Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009578.1 Hibiscus syriacus cultivar Beakdansim tig00116946_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: 651624
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:16022 original size:13 final size:12
Alignment explanation
Indices: 16006--16084 Score: 65
Period size: 13 Copynumber: 6.4 Consensus size: 12
15996 TAAATGTAAA
16006 AAATAAAATATTT
1 AAATAAAATA-TT
*
16019 AAATAAAATAAT
1 AAATAAAATATT
16031 AAA-AAAA-ATT
1 AAATAAAATATT
16041 AAATAATTAAATAATT
1 AAAT-A--AAAT-ATT
*
16057 AAATAAAATACT
1 AAATAAAATATT
*
16069 -AACAAAATATT
1 AAATAAAATATT
16080 AAATA
1 AAATA
16085 TAACAAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
10 5 0.09
11 13 0.25
12 10 0.19
13 14 0.26
14 3 0.06
15 1 0.02
16 7 0.13
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAAATATT
Found at i:16035 original size:22 final size:20
Alignment explanation
Indices: 16002--16046 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
15992 TTTATAAATG
* *
16002 TAAAAAATAAAATATTTAAA
1 TAAAAAATAAAAAAATTAAA
16022 TAAAATAATAAAAAAAATTAAA
1 TAAAA-AAT-AAAAAAATTAAA
16044 TAA
1 TAA
16047 TTAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAAATAAAAAAATTAAA
Found at i:16059 original size:38 final size:39
Alignment explanation
Indices: 15997--16084 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 39
15987 TCCATTTTAT
* *
15997 AAATGTAAAAAATAAAATATTTAAATAAAATAATAA-AAA
1 AAAT-TAAATAATAAAATAATTAAATAAAATAATAACAAA
* *
16036 AAATTAAATAATTAAATAATTAAATAAAATACTAACAAA
1 AAATTAAATAATAAAATAATTAAATAAAATAATAACAAA
*
16075 ATATTAAATA
1 AAATTAAATA
16085 TAACAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 27 0.63
39 16 0.37
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (39 bp):
AAATTAAATAATAAAATAATTAAATAAAATAATAACAAA
Found at i:16090 original size:17 final size:18
Alignment explanation
Indices: 16062--16095 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16052 TAATTAAATA
16062 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
16080 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
16096 ACCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:20394 original size:10 final size:10
Alignment explanation
Indices: 20379--20410 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20369 TTGTCGATGC
20379 TAAAAATAAA
1 TAAAAATAAA
20389 TAAAAATAAA
1 TAAAAATAAA
20399 T--AAATAAA
1 TAAAAATAAA
20407 TAAA
1 TAAA
20411 TTATTCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:35198 original size:21 final size:21
Alignment explanation
Indices: 35172--35216 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
35162 GGATATACTC
35172 TAGTTCAATTCTAAGGCACTT
1 TAGTTCAATTCTAAGGCACTT
* *
35193 TAGTTCAGTTCTAAGGCATTT
1 TAGTTCAATTCTAAGGCACTT
35214 TAG
1 TAG
35217 GAAAGCACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (21 bp):
TAGTTCAATTCTAAGGCACTT
Found at i:36226 original size:33 final size:32
Alignment explanation
Indices: 36165--36228 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
36155 AAGGGGTTTT
*
36165 GGTTCTAGTTTAGCCTGCTAAAAGCTAGGGAAA
1 GGTTCTAGTTTAGCCTGC-AAAAACTAGGGAAA
36198 GGTTCTAGTTTAGCCCATG-AAAAACTAGGGA
1 GGTTCTAGTTTAG-CC-TGCAAAAACTAGGGA
36229 GTTATAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 24 0.86
34 2 0.07
35 2 0.07
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (32 bp):
GGTTCTAGTTTAGCCTGCAAAAACTAGGGAAA
Found at i:39253 original size:20 final size:20
Alignment explanation
Indices: 39228--39268 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39218 ACCTTAGGCA
39228 AAGGTAGTACCGATACCATC
1 AAGGTAGTACCGATACCATC
* *
39248 AAGGTAGTACTGATACTATC
1 AAGGTAGTACCGATACCATC
39268 A
1 A
39269 TGAAAGCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
AAGGTAGTACCGATACCATC
Found at i:44160 original size:2 final size:2
Alignment explanation
Indices: 44153--44179 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44143 TATAATAATT
44153 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
44180 GATTTTATAA
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:44165 original size:52 final size:51
Alignment explanation
Indices: 44069--44167 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 51
44059 ATTTGAATTT
* * * *
44069 TTTTATAATAATAACTTGATTTTATAATAATTTATGTATGTATATATTTGA
1 TTTTATAATAATAACCTAATTTTATAATAATTTATATATATATATATTTGA
44120 TTTTATAATAATTAACCTAATTTTATAATAATTTATATATATATATAT
1 TTTTATAATAA-TAACCTAATTTTATAATAATTTATATATATATATAT
44168 ATATATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 11 0.26
52 32 0.74
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (51 bp):
TTTTATAATAATAACCTAATTTTATAATAATTTATATATATATATATTTGA
Found at i:44230 original size:33 final size:34
Alignment explanation
Indices: 44190--44257 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
44180 GATTTTATAA
44190 TAATTAACTTGATTTTATAAT-AATTATGTATTT
1 TAATTAACTTGATTTTATAATGAATTATGTATTT
* *
44223 TAATTAACTTTATTTTATAATGATTTATGTATTT
1 TAATTAACTTGATTTTATAATGAATTATGTATTT
44257 T
1 T
44258 TTTAGTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (34 bp):
TAATTAACTTGATTTTATAATGAATTATGTATTT
Found at i:47139 original size:20 final size:20
Alignment explanation
Indices: 47114--47166 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
47104 TCTCTTCTTT
47114 TTCTTTCTTTCTCATTTATC
1 TTCTTTCTTTCTCATTTATC
* * *
47134 TTCTTTCTTCCTCTTTTCTC
1 TTCTTTCTTTCTCATTTATC
*
47154 TTCTTTTTTTCTC
1 TTCTTTCTTTCTC
47167 CCATTCTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTTCTTTCTCATTTATC
Found at i:47309 original size:21 final size:21
Alignment explanation
Indices: 47283--47322 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47273 TTCCCTCCCA
47283 CCATTATTGCTGCCCCATAAT
1 CCATTATTGCTGCCCCATAAT
*
47304 CCATTATTGTTGCCCCATA
1 CCATTATTGCTGCCCCATA
47323 CAGGACGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.35
Consensus pattern (21 bp):
CCATTATTGCTGCCCCATAAT
Found at i:49642 original size:19 final size:18
Alignment explanation
Indices: 49603--49646 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
49593 CTATAGCTCT
49603 CATATCATATAACATGGG
1 CATATCATATAACATGGG
*
49621 CATTATCATTATAACAT-TG
1 CA-TATCA-TATAACATGGG
49640 CATATCA
1 CATATCA
49647 CTTGTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 8 0.35
20 8 0.35
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (18 bp):
CATATCATATAACATGGG
Found at i:52558 original size:2 final size:2
Alignment explanation
Indices: 52551--52578 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52541 CAAACTATCC
52551 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
52579 TCTTTCAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59316 original size:31 final size:29
Alignment explanation
Indices: 59257--59317 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
59247 CCAAATTTTG
* *
59257 GTAAAATTTGAAAGTTTAGTGGTTAAAGT
1 GTAAAATTTGAAAATTTAGTGGTCAAAGT
59286 GTAAAATTTGGAATAATTTAG-GGATCAAAGT
1 GTAAAATTT-GAA-AATTTAGTGG-TCAAAGT
59317 G
1 G
59318 GTAATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.33
30 5 0.19
31 13 0.48
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (29 bp):
GTAAAATTTGAAAATTTAGTGGTCAAAGT
Found at i:67877 original size:21 final size:21
Alignment explanation
Indices: 67853--67919 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
67843 ACTTTTTCAT
67853 AGCAGTTGTAACTCAATTTGC
1 AGCAGTTGTAACTCAATTTGC
* * **
67874 AGCAGTCGTGACTCAATTTAT
1 AGCAGTTGTAACTCAATTTGC
** *
67895 AATAGTTATAACTCAATTTGC
1 AGCAGTTGTAACTCAATTTGC
67916 AGCA
1 AGCA
67920 CCATTAATTT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (21 bp):
AGCAGTTGTAACTCAATTTGC
Found at i:68413 original size:20 final size:22
Alignment explanation
Indices: 68390--68430 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
68380 ATGCTTGGAT
*
68390 AAGTGTTCT-AACTT-TTTTTC
