085 -GACGGTTGTCACCATCCCTTTTCAT
1 CGATGGTCGTCACCATCCCTTTTCAT
43935110 GAATAGATAG
Statistics
Matches: 163, Mismatches: 31, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
29 56 0.34
30 102 0.63
31 5 0.03
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (30 bp):
CGATGGTCGTCACCATCCCTTTTCATATTT
Found at i:43935101 original size:119 final size:118
Alignment explanation
Indices: 43934890--43935165 Score: 356
Period size: 119 Copynumber: 2.3 Consensus size: 118
43934880 GGTTGTCACC
43934890 ATCCCTTTTCATAGTTTGATAGCCAAACCTATCCCTTTTCATAGTTCGATGGTCGTCACCATCCC
1 ATCCCTTTTCATA-TTTGATAGCCAAACCTATCCCTTTTCATAGTTCGATGGTCGTCACCATCCC
* * * *
43934955 TTTTCATTGTTGATGGTCATCACCATCCCTTTTCAT-AATTCGGTAGCCGAAGCT
65 TTTTCATTATTGACGGTCATCACCATCCCTTTTCATGAA-TAGATAGCCGAAGCT
** * * * *
43935009 ATCCCTTTTCATATTTCGATATTCGAAGCTATCCCTTTTTATATTTCGATGGTCGTCACCATCCC
1 ATCCCTTTTCATATTT-GATAGCCAAACCTATCCCTTTTCATAGTTCGATGGTCGTCACCATCCC
** * *
43935074 TTTTCATTATTGACGGTTGTCACCATCCCTTTTCATGAATAGATAGTCGAATCT
65 TTTTCATTATTGACGGTCATCACCATCCCTTTTCATGAATAGATAGCCGAAGCT
* **
43935128 ATCCCTTTTCATATTTTGATAGCTAAAGTTATCCCTTT
1 ATCCCTTTTCATA-TTTGATAGCCAAACCTATCCCTTT
43935166 GTAACAGCCC
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
118 3 0.02
119 127 0.94
120 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (118 bp):
ATCCCTTTTCATATTTGATAGCCAAACCTATCCCTTTTCATAGTTCGATGGTCGTCACCATCCCT
TTTCATTATTGACGGTCATCACCATCCCTTTTCATGAATAGATAGCCGAAGCT
Found at i:43935102 original size:89 final size:88
Alignment explanation
Indices: 43934885--43935143 Score: 224
Period size: 89 Copynumber: 2.9 Consensus size: 88
43934875 ACGATGGTTG
* * * * * * * *
43934885 TCACCATCCCTTTTCATAGTTTGATAGCCAAACCTATCCCTTTTCAT-AGTTCGATGGTCGTCA-
1 TCACCATCCCTTTTCATAATTCGGTAGCCAAGCC-ATCCCTTTTCATGA-ATAGATAGTCG-AAG
*
43934948 CCATCCCTTTTCAT-TGTTGATGGTCA
63 CTATCCCTTTTCATAT-TTGATGGTCA
* * * *
43934974 TCACCATCCCTTTTCATAATTCGGTAGCCGAAGCTATCCCTTTTCAT-ATTTCGATATTCGAAGC
1 TCACCATCCCTTTTCATAATTCGGTAGCC-AAGCCATCCCTTTTCATGA-ATAGATAGTCGAAGC
* *
43935038 TATCCCTTTTTATATTTCGATGGTCG
64 TATCCCTTTTCATATTT-GATGGTCA
* * * *
43935064 TCACCATCCCTTTTCATTATTGACGGTTGTC-A-CCATCCCTTTTCATGAATAGATAGTCGAATC
1 TCACCATCCCTTTTCATAATT--CGGTAGCCAAGCCATCCCTTTTCATGAATAGATAGTCGAAGC
43935127 TATCCCTTTTCATATTT
64 TATCCCTTTTCATATTT
43935144 TGATAGCTAA
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
88 1 0.01
89 102 0.72
90 33 0.23
92 6 0.04
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (88 bp):
TCACCATCCCTTTTCATAATTCGGTAGCCAAGCCATCCCTTTTCATGAATAGATAGTCGAAGCTA
TCCCTTTTCATATTTGATGGTCA
Found at i:43935149 original size:30 final size:29
Alignment explanation
Indices: 43934887--43935149 Score: 162
Period size: 30 Copynumber: 8.9 Consensus size: 29
43934877 GATGGTTGTC
* *
43934887 ACCATCCCTTTTCATAGTTT-GATAGCCAA
1 ACCATCCCTTTTCATA-TTTCGATAGTCGA
* * *
43934916 ACCTATCCCTTTTCATAGTTCGATGGTCGTC
1 ACC-ATCCCTTTTCATATTTCGATAGTCG-A
*
43934947 ACCATCCCTTTTCAT-TGTT-GATGGTC-A
1 ACCATCCCTTTTCATAT-TTCGATAGTCGA
* * *
43934974 TCACCATCCCTTTTCATAATTCGGTAGCCGA
1 --ACCATCCCTTTTCATATTTCGATAGTCGA
* *
43935005 AGCTATCCCTTTTCATATTTCGATATTCGA
1 A-CCATCCCTTTTCATATTTCGATAGTCGA
* * * *
43935035 AGCTATCCCTTTTTATATTTCGATGGTCGTC
1 A-CCATCCCTTTTCATATTTCGATAGTCG-A
* * *
43935066 ACCATCCCTTTTCATTATTGACGGTTGTC--
1 ACCATCCCTTTTCA-TATT-TCGATAGTCGA
* *
43935095 ACCATCCCTTTTCATGA-ATAGATAGTCGA
1 ACCATCCCTTTTCAT-ATTTCGATAGTCGA
* *
43935124 ATCTATCCCTTTTCATATTTTGATAG
1 A-CCATCCCTTTTCATATTTCGATAG
43935150 CTAAAGTTAT
Statistics
Matches: 183, Mismatches: 33, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
27 5 0.03
28 1 0.01
29 47 0.26
30 115 0.63
31 9 0.05
32 6 0.03
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.40
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTTCGATAGTCGA
Found at i:43936399 original size:25 final size:25
Alignment explanation
Indices: 43936371--43936488 Score: 121
Period size: 25 Copynumber: 4.7 Consensus size: 25
43936361 GTTACAGATT
*
43936371 TCAGCTCTTATGAGCTTACCGATAC
1 TCAGCTCGTATGAGCTTACCGATAC
*
43936396 TCAGCTCGTATGAGCTTATCGATAC
1 TCAGCTCGTATGAGCTTACCGATAC
* * *
43936421 TCAGCTCGTATAAGCTTACCGTTAT
1 TCAGCTCGTATGAGCTTACCGATAC
* * * *
43936446 TCAGCTTAG-AGGAGCTTACCGTTAT
1 TCAGC-TCGTATGAGCTTACCGATAC
* *
43936471 TCAGCTCGGAGGAGCTTA
1 TCAGCTCGTATGAGCTTA
43936489 TCGTTTACAG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
24 2 0.02
25 77 0.95
26 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTTACCGATAC
Found at i:43937944 original size:17 final size:17
Alignment explanation
Indices: 43937922--43937964 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
43937912 GTGTCTCTTG
43937922 GCCGTGTGAGTCACACA
1 GCCGTGTGAGTCACACA
*
43937939 GCCGTGTGAGTCACATA
1 GCCGTGTGAGTCACACA
43937956 GCCGTGTGA
1 GCCGTGTGA
43937965 CCCTTGCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (17 bp):
GCCGTGTGAGTCACACA
Found at i:43940843 original size:50 final size:50
Alignment explanation
Indices: 43940737--43940979 Score: 324
Period size: 50 Copynumber: 4.7 Consensus size: 50
43940727 GGGAATGAGA
* *
43940737 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA---AG---ATGAGAGG
* *
43940793 TCCTATGTAAGACCATGTCCGGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
** *
43940843 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
* * * *
43940893 TCCCATGTAAGACCATGTATAGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
*
43940943 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
43940980 AGTTCCCATG
Statistics
Matches: 170, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 132 0.78
53 2 0.01
56 36 0.21
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
Found at i:43946422 original size:30 final size:30
Alignment explanation
Indices: 43946380--43946447 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
43946370 AATTCTTTGT
*
43946380 TAAATG-TTTTATTATTTAGTTTTGGGGTC
1 TAAATGTTTTTATTATTTAATTTTGGGGTC
*
43946409 TAAATGTTTTTATTTTTTAATTTTGGGGTC
1 TAAATGTTTTTATTATTTAATTTTGGGGTC
43946439 TAAATGTTT
1 TAAATGTTT
43946448 CTTAACAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 6 0.17
30 30 0.83
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.57
Consensus pattern (30 bp):
TAAATGTTTTTATTATTTAATTTTGGGGTC
Found at i:43950942 original size:16 final size:16
Alignment explanation
Indices: 43950909--43950956 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
43950899 AGATAACCAT
*
43950909 ATAAAAAATTTCAATAA
1 ATAAAAAATAT-AATAA
*
43950926 ATAAAAAATATATTAA
1 ATAAAAAATATAATAA
43950942 ATTAAAATAATATAA
1 A-TAAAA-AATATAA
43950957 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAAATATAATAA
Found at i:43951196 original size:36 final size:36
Alignment explanation
Indices: 43951144--43951215 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
43951134 TTTTAGTTCC
* * *
43951144 CCTTTGCAGACGATTATAGTAACGAGAGCTTAAACT
1 CCTTTGCAGACAATTATAGCAACAAGAGCTTAAACT
43951180 CCTTTGCAGACAATTATAGCAACAAGAGCTTAAACT
1 CCTTTGCAGACAATTATAGCAACAAGAGCTTAAACT
43951216 AACCTAGAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (36 bp):
CCTTTGCAGACAATTATAGCAACAAGAGCTTAAACT
Found at i:43955628 original size:13 final size:13
Alignment explanation
Indices: 43955610--43955640 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43955600 ACAAGTTACC
43955610 TATTGGTTTTGGG
1 TATTGGTTTTGGG
43955623 TATTGGTTTTGGG
1 TATTGGTTTTGGG
*
43955636 AATTG
1 TATTG
43955641 TGTCATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (13 bp):
TATTGGTTTTGGG
Found at i:43958637 original size:39 final size:39
Alignment explanation
Indices: 43958594--43958812 Score: 314
Period size: 39 Copynumber: 5.6 Consensus size: 39
43958584 CATTTTCACT
* * *
43958594 TTTAAGTATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
43958633 TTTAAGCATATACCATAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
43958672 TTTAAGCATATATCATAATTA-TCATATAATCACATAACA
1 TTTAAGCATATATCACAA-TACTCATATAATCACATAACA
* *
43958711 TTCAAGCATATATCACAATACTTATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
