Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005039.1 Hibiscus syriacus cultivar Beakdansim tig00011312_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 112412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:740 original size:30 final size:29
Alignment explanation
Indices: 699--774 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
689 TTAGATAATA
* *
699 ATAATAATTTATAGT-ATTTAGATAAATTT
1 ATAATATTTTATAATCATTTA-ATAAATTT
*
728 ATTAATATTTTATAATCTTTTAATAAATTT
1 A-TAATATTTTATAATCATTTAATAAATTT
758 ATAAGTATTTTTATAAT
1 ATAA-TA-TTTTATAAT
775 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.10
30 23 0.57
31 13 0.32
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (29 bp):
ATAATATTTTATAATCATTTAATAAATTT
Found at i:786 original size:30 final size:29
Alignment explanation
Indices: 715--789 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
705 ATTTATAGTA
715 TTTAGATAAATTTATTAATATTTTATAATCT
1 TTTA-ATAAATTTA-TAATATTTTATAATCT
*
746 TTTAATAAATTTATAAGTATTTTTATAATTT
1 TTTAATAAATTTATAA-TA-TTTTATAATCT
*
777 TTTTA-AAATTTAT
1 TTTAATAAATTTAT
790 TGAAGAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 3 0.08
30 19 0.47
31 18 0.45
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTAATAAATTTATAATATTTTATAATCT
Found at i:7496 original size:23 final size:23
Alignment explanation
Indices: 7452--7496 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7442 GGTGGCTATT
* *
7452 CGACGATGACGATAAGTGATGAA
1 CGACGACGACGATAAGTAATGAA
7475 CGACGACGACTGATAA-TAATGA
1 CGACGACGAC-GATAAGTAATGA
7497 GGTTTGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.18
Consensus pattern (23 bp):
CGACGACGACGATAAGTAATGAA
Found at i:7931 original size:2 final size:2
Alignment explanation
Indices: 7920--7970 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
7910 TTTTAGGTGG
7920 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7961 TA TA TA TA TA
1 TA TA TA TA TA
7971 AAACTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8492 original size:17 final size:17
Alignment explanation
Indices: 8464--8505 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
8454 TTTTAAAAAA
8464 TATTATTTATTTATTTAT
1 TATTA-TTATTTATTTAT
*
8482 TATTATTATTTTTTTAT
1 TATTATTATTTATTTAT
*
8499 TAATATT
1 TATTATT
8506 TTTGTAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTATTTATTTAT
Found at i:8577 original size:23 final size:23
Alignment explanation
Indices: 8551--8594 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
8541 CTACCGTACC
* * *
8551 ATTAATCTTATTCCACTACTACT
1 ATTAATCCTACTCCACCACTACT
8574 ATTAATCCTACTCCACCACTA
1 ATTAATCCTACTCCACCACTA
8595 TTACATGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTAATCCTACTCCACCACTACT
Found at i:13134 original size:16 final size:15
Alignment explanation
Indices: 13108--13153 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
13098 AGATCTAATC
* *
13108 AAGAACAAAAAGAGAA
1 AAGAA-AAAAACAAAA
13124 AAGAAACAAAACAAAA
1 AAGAAA-AAAACAAAA
13140 AAGAAAAAAACAAA
1 AAGAAAAAAACAAA
13154 GGAAAAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAACAAAA
Found at i:13160 original size:20 final size:22
Alignment explanation
Indices: 13111--13153 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13101 TCTAATCAAG
13111 AACAAAAAGAGAAAAGAAACAA
1 AACAAAAAGAGAAAAGAAACAA
13133 AACAAAAA-AGAAAA-AAACAA
1 AACAAAAAGAGAAAAGAAACAA
13153 A
1 A
13154 GGAAAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (22 bp):
AACAAAAAGAGAAAAGAAACAA
Found at i:13161 original size:42 final size:42
Alignment explanation
Indices: 13114--13203 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
13104 AATCAAGAAC
13114 AAAAAGAGAAAAGAAACAAAACAAAAAAG-AA-AAAAACAAAGG
1 AAAAAGAGAAAAGAAA-AAAA-AAAAAAGAAACAAAAACAAAGG
** * * *
13156 AAAAAGCTAAGAGAAAATAAAAAAGAGAAACAAAAACAAAGG
1 AAAAAGAGAAAAGAAAAAAAAAAAAAGAAACAAAAACAAAGG
13198 AAAAAG
1 AAAAAG
13204 TGAAGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.15
41 5 0.12
42 30 0.73
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.02
Consensus pattern (42 bp):
AAAAAGAGAAAAGAAAAAAAAAAAAAGAAACAAAAACAAAGG
Found at i:13285 original size:20 final size:19
Alignment explanation
Indices: 13246--13285 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13236 AGATTCTCTC
*
13246 TATTCAAATTACGCATCGA
1 TATTCAAATTACGAATCGA
*
13265 TATTCAAATTATGAAATCGA
1 TATTCAAATTACG-AATCGA
13285 T
1 T
13286 TAAGCACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (19 bp):
TATTCAAATTACGAATCGA
Found at i:16553 original size:3 final size:3
Alignment explanation
Indices: 16547--16603 Score: 89
Period size: 3 Copynumber: 18.7 Consensus size: 3
16537 AAAAAAATAG
16547 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
16594 TAT T-T TAT TA
1 TAT TAT TAT TA
16604 ATGTTTTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21989 original size:17 final size:17
Alignment explanation
Indices: 21936--22026 Score: 53
Period size: 17 Copynumber: 5.2 Consensus size: 17
21926 AAGAAACAAC
*
21936 AAAAATAAAACAAATTAA
1 AAAAATAAAACAAAAT-A
**
21954 ATAAAATGGGAACACAAATA
1 A-AAAAT-AAAACA-AAATA
21974 AAAAATAAAACAAAATA
1 AAAAATAAAACAAAATA
* *
21991 AGAAAA-ATAA-GAAATA
1 A-AAAATAAAACAAAATA
*
22007 AAACA-AAAACAAAAATA
1 AAAAATAAAAC-AAAATA
22024 AAA
1 AAA
22027 CAACGATAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
15 6 0.11
16 6 0.11
17 17 0.30
18 9 0.16
19 10 0.18
20 6 0.11
21 3 0.05
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAATAAAACAAAATA
Found at i:22027 original size:17 final size:17
Alignment explanation
Indices: 21964--22029 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
21954 ATAAAATGGG
* *
21964 AACACAAATAAAAAATAA
1 AACAAAAATAAAACA-AA
21982 AAC-AAAATAAGAA-AAA
1 AACAAAAATAA-AACAAA
* *
21998 TA-AGAAATAAAACAAA
1 AACAAAAATAAAACAAA
22014 AACAAAAATAAAACAA
1 AACAAAAATAAAACAA
22030 CGATAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 2 0.05
16 13 0.33
17 19 0.49
18 5 0.13
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (17 bp):
AACAAAAATAAAACAAA
Found at i:22037 original size:17 final size:17
Alignment explanation
Indices: 21974--22089 Score: 67
Period size: 19 Copynumber: 6.6 Consensus size: 17
21964 AACACAAATA
* *
21974 AAAAATAAAACAAAATAAG
1 AAAAATAAAA-ATAA-AAC
21993 AAAAATAAGAAATAAAAC
1 AAAAATAA-AAATAAAAC
*
22011 AAAAACAAAAATAAAAC
1 AAAAATAAAAATAAAAC
** *
22028 AACGATAAAAA-AGAA-
1 AAAAATAAAAATAAAAC
* * *
22043 AAAAATAGAATTAAATAA
1 AAAAATAAAAATAAA-AC
22061 AAGAAATAAAAGA-AACAAC
1 AA-AAATAAAA-ATAA-AAC
22080 AAAAATAAAA
1 AAAAATAAAA
22090 CAAATAAGGC
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.09
16 5 0.07
17 18 0.24
18 19 0.25
19 23 0.31
20 3 0.04
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (17 bp):
AAAAATAAAAATAAAAC
Found at i:22047 original size:32 final size:31
Alignment explanation
Indices: 21969--22093 Score: 91
Period size: 32 Copynumber: 4.0 Consensus size: 31
21959 ATGGGAACAC
*
21969 AAATAAAA-AATAAAAC-AAAATAAGAAAAATAAG
1 AAATAAAAGAA-AAAACAAAAAT-A-AAACA-AAG
* *
22002 AAATAAAA-CAAAAACAAAAATAAAACAACG
1 AAATAAAAGAAAAAACAAAAATAAAACAAAG
*
22032 ATAA-AAAAGAAAAAA-ATAGAATTAAATA-AAAG
1 A-AATAAAAGAAAAAACA-A-AAATAAA-ACAAAG
*
22064 AAATAAAAGAAACAACAAAAATAAAACAAA
1 AAATAAAAGAAAAAACAAAAATAAAACAAA
22094 TAAGGCAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
30 9 0.12
31 23 0.31
32 27 0.36
33 16 0.21
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (31 bp):
AAATAAAAGAAAAAACAAAAATAAAACAAAG
Found at i:22069 original size:9 final size:8
Alignment explanation
Indices: 21969--22096 Score: 66
Period size: 9 Copynumber: 14.8 Consensus size: 8
21959 ATGGGAACAC
21969 AAAT-AAA
1 AAATAAAA
21976 AAATAAAACA
1 AAAT-AAA-A
21986 AAATAAGAA
1 AAATAA-AA
*
21995 AAAT-AAG
1 AAATAAAA
22002 AAATAAAA
1 AAATAAAA
22010 CAAA-AACAA
1 -AAATAA-AA
22019 AAATAAAA
1 AAATAAAA
22027 CAACGAT-AAA
1 -AA--ATAAAA
*
22037 AAAGAAAA
1 AAATAAAA
*
22045 AAATAGAATT
1 AAATA-AA-A
22055 AAATAAAA
1 AAATAAAA
22063 GAAATAAAA
1 -AAATAAAA
*
22072 GAAACAACAA
1 -AAATAA-AA
22082 AAATAAAA
1 AAATAAAA
22090 CAAATAA
1 -AAATAA
22097 GGCAAAAACA
Statistics
Matches: 96, Mismatches: 8, Indels: 32
0.71 0.06 0.24
Matches are distributed among these distances:
7 10 0.10
8 19 0.20
9 49 0.51
10 16 0.17
11 2 0.02
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.11
Consensus pattern (8 bp):
AAATAAAA
Found at i:22177 original size:20 final size:21
Alignment explanation
Indices: 22136--22178 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
22126 ATTTAATGGT
22136 TAATAAAACAAGTAAAAAATA
1 TAATAAAACAAGTAAAAAATA
* *
22157 TAATAAAAGAA-TAATAAATA
1 TAATAAAACAAGTAAAAAATA
22177 TA
1 TA
22179 TATCAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