1 AAGTGTCCTCAACTTGTTTTTC
68410 AAGTGTCCTCAACTTGTTTTT
1 AAGTGTCCTCAACTTGTTTTT
68431 ATATGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (22 bp):
AAGTGTCCTCAACTTGTTTTTC
Found at i:68429 original size:21 final size:20
Alignment explanation
Indices: 68390--68429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
68380 ATGCTTGGAT
* *
68390 AAGTGTTCTAACTTTTTTTC
1 AAGTGTCCTAACTTGTTTTC
68410 AAGTGTCCTCAACTTGTTTT
1 AAGTGTCCT-AACTTGTTTT
68430 TATATGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.50
Consensus pattern (20 bp):
AAGTGTCCTAACTTGTTTTC
Found at i:68732 original size:17 final size:16
Alignment explanation
Indices: 68706--68737 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
68696 TTTAGAGGAT
68706 TAAATTTAATAAATGA
1 TAAATTTAATAAATGA
68722 TAAAGTTTAATAAATG
1 TAAA-TTTAATAAATG
68738 GTTAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAATTTAATAAATGA
Found at i:69970 original size:49 final size:49
Alignment explanation
Indices: 69913--70156 Score: 362
Period size: 49 Copynumber: 5.0 Consensus size: 49
69903 AAATGAATGG
* * *
69913 ATGAAAGTTAAATGCATAATGGTGCATTTCGACATAAAATGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* * **
69962 ATGAAAGTTAAATGCATAACGCTGCATTTCGGCATAACATATGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* *
70011 ATGAAAATTTAAATGCATAACGGTGCATTTCGGTATAAAAGGTGCCACTA
1 ATG-AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* * *
70061 ATGAAAGTTAAATGCATAAAGGTGCATTTCGGCATAAAAGGTGTCACGA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
*
70110 ATGAAAGTTAAATGCATAACGGTGTATTTCGGCATAAAAGGTGCCAC
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
70157 CCATGGTATT
Statistics
Matches: 175, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
49 132 0.75
50 43 0.25
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (49 bp):
ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
Found at i:70049 original size:99 final size:98
Alignment explanation
Indices: 69913--70156 Score: 362
Period size: 99 Copynumber: 2.5 Consensus size: 98
69903 AAATGAATGG
* * *
69913 ATGAAAGTTAAATGCATAATGGTGCATTTCGACATAAAATGTGCCACTAATGAAAGTTAAATGCA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCA
* * * *
69978 TAACGCTGCATTTCGGCATAACATATGCCACTA
66 TAAAGCTGCATTTCGGCATAAAAGATGCCACGA
* *
70011 ATGAAAATTTAAATGCATAACGGTGCATTTCGGTATAAAAGGTGCCACTAATGAAAGTTAAATGC
1 ATG-AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGC
* * *
70076 ATAAAGGTGCATTTCGGCATAAAAGGTGTCACGA
65 ATAAAGCTGCATTTCGGCATAAAAGATGCCACGA
*
70110 ATGAAAGTTAAATGCATAACGGTGTATTTCGGCATAAAAGGTGCCAC
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
70157 CCATGGTATT
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
98 44 0.34
99 86 0.66
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (98 bp):
ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCA
TAAAGCTGCATTTCGGCATAAAAGATGCCACGA
Found at i:76481 original size:49 final size:49
Alignment explanation
Indices: 76424--76715 Score: 514
Period size: 49 Copynumber: 6.0 Consensus size: 49
76414 AAATGAATGG
*
76424 ATGAAAGTTAAATGCATAATGGTGCATTTCGGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* *
76473 ATGAAAGTTAAATACAAAACGGTGCATTTCGGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
*
76522 ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
*
76571 ATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
*
76620 ATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCA-TGA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT-A
76669 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
76716 CCATGGTATT
Statistics
Matches: 232, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
48 1 0.00
49 231 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (49 bp):
ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
Found at i:81537 original size:14 final size:15
Alignment explanation
Indices: 81505--81541 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
81495 AGGGGTGTTA
81505 TTTAAAAAAATATTT
1 TTTAAAAAAATATTT
*
81520 TTTAAGAAAATA-TT
1 TTTAAAAAAATATTT
81534 TTTAAAAA
1 TTTAAAAA
81542 GAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TTTAAAAAAATATTT
Found at i:81782 original size:31 final size:31
Alignment explanation
Indices: 81716--81792 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
81706 AGCCTTATAT
** *
81716 TTATGTATATTAAATAATTTATTTTAAAAAA
1 TTATGTATATTGTATAATTTATTTCAAAAAA
*
81747 -TATGTATATTGTATACTTTATTTCAAAAAA
1 TTATGTATATTGTATAATTTATTTCAAAAAA
81777 TTATGTATATTGTATA
1 TTATGTATATTGTATA
81793 TTTTGAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 26 0.63
31 15 0.37
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATGTATATTGTATAATTTATTTCAAAAAA
Found at i:84660 original size:14 final size:14
Alignment explanation
Indices: 84639--84676 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
84629 CCGATCTGAA
84639 CCGAGTCAACTC-T
1 CCGAGTCAACTCGT
84652 CCTGAGTCAACTCGT
1 CC-GAGTCAACTCGT
84667 CCGAGTCAAC
1 CCGAGTCAAC
84677 CCGTTGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 18 0.78
15 3 0.13
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (14 bp):
CCGAGTCAACTCGT
Found at i:91234 original size:18 final size:18
Alignment explanation
Indices: 91209--91251 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
91199 TAAATATTGA
91209 TGAATTTAGAGACTAAA-TT
1 TGAATTTA-AGA-TAAACTT
91228 T-AATTTAAGATAAACTT
1 TGAATTTAAGATAAACTT
91245 TGAATTT
1 TGAATTT
91252 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 11 0.50
19 1 0.05
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (18 bp):
TGAATTTAAGATAAACTT
Found at i:92527 original size:46 final size:46
Alignment explanation
Indices: 92471--92734 Score: 123
Period size: 43 Copynumber: 6.1 Consensus size: 46
92461 GTTAGCGGTG
*
92471 TTTGAGAACAAAAAACACCGCAATAGGTCAAGATCTATAGCGGCATT
1 TTTG-GAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
** ** * *
92518 TTTGGAAC---AAATGCCGCAAAAGGTTGATATCTATAGCGGCGTT
1 TTTGGAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
* ** * *
92561 TTTGGAAC---AAACACCGCAAAAGGTCGATTTCTATTGCGGCGTT
1 TTTGGAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
** * ** * *
92604 TTCT-GAAC--AAAA-GTCGCAAAAGGTCGATTTCTATTGCGGCGTT
1 TT-TGGAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
* ** *
92647 TTTTGAAC--AAAA-GTCGCAAAAGGTC-AGATCTATAGCGGCTTT
1 TTTGGAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
* * * * *
92689 TTTAGATAC---AAACGCCGCAAAAGGTC-ATATCTATAGCAGCGTT
1 TTTGGA-ACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
92732 TTT
1 TTT
92735 TATACAAACG
Statistics
Matches: 189, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.12
43 155 0.82
44 4 0.02
46 4 0.02
47 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
TTTGGAACAAAAAACACCGCAAAAGGTCAAGATCTATAGCGGCATT
Found at i:92550 original size:43 final size:43
Alignment explanation
Indices: 92503--92734 Score: 247
Period size: 43 Copynumber: 5.4 Consensus size: 43
92493 ATAGGTCAAG
* *
92503 ATCTATAGCGGCATTTTTGGAACAAATGCCGCAAAAGGTTGAT
1 ATCTATAGCGGCGTTTTTGGAACAAAAGCCGCAAAAGGTTGAT
*
92546 ATCTATAGCGGCGTTTTTGGAACAAACA-CCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAA-AGCCGCAAAAGGTTGAT
* * * *
92589 TTCTATTGCGGCGTTTTCT-GAACAAAAGTCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTT-TGGAACAAAAGCCGCAAAAGGTTGAT
* * * * * *
92632 TTCTATTGCGGCGTTTTTTGAACAAAAGTCGCAAAAGG-TCAG
1 ATCTATAGCGGCGTTTTTGGAACAAAAGCCGCAAAAGGTTGAT
* * * *
92674 ATCTATAGCGGCTTTTTTAGATACAAACGCCGCAAAAGG-TCAT
1 ATCTATAGCGGCGTTTTTGGA-ACAAAAGCCGCAAAAGGTTGAT
*
92717 ATCTATAGCAGCGTTTTT
1 ATCTATAGCGGCGTTTTT
92735 TATACAAACG
Statistics
Matches: 166, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
42 20 0.12
43 145 0.87
44 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGAACAAAAGCCGCAAAAGGTTGAT
Found at i:92735 original size:86 final size:83