43958750 TTCAAACATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
43958789 TTTAAACATATATCGCAATACTCA
1 TTTAAGCATATATCACAATACTCA
43958813 AAAACATGTT
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
38 2 0.01
39 161 0.98
40 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:43961569 original size:522 final size:522
Alignment explanation
Indices: 43960572--43961619 Score: 1999
Period size: 522 Copynumber: 2.0 Consensus size: 522
43960562 ATGACTAGGT
43960572 CTTACACTATTTGGTCTTCGCTTGCCATAGCCATGGACTTCCATATCAGAATTTGTGTTTACTGT
1 CTTACACTATTTGGTCTTCGCTTGCCATAGCCATGGACTTCCATATCAGAATTTGTGTTTACTGT
* *
43960637 CCCGACGGACTATCACACGCAAGTAGACTCAACATGCAGACTCATGCCTGACTGACTCATTGCAA
66 CCCGACAGACTAGCACACGCAAGTAGACTCAACATGCAGACTCATGCCTGACTGACTCATTGCAA
* *
43960702 TAGACTTCAACATGCAGATGTATTTACGTTTCCAGACATGCAACTCAGACTCATCGTGCAAAAAC
131 TAGACTTCAACATGCAGATGCATTTACGTTTCCAGACATGCAACTCAAACTCATCGTGCAAAAAC
* *
43960767 AATCGTGCTTTAAGCACACTCATGCATGTGCATACTTTTCAATAGAATAGAGACTTATCATTCAA
196 AATCGTACTTTAAGCACACTCATGCATGCGCATACTTTTCAATAGAATAGAGACTTATCATTCAA
43960832 ATCATGCTTTATTGCATATTCATCGTTTTCATACTTTTCTTTTCATAACGAAGGTGCATTGTCAT
261 ATCATGCTTTATTGCATATTCATCGTTTTCATACTTTTCTTTTCATAACGAAGGTGCATTGTCAT
43960897 TTAGGCATCAAGCCACACATGCAAGATTATCAGATGCACATTTACACAGAATCAGTATATCACAC
326 TTAGGCATCAAGCCACACATGCAAGATTATCAGATGCACATTTACACAGAATCAGTATATCACAC
* *
43960962 ATGCATAGCTTTCGTTTTGTTTCACAAATCAATTTTTTAATGTGGAAGAAATAACTATATAAACA
391 ATGCATAGCTTTCGTTTTGTTTCACAAATCAATCTTTTAATGTAGAAGAAATAACTATATAAACA
43961027 TACATGCAACAGACAAAAAAAAGTTCATAAGGTACTCACAGAACCCTCACATTTTTCTCACATAA
456 TACATGCAACAGACAAAAAAAAGTTCATAAGGTACTCACAGAACCCTCACATTTTTCTCACATAA
43961092 TC
521 TC
*
43961094 CTTACACTATTTGGTCTTCGCTTGCCATGGCCATGGACTTCCATATCAGAATTTGTGTTTACTGT
1 CTTACACTATTTGGTCTTCGCTTGCCATAGCCATGGACTTCCATATCAGAATTTGTGTTTACTGT
43961159 CCCGACAGACTAGCACACGCAAGTAGACTCAACATGCAGACTCATGCCTGACTGACTCATTGCAA
66 CCCGACAGACTAGCACACGCAAGTAGACTCAACATGCAGACTCATGCCTGACTGACTCATTGCAA
43961224 TAGACTTCAACATGCAGATGCATTTACGTTTCCAGACATGCAACTCAAACTCATCGTGCAAAAAC
131 TAGACTTCAACATGCAGATGCATTTACGTTTCCAGACATGCAACTCAAACTCATCGTGCAAAAAC
43961289 AATCGTACTTTAAGCACACTCATGCATGCGCATACTTTTCAATAGAATAGAGACTTATCATTCAA
196 AATCGTACTTTAAGCACACTCATGCATGCGCATACTTTTCAATAGAATAGAGACTTATCATTCAA
43961354 ATCATGCTTTATTGCATATTCATCGTTTTCATAC-TTTCTTTTCATAACGAAGGTGCATTGTCAT
261 ATCATGCTTTATTGCATATTCATCGTTTTCATACTTTTCTTTTCATAACGAAGGTGCATTGTCAT
43961418 TTAGGCATCAAGCCACACATGCAAGATTATCAGATGCACATTTACACAGAATCAGTATATCACAC
326 TTAGGCATCAAGCCACACATGCAAGATTATCAGATGCACATTTACACAGAATCAGTATATCACAC
*
43961483 ATGCATAGCTTTCGTTTTGTTTCACAAATCAGTCTTTTAATGTAGAAGAAATAACTATATAAACA
391 ATGCATAGCTTTCGTTTTGTTTCACAAATCAATCTTTTAATGTAGAAGAAATAACTATATAAACA
43961548 TACATGCAACAGACAAAAAAAAGTTCATAAGGTACTCACAGAACCCTCACATTTTTCTCACATAA
456 TACATGCAACAGACAAAAAAAAGTTCATAAGGTACTCACAGAACCCTCACATTTTTCTCACATAA
43961613 TC
521 TC
43961615 CTTAC
1 CTTAC
43961620 CTTTTTCCTC
Statistics
Matches: 516, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
521 229 0.44
522 287 0.56
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (522 bp):
CTTACACTATTTGGTCTTCGCTTGCCATAGCCATGGACTTCCATATCAGAATTTGTGTTTACTGT
CCCGACAGACTAGCACACGCAAGTAGACTCAACATGCAGACTCATGCCTGACTGACTCATTGCAA
TAGACTTCAACATGCAGATGCATTTACGTTTCCAGACATGCAACTCAAACTCATCGTGCAAAAAC
AATCGTACTTTAAGCACACTCATGCATGCGCATACTTTTCAATAGAATAGAGACTTATCATTCAA
ATCATGCTTTATTGCATATTCATCGTTTTCATACTTTTCTTTTCATAACGAAGGTGCATTGTCAT
TTAGGCATCAAGCCACACATGCAAGATTATCAGATGCACATTTACACAGAATCAGTATATCACAC
ATGCATAGCTTTCGTTTTGTTTCACAAATCAATCTTTTAATGTAGAAGAAATAACTATATAAACA
TACATGCAACAGACAAAAAAAAGTTCATAAGGTACTCACAGAACCCTCACATTTTTCTCACATAA
TC
Found at i:43965752 original size:19 final size:19
Alignment explanation
Indices: 43965730--43965814 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
43965720 GTTAAAAACA
*
43965730 TATAAAAAATGTAAAATTT
1 TATAAAAAATATAAAATTT
43965749 TAT-AAAAATAGTAAAATTTTT
1 TATAAAAAATA-TAAAA--TTT
* *
43965770 TATAAAATATATAGAAA-TA
1 TATAAAAAATATA-AAATTT
*
43965789 TAGAAAAAATTATAAAATTT
1 TATAAAAAA-TATAAAATTT
43965809 TATAAA
1 TATAAA
43965815 GTCGTAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
18 6 0.12
19 19 0.37
20 10 0.19
21 8 0.15
22 9 0.17
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAAAAATATAAAATTT
Found at i:43966134 original size:19 final size:18
Alignment explanation
Indices: 43966093--43966134 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
43966083 AATGTTACAA
43966093 TATTTTATATTTTTTTAC
1 TATTTTATATTTTTTTAC
* *
43966111 GATTTTATTATTTTTTTTC
1 TATTTTA-TATTTTTTTAC
43966130 TATTT
1 TATTT
43966135 AATGGTTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (18 bp):
TATTTTATATTTTTTTAC
Found at i:43966162 original size:103 final size:105
Alignment explanation
Indices: 43966028--43966237 Score: 406
Period size: 103 Copynumber: 2.0 Consensus size: 105
43966018 ACAGTTAAAA
43966028 TTAATGGTTAATAGGTCTTTTTGATGCATTTTATATTTTTTTATGATTTTTATAAAATGTTACAA
1 TTAATGGTTAATAGGTCTTTTTGATGCATTTTATATTTTTTTATGATTTTTATAAAATGTTACAA
43966093 TATTTTATATTTTTTTACGATTTTATTATTTTTTTTCTAT
66 TATTTTATATTTTTTTACGATTTTATTATTTTTTTTCTAT
43966133 TTAATGGTT-A-AGGTCTTTTTGATGCATTTTATATTTTTTTATGATTTTTATAAAATGTTACAA
1 TTAATGGTTAATAGGTCTTTTTGATGCATTTTATATTTTTTTATGATTTTTATAAAATGTTACAA
43966196 TATTTTATATTTTTTTACGATTTTATTATTTTTTTTCTAT
66 TATTTTATATTTTTTTACGATTTTATTATTTTTTTTCTAT
43966236 TT
1 TT
43966238 TATTATTTTT
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 95 0.90
104 1 0.01
105 9 0.09
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (105 bp):
TTAATGGTTAATAGGTCTTTTTGATGCATTTTATATTTTTTTATGATTTTTATAAAATGTTACAA
TATTTTATATTTTTTTACGATTTTATTATTTTTTTTCTAT
Found at i:43966237 original size:19 final size:19
Alignment explanation
Indices: 43966196--43966247 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
43966186 AATGTTACAA
43966196 TATTTTA-TATTTTTTTAC
1 TATTTTATTATTTTTTTAC
* *
43966214 GATTTTATTATTTTTTTTC
1 TATTTTATTATTTTTTTAC
43966233 TATTTTATTATTTTT
1 TATTTTATTATTTTT
43966248 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTTTATTATTTTTTTAC
Found at i:43966616 original size:85 final size:85
Alignment explanation
Indices: 43966452--43966615 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 85
43966442 AAATTTAGGA
* *
43966452 GCTTAATTACTTTTATTGAAAAAGTTTAAAGGTATTTTTAATGTATTTTAAAAATTAAATTATCC
1 GCTTAATTACTTTTATTAAAAAAGTTTAAAGATATTTTTAATGTATTTTAAAAATTAAATTATCC
*
43966517 AATTAAGTGTAAAAAGAAAG
66 AATTAAGTGAAAAAAGAAAG
* *
43966537 GCTTAATTA-TTTTCTTTAAAAAAGTTT-AAGA-ATTTTTTTATGTATTTTAAAAATTCAAA-TA
1 GCTTAATTACTTTT-ATTAAAAAAGTTTAAAGATA-TTTTTAATGTATTTTAAAAATT-AAATTA
* *
43966598 TCTAATTGAGTGAAAAAA
63 TCCAATTAAGTGAAAAAA
43966616 AATTTTTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
83 1 0.01
84 45 0.65
85 23 0.33
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (85 bp):
GCTTAATTACTTTTATTAAAAAAGTTTAAAGATATTTTTAATGTATTTTAAAAATTAAATTATCC
AATTAAGTGAAAAAAGAAAG
Found at i:43968335 original size:2 final size:2
Alignment explanation
Indices: 43968328--43968362 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43968318 TCATGGATTT
43968328 TA 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 TA T
43968363 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43972813 original size:18 final size:18
Alignment explanation
Indices: 43972790--43972837 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
43972780 ATATTACCTG
43972790 AAAAATTAAATAAAACAA
1 AAAAATTAAATAAAACAA
* **
43972808 AAAAATTAAATTAAATTA
1 AAAAATTAAATAAAACAA
43972826 AAAAA-TAAATAA
1 AAAAATTAAATAA
43972838 CTAAACATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAATAAAACAA
Found at i:43974930 original size:754 final size:754
Alignment explanation
Indices: 43973483--43974991 Score: 3018
Period size: 754 Copynumber: 2.0 Consensus size: 754
43973473 TGTGTTAATG
43973483 TTTTGCTATTTCAATAAAAATATTATAATTCAAATATAAAGATATAAAGATATTTAAATTGATAT
1 TTTTGCTATTTCAATAAAAATATTATAATTCAAATATAAAGATATAAAGATATTTAAATTGATAT