TAATAAAACAAGTAAAAAATA
Found at i:22256 original size:21 final size:21
Alignment explanation
Indices: 22232--22288 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
22222 ATGTATACGT
**
22232 ATAAATAAAATATTAAAGAAA
1 ATAAATAAAATAAGAAAGAAA
*
22253 AT-AATAATAATAAGAAAGTAA
1 ATAAATAA-AATAAGAAAGAAA
22274 ATAGGAATAAAATAA
1 ATA--AATAAAATAA
22289 ACAACAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
23 5 0.17
24 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAAATAAAATAAGAAAGAAA
Found at i:24325 original size:121 final size:118
Alignment explanation
Indices: 24050--24447 Score: 387
Period size: 121 Copynumber: 3.3 Consensus size: 118
24040 AAGTTGAGCT
* * * * *
24050 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA--T---G-GATGCTGCTTGTGGGCACG
1 TTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGTGA-GTTACTGGTGGGCACG
* * * * *
24109 ATATCCTTCATCGTGAAGTTGAAATCATAGATAGCCCATTCGTTGTGAAGTTGAGCC
65 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAA---AAGCC
*
24166 TTGAATTGGATATCTTTTGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGGGCA
1 TTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAG-TG-A-GTTACTGGTGGGCA
* * *
24231 CAATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAAAGCC
63 CGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAAAGCC
* ** ** * *
24287 TCGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTTGAGTGAGTTGGTTGTGGGCATGA
1 TTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGTGAGTTACTGGTGGGCACGA
* * * * * * *
24352 TATCCTCCGTCGTGGAGTTGAAATCGTGGCTGGCTCTTTCGTTG-CAAAGTTGAGCT
66 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAA----AGCC
*
24408 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC
1 TTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATC
24448 CTTTTCTTTC
Statistics
Matches: 237, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
116 35 0.15
117 3 0.01
118 51 0.22
119 1 0.00
120 2 0.01
121 87 0.37
123 1 0.00
124 57 0.24
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (118 bp):
TTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGTGAGTTACTGGTGGGCACGA
TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAAAGCC
Found at i:24502 original size:58 final size:61
Alignment explanation
Indices: 24407--24566 Score: 240
Period size: 58 Copynumber: 2.7 Consensus size: 61
24397 AAAGTTGAGC
24407 TTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCCTTTT-CTTTCACCAAATT-GG
1 TTTG-ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCCTTTTAC-TTCACCAAATTGGG
24468 -TT-ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT-CTTTTACTTCACCAAATTGGG
1 TTTGATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCCTTTTACTTCACCAAATTGGG
* *
24526 TTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATC
1 TTTGA-TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC
24567 TCGAGTAAGT
Statistics
Matches: 91, Mismatches: 2, Indels: 11
0.88 0.02 0.11
Matches are distributed among these distances:
57 16 0.18
58 38 0.42
59 2 0.02
60 3 0.03
61 32 0.35
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (61 bp):
TTTGATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCCTTTTACTTCACCAAATTGGG
Found at i:24776 original size:14 final size:14
Alignment explanation
Indices: 24757--24783 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24747 CGGTTGCCTG
24757 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
24771 TCTGGAATCTTGA
1 TCTGGAATCTTGA
24784 AGTTCTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:25414 original size:10 final size:10
Alignment explanation
Indices: 25394--25443 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
25384 CCCACCTTAT
25394 TTTTCTTTTTC
1 TTTT-TTTTTC
25405 TTTTTTTTTC
1 TTTTTTTTTC
* *
25415 -TTTTCTTTG
1 TTTTTTTTTC
*
25424 TTATTTTTTC
1 TTTTTTTTTC
25434 TTTTTTTTTC
1 TTTTTTTTTC
25444 AATTTAGGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 7 0.22
10 21 0.66
11 4 0.12
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:25551 original size:81 final size:82
Alignment explanation
Indices: 25399--25557 Score: 196
Period size: 81 Copynumber: 2.0 Consensus size: 82
25389 CTTATTTTTC
* * ** * ** * *
25399 TTTTTCTTTTTTTTTCTTTTCTTTGTTATTTTTTCTTTTTTTTTCAATTTAGGGCGCCCTTTCGG
1 TTTTTCTTTTTTGTTCTTTTCTTTGTTATTTCTTCTTCCTTCTTCAACCTAGGACGCCCTCTCGG
25464 GTTTTTACCCTAAACAT
66 GTTTTTACCCTAAACAT
*
25481 TTTTTCTTTTTTGTTCTTTTCTTT-TCTATTTCTT-TTCCTTCTTCGACCTAGGACGCCCTCTCG
1 TTTTTCTTTTTTGTTCTTTTCTTTGT-TATTTCTTCTTCCTTCTTCAACCTAGGACGCCCTCTCG
*
25544 GGTTTTTATCCTAA
65 GGTTTTTACCCTAA
25558 GGAAATATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 35 0.54
82 30 0.46
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.59
Consensus pattern (82 bp):
TTTTTCTTTTTTGTTCTTTTCTTTGTTATTTCTTCTTCCTTCTTCAACCTAGGACGCCCTCTCGG
GTTTTTACCCTAAACAT
Found at i:30839 original size:2 final size:2
Alignment explanation
Indices: 30829--31226 Score: 68
Period size: 2 Copynumber: 206.0 Consensus size: 2
30819 AATTGAAAAA
*
30829 AT AT A- AT AT AT AT AT AT A- AT AT A- AT AT -T AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
30868 AT AT TT AT AT -T AT AA ACT AT AT AT AT AA AT -T AT AT TT AT GT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
** * * * *
30909 GC AT -T AT AT AT AT AA ACT AT GT AT AT A- AA AT -T AT AA ACT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* *
30950 AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T AT A- AGT -T AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
30988 AT AT AT AT AT AT AT -T AT GT TT AT GT GA- ACT AT GT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT A-T
* * * * * *
31031 AT AT AT GT AT AA ACT AT AA AA AGT AT AT A- AT TT AT A- AA AT AT
1 AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
31073 -T AT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT AA ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* * * * * *
31114 GT AT AA ACT AT AT A- AA AT AT AT AGT TT AT AT GT -T AT A- AT TT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
31155 AT AT -T A- AT AT AGT AT AT GT AT GT AT GT AT GT AT A- ACT A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
31195 AT A- AGT A- AT AT AT AG A- AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31227 TAAAGAAATA
Statistics
Matches: 280, Mismatches: 66, Indels: 100
0.63 0.15 0.22
Matches are distributed among these distances:
1 32 0.11
2 230 0.82
3 18 0.06
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30863 original size:30 final size:29
Alignment explanation
Indices: 30829--30892 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
30819 AATTGAAAAA
*
30829 ATATAATA-TATATATATAATATAATATTAT
1 ATATAA-ACTATATATATAATATAA-ACTAT
* *
30859 ATATAAACTATATTTATATTATAAACTAT
1 ATATAAACTATATATATAATATAAACTAT
30888 ATATA
1 ATATA
30893 TAAATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATAAACTATATATATAATATAAACTAT
Found at i:30976 original size:18 final size:18
Alignment explanation
Indices: 30834--30998 Score: 99
Period size: 18 Copynumber: 8.8 Consensus size: 18
30824 AAAAAATATA
30834 ATATATATA-TAT-AA-T
1 ATATATATATTATAAACT
30849 ATA-ATATTATATATAAACT
1 ATATATA-TAT-TATAAACT
*
30868 ATATTTATATTATAAACT
1 ATATATATATTATAAACT
**
30886 ATATATATAAATTAT-ATTT
1 ATATATAT--ATTATAAACT
*
30905 ATGTGCATTATATATATAAACT
1 ATAT--A-TATAT-TATAAACT
*
30927 ATGTATATAAAATTATAAACT
1 A--TATAT-ATATTATAAACT
*
30948 ATATTTATATTATAAACT
1 ATATATATATTATAAACT
**
30966 ATATA-ATTATTATAAGTT
1 ATATATA-TATTATAAACT
30984 ATATATATATATATA
1 ATATATATAT-TATA
30999 TATTATGTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
14 3 0.03
15 5 0.04
17 4 0.03
18 49 0.42
19 21 0.18
20 9 0.08
21 14 0.12
22 10 0.09
24 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATATATATTATAAACT
Found at i:30997 original size:80 final size:76
Alignment explanation
Indices: 30829--31001 Score: 199
Period size: 80 Copynumber: 2.2 Consensus size: 76
30819 AATTGAAAAA
* *
30829 ATATAATATATATATATAATATAATATTATATATAAACTATATTTATATTATAAACTATATATAT
1 ATATAATATATATATATAATATAATATAAAATATAAACTATATTTATATTATAAACTATATATAT
*
30894 AAATTATATTT
66 AAATTATAGTT
* * *
30905 ATGTGCAT-TATATATATAAACTATGTATATAAAATTATAAACTATATTTATATTATAAACTATA
1 ATAT-AATATATATATAT-AA-TAT-AATATAAAA-TATAAACTATATTTATATTATAAACTATA
*
30969 TA-AT-TATTATAAGTT
61 TATATAAATTAT-AGTT
30984 ATATATATATATATATAT
1 ATATA-ATATATATATAT
31002 TATGTTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
76 12 0.15
77 4 0.05
78 8 0.10
79 16 0.20
80 40 0.50
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (76 bp):
ATATAATATATATATATAATATAATATAAAATATAAACTATATTTATATTATAAACTATATATAT
AAATTATAGTT
Found at i:31088 original size:98 final size:98