Alignment explanation
Indices: 92483--92734 Score: 283
Period size: 86 Copynumber: 2.9 Consensus size: 83
92473 TGAGAACAAA
* * * *
92483 AAACACCGCAATAGGTCAAGATCTATAGCGGCATTTTTGGAACAAATGCCGCAAAAGGTTGATAT
1 AAACACCGCAAAAGGTC-AGATCTATAGCGGC-TTTTTTGAACAAAAGCCGCAAAAGG-TCATAT
92548 CTATAGCGGCGTTTTTGGAAC
63 CTATAGCGGCGTTTTTGGAAC
* * * *
92569 AAACACCGCAAAAGGTC-GATTTCTATTGCGGCGTTTTCTGAACAAAAGTCGCAAAAGGTCGATT
1 AAACACCGCAAAAGGTCAGA--TCTATAGCGGC-TTTTTTGAACAAAAGCCGCAAAAGGTC-ATA
* *
92633 TCTATTGCGGCGTTTTTTGAAC
62 TCTATAGCGGCGTTTTTGGAAC
* *
92655 AAA-AGTCGCAAAAGGTCAGATCTATAGCGGCTTTTTTAGATACAAACGCCGCAAAAGGTCATAT
1 AAACA-CCGCAAAAGGTCAGATCTATAGCGGCTTTTTT-GA-ACAAAAGCCGCAAAAGGTCATAT
*
92719 CTATAGCAGCGTTTTT
63 CTATAGCGGCGTTTTT
92735 TATACAAACG
Statistics
Matches: 140, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
84 7 0.05
85 31 0.22
86 100 0.71
87 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (83 bp):
AAACACCGCAAAAGGTCAGATCTATAGCGGCTTTTTTGAACAAAAGCCGCAAAAGGTCATATCTA
TAGCGGCGTTTTTGGAAC
Found at i:92867 original size:21 final size:21
Alignment explanation
Indices: 92843--92889 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
92833 ACTTTACATC
*
92843 CATAACATCAAACTTGAAATT
1 CATAACAACAAACTTGAAATT
*
92864 CATAACAAGAAACTTGAAATT
1 CATAACAACAAACTTGAAATT
*
92885 TATAA
1 CATAA
92890 TAATAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
CATAACAACAAACTTGAAATT
Found at i:94971 original size:21 final size:21
Alignment explanation
Indices: 94945--95011 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
94935 AACCCCAAAG
*
94945 AAAAATAAAATAAATCCCTGA
1 AAAAATAAAATAAATCCCAGA
*
94966 AAAAATAAAA-ACAA-CCCCGAA
1 AAAAATAAAATA-AATCCCAG-A
*
94987 GAAAAATTAAATAAATCCCAGA
1 -AAAAATAAAATAAATCCCAGA
95009 AAA
1 AAA
95012 TGTGAAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 5 0.13
21 16 0.42
22 12 0.32
23 5 0.13
ACGTcount: A:0.64, C:0.16, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAAATAAAATAAATCCCAGA
Found at i:95696 original size:41 final size:41
Alignment explanation
Indices: 95625--95818 Score: 253
Period size: 41 Copynumber: 4.7 Consensus size: 41
95615 TTTAGTTTAC
* * * *
95625 AAACGCCACTAAAGTAAGAATCTTTTGCGGCGTTTGTATCA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
95666 AAATGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
95707 AAATGCCACGAAAGTACGAGTCTTTAGCGGCGTTTGTATAT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
95748 AAACGCTACAAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
95789 AAACGCCGCTAAAGTATGAATCTTTAGCGG
1 AAACGCCACTAAAGTACGAGTCTTTAGCGG
95819 TAAATTAGTG
Statistics
Matches: 133, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:104182 original size:114 final size:118
Alignment explanation
Indices: 103979--104211 Score: 438
Period size: 114 Copynumber: 2.0 Consensus size: 118
103969 CTGGTTTATT
103979 TACAGTATGTTGTCAATATTTTTTTACTGTATATGACACATTAGGCTTAATAGCTCACTTTCTAG
1 TACAGTATGTTGTCAATATTTTTTTACTGTATATGACACATTAGGCTTAATAGCTCACTTTCTAG
104044 TTTTTTTTTCCAGATTCCTTTTACCATTAAGACTAC-ACC-GTAC-TGAAAGA
66 TTTTTTTTTCCAGATTCCTTTTACCATTAAGACTACAACCTGTACTTGAAAGA
104094 TACAGTATGTTGTCAATATTTTTTTACTGTATATGACACATTA-GCTTAATAGCTCACTTTCTAG
1 TACAGTATGTTGTCAATATTTTTTTACTGTATATGACACATTAGGCTTAATAGCTCACTTTCTAG
104158 TTTTTTTTTCCAGATTCCTTTTACCATTAAGACTACAACCTGTACTTGAAAGA
66 TTTTTTTTTCCAGATTCCTTTTACCATTAAGACTACAACCTGTACTTGAAAGA
104211 T
1 T
104212 CATTTAGTAG
Statistics
Matches: 115, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
114 57 0.50
115 46 0.40
116 4 0.03
117 8 0.07
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (118 bp):
TACAGTATGTTGTCAATATTTTTTTACTGTATATGACACATTAGGCTTAATAGCTCACTTTCTAG
TTTTTTTTTCCAGATTCCTTTTACCATTAAGACTACAACCTGTACTTGAAAGA
Found at i:113085 original size:5 final size:5
Alignment explanation
Indices: 113069--113098 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
113059 AATTAATGTT
113069 AAATA TAAATA AAATA AAATA AAATA AAAT
1 AAATA -AAATA AAATA AAATA AAATA AAAT
113099 TTGAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:114482 original size:20 final size:20
Alignment explanation
Indices: 114457--114494 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
114447 TTGGACCGAA
114457 AAATAAGAA-AAAAATAAATG
1 AAATAA-AATAAAAATAAATG
114477 AAATAAAATAAAAATAAA
1 AAATAAAATAAAAATAAA
114495 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAAATAAAAATAAATG
Found at i:114492 original size:6 final size:6
Alignment explanation
Indices: 114455--114517 Score: 67
Period size: 6 Copynumber: 10.2 Consensus size: 6
114445 GATTGGACCG
*
114455 AAAAAT AAGAA- AAAAAT AAATGAA- ATAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA--AAT A-AAAAT AAAAAT AAAAAT AAAAAT
114504 AAAAACT AAAAAT A
1 AAAAA-T AAAAAT A
114518 TGTATATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 4 0.08
6 33 0.67
7 8 0.16
8 4 0.08
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:114508 original size:13 final size:13
Alignment explanation
Indices: 114481--114517 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
114471 TAAATGAAAT
114481 AAAATAAAAAT-A
1 AAAATAAAAATAA
114493 AAAATAAAAATAA
1 AAAATAAAAATAA
*
114506 AAACTAAAAATA
1 AAAATAAAAATA
114518 TGTATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:114556 original size:16 final size:15
Alignment explanation
Indices: 114526--114566 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
114516 TATGTATATA
114526 TTTCGAAAAATATGT
1 TTTCGAAAAATATGT
*
114541 TTTCGAAACTATATGT
1 TTTCGAAA-AATATGT
*
114557 TTTCCAAAAA
1 TTTCGAAAAA
114567 AACCATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (15 bp):
TTTCGAAAAATATGT
Found at i:114611 original size:37 final size:39
Alignment explanation
Indices: 114550--114631 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 39
114540 TTTTCGAAAC
* *
114550 TATATGTTTTCCAAAAAAACCATTTTTAAAAAGTATATAT
1 TATATGTTTTCC-AAAAAACCATTTTAAAAAACTATATAT
114590 TATATGTTTT-C-AAAAACCATTTTAAAAAACTATATAT
1 TATATGTTTTCCAAAAAACCATTTTAAAAAACTATATAT
114627 TATAT
1 TATAT
114632 ACATTTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 29 0.73
39 1 0.03
40 10 0.25
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (39 bp):
TATATGTTTTCCAAAAAACCATTTTAAAAAACTATATAT
Found at i:114626 original size:39 final size:37
Alignment explanation
Indices: 114550--114650 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 37
114540 TTTTCGAAAC
* *
114550 TATATGTTTTCCAAAAAAACCATTTTTAAAAAGTATA-TA
1 TATATGTTTT-C--AAAAACCATTTTAAAAAAATATATTA
114589 TTATATGTTTTCAAAAACCATTTTAAAAAACTATATATTA
1 -TATATGTTTTCAAAAACCATTTTAAAAAA--ATATATTA
**
114629 TATACATTTTC-AAAA-CATTTTA
1 TATATGTTTTCAAAAACCATTTTA
114651 CATATATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 24 0.44
38 4 0.07
39 14 0.26
40 12 0.22
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (37 bp):
TATATGTTTTCAAAAACCATTTTAAAAAAATATATTA
Found at i:114648 original size:37 final size:37
Alignment explanation
Indices: 114564--114650 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
114554 TGTTTTCCAA
* * *
114564 AAAAACCATTTTTAAAAAGTATATATTATATGTTTTC
1 AAAAACCATTTTAAAAAACTATATATTATATATTTTC
114601 AAAAACCATTTTAAAAAACTATATATTATATACATTTTC
1 AAAAACCATTTTAAAAAACTATATATTATAT--ATTTTC
114640 -AAAA-CATTTTA
1 AAAAACCATTTTA
114651 CATATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
37 36 0.80
38 4 0.09
39 5 0.11
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.40
Consensus pattern (37 bp):
AAAAACCATTTTAAAAAACTATATATTATATATTTTC
Found at i:114701 original size:39 final size:38
Alignment explanation
Indices: 114658--114743 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
114648 TTACATATAT
* * *
114658 TTTCAAAACTGATTTTTTAAAAAACTATATATTATATG-C
1 TTTCAAAAC-CATTTTCT-AAAAACTACATATTATATGTC
*
114697 TTTCAAAAACCATTTTCTAAAAACTACATATTATATGTT