43973548 TTCAATAAAAATATAAAAAAATAATTTATTATAATTCATGATTAAGTTTAATATATGAAATATAA
66 TTCAATAAAAATATAAAAAAATAATTTATTATAATTCATGATTAAGTTTAATATATGAAATATAA
43973613 ATTGTTAAGGCTTACTTGTATAAAACTATCATTTGGCAATCATCACCAATATTATAATGATAAAA
131 ATTGTTAAGGCTTACTTGTATAAAACTATCATTTGGCAATCATCACCAATATTATAATGATAAAA
43973678 ATAAACTTTTAGATATTTTTAAACAATTAATTTAGTTATTTGTTAATTTTTATTTTAATATATAA
196 ATAAACTTTTAGATATTTTTAAACAATTAATTTAGTTATTTGTTAATTTTTATTTTAATATATAA
43973743 ACCCATATTTTTAAATATTAAAATATAGACATTATCAATTCAAATATATAATATTATATATTTAA
261 ACCCATATTTTTAAATATTAAAATATAGACATTATCAATTCAAATATATAATATTATATATTTAA
43973808 AATAAATTTTAATAACGAAATAATTGTATACTCAATATAAAAATTACATAAAGTACATTAGATTA
326 AATAAATTTTAATAACGAAATAATTGTATACTCAATATAAAAATTACATAAAGTACATTAGATTA
43973873 TAAATAAATGTTAAAAATATAATTTAACTCTAAAAATGTTTTTGCGTCTTGGTTTAAAAATACTT
391 TAAATAAATGTTAAAAATATAATTTAACTCTAAAAATGTTTTTGCGTCTTGGTTTAAAAATACTT
43973938 TTAAACTAAAAATGAACTATTTTACGGGTAAATTACACATAAAAGCCCTATTTTTTTAAAATTTA
456 TTAAACTAAAAATGAACTATTTTACGGGTAAATTACACATAAAAGCCCTATTTTTTTAAAATTTA
43974003 TCGAAATAGGCCTGTATTTTATTATTTATTGGAATGGGCTATTTTCTCCGAAATCGAGTCCACAT
521 TCGAAATAGGCCTGTATTTTATTATTTATTGGAATGGGCTATTTTCTCCGAAATCGAGTCCACAT
43974068 CAGCGCGATGTCAGGGGATGTGTCAACAAATTGCGTCCACGTCAGCGCGATTACTTACATGGCAA
586 CAGCGCGATGTCAGGGGATGTGTCAACAAATTGCGTCCACGTCAGCGCGATTACTTACATGGCAA
43974133 CAAATCGCGTCCACGTAAGCGCGATTTGTTGACGTGGAAGCAATAATTCATGAGCAGTTTATGTT
651 CAAATCGCGTCCACGTAAGCGCGATTTGTTGACGTGGAAGCAATAATTCATGAGCAGTTTATGTT
43974198 TTTTAGCTTGGAAAACTTTGAAAGGCCATAACTTTTGGC
716 TTTTAGCTTGGAAAACTTTGAAAGGCCATAACTTTTGGC
43974237 TTTTGCTATTTCAATAAAAATATTATAATTCAAATATAAAGATATAAAGATATTTAAATTGATAT
1 TTTTGCTATTTCAATAAAAATATTATAATTCAAATATAAAGATATAAAGATATTTAAATTGATAT
43974302 TTCAATAAAAATATAAAAAAATAATTTATTATAATTCATGATTAAGTTTAATATATGAAATATAA
66 TTCAATAAAAATATAAAAAAATAATTTATTATAATTCATGATTAAGTTTAATATATGAAATATAA
43974367 ATTGTTAAGGCTTACTTGTATAAAACTATCATTTGGCAATCATCACCAATATTATAATGATAAAA
131 ATTGTTAAGGCTTACTTGTATAAAACTATCATTTGGCAATCATCACCAATATTATAATGATAAAA
43974432 ATAAACTTTTAGATATTTTTAAACAATTAATTTAGTTATTTGTTAATTTTTATTTTAATATATAA
196 ATAAACTTTTAGATATTTTTAAACAATTAATTTAGTTATTTGTTAATTTTTATTTTAATATATAA
43974497 ACCCATATTTTTAAATATTAAAATATAGACATTATCAATTCAAATATATAATATTATATATTTAA
261 ACCCATATTTTTAAATATTAAAATATAGACATTATCAATTCAAATATATAATATTATATATTTAA
43974562 AATAAATTTTAATAACGAAATAATTGTATACTCAATATAAAAATTACATAAAGTACATTAGATTA
326 AATAAATTTTAATAACGAAATAATTGTATACTCAATATAAAAATTACATAAAGTACATTAGATTA
43974627 TAAATAAATGTTAAAAATATAATTTAACTCTAAAAATGTTTTTGCGTCTTGGTTTAAAAATACTT
391 TAAATAAATGTTAAAAATATAATTTAACTCTAAAAATGTTTTTGCGTCTTGGTTTAAAAATACTT
43974692 TTAAACTAAAAATGAACTATTTTACGGGTAAATTACACATAAAAGCCCTATTTTTTTAAAATTTA
456 TTAAACTAAAAATGAACTATTTTACGGGTAAATTACACATAAAAGCCCTATTTTTTTAAAATTTA
43974757 TCGAAATAGGCCTGTATTTTATTATTTATTGGAATGGGCTATTTTCTCCGAAATCGAGTCCACAT
521 TCGAAATAGGCCTGTATTTTATTATTTATTGGAATGGGCTATTTTCTCCGAAATCGAGTCCACAT
43974822 CAGCGCGATGTCAGGGGATGTGTCAACAAATTGCGTCCACGTCAGCGCGATTACTTACATGGCAA
586 CAGCGCGATGTCAGGGGATGTGTCAACAAATTGCGTCCACGTCAGCGCGATTACTTACATGGCAA
43974887 CAAATCGCGTCCACGTAAGCGCGATTTGTTGACGTGGAAGCAATAATTCATGAGCAGTTTATGTT
651 CAAATCGCGTCCACGTAAGCGCGATTTGTTGACGTGGAAGCAATAATTCATGAGCAGTTTATGTT
43974952 TTTTAGCTTGGAAAACTTTGAAAGGCCATAACTTTTGGC
716 TTTTAGCTTGGAAAACTTTGAAAGGCCATAACTTTTGGC
43974991 T
1 T
43974992 CAGTTGTCCG
Statistics
Matches: 755, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
754 755 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (754 bp):
TTTTGCTATTTCAATAAAAATATTATAATTCAAATATAAAGATATAAAGATATTTAAATTGATAT
TTCAATAAAAATATAAAAAAATAATTTATTATAATTCATGATTAAGTTTAATATATGAAATATAA
ATTGTTAAGGCTTACTTGTATAAAACTATCATTTGGCAATCATCACCAATATTATAATGATAAAA
ATAAACTTTTAGATATTTTTAAACAATTAATTTAGTTATTTGTTAATTTTTATTTTAATATATAA
ACCCATATTTTTAAATATTAAAATATAGACATTATCAATTCAAATATATAATATTATATATTTAA
AATAAATTTTAATAACGAAATAATTGTATACTCAATATAAAAATTACATAAAGTACATTAGATTA
TAAATAAATGTTAAAAATATAATTTAACTCTAAAAATGTTTTTGCGTCTTGGTTTAAAAATACTT
TTAAACTAAAAATGAACTATTTTACGGGTAAATTACACATAAAAGCCCTATTTTTTTAAAATTTA
TCGAAATAGGCCTGTATTTTATTATTTATTGGAATGGGCTATTTTCTCCGAAATCGAGTCCACAT
CAGCGCGATGTCAGGGGATGTGTCAACAAATTGCGTCCACGTCAGCGCGATTACTTACATGGCAA
CAAATCGCGTCCACGTAAGCGCGATTTGTTGACGTGGAAGCAATAATTCATGAGCAGTTTATGTT
TTTTAGCTTGGAAAACTTTGAAAGGCCATAACTTTTGGC
Found at i:43981720 original size:11 final size:11
Alignment explanation
Indices: 43981704--43981730 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43981694 TAGAAATTAG
43981704 TTTGTGAAACT
1 TTTGTGAAACT
43981715 TTTGTGAAACT
1 TTTGTGAAACT
43981726 TTTGT
1 TTTGT
43981731 ATTGATTTTT
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:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:43982079 original size:123 final size:124
Alignment explanation
Indices: 43981850--43982097 Score: 453
Period size: 123 Copynumber: 2.0 Consensus size: 124
43981840 TATTGAATTT
43981850 AATTCTAATTTTATAAAGTGTTCACCTTTTGAATCATGATATTAAAATAGTAATTAATATAACAT
1 AATTCTAA-TTTATAAAGTGTTCACCTTTTGAATCATGATATTAAAATAGTAATTAATATAACAT
**
43981915 TGCTACTTCCAGAATCAAATGCTTCTTCTCAAGCTTCTCAAGGAAGCAAAAGAAAATGGG
65 TGCTACTTCCAGAATCAAATGCTTCTTCTCAAGAGTCTCAAGGAAGCAAAAGAAAATGGG
43981975 AATTCTAA-TTATAAAGTGTTCACCTTTTGAATCATGATATTAAAATAGTAATTAATATAACATT
1 AATTCTAATTTATAAAGTGTTCACCTTTTGAATCATGATATTAAAATAGTAATTAATATAACATT
*
43982039 GCTACTTCCAGAATCAAATGCTTCTTTTCAAGAGTCTCAAGGAAGCAAAAGAAAATGGG
66 GCTACTTCCAGAATCAAATGCTTCTTCTCAAGAGTCTCAAGGAAGCAAAAGAAAATGGG
43982098 TTCCAGAAGA
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
123 112 0.93
125 8 0.07
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (124 bp):
AATTCTAATTTATAAAGTGTTCACCTTTTGAATCATGATATTAAAATAGTAATTAATATAACATT
GCTACTTCCAGAATCAAATGCTTCTTCTCAAGAGTCTCAAGGAAGCAAAAGAAAATGGG
Found at i:43983940 original size:18 final size:17
Alignment explanation
Indices: 43983912--43983946 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43983902 NNNNTTAAGA
*
43983912 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43983929 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43983947 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43984197 original size:45 final size:44
Alignment explanation
Indices: 43984107--43984200 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
43984097 TTACACCTCT
* *
43984107 ATTACATTCAACCAAACATAAGAATACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACATAAGAATACTATTACACCTCTAATCC
** *
43984151 ATTACATTCAACCAAACAATTAA-TTTGCTATTACACCTCTAATCC
1 ATTACATTCAACCAAAC-A-TAAGAATACTATTACACCTCTAATCC
43984196 ATTAC
1 ATTAC
43984201 GCCTCTATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 17 0.40
45 23 0.53
46 3 0.07
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (44 bp):
ATTACATTCAACCAAACATAAGAATACTATTACACCTCTAATCC
Found at i:43987676 original size:29 final size:29
Alignment explanation
Indices: 43987618--43987714 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
43987608 CCTAGAGCAA
43987618 CCACAAAGGCTTTCACATATAA-AAAGTTCAG
1 CCACAAAGGC--TCACATATAACAAA-TTCAG
* * * * *
43987649 CCACTAGGGCTCACATGTAACAGATTCAA
1 CCACAAAGGCTCACATATAACAAATTCAG
*
43987678 CCACAAAGGCTTACATATAACAAATTCAG
1 CCACAAAGGCTCACATATAACAAATTCAG
43987707 CCACAAAG
1 CCACAAAG
43987715 ACATCACTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 44 0.81
30 2 0.04
31 8 0.15
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (29 bp):
CCACAAAGGCTCACATATAACAAATTCAG
Found at i:43987708 original size:58 final size:61
Alignment explanation
Indices: 43987598--43987710 Score: 164
Period size: 58 Copynumber: 1.9 Consensus size: 61
43987588 CCACGAAGAT
43987598 TCACATGTAACCTAGAGCAACCACAAAGGCTTTCACATATAAAAAGTTCAGCCACTAGGGC
1 TCACATGTAACCTAGAGCAACCACAAAGGCTTTCACATATAAAAAGTTCAGCCACTAGGGC
*
43987659 TCACATGTAA-C-AGATTCAACCACAAAGGC-TT-ACATATAACAAA-TTCAGCCAC
1 TCACATGTAACCTAGA-GCAACCACAAAGGCTTTCACATATAA-AAAGTTCAGCCAC
43987711 AAAGACATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
58 17 0.35
59 8 0.16
60 14 0.29
61 10 0.20