Alignment explanation
Indices: 30852--31102 Score: 242
Period size: 104 Copynumber: 2.5 Consensus size: 98
30842 ATATAATATA
* * * * *
30852 ATATT-ATA-TATAAACTA-TATTTATATTATAAACTATATATATAAATTATATTTATGTGCATT
1 ATATTAATATTATAAAATATTATTTATATTATATA-TATATATATATATTATATTTATGTGAACT
* *
30914 ATATATATAAACTATGTATATAAAATTATAAACT
65 ATATATATAAACTATATATATAAAATTAAAAACT
* * *
30948 ATATTTATATTATAAACTATATAATTATTATAAGTTATATATATATATATATATTATGTTTATGT
1 ATATTAATATTATAAA--ATATTA-T-TTAT-A-TTATATATATATATATATATTATATTTATGT
* * *
31013 GAACTATGTATATAAACTATATATGTATAAACTATAAAAAGT
60 GAACTATATATATAAACTATATA--TATAAAAT-TAAAAACT
31055 ATA-TAAT-TTATAAAATATTATTTATATTAATATAGTATATATATATAT
1 ATATTAATATTATAAAATATTATTTATATT-ATATA-TATATATATATAT
31103 AAACTATATA
Statistics
Matches: 127, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
96 5 0.04
97 3 0.02
98 6 0.05
99 2 0.02
100 8 0.06
101 18 0.14
102 2 0.02
103 9 0.07
104 42 0.33
105 13 0.10
106 10 0.08
107 9 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (98 bp):
ATATTAATATTATAAAATATTATTTATATTATATATATATATATATATTATATTTATGTGAACTA
TATATATAAACTATATATATAAAATTAAAAACT
Found at i:31110 original size:17 final size:17
Alignment explanation
Indices: 31090--31127 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
31080 ATTAATATAG
31090 TATATATATATATAAAC
1 TATATATATATATAAAC
*
31107 --TATATATGTATAAAC
1 TATATATATATATAAAC
31122 TATATA
1 TATATA
31128 AAATATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
15 14 0.78
17 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
TATATATATATATAAAC
Found at i:31125 original size:77 final size:77
Alignment explanation
Indices: 31021--31171 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
31011 GTGAACTATG
*
31021 TATATAAACTATATATGTATAAACTATA-AAAAGTATATAATTTATAAAATATTATTTATATTAA
1 TATATAAACTATATATGTATAAACTATATAAAA-TATATAATTTATAAAATATAATTTATATTAA
31085 TATAGTATATATA
65 TATAGTATATATA
* ***
31098 TATATAAACTATATATGTATAAACTATATAAAATATATAGTTTATATGTTATAATTTATATTAAT
1 TATATAAACTATATATGTATAAACTATATAAAATATATAATTTATAAAATATAATTTATATTAAT
31163 ATAGTATAT
66 ATAGTATAT
31172 GTATGTATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
77 64 0.94
78 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (77 bp):
TATATAAACTATATATGTATAAACTATATAAAATATATAATTTATAAAATATAATTTATATTAAT
ATAGTATATATA
Found at i:31477 original size:42 final size:42
Alignment explanation
Indices: 31419--31506 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
31409 ACAATAGTTA
* * *
31419 ATATATGTAACTTATAGTATGTGTATTCATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATATAATGTAAACT
31461 ATATATGTAACTTATAGTATATGTATACATATAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATATAATGTAAACT
31503 ATAT
1 ATAT
31507 GCATAAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (42 bp):
ATATATGTAACTTATAGTATATGTATACATATAATGTAAACT
Found at i:31717 original size:37 final size:37
Alignment explanation
Indices: 31657--31727 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
31647 ATAGTTAATA
31657 TATATAATGTAACATATAATATATGTATACATGTAAGC
1 TATATAATGTAACATATAATATATGTAT-CATGTAAGC
* *
31695 TATAT-ATGTAACTTATAGTATATGTATCATGTA
1 TATATAATGTAACATATAATATATGTATCATGTA
31728 TGTATAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 6 0.19
37 20 0.65
38 5 0.16
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (37 bp):
TATATAATGTAACATATAATATATGTATCATGTAAGC
Found at i:31790 original size:24 final size:22
Alignment explanation
Indices: 31713--31823 Score: 101
Period size: 20 Copynumber: 5.2 Consensus size: 22
31703 TAACTTATAG
*
31713 TATATGTATCATGTATGTATAAAC
1 TATA-GTAT-ATGTATATATAAAC
*
31737 TAT-GTATA-GTGTATATAAAC
1 TATAGTATATGTATATATAAAC
*
31757 TAT-GTATA--TATATATAACC
1 TATAGTATATGTATATATAAAC
31776 TATAGTATATGTATATATACAATC
1 TATAGTATATGTATATATA-AA-C
*
31800 TAT-TTATATGT-TATATAAAC
1 TATAGTATATGTATATATAAAC
31820 TATA
1 TATA
31824 TATGTAACCT
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
19 12 0.16
20 27 0.36
21 3 0.04
22 18 0.24
23 8 0.11
24 7 0.09
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (22 bp):
TATAGTATATGTATATATAAAC
Found at i:31808 original size:39 final size:39
Alignment explanation
Indices: 31730--31808 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
31720 ATCATGTATG
* *
31730 TATAAACTATGTATAGTGTATATAAACTATGTATATATA
1 TATAAACTATGTATAGTGTATATAAACAATCTATATATA
* * *
31769 TATAACCTATAGTATA-TGTATATATACAATCTATTTATA
1 TATAAACTAT-GTATAGTGTATATAAACAATCTATATATA
31808 T
1 T
31809 GTTATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (39 bp):
TATAAACTATGTATAGTGTATATAAACAATCTATATATA
Found at i:39345 original size:23 final size:24
Alignment explanation
Indices: 39318--39363 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
39308 TTTTTCTTTG
*
39318 TATAAATTAAATTATA-TAATTTA
1 TATAAATTAAACTATATTAATTTA
39341 TATAAATTAAACTATATTAATTT
1 TATAAATTAAACTATATTAATTT
39364 TCCTTTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAATTAAACTATATTAATTTA
Found at i:39540 original size:16 final size:16
Alignment explanation
Indices: 39521--39598 Score: 120
Period size: 16 Copynumber: 4.9 Consensus size: 16
39511 CATTTACATA
* *
39521 TCAGGTTAAAAACATG
1 TCAGGTTGAAAACAAG
* *
39537 TCAGGTTAAAAACAGG
1 TCAGGTTGAAAACAAG
39553 TCAGGTTGAAAACAAG
1 TCAGGTTGAAAACAAG
39569 TCAGGTTGAAAACAAG
1 TCAGGTTGAAAACAAG
39585 TCAGGTTGAAAACA
1 TCAGGTTGAAAACA
39599 GGTCGGGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (16 bp):
TCAGGTTGAAAACAAG
Found at i:45737 original size:18 final size:20
Alignment explanation
Indices: 45698--45740 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
45688 GAAAGAATGT
45698 AAATAGAAAAATAATGAATA
1 AAATAGAAAAATAATGAATA
*
45718 AAATAG-AAAATGAT-AATA
1 AAATAGAAAAATAATGAATA
45736 AAATA
1 AAATA
45741 ACTAAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (20 bp):
AAATAGAAAAATAATGAATA
Found at i:45803 original size:17 final size:17
Alignment explanation
Indices: 45778--45813 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
45768 ATAAAATGGG
45778 AACACAAATAAATAATAA
1 AACACAAATAAA-AATAA
45796 AACA-AAATAAAAATAA
1 AACACAAATAAAAATAA
45812 AA
1 AA
45814 ATAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (17 bp):
AACACAAATAAAAATAA
Found at i:45810 original size:6 final size:6
Alignment explanation
Indices: 45799--45825 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45789 ATAATAAAAC
45799 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
45826 CAACGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:45836 original size:28 final size:27
Alignment explanation
Indices: 45783--45884 Score: 89
Period size: 28 Copynumber: 3.7 Consensus size: 27
45773 ATGGGAACAC
45783 AAATAAATAATAAAACAAAATAAAAATAA
1 AAATAAA-AATAAAACAAAATAAAAA-AA
*
45812 AAATAAAAATAAAACAACGATAAAAAAA
1 AAATAAAAATAAAACAA-AATAAAAAAA
* ** **
45840 GAA-AAAAATGGAATTAAATAAAAGAAA
1 AAATAAAAATAAAACAAAATAAAA-AAA
* *
45867 CAACAAAAATAAAACAAA
1 AAATAAAAATAAAACAAA
45885 TAAGACAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
26 6 0.10
27 14 0.24
28 24 0.41
29 14 0.24
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (27 bp):
AAATAAAAATAAAACAAAATAAAAAAA
Found at i:45906 original size:2 final size:2
Alignment explanation
Indices: 45899--45941 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
45889 ACAAAAACAA
*
45899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45941 A
1 A
45942 ATTTAATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45977 original size:20 final size:20
Alignment explanation
Indices: 45952--45993 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45942 ATTTAATGGT
45952 TAATAAAACAAGTAA-AAATA
1 TAATAAAACAA-TAATAAATA
*
45972 TAATAAAAGAATAATAAATA
1 TAATAAAACAATAATAAATA
45992 TA
1 TA
45994 TATCAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
TAATAAAACAATAATAAATA
Found at i:46111 original size:3 final size:3
Alignment explanation
Indices: 46105--46157 Score: 88
Period size: 3 Copynumber: 17.0 Consensus size: 3
46095 AACAAAAAAA
46105 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46151 AAAT AAT
1 -AAT AAT
46158 CGTAAAAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49370 original size:17 final size:18
Alignment explanation
Indices: 49344--49386 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49334 ATTATATGAA
*
49344 TATT-TTATTCAT-TTTT
1 TATTATTATTCATGTTAT
*
49360 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
49378 TATTATTAT
1 TATTATTAT
49387 ACGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:49445 original size:2 final size:2
Alignment explanation
Indices: 49438--49504 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