1 TTTC-AAAACCATTTTCTAAAAACTACATATTATATGTC
114736 TTTCAAAA
1 TTTCAAAA
114744 ATATCTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 22 0.54
39 14 0.34
40 5 0.12
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (38 bp):
TTTCAAAACCATTTTCTAAAAACTACATATTATATGTC
Found at i:114719 original size:38 final size:37
Alignment explanation
Indices: 114677--114761 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 37
114667 TGATTTTTTA
*
114677 AAAAACTATATATTATATG-CTTTCAAAAACCATTTTC
1 AAAAACTATATATTATATGTCTTTCAAAAA-CATCTTC
* * *
114714 TAAAAACTACATATTATATGTTTTTCAAAAATATCTTC
1 -AAAAACTATATATTATATGTCTTTCAAAAACATCTTC
114752 AAAAACTATA
1 AAAAACTATA
114762 CTATATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 9 0.22
38 23 0.56
39 9 0.22
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (37 bp):
AAAAACTATATATTATATGTCTTTCAAAAACATCTTC
Found at i:115807 original size:201 final size:201
Alignment explanation
Indices: 115282--115842 Score: 739
Period size: 201 Copynumber: 2.8 Consensus size: 201
115272 AAGTCTTTGT
* *
115282 CAACCTTA-GTCTTCTTCTTGGCTTAAAGATCTCGGTTTAAAATTCAACCGAAAAGTAGTTCCTC
1 CAACC-TAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCGAAAAGTAGTTCCTC
* *
115346 GCTGCTACCATGAGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCATTGAT
65 GCTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGAT
* * * ** *
115411 AGACAACTTTTCTCAACTTAAGCTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAA
130 AGATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAA
115476 TCACAGC
195 TCACAGC
** * * * * *
115483 CAACCTAGGTCTTCTTCTTAACTTAAAGACCTCAATTTAAACTTTAACCGAAAAGTAGTTCTTAG
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCGAAAAGTAGTTCCTCG
* * * * * *
115548 CTGCTACCATGCGATTGGTATGCCCTCGAGCTGAATGAAATTGAATTTGAAAGTTTTCGTTGATA
66 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGATA
* * *
115613 GATAGCCCTCCTCGCCTTGAGCTATGCTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAAT
131 GATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAAT
* *
115678 CGCAGG
196 CACAGC
* * *
115684 CAACCTAGGTTTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAATCGGAAAGTAGTTCCTCG
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCGAAAAGTAGTTCCTCG
* * * * * * **
115749 ATGCTACCATGCGGTTGATATGCCCTTGACCTAAATGGAATCAAACTCAAAAGTTTTCG-TGGCA
66 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGATA
*
115813 GATAGCTCTTCTCGCCTTTAGCTATGCTGT
131 GATAGCTCTTCTCGCCTTAAGCTATGCTGT
115843 GAACGGTTCC
Statistics
Matches: 304, Mismatches: 55, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
200 32 0.11
201 272 0.89
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (201 bp):
CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCGAAAAGTAGTTCCTCG
CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGATA
GATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAAT
CACAGC
Found at i:120286 original size:24 final size:24
Alignment explanation
Indices: 120259--120332 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
120249 GTTAGTTACA
*
120259 GAAGCTTGTGCTTTTGCAGCTGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
* *
120283 GAAGCTTCTACTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
* * *
120307 GAAGCGTGTGTTTTTGCAGGAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
120331 GA
1 GA
120333 GTCTCCTTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.34
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTGCAGCAGAT
Found at i:123957 original size:21 final size:21
Alignment explanation
Indices: 123933--123979 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
123923 GGCAATTTTT
* * *
123933 TATTGTTTATGGTTTGTGGTC
1 TATTGTCTACGGTTTATGGTC
123954 TATTGTCTACGGTTTATGGTC
1 TATTGTCTACGGTTTATGGTC
123975 TATTG
1 TATTG
123980 GTTAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.26, T:0.53
Consensus pattern (21 bp):
TATTGTCTACGGTTTATGGTC
Found at i:124090 original size:45 final size:45
Alignment explanation
Indices: 124001--124311 Score: 552
Period size: 45 Copynumber: 6.9 Consensus size: 45
123991 GTAACCATGT
*
124001 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
124045 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
124090 AAATAATCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
124135 AAATAAGCTTACAAGATTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
124180 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTTGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
124225 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
124270 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTG
124312 ATAAGAAATT
Statistics
Matches: 255, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
44 25 0.10
45 230 0.90
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:124094 original size:24 final size:24
Alignment explanation
Indices: 124067--124185 Score: 62
Period size: 24 Copynumber: 5.2 Consensus size: 24
124057 GAGCTTATGG
124067 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
**
124091 AAT-AATCTTACGAGCT-TA-TGG---
1 AATAAATGGTA--AG-TATATTGGTAA
124112 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* ***
124136 AATAAGCTTACAAG-AT-TATGG---
1 AATAA-ATGGTAAGTATAT-TGGTAA
124157 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
124181 AATAA
1 AATAA
124186 GCTTACGAGC
Statistics
Matches: 67, Mismatches: 12, Indels: 32
0.60 0.11 0.29
Matches are distributed among these distances:
19 1 0.01
20 8 0.12
21 16 0.24
22 6 0.09
23 6 0.09
24 21 0.31
25 8 0.12
26 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:128896 original size:21 final size:22
Alignment explanation
Indices: 128848--128901 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
128838 CCCTCTAGGG
128848 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGG-AT
*
128871 GTATCGGTACACATTCAAGG-T
1 GTATCGATACACATTCAAGGAT
128892 GTATCGATAC
1 GTATCGATAC
128902 CTAGCAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.34
23 19 0.66
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (22 bp):
GTATCGATACACATTCAAGGAT
Found at i:132717 original size:63 final size:64
Alignment explanation
Indices: 132588--132709 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 64
132578 TTTATACGAC
* ** * ** *
132588 GACTAAATTATAAATAAAATAAAATTCGAATACTAAATTAAAATATATGGAAATTTATTACAGT
1 GACTAAATTATAAATAAAACAAAATTAAAAGACTAAATTAAAATATATAAAAATTGATTACAGT
*
132652 GACTAAATTAT-AATAAAACAAAATTAAAAGA-TATAATTAAAATGTATAAAAATTGATT
1 GACTAAATTATAAATAAAACAAAATTAAAAGACTA-AATTAAAATATATAAAAATTGATT
132710 TTAGTGACCA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.04
63 36 0.73
64 11 0.22
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (64 bp):
GACTAAATTATAAATAAAACAAAATTAAAAGACTAAATTAAAATATATAAAAATTGATTACAGT
Found at i:133651 original size:3 final size:3
Alignment explanation
Indices: 133645--133682 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
133635 ATTTATTATT
*
133645 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
133683 ATAGGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:133964 original size:63 final size:64
Alignment explanation
Indices: 133860--133991 Score: 160
Period size: 63 Copynumber: 2.1 Consensus size: 64
133850 TATATATACG
* ** * * ** *
133860 GTGACTAAATTATAAATAAAATAAAATTTGAATATTGAATTAAAATATATGGAAATTTATTGTA
1 GTGACTAAATTATAAATAAAACAAAATTAAAAGATTGAATTAAAACATATAAAAATTGATTGTA
*
133924 GTGACTAAATTAT-AATAAAACAAAATTAAAAGATAT-AATTAAAACATATAAAAATTGATTTTA
1 GTGACTAAATTATAAATAAAACAAAATTAAAAGAT-TGAATTAAAACATATAAAAATTGATTGTA
133987 GTGAC
1 GTGAC
133992 CAAAATGGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 44 0.76
64 14 0.24
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (64 bp):
GTGACTAAATTATAAATAAAACAAAATTAAAAGATTGAATTAAAACATATAAAAATTGATTGTA
Found at i:133965 original size:13 final size:13
Alignment explanation