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (61 bp):
TCACATGTAACCTAGAGCAACCACAAAGGCTTTCACATATAAAAAGTTCAGCCACTAGGGC
Found at i:43987908 original size:54 final size:54
Alignment explanation
Indices: 43987839--43988037 Score: 319
Period size: 54 Copynumber: 3.7 Consensus size: 54
43987829 ACATGACGCA
43987839 ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCATTTCCCCATATGATGTC
1 ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCATTTCCCCATATGATGTC
* * * * *
43987893 ATAGTCTCAGGCTAGGTCTTATAGTATATAGTCTTCATTTCCCCATATGATGTC
1 ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCATTTCCCCATATGATGTC
* *
43987947 ATAGTCCTAGACTAGGTCTTACACTATATGGTATTCATTTCCCCATATGAT-TC
1 ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCATTTCCCCATATGATGTC
43988000 TATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCA
1 -ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCA
43988038 CTTACCATAT
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.02
54 128 0.98
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (54 bp):
ATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCATTTCCCCATATGATGTC
Found at i:43992809 original size:19 final size:20
Alignment explanation
Indices: 43992758--43992810 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
43992748 CACTTTCTAT
*
43992758 ATTTT-ATAATATTTCAAATA
1 ATTTTCATAAT-TTTCAAACA
43992778 ATTTTC-TATATTTT-AAACA
1 ATTTTCATA-ATTTTCAAACA
43992797 ATTTTCATAATTTT
1 ATTTTCATAATTTT
43992811 TATAGCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 15 0.52
20 12 0.41
21 2 0.07
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTCATAATTTTCAAACA
Found at i:43995277 original size:19 final size:19
Alignment explanation
Indices: 43995253--43995289 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43995243 AGTATTAAAC
* *
43995253 TACTAAATATTCTAAAAAG
1 TACTAAAAATTATAAAAAG
43995272 TACTAAAAATTATAAAAA
1 TACTAAAAATTATAAAAA
43995290 AAATATTATA
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:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (19 bp):
TACTAAAAATTATAAAAAG
Found at i:43995705 original size:15 final size:17
Alignment explanation
Indices: 43995684--43995718 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
43995674 TAAAAAAATC
*
43995684 AAAAAAAAAT-ATTTTT
1 AAAAAAAATTCATTTTT
43995700 AAAAAAAATTCATTTTT
1 AAAAAAAATTCATTTTT
43995717 AA
1 AA
43995719 TATTCCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAAAAATTCATTTTT
Found at i:43999455 original size:26 final size:25
Alignment explanation
Indices: 43999420--43999606 Score: 73
Period size: 24 Copynumber: 7.6 Consensus size: 25
43999410 GTAGCTCTTA
*
43999420 TGAGCGTCCCGTTATATGGCTCTTCG
1 TGAGCTTCCCGTTA-ATGGCTCTTCG
* **
43999446 TGAGCTTCCCGATTAAAGGCTCTTTA
1 TGAGCTTCCCG-TTAATGGCTCTTCG
** * * *
43999472 TGAGCTTCTTGTTAGT-GCTC-GCT
1 TGAGCTTCCCGTTAATGGCTCTTCG
* ** * *
43999495 TGAACTTCCCGTTATATAACT-ATCT
1 TGAGCTTCCCGTTA-ATGGCTCTTCG
* *
43999520 TGTGCTTCCCGTTAATTGCTCTTCG
1 TGAGCTTCCCGTTAATGGCTCTTCG
* * * * *
43999545 -GAGCTACCCGTTAATTGATTTTTG
1 TGAGCTTCCCGTTAATGGCTCTTCG
* *
43999569 -GAG-TTACCTGTT-ATAGGCTCTTTG
1 TGAGCTT-CCCGTTAAT-GGCTCTTCG
43999593 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
43999607 TATTACCCGG
Statistics
Matches: 117, Mismatches: 34, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
23 14 0.12
24 42 0.36
25 29 0.25
26 29 0.25
27 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
TGAGCTTCCCGTTAATGGCTCTTCG
Found at i:44013438 original size:19 final size:19
Alignment explanation
Indices: 44013414--44013455 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
44013404 TTCCATAGTC
44013414 TGTTGCATATATAGATCCT
1 TGTTGCATATATAGATCCT
*
44013433 TGTTGCATATATAGATTCT
1 TGTTGCATATATAGATCCT
44013452 TGTT
1 TGTT
44013456 AACTTCTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.48
Consensus pattern (19 bp):
TGTTGCATATATAGATCCT
Found at i:44014345 original size:60 final size:60
Alignment explanation
Indices: 44014272--44014390 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
44014262 ATCCAGATAC
44014272 TGATGCTGATTCTGACTAGGAAACAGGGTAAGAGAAATGTTAATTCATCAGCTGTTCATT
1 TGATGCTGATTCTGACTAGGAAACAGGGTAAGAGAAATGTTAATTCATCAGCTGTTCATT
44014332 TGATGCTGATTCTGACTAGGAAACAGGGTAAGAGAAATGTTAATTCATCAGCTGTTCAT
1 TGATGCTGATTCTGACTAGGAAACAGGGTAAGAGAAATGTTAATTCATCAGCTGTTCAT
44014391 CAAAATGAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (60 bp):
TGATGCTGATTCTGACTAGGAAACAGGGTAAGAGAAATGTTAATTCATCAGCTGTTCATT
Found at i:44016843 original size:5 final size:5
Alignment explanation
Indices: 44016828--44016868 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
44016818 TTTAAAAAAA
44016828 TATATT TATAT TATAT TATAT TATAT TAATAT T-TAT T-TAT T
1 TATA-T TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT T
44016869 GAAATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 17 0.50
6 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:44016852 original size:21 final size:19
Alignment explanation
Indices: 44016828--44016868 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
44016818 TTTAAAAAAA
*
44016828 TATATTTATATTATATTATAT
1 TATATTAATATT-TATT-TAT
44016849 TATATTAATATTTATTTAT
1 TATATTAATATTTATTTAT
44016868 T
1 T
44016869 GAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTAATATTTATTTAT
Found at i:44021897 original size:13 final size:14
Alignment explanation
Indices: 44021879--44021911 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
44021869 GTTTCAAAAG
44021879 TTGCTTTTATG-CT
1 TTGCTTTTATGACT
44021892 TTGCTTTTATGACT
1 TTGCTTTTATGACT
44021906 TT-CTTT
1 TTGCTTT
44021912 AGAAGAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.09, C:0.15, G:0.12, T:0.64
Consensus pattern (14 bp):
TTGCTTTTATGACT
Found at i:44023280 original size:20 final size:20
Alignment explanation
Indices: 44023257--44023295 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44023247 AATTTAAAAA
44023257 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* *
44023277 TATATAAATTTATTAATAT
1 TATAAAAAATTATTAATAT
44023296 ATGTAATAAT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:44023357 original size:17 final size:17
Alignment explanation
Indices: 44023335--44023369 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44023325 TCTGCCAAAT
44023335 AACATAAAATATTTTAC
1 AACATAAAATATTTTAC
44023352 AACATAAAATATTTTAC
1 AACATAAAATATTTTAC
44023369 A
1 A
44023370 CAGATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (17 bp):
AACATAAAATATTTTAC
Found at i:44023436 original size:15 final size:14
Alignment explanation
Indices: 44023396--44023434 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
44023386 CCAGAAAATA
44023396 TTTTCAGTAAATCAT
1 TTTTCAG-AAATCAT
*
44023411 TTTTTAGAAATCAT
1 TTTTCAGAAATCAT
*
44023425 TTTTCGGAAA
1 TTTTCAGAAA
44023435 ATATTTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (14 bp):
TTTTCAGAAATCAT
Found at i:44038956 original size:22 final size:24
Alignment explanation
Indices: 44038926--44038969 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
44038916 ACATATAAAT
44038926 AAATAATTTAT-TATATATTTTAA
1 AAATAATTTATGTATATATTTTAA
44038949 AAAT-ATTTATGTATATATTTT
1 AAATAATTTATGTATATATTTT
44038970 TGAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
AAATAATTTATGTATATATTTTAA
Found at i:44039386 original size:22 final size:23
Alignment explanation
Indices: 44039361--44039403 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
44039351 AAAAATAAAT
44039361 AAATATTTAT-TATATATTTTAA
1 AAATATTTATGTATATATTTTAA
44039383 AAATATTTATGTATATATTTT
1 AAATATTTATGTATATATTTT
44039404 TGAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AAATATTTATGTATATATTTTAA
Found at i:44039739 original size:434 final size:435
Alignment explanation
Indices: 44038920--44039788 Score: 1731
Period size: 434 Copynumber: 2.0 Consensus size: 435
44038910 GTCCATACAT
44038920 ATAAATAAATAATTTATTATATATTTTAAAAATATTTATGTATATATTTTTGAATTATTTAGAAT
1 ATAAATAAATAATTTATTATATATTTTAAAAATATTTATGTATATATTTTTGAATTATTTAGAAT