49428 TACTATATTT
49438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49480 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 T
49505 GTTTCTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49574 original size:82 final size:83
Alignment explanation
Indices: 49490--49647 Score: 207
Period size: 82 Copynumber: 1.9 Consensus size: 83
49480 TATATATATA
* * ** *
49490 TATATATATATATATGTT-T-C-TTTAATATTTTACTTATATGTCTATTATTACTATATATATT-
1 TATATATATAAATAT-TTATACTTTTAATAGTTTACTTATATACCTATTATTAATATATATATTC
49551 GTAATTATCTTTATCTAGT
65 GTAATTATCTTTATCTAGT
* *
49570 TATATATATAAATATTTATACTTTTAATAGTTTATTTATATACCTATTATTAATATATATATTCT
1 TATATATATAAATATTTATACTTTTAATAGTTTACTTATATACCTATTATTAATATATATATTCG
*
49635 TAATTATTTTTAT
66 TAATTATCTTTAT
49648 TTGATTATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 2 0.03
80 15 0.23
81 1 0.02
82 36 0.55
83 12 0.18
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (83 bp):
TATATATATAAATATTTATACTTTTAATAGTTTACTTATATACCTATTATTAATATATATATTCG
TAATTATCTTTATCTAGT
Found at i:49710 original size:4 final size:4
Alignment explanation
Indices: 49703--49731 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
49693 TATATATATA
49703 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
49732 TCATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:49979 original size:36 final size:38
Alignment explanation
Indices: 49930--50005 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
49920 AGTGAGAGGG
* *
49930 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATATATATATA
*
49966 TAGCTTATT-TATTTTATTAATACTTTGATATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATATATATATA
50004 TA
1 TA
50006 TATATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.35
37 7 0.21
38 15 0.44
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATAAATACTTTGATATATATATA
Found at i:50000 original size:2 final size:2
Alignment explanation
Indices: 49993--50018 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49983 TAATACTTTG
49993 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50019 TTCATTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50092 original size:9 final size:9
Alignment explanation
Indices: 50078--50102 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
50068 CCATATCTTA
50078 TTTATTTAT
1 TTTATTTAT
50087 TTTATTTAT
1 TTTATTTAT
50096 TTTATTT
1 TTTATTT
50103 TTTCCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:54584 original size:10 final size:10
Alignment explanation
Indices: 54561--54595 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
54551 AGATTCAATC
54561 AAGAACAAAA
1 AAGAACAAAA
54571 AAGAA-AAAA
1 AAGAACAAAA
54580 CAAGAACAAAA
1 -AAGAACAAAA
54591 AAGAA
1 AAGAA
54596 AAGAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (10 bp):
AAGAACAAAA
Found at i:54585 original size:20 final size:20
Alignment explanation
Indices: 54560--54597 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
54550 AAGATTCAAT
54560 CAAGAACAAAAAAGAAAAAA
1 CAAGAACAAAAAAGAAAAAA
54580 CAAGAACAAAAAAGAAAA
1 CAAGAACAAAAAAGAAAA
54598 GAAGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
CAAGAACAAAAAAGAAAAAA
Found at i:54613 original size:22 final size:21
Alignment explanation
Indices: 54564--54613 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
54554 TTCAATCAAG
*
54564 AACAAAAAAGAAAA-AACAAG
1 AACAAAAAAGAAAAGAACAAA
54584 AACAAAAAAGAAAAGAAGCAAA
1 AACAAAAAAGAAAAGAA-CAAA
54606 AATCAAAA
1 AA-CAAAA
54614 GGAAAAGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 5 0.19
23 5 0.19
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (21 bp):
AACAAAAAAGAAAAGAACAAA
Found at i:55691 original size:18 final size:18
Alignment explanation
Indices: 55668--55703 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55658 TCAACATCAA
*
55668 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
55686 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
55704 GGATTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:56245 original size:38 final size:36
Alignment explanation
Indices: 56169--56238 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
56159 GTGCTCACCA
*
56169 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAACT
56205 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
56239 ACCTTTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAACT
Found at i:56260 original size:29 final size:32
Alignment explanation
Indices: 56222--56280 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
56212 TCTTGAGACA
56222 GTTTCCCTTG-AA-A-AAAAACCTTTGAAATT
1 GTTTCCCTTGAAACACAAAAACCTTTGAAATT
*
56251 GTTTCTCTTGAAACACAAAAACCTTTGAAA
1 GTTTCCCTTGAAACACAAAAACCTTTGAAA
56281 CATAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
30 2 0.08
31 1 0.04
32 14 0.54
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (32 bp):
GTTTCCCTTGAAACACAAAAACCTTTGAAATT
Found at i:57263 original size:106 final size:106
Alignment explanation
Indices: 57075--57640 Score: 880
Period size: 106 Copynumber: 5.3 Consensus size: 106
57065 CGCATCCACG
* * *
57075 ATTTCAACTCCACAACGGAGGATATTGCGTCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAGCGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTTCACAACGAA
* * *
57140 GGGGCGGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
57184 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
57249 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* ** *
57290 ATTTCAACTTCACAACGAAGGGCATTGGACTCGAGACAACAAAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
57355 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** *
57396 ATTTCAACTTCACAGCGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
57461 ACGACTGGTTGTTAACAAACAATTTCCCAATTTCAGAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
57502 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCATAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
57567 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** * *
57608 ATTTCAACTTCATGGCGGAGAATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
57641 GAACAATACT
Statistics
Matches: 427, Mismatches: 30, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
106 402 0.94
108 1 0.00
109 24 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:59141 original size:34 final size:33
Alignment explanation
Indices: 59066--59142 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
59056 TATATAAGTC
*
59066 TATATTATATATATATTGTAATTATATTTATTAGT
1 TATA-TATATATATATTGT-ATTATATTTAATAGT
59101 TATATATATATATATT-T-TTATACTTTTAATAGT
1 TATATATATATATATTGTATTATA--TTTAATAGT
59134 TAT-TATATA
1 TATATATATA
59143 CCTATTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 5 0.13
32 6 0.15
33 12 0.31
34 12 0.31
35 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (33 bp):
TATATATATATATATTGTATTATATTTAATAGT
Found at i:59472 original size:34 final size:38
Alignment explanation
Indices: 59425--59499 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 38
59415 AGTAAGAGGG
59425 TAGCTTTTCTATTTTA-AATA-TTG-T-TGTATATATA
1 TAGCTTTTCTATTTTATAATACTTGATGTGTATATATA
59459 TAGCTTATT-TATTTTATTAATACTTGATGTGTATATATA
1 TAGCTT-TTCTATTTTA-TAATACTTGATGTGTATATATA
59498 TA
1 TA
59500 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
34 13 0.37
35 2 0.06
36 4 0.11
37 3 0.09
38 1 0.03
39 12 0.34
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATAATACTTGATGTGTATATATA
Found at i:59497 original size:2 final size:2
Alignment explanation
Indices: 59490--59516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59480 ACTTGATGTG
59490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59517 TATTTTTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59589 original size:9 final size:9
Alignment explanation
Indices: 59575--59599 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59565 CCTTGTCTTA
59575 TTTATTTAT
1 TTTATTTAT
59584 TTTATTTAT
1 TTTATTTAT
59593 TTTATTT
1 TTTATTT
59600 TTCCCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:65091 original size:2 final size:2
Alignment explanation
Indices: 65084--65120 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65074 TTCAGGTTTA
65084 AT AT AT AT AT 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 AT AT AT AT AT A
65121 ATAGTATAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75663 original size:3 final size:3
Alignment explanation
Indices: 75655--75703 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
75645 ATGTAAATTA
* *
75655 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
75703 A
1 A
75704 TACAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:76010 original size:46 final size:43
Alignment explanation