Indices: 133934--133974 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
133924 GTGACTAAAT
133934 TATAA-TAAAACA
1 TATAATTAAAACA
*
133946 -A-AATTAAAAGA
1 TATAATTAAAACA
133957 TATAATTAAAACA
1 TATAATTAAAACA
133970 TATAA
1 TATAA
133975 AAATTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 2 0.08
11 7 0.29
12 1 0.04
13 14 0.58
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (13 bp):
TATAATTAAAACA
Found at i:133977 original size:23 final size:23
Alignment explanation
Indices: 133934--133977 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
133924 GTGACTAAAT
*
133934 TATAATAAAACAAAATTAAAAGA
1 TATAATAAAACAAAATAAAAAGA
*
133957 TATAATTAAAAC-ATATAAAAA
1 TATAA-TAAAACAAAATAAAAA
133978 TTGATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
TATAATAAAACAAAATAAAAAGA
Found at i:134208 original size:21 final size:21
Alignment explanation
Indices: 134144--134200 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
134134 TCTTTGGTTG
*
134144 TCTCTCTAAAGAGAGAGAACC
1 TCTCCCTAAAGAGAGAGAACC
134165 TCTCCCTAAAGAGAGAGAACC
1 TCTCCCTAAAGAGAGAGAACC
134186 TCTCCCTAAAGAGAG
1 TCTCCCTAAAGAGAG
134201 TTTCCCTCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
TCTCCCTAAAGAGAGAGAACC
Found at i:135005 original size:3 final size:3
Alignment explanation
Indices: 134999--135036 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
134989 ATTTATTATT
*
134999 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
135037 ATGGGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:135391 original size:39 final size:39
Alignment explanation
Indices: 135337--135569 Score: 322
Period size: 39 Copynumber: 6.0 Consensus size: 39
135327 AGGTTGAATA
*
135337 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
*
135376 AGTTCTTTAGACTATGAACTCCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * * * *
135415 AGTTCTTCAGACTATGAACTTCTTTTTCTTCTTTAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * * *
135454 AATTCTTCATATTATGAACTCATTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
135493 AGTTATTCAGATTATAAACTCCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* *
135532 AGTTCTTCAGATTATGAACTCCTTCTTTCTCTTCAGAT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGAT
135570 TATGAACTCT
Statistics
Matches: 169, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 169 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
Found at i:135392 original size:123 final size:123
Alignment explanation
Indices: 135173--135398 Score: 339
Period size: 123 Copynumber: 1.8 Consensus size: 123
135163 TTGATGTTGT
* *
135173 TCTATCTCCTTCTGCGATAAAATCTAGCAAAAGGTCAATTAAATTCTTCATATTATGAACTTCTT
1 TCTATCTCCTTCTGCGATAAAATCTAGCAAAAGGTCAATTAAATTCTTCAGACTATGAACTTCTT
*
135238 CTTCCTCTTCAGATGAGTTCGTCAGATTATGAACTCCTGTCTGAAAATGTTCTCTTGC
66 CTTCCTCTTCAGATGAGTTCGTCAGACTATGAACTCCTGTCTGAAAATGTTCTCTTGC
* * * *
135296 TCTATCTCTTTCTGCGATAAAGT-TAAGCAAAAGGTTGAA-TAAGTTCTTCAGACTATGAACTTC
1 TCTATCTCCTTCTGCGATAAAATCT-AGCAAAAGG-TCAATTAAATTCTTCAGACTATGAACTTC
* *
135359 TTCTTCCTCTTCAGATGAGTTCTTTAGACTATGAACTCCT
64 TTCTTCCTCTTCAGATGAGTTCGTCAGACTATGAACTCCT
135399 TCTTCCTCTT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
122 1 0.01
123 88 0.96
124 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (123 bp):
TCTATCTCCTTCTGCGATAAAATCTAGCAAAAGGTCAATTAAATTCTTCAGACTATGAACTTCTT
CTTCCTCTTCAGATGAGTTCGTCAGACTATGAACTCCTGTCTGAAAATGTTCTCTTGC
Found at i:135568 original size:26 final size:26
Alignment explanation
Indices: 135535--135592 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
135525 TCAGATGAGT
135535 TCTTCAGATTATGAACTCCTTCTTT-C
1 TCTTCAGATTATGAACT-CTTCTTTCC
*
135561 TCTTCAGATTATGAACTCTTTTTTCC
1 TCTTCAGATTATGAACTCTTCTTTCC
135587 TCTTCA
1 TCTTCA
135593 AACAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.48
Consensus pattern (26 bp):
TCTTCAGATTATGAACTCTTCTTTCC
Found at i:135584 original size:143 final size:143
Alignment explanation
Indices: 135418--135712 Score: 387
Period size: 143 Copynumber: 2.1 Consensus size: 143
135408 TCAGATGAGT
* * * * *
135418 TCTTCAGACTATGAACTTCTTTTTCTTCTTTAGACGAA-TTCTTCATATTATGAACTCATTCTTC
1 TCTTCAGACTATGAACTTCTTTTTCCTCTTCAAAC-AAGTTATTCAGATTATGAACTCATTCTTC
* * * * *
135482 CTCTTCAGATGAGTTATTCAGATTATAAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTAT
65 CTCTTCAGACGAGTTATTCAGATTATAAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTAT
*
135547 GAACTCCTTCTTTC
130 GAACTCCTTCTTCC
* *
135561 TCTTCAGATTATGAAC-TCTTTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTC
1 TCTTCAGACTATGAACTTC-TTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCATTCTTC
* * * * *
135625 CTCTTTAGACGAGTTCTTCATATTATGAACTTATTCTTCCTCTTCAAACGAGTTATTCAGATTAT
65 CTCTTCAGACGAGTTATTCAGATTATAAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTAT
135690 GAACTCCTTCTTCC
130 GAACTCCTTCTTCC
*
135704 TCTTTAGAC
1 TCTTCAGAC
135713 GAGTTCTTCA
Statistics
Matches: 130, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
142 4 0.03
143 126 0.97
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.43
Consensus pattern (143 bp):
TCTTCAGACTATGAACTTCTTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCATTCTTCC
TCTTCAGACGAGTTATTCAGATTATAAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTATG
AACTCCTTCTTCC
Found at i:135587 original size:65 final size:65
Alignment explanation
Indices: 135498--135629 Score: 192
Period size: 65 Copynumber: 2.0 Consensus size: 65
135488 AGATGAGTTA
* ** * *
135498 TTCAGATTATAAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTTCTC
1 TTCAGATTATAAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCCTC
* * *
135563 TTCAGATTATGAACTCTTTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCCTC
1 TTCAGATTATAAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCCTC
135628 TT
1 TT
135630 TAGACGAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.44
Consensus pattern (65 bp):
TTCAGATTATAAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCCTC
Found at i:135606 original size:39 final size:39
Alignment explanation
Indices: 135563--135730 Score: 228
Period size: 39 Copynumber: 4.3 Consensus size: 39
135553 CTTCTTTCTC
* * *
135563 TTCAGATTATGAACTCTTTTTTCCTCTTCAAACAAGTTA
1 TTCAGATTATGAACTCCTTCTTCCTCTTCAAACGAGTTA
* * *
135602 TTCAGATTATGAACTCCTTCTTCCTCTTTAGACGAGTTC
1 TTCAGATTATGAACTCCTTCTTCCTCTTCAAACGAGTTA
* **
135641 TTCATATTATGAACTTATTCTTCCTCTTCAAACGAGTTA
1 TTCAGATTATGAACTCCTTCTTCCTCTTCAAACGAGTTA
* * *
135680 TTCAGATTATGAACTCCTTCTTCCTCTTTAGACGAGTTC
1 TTCAGATTATGAACTCCTTCTTCCTCTTCAAACGAGTTA
135719 TTCAGATTATGA
1 TTCAGATTATGA
135731 TTTCCATCTG
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (39 bp):
TTCAGATTATGAACTCCTTCTTCCTCTTCAAACGAGTTA
Found at i:135643 original size:78 final size:78
Alignment explanation
Indices: 135561--135730 Score: 297
Period size: 78 Copynumber: 2.2 Consensus size: 78
135551 TCCTTCTTTC
*
135561 TCTTCAGATTATGAACTCT-TTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTC
1 TCTTCAGATTATGAACT-TATTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTC
135625 CTCTTTAGACGAGT
65 CTCTTTAGACGAGT
* *
135639 TCTTCATATTATGAACTTATTCTTCCTCTTCAAACGAGTTATTCAGATTATGAACTCCTTCTTCC
1 TCTTCAGATTATGAACTTATTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCC
135704 TCTTTAGACGAGT
66 TCTTTAGACGAGT
135717 TCTTCAGATTATGA
1 TCTTCAGATTATGA
135731 TTTCCATCTG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
77 1 0.01
78 86 0.99
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (78 bp):
TCTTCAGATTATGAACTTATTCTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCC
TCTTTAGACGAGT
Found at i:135647 original size:182 final size:182
Alignment explanation
Indices: 135379--135730 Score: 533
Period size: 182 Copynumber: 1.9 Consensus size: 182
135369 TCAGATGAGT
* * ** * * * *
135379 TCTTTAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTTCTTTTTCT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGACTATGAACTCCTTCTTCC
* *
135444 TCTTTAGACGAATTCTTCATATTATGAACTCATTCTTCCTCTTCAGATGAGTTATTCAGATTATA
66 TCTTTAGACGAATTCTTCATATTATGAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTATA
*
135509 AACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTTC
131 AACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTTC
* * * *
135561 TCTTCAGATTATGAACTCTTTTTTCCTCTTCAAACAAGTTATTCAGATTATGAACTCCTTCTTCC
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGACTATGAACTCCTTCTTCC
* * *
135626 TCTTTAGACGAGTTCTTCATATTATGAACTTATTCTTCCTCTTCAAACGAGTTATTCAGATTATG
66 TCTTTAGACGAATTCTTCATATTATGAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTATA
*
135691 AACTCCTTCTTCCTCTTTAGACGAGTTCTTCAGATTATGA
131 AACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGA
135731 TTTCCATCTG
Statistics
Matches: 151, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
182 151 1.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (182 bp):
TCTTCAGACTATGAACTCCTTCTTCCTCTTCAAACAAGTTATTCAGACTATGAACTCCTTCTTCC
TCTTTAGACGAATTCTTCATATTATGAACTCATTCTTCCTCTTCAAACGAGTTATTCAGATTATA
AACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTTC
Found at i:136970 original size:54 final size:54
Alignment explanation
Indices: 136888--137036 Score: 219
Period size: 54 Copynumber: 2.8 Consensus size: 54
136878 CACTGGTTCA
* *
136888 TAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCTACAT-TTTCG
1 TAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCACATGTTT-G
* *
136942 TAAAACATTTGAAAACACATTCATCATTTCCTATGGCTTCTGCCCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCACATGTTTG
* * *
136996 TAAAACATTTGACAACAGATTCATCTTTTCCTATGGTTTCT
1 TAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCT
137037 ACACATATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 83 0.97
55 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCACATGTTTG
Found at i:138648 original size:18 final size:18
Alignment explanation
Indices: 138625--138662 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
138615 TCAGGAACAT
138625 TTTTGGGATGTGTGGTGC
1 TTTTGGGATGTGTGGTGC
*
138643 TTTTGGTATGTGTGGTGC
1 TTTTGGGATGTGTGGTGC
138661 TT
1 TT
138663 CATCAAGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.39, T:0.50
Consensus pattern (18 bp):
TTTTGGGATGTGTGGTGC
Found at i:146622 original size:21 final size:21
Alignment explanation
Indices: 146596--146652 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
146586 AGAGCGTGGG
146596 GGGAATCGGTTCCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
146617 GGGAATCGGTTCCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
146638 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
146653 AAGTGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:147101 original size:13 final size:13
Alignment explanation
Indices: 147083--147107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147073 AAATCAAGTT
147083 AAAAAAAATTACA
1 AAAAAAAATTACA
147096 AAAAAAAATTAC
1 AAAAAAAATTAC
147108 TCCCCCTTAC
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTACA
Found at i:149420 original size:21 final size:21
Alignment explanation
Indices: 149394--149474 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
149384 CAGAACCCCA
*
149394 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
149415 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* *
149438 AGGGGGAATCGGTT-CCCTCA-
1 GGGGGGAATCGATTCCCCT-AT
*
149458 GGGGGGGATCGATTCCC
1 GGGGGGAATCGATTCCC
149475 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:157124 original size:2 final size:2
Alignment explanation
Indices: 157117--157187 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
157107 TCAATCTACA
157117 AT AT AT AT AT AT AT AT A- AT AT AT -T 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 AT AT AT AT AT
157157 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 A
157188 CAAAATACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:162211 original size:181 final size:183
Alignment explanation
Indices: 161907--162270 Score: 714
Period size: 181 Copynumber: 2.0 Consensus size: 183
161897 TCCGGTTTCA
161907 TCCTGAAATTTTCATAGCTATGAGTAAGAAGACTAATTTTGGATTCTTTTACCTCCTTGGTGCCT
1 TCCTGAAATTTTCATAGCTATGAGTAAGAAGACTAATTTTGGATTCTTTTACCTCCTTGGTGCCT
161972 TCATGAGTGACTTGTAGTTTATCCCATATCTCCTTGGCGGTTGTACAAGATGAAACTCTCCCGTA
66 TCATGAGTGACTTGTAGTTTATCCCATATCTCCTTGGCGGTTGTACAAGATGAAACTCTCCCGTA
162037 TTTATCTGGTCTAAGTGCGCAGAAAATAATATGGATAGCC-TTG-GTTAAGTT
131 TTTATCTGGTCTAAGTGCGCAGAAAATAATATGGATAGCCTTTGAGTTAAGTT
162088 TCCTGAAATTTTCATAGCTATGAGTAAGAAGACTAATTTTGGATTCTTTTACCTCCTTGGTGCCT
1 TCCTGAAATTTTCATAGCTATGAGTAAGAAGACTAATTTTGGATTCTTTTACCTCCTTGGTGCCT
162153 TCATGAGTGACTTGTAGTTTATCCCATATCTCCTTGGCGGTTGTACAAGATGAAACTCTCCCGTA
66 TCATGAGTGACTTGTAGTTTATCCCATATCTCCTTGGCGGTTGTACAAGATGAAACTCTCCCGTA
162218 TTTATCTGGTCTAAGTGCGCAGAAAATAATATGGATAGCCTTTGAGTTAAGTT
131 TTTATCTGGTCTAAGTGCGCAGAAAATAATATGGATAGCCTTTGAGTTAAGTT
162271 GGAACATTCT
Statistics
Matches: 181, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
181 170 0.94
182 3 0.02
183 8 0.04
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (183 bp):
TCCTGAAATTTTCATAGCTATGAGTAAGAAGACTAATTTTGGATTCTTTTACCTCCTTGGTGCCT
TCATGAGTGACTTGTAGTTTATCCCATATCTCCTTGGCGGTTGTACAAGATGAAACTCTCCCGTA
TTTATCTGGTCTAAGTGCGCAGAAAATAATATGGATAGCCTTTGAGTTAAGTT
Found at i:164442 original size:12 final size:12
Alignment explanation
Indices: 164415--164456 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
164405 AAGTTTGTAA
164415 AATAA-AAAAAT
1 AATAATAAAAAT
*
164426 AATAATCAAAAT
1 AATAATAAAAAT
*
164438 GATAATAAAAAT
1 AATAATAAAAAT
164450 AAATAAT
1 -AATAAT
164457 TCCTACTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:165806 original size:176 final size:179
Alignment explanation
Indices: 165605--165959 Score: 689
Period size: 176 Copynumber: 2.0 Consensus size: 179
165595 AGAAGTGAGG
165605 GGTCAATTGCATAAATATAAAAAATATAAATAGGGATTAAATTGAATAAATTCAAAATTTAAGGG
1 GGTCAATTGCATAAATATAAAAAATATAAATAGGGATTAAATTGAATAAATTCAAAATTTAAGGG
165670 AAAATTTATAATAGGTGACCAAAATGGATTTCACATC-AAACTTAGGGACTATAGAAATAATTTA
66 AAAATTTATAATAGGTGACCAAAATGGATTTCACATCAAAACTTAGGGACTATAGAAATAATTTA
165734 AGAAGTTCATATTTACAT-AAGGTCCTCCCTATAAATAGCCC-TAAATC
131 AGAAGTTCATATTTACATAAAGGTCCTCCCTATAAATAGCCCATAAATC
165781 GGTCAATTGCATAAATATAAAAAATATAAATAGGGATTAAATTGAATAAATTCAAAATTTAAGGG
1 GGTCAATTGCATAAATATAAAAAATATAAATAGGGATTAAATTGAATAAATTCAAAATTTAAGGG
165846 AAAATTTATAATAGGTGACCAAAATGGATTTCACATCAAAACTTAGGGACTATAGAAATAATTTA
66 AAAATTTATAATAGGTGACCAAAATGGATTTCACATCAAAACTTAGGGACTATAGAAATAATTTA
165911 AGAAGTTCATATTTACATAAAGGTCCTCCCTATAAATAGCCCATAAATC
131 AGAAGTTCATATTTACATAAAGGTCCTCCCTATAAATAGCCCATAAATC
165960 AAAAAAAATA
Statistics
Matches: 176, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
176 102 0.58
177 45 0.26
178 23 0.13
179 6 0.03
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (179 bp):
GGTCAATTGCATAAATATAAAAAATATAAATAGGGATTAAATTGAATAAATTCAAAATTTAAGGG
AAAATTTATAATAGGTGACCAAAATGGATTTCACATCAAAACTTAGGGACTATAGAAATAATTTA
AGAAGTTCATATTTACATAAAGGTCCTCCCTATAAATAGCCCATAAATC
Found at i:166842 original size:9 final size:8
Alignment explanation
Indices: 166829--166886 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 8
166819 GATTGGACCG
166829 AAAAATAA
1 AAAAATAA
166837 GAAAAATAA
1 -AAAAATAA
166846 TAAAAATAA
1 -AAAAATAA
*
166855 ATAAATAAA
1 AAAAAT-AA
166864 ATAAAATAAA
1 A-AAAAT-AA
166874 ATAAAATAA
1 A-AAAATAA
166883 AAAA
1 AAAA
166887 CAGAAAACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
8 8 0.18
9 22 0.50
10 14 0.32
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:166867 original size:5 final size:5
Alignment explanation
Indices: 166830--166884 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
166820 ATTGGACCGA
* *