44038985 TAAAATTAAATTGAGATCATGCGTTAAATTTTTTTTAAAAAATTATGATTAAATTATTATTTTAT
66 TAAAATTAAATTGAGATCATGCGTTAAATTTTTTTTAAAAAATTATGATTAAATTATTATTTTAT
44039050 TGATTTTTTAATTTCCATGTCACCTTCTTGTCAAACATTTAACGCCCTAAACAAAAATGGACAAA
131 TGATTTTTTAATTTCCATGTCACCTTCTTGTCAAACATTTAACGCCCTAAACAAAAATGGACAAA
44039115 AGAAACTCGATTAGTTGAATGGTTAATGTAAAAAATTTCATAATTGAATGAAAAAAAAATATGAG
196 AGAAACTCGATTAGTTGAATGGTTAATGTAAAAAATTTCATAATTGAATGAAAAAAAAATATGAG
44039180 TCCATAATTGAGTAACCTATGATACAATTTACCCTAATTTTTGCTCTATCAAAATTACAACATTT
261 TCCATAATTGAGTAACCTATGATACAATTTACCCTAATTTTTGCTCTATCAAAATTACAACATTT
44039245 CTCGATTAATGTACCGAATATTGTACCTAAAAGATATTAGGTAATCCAATGATAAAATACCAAGC
326 CTCGATTAATGTACCGAATATTGTACCTAAAAGATATTAGGTAATCCAATGATAAAATACCAAGC
44039310 ATGATTTGATGTCGATTGCCAAAATCTCCACCTCCTAAAAAAAAA
391 ATGATTTGATGTCGATTGCCAAAATCTCCACCTCCTAAAAAAAAA
44039355 ATAAATAAAT-ATTTATTATATATTTTAAAAATATTTATGTATATATTTTTGAATTATTTAGAAT
1 ATAAATAAATAATTTATTATATATTTTAAAAATATTTATGTATATATTTTTGAATTATTTAGAAT
44039419 TAAAATTAAATTGAGATCATGCGTTAAATTTTTTTTAAAAAATTATGATTAAATTATTATTTTAT
66 TAAAATTAAATTGAGATCATGCGTTAAATTTTTTTTAAAAAATTATGATTAAATTATTATTTTAT
44039484 TGATTTTTTAATTTCCATGTCACCTTCTTGTCAAACATTTAACGCCCTAAACAAAAATGGACAAA
131 TGATTTTTTAATTTCCATGTCACCTTCTTGTCAAACATTTAACGCCCTAAACAAAAATGGACAAA
44039549 AGAAACTCGATTAGTTGAATGGTTAATGTAAAAAATTTCATAATTGAATGAAAAAAAAATATGAG
196 AGAAACTCGATTAGTTGAATGGTTAATGTAAAAAATTTCATAATTGAATGAAAAAAAAATATGAG
44039614 TCCATAATTGAGTAACCTATGATACAATTTACCCTAATTTTTGCTCTATCAAAATTACAACATTT
261 TCCATAATTGAGTAACCTATGATACAATTTACCCTAATTTTTGCTCTATCAAAATTACAACATTT
44039679 CTCGATTAATGTACCGAATATTGTACCTAAAAGATATTAGGTAATCCAATGATAAAATACCAAGC
326 CTCGATTAATGTACCGAATATTGTACCTAAAAGATATTAGGTAATCCAATGATAAAATACCAAGC
44039744 ATGATTTGATGTCGATTGCCAAAATCTCCACCTCCTAAAAAAAAA
391 ATGATTTGATGTCGATTGCCAAAATCTCCACCTCCTAAAAAAAAA
44039789 TGTGCCTCCA
Statistics
Matches: 434, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
434 424 0.98
435 10 0.02
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (435 bp):
ATAAATAAATAATTTATTATATATTTTAAAAATATTTATGTATATATTTTTGAATTATTTAGAAT
TAAAATTAAATTGAGATCATGCGTTAAATTTTTTTTAAAAAATTATGATTAAATTATTATTTTAT
TGATTTTTTAATTTCCATGTCACCTTCTTGTCAAACATTTAACGCCCTAAACAAAAATGGACAAA
AGAAACTCGATTAGTTGAATGGTTAATGTAAAAAATTTCATAATTGAATGAAAAAAAAATATGAG
TCCATAATTGAGTAACCTATGATACAATTTACCCTAATTTTTGCTCTATCAAAATTACAACATTT
CTCGATTAATGTACCGAATATTGTACCTAAAAGATATTAGGTAATCCAATGATAAAATACCAAGC
ATGATTTGATGTCGATTGCCAAAATCTCCACCTCCTAAAAAAAAA
Found at i:44047065 original size:12 final size:13
Alignment explanation
Indices: 44047048--44047076 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44047038 TATTTCGACG
44047048 TCTTAGAGAATT-
1 TCTTAGAGAATTC
44047060 TCTTAGAGAATTC
1 TCTTAGAGAATTC
44047073 TCTT
1 TCTT
44047077 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (13 bp):
TCTTAGAGAATTC
Found at i:44049398 original size:48 final size:48
Alignment explanation
Indices: 44049346--44049439 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 48
44049336 AAGCTGTCAG
* * * *
44049346 AAATAGTGCAG-TAATCCGCTAGAATTAGATAAGTGTGATCAAGCCACC
1 AAATA-TGCAGATAAACCGCCAGAATCAGATAAGGGTGATCAAGCCACC
* * *
44049394 AAATATGCAGATAAACTGCCAGAATCAGATATGGGTGGTCAAGCCA
1 AAATATGCAGATAAACCGCCAGAATCAGATAAGGGTGATCAAGCCA
44049440 TCATAATCGC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 5 0.13
48 33 0.87
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (48 bp):
AAATATGCAGATAAACCGCCAGAATCAGATAAGGGTGATCAAGCCACC
Found at i:44065705 original size:29 final size:30
Alignment explanation
Indices: 44065659--44065717 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
44065649 GAATTGGATC
*
44065659 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATCGCACA
*
44065689 AAATCAAAATTT-ATGTATACAATCGCACA
1 AAATCAAAATTTCATGTATAAAATCGCACA
44065718 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATCGCACA
Found at i:44078477 original size:22 final size:21
Alignment explanation
Indices: 44078438--44078479 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
44078428 TGGGTGAAAG
*
44078438 AAAATATTTTATATTTTATTA
1 AAAATATTTTATAATTTATTA
*
44078459 AAAATATTTTTTTAATTTATT
1 AAAATA-TTTTATAATTTATT
44078480 CAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAAATATTTTATAATTTATTA
Found at i:44079229 original size:19 final size:20
Alignment explanation
Indices: 44079207--44079244 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44079197 AGCATTTAGG
*
44079207 AAAAAAATGTTTTT-ATTTT
1 AAAAAAATCTTTTTCATTTT
44079226 AAAAAAATCTTTTTCATTT
1 AAAAAAATCTTTTTCATTT
44079245 CTCACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
AAAAAAATCTTTTTCATTTT
Found at i:44081022 original size:32 final size:33
Alignment explanation
Indices: 44080976--44081040 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
44080966 GTTAAAGAGA
44080976 ATGATTTTTTTTCTTCAATTGTGCTGAATTCTT
1 ATGATTTTTTTTCTTCAATTGTGCTGAATTCTT
44081009 ATGA-TTTTTTTCTTCAATTGTGCTGAATTCTT
1 ATGATTTTTTTTCTTCAATTGTGCTGAATTCTT
44081041 TTTCTTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.57
Consensus pattern (33 bp):
ATGATTTTTTTTCTTCAATTGTGCTGAATTCTT
Found at i:44085882 original size:28 final size:29
Alignment explanation
Indices: 44085837--44085895 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
44085827 ATTTAAAAAC
*
44085837 ATAAAAATAAATATTAAAACAAGAAACAA
1 ATAAAAATAAATACTAAAACAAGAAACAA
* * *
44085866 ATAAAAAT-TATACTAAAACAATACACAA
1 ATAAAAATAAATACTAAAACAAGAAACAA
44085894 AT
1 AT
44085896 TGAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (29 bp):
ATAAAAATAAATACTAAAACAAGAAACAA
Found at i:44088847 original size:22 final size:24
Alignment explanation
Indices: 44088803--44088847 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
44088793 GTATTTGTAT
* *
44088803 GATTTGATTTCAATGTTATTTTGG
1 GATTTGATTTCAATGTGAATTTGG
44088827 GATTTG-TTT-AATGTGAATTTG
1 GATTTGATTTCAATGTGAATTTG
44088848 AGTTTGTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.53
Consensus pattern (24 bp):
GATTTGATTTCAATGTGAATTTGG
Found at i:44089318 original size:21 final size:21
Alignment explanation
Indices: 44089271--44089319 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
44089261 CGGCCCGTTT
* *
44089271 TTAAATTAAAATTATTTTTAA
1 TTAAATTAAAATAATTGTTAA
*
44089292 TAAAATTAAAACTAATTGTT-A
1 TTAAATTAAAA-TAATTGTTAA
44089313 TTAAATT
1 TTAAATT
44089320 TAATTGGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATTAAAATAATTGTTAA
Found at i:44089426 original size:16 final size:16
Alignment explanation
Indices: 44089418--44089461 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
44089408 ATTATTAATT
*
44089418 TTATTAATTTTATTAA
1 TTATTAATTGTATTAA
44089434 TTATTAATTGTATTAA
1 TTATTAATTGTATTAA
44089450 TTGTATTAATTG
1 -T-TATTAATTG
44089462 CTAATTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 1 0.04
18 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
TTATTAATTGTATTAA
Found at i:44089435 original size:25 final size:25
Alignment explanation
Indices: 44089407--44089460 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
44089397 AAATTTATCA
* *
44089407 AATTATTAATTTTATTAATTTTATT
1 AATTATTAATTGTATTAATTGTATT
44089432 AATTATTAATTGTATTAATTGTATT
1 AATTATTAATTGTATTAATTGTATT
44089457 AATT
1 AATT
44089461 GCTAATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
AATTATTAATTGTATTAATTGTATT
Found at i:44089461 original size:9 final size:9
Alignment explanation
Indices: 44089410--44089461 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
44089400 TTTATCAAAT
*
44089410 TATTAATTT
1 TATTAATTG
*
44089419 TATTAATTT
1 TATTAATTG
44089428 TATTAA-T-
1 TATTAATTG
44089435 TATTAATTG
1 TATTAATTG
44089444 TATTAATTG
1 TATTAATTG
44089453 TATTAATTG
1 TATTAATTG
44089462 CTAATTTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 6 0.15
8 2 0.05
9 33 0.80
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (9 bp):
TATTAATTG
Found at i:44089466 original size:25 final size:25
Alignment explanation
Indices: 44089407--44089467 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