Indices: 75947--76192 Score: 184
Period size: 46 Copynumber: 5.7 Consensus size: 43
75937 TCGAGGGTTG
*
75947 ACACTGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT--AGG-GATA
* * * * * ** *
75993 ACATGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGG-TG
1 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAGGGATA
* *
76035 ACACGGCTCATACGTGATGAAGAGATCTGG---TC-AGGGAATG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAGGG-ATA
76075 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT--AGG-GATA
* * * * ** *
76121 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGG-TG
1 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAGGGATA
*
76163 ACACGGCTCATACGTGATGAAGAGATCTGG
1 ACACGGCTCATACGTGATGAAGAGTTCTGG
76193 TCTGGGGATG
Statistics
Matches: 160, Mismatches: 27, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
38 4 0.03
39 2 0.01
40 31 0.19
41 2 0.01
42 49 0.31
43 4 0.03
44 6 0.04
46 59 0.37
47 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (43 bp):
ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAGGGATA
Found at i:76056 original size:88 final size:83
Alignment explanation
Indices: 75869--76064 Score: 232
Period size: 88 Copynumber: 2.3 Consensus size: 83
75859 GGATGCCACT
* * * * *
75869 GCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACATGGTTCCTACGTGATGAGGAAATC
1 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGGTAACATGGTTCCTACGTGATGAGGAAAGC
*
75934 TAGTCGAGGGTTGACACT
66 TAGTCGAGGGTTGACACG
*
75952 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGAC
1 GCTCATACGTGATGAAGAGTTCTGGCCATCT-AAGG-G-TAACATGGTTCCTACGTGATGAGGAA
* * *
76017 GGCTGGTTATCTAGGG-TGACACG
63 AGCTAG---TCGAGGGTTGACACG
*
76040 GCTCATACGTGATGAAGAGATCTGG
1 GCTCATACGTGATGAAGAGTTCTGG
76065 TCAGGGAATG
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
83 28 0.29
84 4 0.04
85 1 0.01
86 27 0.28
88 30 0.31
89 6 0.06
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (83 bp):
GCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGGTAACATGGTTCCTACGTGATGAGGAAAGC
TAGTCGAGGGTTGACACG
Found at i:76087 original size:40 final size:41
Alignment explanation
Indices: 75858--76222 Score: 181
Period size: 40 Copynumber: 8.6 Consensus size: 41
75848 TTGGTTGTTG
* * * * *
75858 GGGATGCCACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAA
1 GGGATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC-AA
* * * * * * *
75902 GGG-TGACATGGTTCCTACGTGATGAGGAAATCTAG-TCGA
1 GGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCAA
* * *
75941 GGGTTGACACTGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGGATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC--AA
* * * * * * *
75986 GGTGATAACATGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GG-GATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATCAA
76030 GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-A
1 GGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCAA
*
76068 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC--AA
* * * * * *
76114 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GG-GATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATCAA
**
76158 GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTG
1 GGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCAA
** *
76197 GGGATGACACGATTCCTACGTGATGA
1 GGGATGACACGGCTCATACGTGATGA
76223 GGACGGTTGG
Statistics
Matches: 245, Mismatches: 55, Indels: 46
0.71 0.16 0.13
Matches are distributed among these distances:
38 4 0.02
39 12 0.05
40 76 0.31
41 2 0.01
42 49 0.20
43 28 0.11
44 9 0.04
45 3 0.01
46 59 0.24
47 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (41 bp):
GGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCAA
Found at i:76129 original size:128 final size:127
Alignment explanation
Indices: 75901--76222 Score: 500
Period size: 128 Copynumber: 2.5 Consensus size: 127
75891 GGGTCGTCTA
* * * * * * * *
75901 AGGGTGACATGGTTCCTACGTGATGAGGAAATCTAGTCGAGGGTTGACACTGCTCATACGTGATG
1 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-AGGGATGACACGGCTCATACGTGATG
*
75966 AAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCT
65 AAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
76029 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGAATGACACGGCTCATACGTGATG
1 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGG-ATGACACGGCTCATACGTGATG
76094 AAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
65 AAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
* ** *
76157 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGATTCCTACGTGATG
1 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-AGGGATGACACGGCTCATACGTGATG
76222 A
65 A
76223 GGACGGTTGG
Statistics
Matches: 179, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
127 4 0.02
128 172 0.96
129 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (127 bp):
AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGATGACACGGCTCATACGTGATGA
AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
Found at i:76182 original size:88 final size:82
Alignment explanation
Indices: 76073--76228 Score: 222
Period size: 88 Copynumber: 1.8 Consensus size: 82
76063 GGTCAGGGAA
* * *
76073 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGATTCCTACGTGA
76138 TGAGGACGGCTGGTTATCTAGGG
60 TGAGGACGGCTGGTTATCTAGGG
*
76161 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGATTCCTACGTGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGATTCCTACGTGATGAGGA
76226 CGG
66 CGG
76229 TTGGCCATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
82 30 0.47
85 3 0.05
88 31 0.48
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (82 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGATTCCTACGTGATGAGGA
CGGCTGGTTATCTAGGG
Found at i:76302 original size:28 final size:28
Alignment explanation
Indices: 76271--76347 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
76261 AAACCAAATT
76271 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
76299 AAAGATTCGTTTCAAGAA-AAACAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
76327 AAAGATGATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
76348 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 29 0.71
29 2 0.05
30 3 0.07
31 7 0.17
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:76414 original size:26 final size:27
Alignment explanation
Indices: 76373--76423 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
76363 AGACAAAATT
76373 TTGTTTCAAAGGAAAC-GACTCAAAGA
1 TTGTTTCAAAGGAAACTGACTCAAAGA
*
76399 TTGTTT-AAAGGAAAACTGTCTCAAA
1 TTGTTTCAAAGG-AAACTGACTCAAA
76424 TGAGACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (27 bp):
TTGTTTCAAAGGAAACTGACTCAAAGA
Found at i:76416 original size:63 final size:62
Alignment explanation
Indices: 76349--76466 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
76339 TTTCAAAAGC
*
76349 AACTGTCTCCAAA-GAGACAAAATTTTGTTTCAAA-GGAAACGA-CTCAAAGATTGTTTAAAGGA
1 AACTGTCT-CAAATGAGACAAAA-TTCGTTT-AAAGGGAAACGATCTCAAAGA-TGTTTAAAGGA
76411 A
62 A
*
76412 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGTTT
76467 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 3 0.06
62 22 0.44
63 25 0.50
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (62 bp):
AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGTTTAAAGGAA
Found at i:76752 original size:40 final size:40
Alignment explanation
Indices: 76708--76787 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
76698 GTTTTAATAG
*
76708 AAACGATATCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
*
76748 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
76788 CGAGAGACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (40 bp):
AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
Found at i:76848 original size:31 final size:30
Alignment explanation
Indices: 76800--76865 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
76790 AGAGACAAAA
* *
76800 TTTTGTTTCAAAGGAAACAAACTCAAAGAT
1 TTTTTTTTCAAAAGAAACAAACTCAAAGAT
*
76830 TTTTTTTTCCAAAAGAAACAATCTCAAAGAT
1 TTTTTTTT-CAAAAGAAACAAACTCAAAGAT
76861 TTTTT
1 TTTTT
76866 CACAAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTTTTTCAAAAGAAACAAACTCAAAGAT
Found at i:76962 original size:63 final size:62
Alignment explanation
Indices: 76839--76982 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 62
76829 TTTTTTTTTC
*
76839 CAAAAGAAACA-ATCTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1 CAAAAGAAACAGA-CTCAAAGATTTTTTCAAAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
* ** * *
76901 C-AAAGTAAATAGACTCAAAGATTTTTTCAAAAGAAATTGTCTTTA-AGAGATAAAATTTTGTTT
1 CAAAAG-AAACAGACTCAAAGATTTTTTC-AAA-AAATTGTCTCAAGAGAGACAAAACTTTGTTT