166830 AAAAT AAGA- AAAAT AATA- AAAAT -AAAT -AAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
166876 AAAAT AAAA
1 AAAAT AAAA
166885 AACAGAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
4 14 0.33
5 29 0.67
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:167001 original size:37 final size:37
Alignment explanation
Indices: 166938--167140 Score: 148
Period size: 37 Copynumber: 5.4 Consensus size: 37
166928 CAAAACTATC
*
166938 TGTTTTCCAAAAAATCATTTT-TAAAACTATATATTATA
1 TGTTTT-C-AAAAATCATTTTAAAAAACTATATATTATA
166976 TGTTTTCAAAAATCATTTTAAAAAACTATATATTATA
1 TGTTTTCAAAAATCATTTTAAAAAACTATATATTATA
**
167013 TACGTTTTCAAAAAAT-ATGTTTTCAAAAC-ATAT-TATATA
1 T--GTTTTC-AAAAATCAT-TTTAAAAAACTATATAT-TATA
* * * *
167052 TATTTTC-AAAACCGGTTTTTTAAAAAACTCTATATTATA
1 TGTTTTCAAAAATC---ATTTTAAAAAACTATATATTATA
* * * ** *
167091 TGCTTTCAAAAACCGTTTTCTAAAA-TCTATATTATA
1 TGTTTTCAAAAATCATTTTAAAAAACTATATATTATA
167127 TGTTTTTCAAAAAT
1 TG-TTTTCAAAAAT
167141 TATACTATAT
Statistics
Matches: 135, Mismatches: 16, Indels: 29
0.75 0.09 0.16
Matches are distributed among these distances:
35 4 0.03
36 25 0.19
37 40 0.30
38 15 0.11
39 30 0.22
40 21 0.16
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (37 bp):
TGTTTTCAAAAATCATTTTAAAAAACTATATATTATA
Found at i:167036 original size:15 final size:15
Alignment explanation
Indices: 167016--167045 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
167006 TATTATATAC
167016 GTTTTCAAAAAATAT
1 GTTTTCAAAAAATAT
*
167031 GTTTTCAAAACATAT
1 GTTTTCAAAAAATAT
167046 TATATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (15 bp):
GTTTTCAAAAAATAT
Found at i:167144 original size:23 final size:24
Alignment explanation
Indices: 167106--167150 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
167096 TCAAAAACCG
* *
167106 TTTTCTAAAATCTATATTATATGT
1 TTTTCAAAAATCTATACTATATGT
167130 TTTTCAAAAAT-TATACTATAT
1 TTTTCAAAAATCTATACTATAT
167151 TATTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTTCAAAAATCTATACTATATGT
Found at i:170550 original size:13 final size:12
Alignment explanation
Indices: 170532--170565 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
170522 TTAGACATAT
170532 TTTTAATATAATA
1 TTTTAA-ATAATA
170545 TTTTAAA-AATA
1 TTTTAAATAATA
170556 TTTTAAATAA
1 TTTTAAATAA
170566 ATGAAGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 3 0.15
13 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTTAAATAATA
Found at i:172885 original size:13 final size:14
Alignment explanation
Indices: 172854--172899 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
172844 GTGTCATGTT
*
172854 CATATTTTTAAAAA
1 CATATTTTTAAATA
172868 CATATTTTTAAATA
1 CATATTTTTAAATA
172882 -ATATTTTTAAATA
1 CATATTTTTAAATA
*
172895 TATAT
1 CATAT
172900 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 13 0.43
14 17 0.57
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (14 bp):
CATATTTTTAAATA
Found at i:180275 original size:19 final size:19
Alignment explanation
Indices: 180251--180291 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
180241 ATCTTCATCG
*
180251 AAATCGCCGTAGTAAATCT
1 AAATCGCCGCAGTAAATCT
180270 AAATCGCCGCAGTAAATCT
1 AAATCGCCGCAGTAAATCT
180289 AAA
1 AAA
180292 GCAACAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (19 bp):
AAATCGCCGCAGTAAATCT
Found at i:189465 original size:27 final size:26
Alignment explanation
Indices: 189435--189489 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
189425 GAAATATGTA
* *
189435 TTTTTAATTTAAATATCTAAATTAATT
1 TTTTTAATTAAAATAACTAAA-TAATT
* *
189462 TTTTTTATTAAAATAAGTAAATAATT
1 TTTTTAATTAAAATAACTAAATAATT
189488 TT
1 TT
189490 ATGTAATAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTTAATTAAAATAACTAAATAATT
Found at i:189973 original size:32 final size:32
Alignment explanation
Indices: 189932--189993 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
189922 TCTTTTCACC
*
189932 TTAAATGCATCATTGGCCAATAAATTATACCA
1 TTAAATGCATCATTGGCCAATAAACTATACCA
* * *
189964 TTAAATGCATTATTGTCCCATAAACTATAC
1 TTAAATGCATCATTGGCCAATAAACTATAC
189994 TATTTGTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (32 bp):
TTAAATGCATCATTGGCCAATAAACTATACCA
Found at i:190440 original size:36 final size:35
Alignment explanation
Indices: 190386--190465 Score: 124
Period size: 36 Copynumber: 2.3 Consensus size: 35
190376 AGGAGAGATG
190386 TTTTGTTTTCAACCTATTGCTTTGCATTTAAATATA
1 TTTTGTTTTCAACCTATTGCTTTGCATTTAAAT-TA
* *
190422 TTTTGTTTTCAGCTTATTGCTTTGCATTTAAATTA
1 TTTTGTTTTCAACCTATTGCTTTGCATTTAAATTA
*
190457 TTTAGTTTT
1 TTTTGTTTT
190466 TTTTTTGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 10 0.24
36 31 0.76
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTTGTTTTCAACCTATTGCTTTGCATTTAAATTA
Found at i:192055 original size:18 final size:20
Alignment explanation
Indices: 192019--192055 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
192009 GATAAAAAAA
*
192019 ATATTAACAATTTTATAAAT
1 ATATTAACAATTATATAAAT
192039 ATATTAA-AATTAT-TAAA
1 ATATTAACAATTATATAAA
192056 ATTTATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 5 0.31
20 7 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTAACAATTATATAAAT
Found at i:193286 original size:21 final size:21
Alignment explanation
Indices: 193248--193287 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
193238 TATTCGAGTG
**
193248 AAACATTAATTTAATCCATTA
1 AAACATTAAAATAATCCATTA
*
193269 AAACATTAAAATATTCCAT
1 AAACATTAAAATAATCCAT
193288 ACTGGAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (21 bp):
AAACATTAAAATAATCCATTA
Found at i:198760 original size:17 final size:16
Alignment explanation
Indices: 198738--198771 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
198728 TAAAGACAGT
198738 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
198755 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
198771 A
1 A
198772 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:199273 original size:24 final size:24
Alignment explanation
Indices: 199246--199296 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
199236 ATAAAGAACC
*
199246 AAAAATAAA-CTTAAATATACCATT
1 AAAAATAAAGCTTAAACA-ACCATT
*
199270 AAAAATAAAGTTTAAACAACCATT
1 AAAAATAAAGCTTAAACAACCATT
199294 AAA
1 AAA
199297 TCAACCACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAAATAAAGCTTAAACAACCATT
Found at i:208942 original size:17 final size:16
Alignment explanation
Indices: 208920--208953 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
208910 TAAAGACAGT
208920 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
208937 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
208953 A
1 A
208954 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:209457 original size:24 final size:24
Alignment explanation
Indices: 209430--209478 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
209420 AAAGAACCAC
*
209430 AAATAAA-CTTAAATATACCATTAA
1 AAATAAAGCTTAAACA-ACCATTAA
*
209454 AAATAAAGTTTAAACAACCATTAA
1 AAATAAAGCTTAAACAACCATTAA
209478 A
1 A
209479 TCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATAAAGCTTAAACAACCATTAA
Found at i:215113 original size:16 final size:16
Alignment explanation
Indices: 215092--215123 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
215082 ATCGTCGACA
215092 AAAATTCACTATTCAC
1 AAAATTCACTATTCAC
215108 AAAATTCACTATTCAC
1 AAAATTCACTATTCAC
215124 GTAAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTCACTATTCAC
Found at i:215629 original size:13 final size:13
Alignment explanation
Indices: 215611--215636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
215601 GTCCAGCCTG
215611 CCATTCTAGAATT
1 CCATTCTAGAATT
215624 CCATTCTAGAATT
1 CCATTCTAGAATT
215637 TTGACTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CCATTCTAGAATT
Found at i:227088 original size:22 final size:23
Alignment explanation
Indices: 227063--227106 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