44089397 AAATTTATCA
* * *
44089407 AATTATTAATTTTATTAATTTTATT
1 AATTACTAATTGTATTAATTGTATT
*
44089432 AATTATTAATTGTATTAATTGTATT
1 AATTACTAATTGTATTAATTGTATT
*
44089457 AATTGCTAATT
1 AATTACTAATT
44089468 TGCTATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
AATTACTAATTGTATTAATTGTATT
Found at i:44089656 original size:20 final size:20
Alignment explanation
Indices: 44089631--44089671 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
44089621 AGTAGAAGAC
*
44089631 TAAGAATAGAATTTAACCTT
1 TAAGAACAGAATTTAACCTT
44089651 TAAGAACAGAATTTAACCTT
1 TAAGAACAGAATTTAACCTT
44089671 T
1 T
44089672 CTTTGACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (20 bp):
TAAGAACAGAATTTAACCTT
Found at i:44090545 original size:15 final size:15
Alignment explanation
Indices: 44090525--44090556 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44090515 AGAAACCTCG
44090525 TCGTCATCGTCGTCA
1 TCGTCATCGTCGTCA
*
44090540 TCGTCATCGTTGTCA
1 TCGTCATCGTCGTCA
44090555 TC
1 TC
44090557 ATCCTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (15 bp):
TCGTCATCGTCGTCA
Found at i:44092707 original size:21 final size:21
Alignment explanation
Indices: 44092681--44092724 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
44092671 GAATATGTTC
44092681 TATATAATAATATAATAATATAT
1 TATATAAT-AT-TAATAATATAT
* *
44092704 TATATATTATTTATAATATAT
1 TATATAATATTAATAATATAT
44092725 ACAACAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATAATATTAATAATATAT
Found at i:44093006 original size:22 final size:22
Alignment explanation
Indices: 44092981--44093052 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
44092971 CTTTTAAATT
44092981 AATAACTCTTTAATTTGCTATA
1 AATAACTCTTTAATTTGCTATA
* * *** *
44093003 AATAA-TATATAGAATTTTAAATT
1 AATAACTCT-T-TAATTTGCTATA
44093026 AATAACTCTTTAATTTGCTATA
1 AATAACTCTTTAATTTGCTATA
44093048 AATAA
1 AATAA
44093053 TGAAAATTGT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 2 0.06
22 18 0.51
23 13 0.37
24 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (22 bp):
AATAACTCTTTAATTTGCTATA
Found at i:44094948 original size:13 final size:13
Alignment explanation
Indices: 44094930--44094954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44094920 CAAACCCGTA
44094930 CCTGTACCAAACT
1 CCTGTACCAAACT
44094943 CCTGTACCAAAC
1 CCTGTACCAAAC
44094955 GAAGAAGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.20
Consensus pattern (13 bp):
CCTGTACCAAACT
Found at i:44097689 original size:302 final size:301
Alignment explanation
Indices: 44097055--44097826 Score: 1159
Period size: 302 Copynumber: 2.6 Consensus size: 301
44097045 GCGGATTTAC
* * *** * * *
44097055 TATCAGAAGGGCCACTTTTACACACCTTATCATCACAGATAGGAGCAAAAGATTTTG---CATCT
1 TATCAGAAGGGCCACTCTCATGGACCTTATCATCACAGGTAGAATCAAAAGATTTTGTATCATCT
* *
44097117 ACCTCGCACATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTTTTAA
66 ACCTCGAACATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTTTTGA
*
44097182 ACAAACCCTGCAACCAAAACATAAAAAAAAACCCATGAATTTTCCTGTCACTGAAGTTTTCAAAC
131 ACAAACCCTGCAACCAAAACAT-AAAAGAAA-CCATGAATTTTCCTGTCACTGAAGTTTTCAAAC
44097247 AAAAAAGTTAAAAGACTACACTGTTATTGAAAATAATTTGCACTAAGCAATAAGAAATGTACAAA
194 AAAAAAGTTAAAAGACTACACTGTTATTGAAAATAATTTGCACTAAGCAATAAGAAATGTACAAA
*
44097312 AACCTTTTGTTGTCAATCCCCTCCTTGGTTTGGACTGGTTTGA
259 AACCTTTTGTTGTCAATCCCCTCCTTGGCTTGGACTGGTTTGA
* * *
44097355 TATCAGAAGGGCCACTCCCATGGACGTTATCATCACGGGTAGAATCAAAAGATTTTGTATCATCT
1 TATCAGAAGGGCCACTCTCATGGACCTTATCATCACAGGTAGAATCAAAAGATTTTGTATCATCT
*
44097420 ACCTCGAACATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTCTTGA
66 ACCTCGAACATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTTTTGA
44097485 ACAAACCCTGCAACCAAAACATAAAAGAAACCATGAATTTTACTCTGTCACTGAAGTTTTCAAAC
131 ACAAACCCTGCAACCAAAACATAAAAGAAACCATGAATTTT-C-CTGTCACTGAAGTTTTCAAAC
44097550 AAAAAAGTT-AAAGACTACACTGTTATTGAAAATAATTTGCACTAAGCAATAAGAAATGTACAAA
194 AAAAAAGTTAAAAGACTACACTGTTATTGAAAATAATTTGCACTAAGCAATAAGAAATGTACAAA
44097614 AACCTTTTGTTGTCAATCCCCTCCTTGGCTTGGACTGGTTTGA
259 AACCTTTTGTTGTCAATCCCCTCCTTGGCTTGGACTGGTTTGA
44097657 TATCAGAAGGGCCACTCTCATGGACCTTATCATCACAGGTAGAATCAAAAGATTTTGTATCATCT
1 TATCAGAAGGGCCACTCTCATGGACCTTATCATCACAGGTAGAATCAAAAGATTTTGTATCATCT
* * * * * **
44097722 ACCTC-AATTACATATTCAGTTGTTTC---TGCTTGGGTTTTATGCCTAGCAGATTGCCTTTTTG
66 ACCTCGAA-CATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTTTTG
* * * * **
44097783 CATACATCCTGCTAA-GGAAACATAAAAGAAACCAT-AATTTTCCT
130 AACAAACCCTGC-AACCAAAACATAAAAGAAACCATGAATTTTCCT
44097827 TTTTCATTGG
Statistics
Matches: 432, Mismatches: 33, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
296 2 0.00
297 1 0.00
298 6 0.01
299 56 0.13
300 48 0.11
301 13 0.03
302 187 0.43
303 119 0.28
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (301 bp):
TATCAGAAGGGCCACTCTCATGGACCTTATCATCACAGGTAGAATCAAAAGATTTTGTATCATCT
ACCTCGAACATATATTCAGTAGTTTCAGGTTCTTGGGCTTTAAACCTAGCAGATTGCCTTTTTGA
ACAAACCCTGCAACCAAAACATAAAAGAAACCATGAATTTTCCTGTCACTGAAGTTTTCAAACAA
AAAAGTTAAAAGACTACACTGTTATTGAAAATAATTTGCACTAAGCAATAAGAAATGTACAAAAA
CCTTTTGTTGTCAATCCCCTCCTTGGCTTGGACTGGTTTGA
Found at i:44098170 original size:66 final size:66
Alignment explanation
Indices: 44098059--44098186 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
44098049 CTCTTTCTGG
* ** * * *
44098059 TCATATTACACGGTTTATTCTCTTCATCTTCTCCTTTAAGAGATTCACCTGTCTCGCCACACCCG
1 TCATATTACAAGGTTTATTCTCGCCATCTTCTCCATCAAGAGATTCACCTGCCTCGCCACACCCG
44098124 T
66 T
* * * * *
44098125 TCATATTACAAGGTTTATTTTCGCCATCTTCTTCATCATGTGATTCACCTGCCTTGCCACAC
1 TCATATTACAAGGTTTATTCTCGCCATCTTCTCCATCAAGAGATTCACCTGCCTCGCCACAC
44098187 TTGTTTGTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.20, C:0.30, G:0.11, T:0.38
Consensus pattern (66 bp):
TCATATTACAAGGTTTATTCTCGCCATCTTCTCCATCAAGAGATTCACCTGCCTCGCCACACCCG
T
Found at i:44101532 original size:18 final size:18
Alignment explanation
Indices: 44101496--44101532 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44101486 AAATAATTTA
*
44101496 AAAATATTTTTTATTTTT
1 AAAATATTTTTTATGTTT
*
44101514 AAAATATTTTTTGTGTTT
1 AAAATATTTTTTATGTTT
44101532 A
1 A
44101533 TTAAAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
AAAATATTTTTTATGTTT
Found at i:44102491 original size:18 final size:20
Alignment explanation
Indices: 44102450--44102492 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44102440 GACTGAAAAG
*
44102450 TATTTTTATAATATTTTTAC
1 TATTTCTATAATATTTTTAC
44102470 TATTTCTATAAT-TTTTTA-
1 TATTTCTATAATATTTTTAC
44102488 TATTT
1 TATTT
44102493 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 6 0.27
20 11 0.50
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTCTATAATATTTTTAC
Found at i:44104724 original size:9 final size:9
Alignment explanation
Indices: 44104702--44104736 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
44104692 ATGATGCTCG
44104702 TTTTAAATTA
1 TTTTAAA-TA
44104712 TTTTAAATA
1 TTTTAAATA
44104721 TTTTTAAATA
1 -TTTTAAATA
44104731 TTTTAA
1 TTTTAA
44104737 TTACATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAAATA
Found at i:44105263 original size:2 final size:2
Alignment explanation
Indices: 44105256--44105282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44105246 TACTCGAATC
44105256 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44105283 ACACATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44106140 original size:25 final size:25
Alignment explanation
Indices: 44106112--44106161 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
44106102 CTCAATAACT
44106112 TAAATGAAAACTTTCAAATAGTTTA
1 TAAATGAAAACTTTCAAATAGTTTA
44106137 TAAATGAAAACTTTCAAATAGTTTA
1 TAAATGAAAACTTTCAAATAGTTTA
44106162 ATGGCCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (25 bp):
TAAATGAAAACTTTCAAATAGTTTA
Found at i:44116526 original size:16 final size:16
Alignment explanation
Indices: 44116505--44116569 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
44116495 TGCTCGTAAT
44116505 AATTTGAGTTTGAGAA
1 AATTTGAGTTTGAGAA