76964 CAAAAGAAACAGACTCAAA
1 CAAAAGAAACAGACTCAAA
76983 TGATGGATCT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
61 4 0.06
62 20 0.29
63 32 0.46
64 14 0.20
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (62 bp):
CAAAAGAAACAGACTCAAAGATTTTTTCAAAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
Found at i:77251 original size:63 final size:64
Alignment explanation
Indices: 77137--77367 Score: 213
Period size: 63 Copynumber: 3.6 Consensus size: 64
77127 ACTCAAAGAT
* ** ** * *
77137 TTTCAAAATG-AACATATTCAAAGATTTACTTCAAAAGAAACGGTCTCAAGAGATACAAAATTCA
1 TTTCAAAA-GAAACAAATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTCA
* * * * * **
77201 TTT-AAGAGAAACAGATTTAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAATTTTG
1 TTTCAAAAGAAACAAATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTCA
*
77264 TTTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAATTT
1 TTTCAAAAGAAACAAATTCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAA-TT
**
77328 TG
63 CA
* *
77330 TTTCCAAA-AAACAAACTCAAAGA--TTTTTCAAAAGAAAC
1 TTTCAAAAGAAACAAATTCAAAGATTTTTTTCAAAAGAAAC
77368 GACTCAAAGA
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
61 13 0.09
62 3 0.02
63 48 0.34
64 19 0.13
65 22 0.15
66 37 0.26
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (64 bp):
TTTCAAAAGAAACAAATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTCA
Found at i:77268 original size:36 final size:35
Alignment explanation
Indices: 77223--77338 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 35
77213 AGATTTAAAG
*
77223 ATTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAA
1 ATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AA
* * *
77258 ATTTTGTTTCAAAAGAAACAAAC-TCA-A-AG--A
1 ATTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA
*
77288 TTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAA
1 ATTTTGTTTCAAAAGAAACTATCTTAAGAGAG-AAA
77324 ATTTTGTTTCCAAAA
1 ATTTTGTTT-CAAAA
77339 AACAAACTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
30 21 0.33
31 2 0.03
32 1 0.02
33 4 0.06
34 1 0.02
35 7 0.11
36 23 0.36
37 5 0.08
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (35 bp):
ATTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA
Found at i:77311 original size:66 final size:65
Alignment explanation
Indices: 77166--77357 Score: 228
Period size: 66 Copynumber: 3.0 Consensus size: 65
77156 AAAGATTTAC
** * * * ** * * * *
77166 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCATTT-AAGAGAAACAGATTTAAAGA-TTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTT
*
77229 TTCAAAAGAAATTATCTTAAGAGAGACAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTG
1 TTCAAAAGAAACTATCTTAAGAGAGACAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT-
77294 T
65 T
* *
77295 TTCAAAAGAAACTATCTTAAGAGAGAAAAATTTTGTTTCCAAA-AAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
77358 CAAAAGAAAC
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
63 30 0.27
64 16 0.14
65 24 0.22
66 41 0.37
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (65 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTT
Found at i:77316 original size:29 final size:30
Alignment explanation
Indices: 77259--77589 Score: 181
Period size: 29 Copynumber: 11.1 Consensus size: 30
77249 GAGAGACAAA
77259 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
77289 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
*
77325 TTTTGTTTCCAAA-AAACAAACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
77353 --TT-TTTCAAAAGAAAC-GACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
77379 ATTT-ATTCAAAAGGAACAAACTCCAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
77408 TTTT-ATTCAAAAGGAACAAACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* *** *
77436 TTTT-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAACTC-A-A-AG----AT
* * * * *
77472 CTTTGTTTTAAAATAAATAGACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
77501 -TTT-TTTCAAAAGAAAC-AACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
77528 ATTT-ATTCAAAAGGAACAAACTCCAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
77557 TTTT-ATTCAAAAGGAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
77586 TTTT
1 TTTT
77590 CAAGAGAAAC
Statistics
Matches: 240, Mismatches: 38, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
25 16 0.07
26 15 0.06
27 10 0.04
28 47 0.20
29 78 0.32
30 22 0.09
31 4 0.02
32 3 0.01
33 3 0.01
34 4 0.02
35 8 0.03
36 17 0.07
37 13 0.05
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:77459 original size:28 final size:28
Alignment explanation
Indices: 77324--77589 Score: 193
Period size: 29 Copynumber: 9.2 Consensus size: 28
77314 AGAGAGAAAA
*
77324 ATTTTGTTTCCAAA-AAACAAACTCAAAG
1 ATTTT-TTTCAAAAGAAACAAACTCAAAG
*
77352 A--TTTTTCAAAAGAAAC-GACTCAAAG
1 ATTTTTTTCAAAAGAAACAAACTCAAAG
* * *
77377 ATATTTATTCAAAAGGAACAAACTCCAAG
1 AT-TTTTTTCAAAAGAAACAAACTCAAAG
*
77406 ATTTTTATTCAAAAGGAACAAACTCAAAG
1 ATTTTT-TTCAAAAGAAACAAACTCAAAG
* ***
77435 ATTTTTTTCAAGAGAAACTGTCTCAAGAGAG
1 ATTTTTTTCAAAAGAAACAAACTC-A-A-AG
* * * * *
77466 ACAAAACTTTGTTTTAAAATAAATAGACTCAAAG
1 -----A-TTTTTTTCAAAAGAAACAAACTCAAAG
77500 A-TTTTTTCAAAAGAAAC-AACTCAAAG
1 ATTTTTTTCAAAAGAAACAAACTCAAAG
* * *
77526 ATATTTATTCAAAAGGAACAAACTCCAAG
1 AT-TTTTTTCAAAAGAAACAAACTCAAAG
*
77555 ATTTTTATTCAAAAGGAACAAACTCAAAG
1 ATTTTT-TTCAAAAGAAACAAACTCAAAG
77584 ATTTTT
1 ATTTTT
77590 CAAGAGAAAC
Statistics
Matches: 189, Mismatches: 30, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
25 16 0.08
26 15 0.08
27 12 0.06
28 47 0.25
29 75 0.40
30 1 0.01
31 2 0.01
34 2 0.01
35 1 0.01
36 2 0.01
37 16 0.08
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.29
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAAACTCAAAG
Found at i:77548 original size:149 final size:146
Alignment explanation
Indices: 77265--77617 Score: 548
Period size: 149 Copynumber: 2.4 Consensus size: 146
77255 CAAATTTTGT
* * * * *
77265 TTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAATTTTG
1 TTCAAAAGGAACAAACTCAAAGA-TTTT-TTTCAAGAGAAACTGTCTCAAGAGAGAAAAACTTTG
* *
77330 TTTCCAAAAAACAAACTCAAAGATTTTTCAAAAGAAACGACTCAAAGATATTTATTCAAAAGGAA
64 TTTCAAAAAAACAAACTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAA
77395 CAAACTCCAAGATTTTTA
129 CAAACTCCAAGATTTTTA
77413 TTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAACTTTGT
* * *
77478 TTTAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGA
65 TTCAAAA-AAACAAACTCAAAGA-TTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGA
77543 ACAAACTCCAAGATTTTTA
128 ACAAACTCCAAGATTTTTA
*
77562 TTCAAAAGGAACAAACTCAAAGA--TTTTTCAAGAGAAACTGTCTCAAGAGACAAAAA
1 TTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGAAAAA
77618 TCGTTTTAAA
Statistics
Matches: 191, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
146 28 0.15
147 46 0.24
148 35 0.18
149 82 0.43
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (146 bp):
TTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGAAAAACTTTGTT
TCAAAAAAACAAACTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACA
AACTCCAAGATTTTTA
Found at i:77959 original size:36 final size:35
Alignment explanation
Indices: 77865--77961 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 35
77855 TTAAGATATA
* * **
77865 GTCTCAAATGAGACCAAATTTGTTTTTATAGAAATT
1 GTCTCAAGTGAGA-CAAATTTGTTTTTAGAGAAAAC
*
77901 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAA-TTTGTTTTTAGAGAAAAC
*
77936 GATCTCAAGTGAGATCAACTTTGTTT
1 G-TCTCAAGTGAGA-CAAATTTGTTT
77962 AATGTGAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
35 10 0.20
36 38 0.75
37 3 0.06
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (35 bp):
GTCTCAAGTGAGACAAATTTGTTTTTAGAGAAAAC
Found at i:78081 original size:105 final size:101
Alignment explanation
Indices: 77901--78133 Score: 290
Period size: 105 Copynumber: 2.3 Consensus size: 101
77891 TATAGAAATT
* *
77901 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
77966 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
78003 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
78067 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
78108 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
78134 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.18
103 2 0.02
104 4 0.04
105 77 0.68
106 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:78656 original size:16 final size:15
Alignment explanation
Indices: 78609--78660 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
78599 ATATGTATAT
78609 ATGTATGTATGAATTG
1 ATGTATGTATG-ATTG
78625 ATGTATGTAT-A-T-
1 ATGTATGTATGATTG
78637 ATGTATGTATGAGTTG
1 ATGTATGTATGA-TTG
78653 ATGTATGT
1 ATGTATGT
78661 TTCTCAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.31
13 2 0.06
14 1 0.03
15 1 0.03
16 18 0.56
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (15 bp):
ATGTATGTATGATTG
Found at i:78660 original size:4 final size:4
Alignment explanation
Indices: 78575--78647 Score: 73
Period size: 4 Copynumber: 19.0 Consensus size: 4
78565 ATGCAAATTT
* *
78575 TATG TAT- TATG TATG TATG --TG TATA TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
78620 AAT- TGATG TATG TATA TATG TATG TATG
1 TATG T-ATG TATG TATG TATG TATG TATG
78648 AGTTGATGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 3 0.05
4 50 0.89
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:79837 original size:12 final size:11
Alignment explanation
Indices: 79809--79846 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
79799 TCTTCTTTTG
*
79809 TTCTTTGCTTT
1 TTCTTTGATTT
79820 TTCTTTGATTT
1 TTCTTTGATTT
79831 TTGCTTTGATTT
1 TT-CTTTGATTT
79843 TTCT
1 TTCT
79847 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:80540 original size:26 final size:26
Alignment explanation
Indices: 80462--80543 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
80452 TTTCAAGGTG
80462 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
80488 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
80509 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
80534 GATAGAATGT
1 GAAAGAATGT
80544 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.51
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:80542 original size:46 final size:45
Alignment explanation
Indices: 80450--80543 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
80440 ATAAATACAG
* * *
80450 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
80495 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
80541 TGT
1 TGT
80544 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:86520 original size:3 final size:3
Alignment explanation
Indices: 86512--86581 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
86502 ATGTAAATTA
86512 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
86560 AAT AAT AAT AAC GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
86582 TACAAAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:88020 original size:14 final size:14
Alignment explanation
Indices: 88001--88028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
87991 CTTTATGTAT
88001 GTTGACCTTTTGAC
1 GTTGACCTTTTGAC
88015 GTTGACCTTTTGAC
1 GTTGACCTTTTGAC
88029 TTTACATATG
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:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
GTTGACCTTTTGAC
Found at i:91186 original size:19 final size:19
Alignment explanation
Indices: 91162--91198 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
91152 ATGATCAACA
*
91162 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
91181 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
91199 CAGTATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:91328 original size:20 final size:20
Alignment explanation
Indices: 91305--91419 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
91295 GAATATGTAA
*
91305 ATCGCAACGCTATTCTGACT
1 ATCGCAACGCGATTCTGACT
* ** *
91325 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
*
91346 ATCGCAACGCGGTTCTGACT
1 ATCGCAACGCGATTCTGACT
* ** *
91366 ATCGCAACGTGATGAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
91387 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
91407 ATCGCAACGCGAT
1 ATCGCAACGCGAT
91420 AATACAAATT
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.06
20 37 0.53
21 25 0.36
22 4 0.06
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:91351 original size:21 final size:21
Alignment explanation
Indices: 91325--91440 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
91315 TATTCTGACT
*
91325 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* ** *
91346 ATCGCAACGCGGTTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
* *
91366 ATCGCAACGTGATGATACAAA
1 ATCGCAACGCGATAATACAAA
** *
91387 ATCGCAACGCGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
91407 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* *
91428 TTCGCAATGCGAT
1 ATCGCAACGCGAT
91441 TTTCAAAGTG
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.06
20 26 0.37
21 36 0.51
22 4 0.06
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:91355 original size:41 final size:41
Alignment explanation
Indices: 91303--91441 Score: 215
Period size: 41 Copynumber: 3.4 Consensus size: 41
91293 GCGAATATGT
* *
91303 AAATCGCAACGCTATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* * *
91344 AAATCGCAACGCGGTTCTGACTATCGCAACGTGATGATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
91385 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* *
91426 AATTCGCAATGCGATT
1 AAATCGCAACGCGATT
91442 TTCAAAGTGC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:91604 original size:22 final size:22
Alignment explanation
Indices: 91579--91636 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
91569 TCACTCTCTA
*
91579 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
91601 CGGCGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
*
91623 CGACGAAATCCGTC
1 CGGCGAAATCCGTC
91637 TATCTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.17
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:92019 original size:14 final size:14
Alignment explanation
Indices: 92000--92026 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
91990 AACGCGAAAT
92000 AAAAATCGCAATGA
1 AAAAATCGCAATGA
92014 AAAAATCGCAATG
1 AAAAATCGCAATG
92027 CGATTTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATCGCAATGA
Found at i:94049 original size:19 final size:19
Alignment explanation
Indices: 94003--94050 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
93993 ACGCGATTCG
* *
94003 CATTGCGATTTTGGTTTCG
1 CATTGCGATTTTGATTTCA
* * *
94022 CGTTACGATTTTTATTTCA
1 CATTGCGATTTTGATTTCA
94041 CATTGCGATT
1 CATTGCGATT
94051 ATCCCATTGC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (19 bp):
CATTGCGATTTTGATTTCA
Found at i:94082 original size:20 final size:20
Alignment explanation
Indices: 94057--94143 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
94047 GATTATCCCA
*
94057 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAATTTCGCG
94077 TTGCGATAGTC-ATTTGCGCG
1 TTGCGATAGTCAATTT-CGCG
* *
94097 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCG
* *
94117 TTGCAATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCG
94137 TTGCGAT
1 TTGCGAT
94144 TTTAAGTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCG
Found at i:94751 original size:42 final size:42
Alignment explanation
Indices: 94660--94751 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
94650 TCTCCTATCG
* *
94660 TTCAAGAGGCCTCTATCATCCCTCAAGAGTCCTCTCACACCG
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCTCTCACACCA
* * ** * *
94702 TTTAAGAGGCCCCTGTCATCGTTGAAGAGGTCC-CTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCTCTCACACCA
94744 TTCAAGAG
1 TTCAAGAG
94752 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 36 0.90
43 4 0.10
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCTCTCACACCA
Found at i:96303 original size:20 final size:20
Alignment explanation
Indices: 96278--96355 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
96268 AGGTACACTT
**
96278 TCGCAACGTTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
96298 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
96318 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
96338 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
96356 TTCGCGTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:96412 original size:34 final size:34
Alignment explanation
Indices: 96345--96629 Score: 260
Period size: 34 Copynumber: 8.4 Consensus size: 34
96335 AAATCGCAAC
* * *
96345 GCGAAAGTC-AATTCGCGTTGTGATTTTTACGTT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
* * *
96378 GCGATAGTCTAATACGCTTTGCGATTTTCT-CGTT
1 GCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTT
* *
96412 GCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTTGCGAT--T----TTTGCGTT
*
96452 GCGATAGTCAAATTCGCGTTGCAATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
*
96486 GCGATAGTCAAATTCGCGTTGCGATTTTTGCTTT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
* * *
96520 GCGATAGTCAAATTCGCGTTGCGCTTTTTTCTTT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
** ** ** *
96554 GCGATAGTCAAATT---AAT-C-AAATTCACATT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
*
96583 GCAATAGTCAAATTCGCGTTGCGATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
*