44116521 AATTTGAGTTTGA-AA
1 AATTTGAGTTTGAGAA
* * ***
44116536 AAGCTCGAGACCGAGAA
1 AA-TTTGAGTTTGAGAA
44116553 AATTTGAGTTTG-GAA
1 AATTTGAGTTTGAGAA
44116568 AA
1 AA
44116570 GCCTGAGTCT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
15 9 0.24
16 24 0.65
17 4 0.11
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (16 bp):
AATTTGAGTTTGAGAA
Found at i:44122315 original size:147 final size:147
Alignment explanation
Indices: 44122048--44122488 Score: 589
Period size: 147 Copynumber: 3.0 Consensus size: 147
44122038 TCTTTCTTTT
* * * *
44122048 CTACATTAACTTTATCTTCCACAA-CCAAGGAATCAACCCTTTCGGTGACCTCCTCCTTAAGTTC
1 CTACATTAACTTTATCTTCCACAACCCCA-GAATCATCCATTTCGGTAACCTCCTCCTTAAGTTC
* * *
44122112 AGACGTCAGGTTATCTTCCTTGATTGCATTTTCAGCATCTCCAATGTTTGATGAAATGCCACACT
65 AGATGTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTTGATGAAATGCCACGCT
* *
44122177 GAACTATCGTCCACTTGG
130 GAACTATAGTCGACTTGG
* *
44122195 CTACATTAACTTTATCTGCTACAACCCCAGAATCATCCATTTCGGTAACCTCCTCCTTAAGTTCA
1 CTACATTAACTTTATCTTCCACAACCCCAGAATCATCCATTTCGGTAACCTCCTCCTTAAGTTCA
* ** * * *
44122260 GATGTTAGGTTATCTTCCTTAATTGCACCTTCAGCATCTCCAATGTTCGATGAAATGTCAGGCTG
66 GATGTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTTGATGAAATGCCACGCTG
* * *
44122325 AACTATTGTAGACTTCG
131 AACTATAGTCGACTTGG
* * *
44122342 CTACATTAACTTTAACTTCCACAACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTAAGTTGA
1 CTACATTAACTTTATCTTCCACAACCCCAGAATCATCCATTTCGGTAACCTCCTCCTTAAGTTCA
* * * * * *
44122407 GATGTCAGGTTATCTTCCTTCATTACGTTTTCTGCATCT-AAATTGTTTGATGAAATGCCATGCT
66 GATGTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAA-TGTTTGATGAAATGCCACGCT
44122471 GAACTATAGTCGACTTGG
130 GAACTATAGTCGACTTGG
44122489 GTTCAAAACT
Statistics
Matches: 254, Mismatches: 38, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
146 2 0.01
147 249 0.98
148 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (147 bp):
CTACATTAACTTTATCTTCCACAACCCCAGAATCATCCATTTCGGTAACCTCCTCCTTAAGTTCA
GATGTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTTGATGAAATGCCACGCTG
AACTATAGTCGACTTGG
Found at i:44126336 original size:2 final size:2
Alignment explanation
Indices: 44126329--44126369 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
44126319 TTATCTGATT
44126329 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
44126370 TTGCTATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:44128929 original size:3 final size:3
Alignment explanation
Indices: 44128923--44128956 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
44128913 AGTATTGCAC
44128923 CAT CAT CAT CA- CAAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT C-AT CAT CAT CAT CAT CAT CAT C
44128957 TTAATATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:44130423 original size:19 final size:20
Alignment explanation
Indices: 44130379--44130424 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
44130369 AGTAATATAA
44130379 TATATATTTATTTTAATTGAG
1 TATATA-TTATTTTAATTGAG
*
44130400 -A-ATATTATTTT-ATTTAG
1 TATATATTATTTTAATTGAG
44130417 TATATATT
1 TATATATT
44130425 TAATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 8 0.36
20 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TATATATTATTTTAATTGAG
Found at i:44135526 original size:14 final size:14
Alignment explanation
Indices: 44135491--44135527 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
44135481 AAATGAAGGA
*
44135491 AATAATAGGA-ATG
1 AATAAAAGGAGATG
44135504 AAT-AAAGGAGATG
1 AATAAAAGGAGATG
44135517 AATAAAAGGAG
1 AATAAAAGGAG
44135528 GGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 9 0.43
14 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (14 bp):
AATAAAAGGAGATG
Found at i:44136668 original size:18 final size:18
Alignment explanation
Indices: 44136629--44136670 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44136619 ATAATGTGTT
* **
44136629 TTTATATGTTTTTGTACT
1 TTTATATGTTTTTATAAA
44136647 TTTATATGTTTTTATAAA
1 TTTATATGTTTTTATAAA
44136665 TTTATA
1 TTTATA
44136671 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (18 bp):
TTTATATGTTTTTATAAA
Found at i:44136683 original size:16 final size:18
Alignment explanation
Indices: 44136647--44136693 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
44136637 TTTTTGTACT
* *
44136647 TTTATATGTTTTTATAAA
1 TTTATATATATTTATAAA
44136665 TTTATA-ATATTTA-AAA
1 TTTATATATATTTATAAA
*
44136681 TTTGTATATATTT
1 TTTATATATATTT
44136694 GTATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 11 0.44
18 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTATATATATTTATAAA
Found at i:44145068 original size:13 final size:13
Alignment explanation
Indices: 44145047--44145123 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
44145037 ACACTCAAAT
* *
44145047 TTCTAAAAAGTAC
1 TTCTCAAAAGCAC
*
44145060 TTCTCAAAATCAC
1 TTCTCAAAAGCAC
44145073 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
44145086 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
44145099 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
44145112 TTCTCAAAAGCA
1 TTCTCAAAAGCA
44145124 ATGAAGAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:44149520 original size:3 final size:3
Alignment explanation
Indices: 44149512--44149542 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
44149502 GATTTAGTCC
44149512 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44149543 TTCATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44149662 original size:21 final size:20
Alignment explanation
Indices: 44149626--44149665 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
44149616 CATTACATAT
*
44149626 ATTTTATCTAATATATATAA
1 ATTTTATATAATATATATAA
44149646 ATTTTATATATATATATATA
1 ATTTTATATA-ATATATATA
44149666 TGCATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTATATAATATATATAA
Found at i:44160323 original size:63 final size:63
Alignment explanation
Indices: 44160236--44160357 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
44160226 ACTGTTTGCT
* * * *
44160236 ATTAGGGACCACACGGGCCAGAGACACTGGCACGTGTCTAGGCCGTGTGA-TTCACTGTTCACC
1 ATTAAGGACCACACAGGCCAGAGACACGGGCACGTGTCCAGGCCGTGTGACTT-ACTGTTCACC
* * *
44160299 ATTAAGGACCACATAGGCTAGAGACACGGGCATGTGTCCAGGCCGTGTGACTTACTGTT
1 ATTAAGGACCACACAGGCCAGAGACACGGGCACGTGTCCAGGCCGTGTGACTTACTGTT
44160358 TGCAAATTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 49 0.96
64 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (63 bp):
ATTAAGGACCACACAGGCCAGAGACACGGGCACGTGTCCAGGCCGTGTGACTTACTGTTCACC
Found at i:44160895 original size:29 final size:30
Alignment explanation
Indices: 44160859--44160918 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
44160849 AAACCTTTTT
*
44160859 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCT-AAAACTTTTACTCCTCTCCC
44160889 ACTTTCCCCTAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCTAAAACTTTTACTCCTCTCCC
44160919 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.38
Consensus pattern (30 bp):
ACTTTCCCCTAAAACTTTTACTCCTCTCCC
Found at i:44162093 original size:17 final size:17
Alignment explanation
Indices: 44162044--44162086 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44162034 TCTTTATTCA
* * *
44162044 AAAAAAAAAAAAAAAAG
1 AAAAAGAAAAACAGAAG
44162061 AAAAAGAAAAACAGAAG
1 AAAAAGAAAAACAGAAG
*
44162078 AAGAAGAAA
1 AAAAAGAAA
44162087 GAAAGAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAACAGAAG
Found at i:44163564 original size:138 final size:139
Alignment explanation
Indices: 44163291--44163566 Score: 482
Period size: 139 Copynumber: 2.0 Consensus size: 139
44163281 TTTAAGAAAA
* * **
44163291 TTGAACATACCGTGTTAAAACACATCAATATTCCATCCAAATCCGAGTGACGTTGAGGCTGATGT
1 TTGAACATACCGTGTTAAAACACATCAATATTCCATCCAAATCCAAGTAACGTTGAGGCCAATGT
44163356 AATTTTAAACTCTTACAAGTCACCGTTGATCAGAGATCCTAGAATTCCAGCCTTGAGGGTATAGT
66 AATTTTAAACTCTTACAAGTCACCGTTGATCAGAGATCCTAGAATTCCAGCCTTGAGGGTATAGT
44163421 AAGCAGCAG
131 AAGCAGCAG
*
44163430 TTGAACATACCGTGTTAAAACACATCAATATTCCATCCAAATCCAAGTAACGTTGGGGCCAATGT
1 TTGAACATACCGTGTTAAAACACATCAATATTCCATCCAAATCCAAGTAACGTTGAGGCCAATGT