96617 GCGATATTCAAAT
1 GCGATAGTCAAAT
96630 GAATGTGTAA
Statistics
Matches: 204, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
29 18 0.09
30 1 0.00
31 1 0.00
32 1 0.00
33 9 0.04
34 142 0.70
35 1 0.00
36 1 0.00
38 1 0.00
40 29 0.14
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (34 bp):
GCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
Found at i:96433 original size:20 final size:20
Alignment explanation
Indices: 96408--96542 Score: 132
Period size: 20 Copynumber: 7.3 Consensus size: 20
96398 GCGATTTTCT
*
96408 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
96428 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
96448 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
96468 CGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
96482 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
96502 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
96516 CTTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
96536 CGTTGCG
1 CGTTGCG
96543 CTTTTTTCTT
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 1 0.01
20 64 0.70
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:96456 original size:54 final size:54
Alignment explanation
Indices: 96374--96542 Score: 164
Period size: 54 Copynumber: 3.1 Consensus size: 54
96364 GTGATTTTTA
* * * * *
96374 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAAATTCG
* ** ** * * *
96428 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG-TTG-CAATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATT-GCGATAGTCAA-ATTCG
*
96482 CGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCTTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CATTGCGATAGTCAAATTCG
96536 CGTTGCG
1 CGTTGCG
96543 CTTTTTTCTT
Statistics
Matches: 88, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
53 6 0.07
54 76 0.86
55 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAAATTCG
Found at i:96492 original size:108 final size:107
Alignment explanation
Indices: 96345--96542 Score: 290
Period size: 108 Copynumber: 1.8 Consensus size: 107
96335 AAATCGCAAC
** * *
96345 GCGAAAGTCAATTCGCGTTGTGATTTTTACGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-C
1 GCGAAAGTCAATTCGCGTTGCAATTTTTACGTTGCGATAGTCAAATACGCGTTGCGATTTT-TGC
96409 GTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTT
65 GTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTT
* * *
96452 GCGATAGTCAAATTCGCGTTGCAATTTTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGC
1 GCGAAAGTC-AATTCGCGTTGCAATTTTTACGTTGCGATAGTCAAATACGCGTTGCGATTTTTGC
* *
96517 TTTGCGATAGTCAAATTCGCGTTGCG
65 GTTGCGATAGTCAAATTCCCGTTGCG
96543 CTTTTTTCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
107 9 0.11
108 71 0.89
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (107 bp):
GCGAAAGTCAATTCGCGTTGCAATTTTTACGTTGCGATAGTCAAATACGCGTTGCGATTTTTGCG
TTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTT
Found at i:98895 original size:15 final size:14
Alignment explanation
Indices: 98859--98895 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
98849 TCTCGTGGCA
98859 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAT
98873 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAT
98887 TTCTTCTTC
1 TT-TTCTTC
98896 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (14 bp):
TTTTCTTCGGGGAT
Found at i:99122 original size:24 final size:24
Alignment explanation
Indices: 99088--99141 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
99078 CTGAAACATC
99088 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
99112 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
99136 ATCAAA
1 ATCAAA
99142 TTTTCGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:99818 original size:17 final size:17
Alignment explanation
Indices: 99796--99833 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
99786 CGGATGGGGA
99796 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
99813 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
99830 AGGA
1 AGGA
99834 ACGGATATCG
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:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:100005 original size:20 final size:20
Alignment explanation
Indices: 99980--100017 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
99970 GAAATTCAGT
99980 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
100000 GTTGCGATAGTCAGAATC
1 GTTGCGATAGTCAGAATC
100018 ATGTTGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:100023 original size:20 final size:20
Alignment explanation
Indices: 99979--100023 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
99969 TGAAATTCAG
*
99979 TGTTGCGATAGTCAGAATCG
1 TGTTGCGATAGTCAGAATCA
*
99999 CGTTGCGATAGTCAGAATCA
1 TGTTGCGATAGTCAGAATCA
100019 TGTTG
1 TGTTG
100024 TGATTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (20 bp):
TGTTGCGATAGTCAGAATCA
Found at i:100290 original size:2 final size:2
Alignment explanation
Indices: 100283--100314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100273 AATATTGAAC
100283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100315 TATTGATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101333 original size:11 final size:11
Alignment explanation
Indices: 101317--101376 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
101307 TTTACCGTCC
101317 ATTTTATTTTT
1 ATTTTATTTTT
101328 ATTTTA-TTTT
1 ATTTTATTTTT
*
101338 AGTTCTT-TTTAT
1 A-TT-TTATTTTT
**
101350 ATTTTATTCCT
1 ATTTTATTTTT
101361 ATTTTATTTTTT
1 ATTTTA-TTTTT
101373 ATTT
1 ATTT
101377 ATTCAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.18
11 19 0.49
12 13 0.33
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:101367 original size:18 final size:16
Alignment explanation
Indices: 101317--101375 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
101307 TTTACCGTCC
*
101317 ATTTTATT-TTTATTTT
1 ATTTTATTCTTT-TTAT
101333 ATTTTAGTTCTTTTTAT
1 ATTTTA-TTCTTTTTAT
101350 ATTTTATTCCTATTTTAT
1 ATTTTATT-CT-TTTTAT
*
101368 TTTTTATT
1 ATTTTATT
101376 TATTCAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 8 0.22
17 13 0.35
18 16 0.43
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (16 bp):
ATTTTATTCTTTTTAT
Found at i:101409 original size:2 final size:2
Alignment explanation
Indices: 101402--101440 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
101392 CATTTTATTT
101402 TA TA 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 TA TA T
101441 TTTTTTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101666 original size:22 final size:24
Alignment explanation
Indices: 101641--101690 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
101631 TTATATATGT
101641 TTTTAT-TATTATTATT-TTTTTC
1 TTTTATGTATTATTATTGTTTTTC
*
101663 TTTT-TGTATTTTTATTGTTTTTC
1 TTTTATGTATTATTATTGTTTTTC
*
101686 CTTTA
1 TTTTA
101691 CCTAACATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 9 0.39
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTATGTATTATTATTGTTTTTC
Found at i:101769 original size:13 final size:14
Alignment explanation
Indices: 101714--101770 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
101704 ATATATTATA
101714 TATT-TTTTCTTTT
1 TATTATTTTCTTTT
101727 TA-TATTTTCTATTT
1 TATTATTTTCT-TTT
* * *
101741 TTTTA-TTACTTAT
1 TATTATTTTCTTTT
101754 TATTATTTT-TTTT
1 TATTATTTTCTTTT
101767 TATT
1 TATT
101771 TGACTTGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
12 1 0.03
13 21 0.62
14 10 0.29
15 2 0.06
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTATTTTCTTTT
Found at i:103202 original size:24 final size:24
Alignment explanation
Indices: 103175--103226 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
103165 TTTTTTGAGT
*
103175 TTTTTTTAAT-TATAATATTAAATA
1 TTTTTTAAATATATAATATTAAA-A
* *
103199 TTTTTTAAATATATATTTTTAAAA
1 TTTTTTAAATATATAATATTAAAA
103223 TTTT
1 TTTT
103227 ATATGCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTTAAATATATAATATTAAAA
Found at i:105417 original size:24 final size:24
Alignment explanation
Indices: 105390--105445 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
105380 TAGAAGTTCG
105390 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
105414 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
105438 ATTGAAGC
1 ATTGAAGC
105446 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:109866 original size:20 final size:20
Alignment explanation
Indices: 109841--109884 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
109831 TCAAAATCAT
*
109841 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
109861 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
109881 TTTT
1 TTTT
109885 AAGAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Done.