* *
44163495 AATTTT-AACTCTTACAAGTCATCGTTGATCAGAGATCCTAGAATTCTAGCCTTGAGGGTATAGT
66 AATTTTAAACTCTTACAAGTCACCGTTGATCAGAGATCCTAGAATTCCAGCCTTGAGGGTATAGT
44163559 AAGCAGCA
131 AAGCAGCA
44163567 CCCATTCTTG
Statistics
Matches: 130, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
138 64 0.49
139 66 0.51
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (139 bp):
TTGAACATACCGTGTTAAAACACATCAATATTCCATCCAAATCCAAGTAACGTTGAGGCCAATGT
AATTTTAAACTCTTACAAGTCACCGTTGATCAGAGATCCTAGAATTCCAGCCTTGAGGGTATAGT
AAGCAGCAG
Found at i:44176798 original size:3 final size:3
Alignment explanation
Indices: 44176785--44176837 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
44176775 AATATAAATG
* *
44176785 TAA TGA TAA TAA TAA TAA CT-T TAA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA
44176831 TAA TAA T
1 TAA TAA T
44176838 GTCAACTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:44180090 original size:40 final size:40
Alignment explanation
Indices: 44179998--44180107 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 40
44179988 AACCTAATTA
* ** *
44179998 TTTTAAATATTTTATTAACAACTTTATGCTTTTTATAATG
1 TTTTAAATATTTTATTAACAATTTTATAATTTTTATAATC
*
44180038 TTTTCTAA-ATTTTATTAACAATTTTAATAATTTTCTAT-A-C
1 TTTT-AAATATTTTATTAACAATTTT-ATAATTTT-TATAATC
* *
44180078 TTTTAAATATTTT-TTTATAATTTTATAATT
1 TTTTAAATATTTTATTAACAATTTTATAATT
44180108 AATATTTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
38 6 0.10
39 11 0.19
40 29 0.50
41 9 0.16
42 3 0.05
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (40 bp):
TTTTAAATATTTTATTAACAATTTTATAATTTTTATAATC
Found at i:44180091 original size:20 final size:20
Alignment explanation
Indices: 44180057--44180102 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
44180047 TTTTATTAAC
44180057 AATTTT-AATAATTTTCTAT
1 AATTTTAAATAATTTTCTAT
* * *
44180076 ACTTTTAAATATTTTTTTAT
1 AATTTTAAATAATTTTCTAT
44180096 AATTTTA
1 AATTTTA
44180103 TAATTAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTAAATAATTTTCTAT
Found at i:44180103 original size:8 final size:8
Alignment explanation
Indices: 44180090--44180139 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
44180080 TTAAATATTT
44180090 TTTTATAA
1 TTTTATAA
44180098 TTTTATAA
1 TTTTATAA
* **
44180106 TTAATATTT
1 TT-TTATAA
44180115 TTTTATAA
1 TTTTATAA
44180123 TTTTATAA
1 TTTTATAA
44180131 TTTTATAA
1 TTTTATAA
44180139 T
1 T
44180140 ATTTTTTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 30 0.86
9 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:44180116 original size:25 final size:25
Alignment explanation
Indices: 44180083--44180132 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
44180073 TATACTTTTA
44180083 AATATTTTTTTATAATTTTATAATT
1 AATATTTTTTTATAATTTTATAATT
44180108 AATATTTTTTTATAATTTTATAATT
1 AATATTTTTTTATAATTTTATAATT
44180133 TTATAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
AATATTTTTTTATAATTTTATAATT
Found at i:44180582 original size:18 final size:17
Alignment explanation
Indices: 44180561--44180607 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
44180551 TTTTTGTCCT
*
44180561 TTTATATATTTTTATAAA
1 TTTATATATATTT-TAAA
44180579 TTTATA-ATATTTTAAA
1 TTTATATATATTTTAAA
*
44180595 TTTGTATATATTT
1 TTTATATATATTT
44180608 GTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 11 0.42
18 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTATATATATTTTAAA
Found at i:44180597 original size:26 final size:26
Alignment explanation
Indices: 44180568--44180628 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
44180558 CCTTTTATAT
*
44180568 ATTTTTATAAATTTATAATATTTTAA
1 ATTTGTATAAATTTATAATATTTTAA
* * * *
44180594 ATTTGTATATATTTGTATTATTTTTAT
1 ATTTGTATAAATTTATAATA-TTTTAA
44180621 ATTTGTAT
1 ATTTGTAT
44180629 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (26 bp):
ATTTGTATAAATTTATAATATTTTAA
Found at i:44180621 original size:17 final size:17
Alignment explanation
Indices: 44180601--44180636 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
44180591 TAAATTTGTA
44180601 TATATTTGTATTATTTT
1 TATATTTGTATTATTTT
44180618 TATATTTGTATTATTTT
1 TATATTTGTATTATTTT
44180635 TA
1 TA
44180637 ATATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TATATTTGTATTATTTT
Found at i:44180631 original size:11 final size:10
Alignment explanation
Indices: 44180563--44180633 Score: 59
Period size: 10 Copynumber: 7.9 Consensus size: 10
44180553 TTTGTCCTTT
*
44180563 TATATATTTT
1 TATATATTTG
* *
44180573 TATAAATTTA
1 TATATATTTG
44180583 TA-ATATTT-
1 TATATATTTG
44180591 TA-A-ATTTG
1 TATATATTTG
44180599 TATATATTTG
1 TATATATTTG
44180609 TAT-TATTT-
1 TATATATTTG
44180617 T-TATATTTG
1 TATATATTTG
44180626 TAT-TATTT
1 TATATATTT
44180634 TTAATATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
7 5 0.10
8 11 0.21
9 17 0.33
10 19 0.37
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (10 bp):
TATATATTTG
Found at i:44184895 original size:20 final size:20
Alignment explanation
Indices: 44184867--44184914 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
44184857 TAACAACTTT
* *
44184867 AATAATTTTCCATATTTTTA
1 AATATTTTTCCATAATTTTA
*
44184887 AATATTTTTTCATAATTTTA
1 AATATTTTTCCATAATTTTA
44184907 AA-ATTTTT
1 AATATTTTT
44184915 ATTTTTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTTTCCATAATTTTA
Found at i:44184982 original size:9 final size:9
Alignment explanation
Indices: 44184970--44185057 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
44184960 TTTTTGCAAT
44184970 TTTTTATAA
1 TTTTTATAA
*
44184979 TTTTAATAA
1 TTTTTATAA
*
44184988 TTTATAT-A
1 TTTTTATAA
*
44184996 TCATTTATAA
1 T-TTTTATAA
44185006 TATTTT-TAA
1 T-TTTTATAA
*
44185015 TTTGTATATA
1 TTTTTATA-A
** *
44185025 TTTCAATTA
1 TTTTTATAA
44185034 TTTTTAT-A
1 TTTTTATAA
*
44185042 TTTTTATGA
1 TTTTTATAA
44185051 TTTTTAT
1 TTTTTAT
44185058 TATAAAATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 13 0.21
9 37 0.61
10 11 0.18
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:44185002 original size:27 final size:26
Alignment explanation
Indices: 44184972--44185027 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
44184962 TTTGCAATTT
44184972 TTTATAAT-TTTAATAATTTATATATCA
1 TTTATAATATTT-ATAATTTATATAT-A
* *
44184999 TTTATAATATTTTTAATTTGTATATA
1 TTTATAATATTTATAATTTATATATA
44185025 TTT
1 TTT
44185028 CAATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 19 0.73
28 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATAATATTTATAATTTATATATA
Found at i:44187101 original size:20 final size:21
Alignment explanation
Indices: 44187064--44187103 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44187054 TTTTAATAGT
44187064 TTTTAAATTTTATTAAAAAAA
1 TTTTAAATTTTATTAAAAAAA
*
44187085 TTTTATATTTT-TTAAAAAA
1 TTTTAAATTTTATTAAAAAA
44187104 TTATGAATTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAAATTTTATTAAAAAAA
Found at i:44196411 original size:15 final size:15
Alignment explanation
Indices: 44196391--44196421 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44196381 GGTTAGTGTT
44196391 GGAGTTGAGTTTGGG
1 GGAGTTGAGTTTGGG
44196406 GGAGTTGAGTTTGGG
1 GGAGTTGAGTTTGGG
44196421 G
1 G
44196422 TTGGAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.55, T:0.32
Consensus pattern (15 bp):
GGAGTTGAGTTTGGG
Found at i:44196915 original size:16 final size:16
Alignment explanation
Indices: 44196894--44196926 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44196884 CGTCATTGTC
44196894 AATAAAATTTATCAAA
1 AATAAAATTTATCAAA
44196910 AATAAAATTTATCAAA
1 AATAAAATTTATCAAA
44196926 A
1 A
44196927 GTAATACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAAATTTATCAAA
Found at i:44204783 original size:16 final size:17
Alignment explanation
Indices: 44204746--44204787 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
44204736 AATTATAATG
*
44204746 AAATAAAATATTTATTA
1 AAATAAAATATTTATAA
*
44204763 AAATATAATATTT-TAA
1 AAATAAAATATTTATAA
44204779 AAATAAAAT
1 AAATAAAAT
44204788 GAATAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAATATTTATAA
Done.