227053 ACGGTTTTAT
* *
227063 AATTGAAAGAAA-ATAAATAAAG
1 AATTGAAACAAAGAAAAATAAAG
227085 AATTGAAACAAAGAAAAATAAA
1 AATTGAAACAAAGAAAAATAAA
227107 ATAAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.16
Consensus pattern (23 bp):
AATTGAAACAAAGAAAAATAAAG
Found at i:228301 original size:25 final size:25
Alignment explanation
Indices: 228250--228301 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
228240 ATATTGGTCT
* *
228250 CACCTATAATTTAATTGCACTCTAA
1 CACCTATAATTTAATTGCACACCAA
* *
228275 CACCTATAATTTCATTGGACACCAA
1 CACCTATAATTTAATTGCACACCAA
228300 CA
1 CA
228302 TCGCTAGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (25 bp):
CACCTATAATTTAATTGCACACCAA
Found at i:229842 original size:3 final size:3
Alignment explanation
Indices: 229834--229902 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
229824 AATTTTTTGT
* **
229834 TTA TTA TTA ATA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
229882 TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA
229903 CAAGCCCAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:231381 original size:27 final size:26
Alignment explanation
Indices: 231348--231419 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
231338 ATATAGTTCT
*
231348 AATTTTATTTTTATTATTGTTTATTTA
1 AATTTTATTTTTATTATT-TATATTTA
** * *
231375 TGTTTTAATTTTACTTGTTTATATTTA
1 AATTTTATTTTTA-TTATTTATATTTA
*
231402 AATATTATTTTTATTATT
1 AATTTTATTTTTATTATT
231420 ATAGTCATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
26 4 0.12
27 26 0.76
28 4 0.12
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (26 bp):
AATTTTATTTTTATTATTTATATTTA
Found at i:234630 original size:36 final size:35
Alignment explanation
Indices: 234580--234668 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
234570 GAGTAACACC
* * *
234580 TTTT-CATATATGCATTTACATTTTGTATTCTTACT
1 TTTTACATTTATGCATTTACAGTTTGCATTCTTA-T
*
234615 TTTTACATCTT-TGCATTACACAGTTTGCATTCTTAT
1 TTTTACAT-TTATGCATT-TACAGTTTGCATTCTTAT
*
234651 TTTTGCATTTATGCATTT
1 TTTTACATTTATGCATTT
234669 TCGCATTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
35 6 0.14
36 23 0.52
37 15 0.34
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (35 bp):
TTTTACATTTATGCATTTACAGTTTGCATTCTTAT
Found at i:237545 original size:18 final size:17
Alignment explanation
Indices: 237522--237636 Score: 92
Period size: 18 Copynumber: 6.6 Consensus size: 17
237512 GTAAAGAAAG
237522 AAGAAAGAAAA-AAAAGAA
1 AAGAAA-AAAAGAAAA-AA
*
237540 AAGAAAAAAAGGAAAAAT
1 AAGAAAAAAA-GAAAAAA
237558 AAGAAAAAAAGAAAAAA
1 AAGAAAAAAAGAAAAAA
**
237575 AAGATAAAAGATCAAAAAA
1 AAGA-AAAA-AAGAAAAAA
* *
237594 AAG-AAGAAGGAAAAAA
1 AAGAAAAAAAGAAAAAA
*
237610 GAAGGAAAAAAG-AAAAA
1 -AAGAAAAAAAGAAAAAA
*
237627 AGGAAAAAAA
1 AAGAAAAAAA
237637 ATTTGAACCA
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
16 15 0.19
17 25 0.31
18 26 0.32
19 14 0.17
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAAGAAAAAA
Found at i:237549 original size:8 final size:8
Alignment explanation
Indices: 237522--237636 Score: 72
Period size: 9 Copynumber: 13.2 Consensus size: 8
237512 GTAAAGAAAG
237522 AAGAAAGAA
1 AAGAAA-AA
*
237531 AAAAAAGAA
1 AAGAAA-AA
237540 AAGAAAAA
1 AAGAAAAA
237548 AAGGAAAAA
1 AA-GAAAAA
237557 TAAGAAAAA
1 -AAGAAAAA
237566 AAGAAAAAA
1 AAG-AAAAA
237575 AAGATAAAA
1 AAGA-AAAA
237584 GATCA-AAAAA
1 -A--AGAAAAA
*
237594 AAGAAGAAGG
1 AAGAA-AA-A
*
237604 AA-AAAAG
1 AAGAAAAA
*
237611 AAGGAAAA
1 AAGAAAAA
237619 AAGAAAAA
1 AAGAAAAA
*
237627 AGGAAAAA
1 AAGAAAAA
237635 AA
1 AA
237637 ATTTGAACCA
Statistics
Matches: 87, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
7 4 0.05
8 30 0.34
9 42 0.48
10 9 0.10
11 1 0.01
12 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:237564 original size:17 final size:17
Alignment explanation
Indices: 237533--237627 Score: 77
Period size: 17 Copynumber: 5.4 Consensus size: 17
237523 AGAAAGAAAA
237533 AAAAGAAAAGAAAAAAAGG
1 AAAA-AAAAG-AAAAAAGG
* *
237552 AAAAATAAGAAAAAAAG
1 AAAAAAAAGAAAAAAGG
**
237569 AAAAAAAAGATAAAAGATC
1 AAAAAAAAGA-AAAA-AGG
*
237588 AAAAAAAAG-AAGAAGG
1 AAAAAAAAGAAAAAAGG
237604 AAAAAAGAAGGAAAAAA-G
1 AAAAAA-AA-GAAAAAAGG
237622 AAAAAA
1 AAAAAA
237628 GGAAAAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.11
17 21 0.34
18 16 0.26
19 18 0.29
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAGG
Found at i:237574 original size:26 final size:26
Alignment explanation
Indices: 237538--237634 Score: 99
Period size: 26 Copynumber: 3.7 Consensus size: 26
237528 GAAAAAAAAG
*
237538 AAAAGAAAAAAAGGAAAAATAAGAAA
1 AAAAGAAAAAAAGGAAAAAGAAGAAA
* **
237564 AAAAGAAAAAAAAGATAAAAGATCAAA
1 AAAAGAAAAAAAGGA-AAAAGAAGAAA
* * *
237591 AAAA-AGAAGAAGGAAAAAAGAAGGAA
1 AAAAGAAAAAAAGG-AAAAAGAAGAAA
237617 AAAAG-AAAAAAGGAAAAA
1 AAAAGAAAAAAAGGAAAAA
237635 AAATTTGAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
25 5 0.09
26 38 0.68
27 13 0.23
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAAGAAAAAAAGGAAAAAGAAGAAA
Found at i:237626 original size:7 final size:7
Alignment explanation
Indices: 237514--237635 Score: 58
Period size: 7 Copynumber: 17.4 Consensus size: 7
237504 CTCATTCAGT
237514 AAAGAAA
1 AAAGAAA
*
237521 GAAGAAA
1 AAAGAAA
*
237528 GAA-AAA
1 AAAGAAA
237534 AAAGAAA
1 AAAGAAA
*
237541 AGA-AAA
1 AAAGAAA
*
237547 AAAGGAA
1 AAAGAAA
*
237554 AAATAAGA
1 AAAGAA-A
237562 AAA-AAA
1 AAAGAAA
*
237568 GAA-AAA
1 AAAGAAA
*
237574 AAAGATA
1 AAAGAAA
237581 AAAGATCAA
1 AAAGA--AA
237590 AAA-AAA
1 AAAGAAA
*
237596 GAAGAAGGA
1 AAAGAA--A
*
237605 AAA-AAG
1 AAAGAAA
*
237611 AAGGAAA
1 AAAGAAA
237618 AAAGAAA
1 AAAGAAA
237625 AAAGGAAA
1 AAA-GAAA
237633 AAA
1 AAA
237636 AATTTGAACC
Statistics
Matches: 87, Mismatches: 17, Indels: 21
0.70 0.14 0.17
Matches are distributed among these distances:
6 24 0.28
7 42 0.48
8 14 0.16
9 7 0.08
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:237637 original size:11 final size:11
Alignment explanation
Indices: 237592--237623 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
237582 AAGATCAAAA
237592 AAAAGAAGAAGG
1 AAAA-AAGAAGG
237604 AAAAAAGAAGG
1 AAAAAAGAAGG
237615 AAAAAAGAA
1 AAAAAAGAA
237624 AAAAGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGG
Found at i:239979 original size:114 final size:114
Alignment explanation
Indices: 239765--239982 Score: 319
Period size: 114 Copynumber: 1.9 Consensus size: 114
239755 GTTTCTCGTA
* * **
239765 GTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTTTG
1 GTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTATTTGAGTTATCTGATCTGGTTCGG
* * * *
239830 TATGAACCCTAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCATC
66 TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAATTTGCTCATC
* *
239879 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTCGG
1 GTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTATTTGAGTTATCTGATCTGGTTCGG
* * *
239944 TAGGAACCCCAGAACCAATCATTGGAATAGGAAGATGAA
66 TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAA
239983 CTGCATGATC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
GTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTATTTGAGTTATCTGATCTGGTTCGG
TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAATTTGCTCATC
Found at i:240198 original size:31 final size:32
Alignment explanation
Indices: 240160--240223 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
240150 GCACATATAA
*
240160 AATCTGTC-AACTCTGCAATTGATGAATTCAG
1 AATCTGTCAAACTCTACAATTGATGAATTCAG
240191 AATCTGTCAAACTCTACAATTGATGAATTCAG
1 AATCTGTCAAACTCTACAATTGATGAATTCAG
240223 A
1 A
240224 CCACATCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (32 bp):
AATCTGTCAAACTCTACAATTGATGAATTCAG
Found at i:243330 original size:75 final size:76
Alignment explanation
Indices: 243158--243490 Score: 562
Period size: 76 Copynumber: 4.4 Consensus size: 76
243148 CTATTTCCCA
243158 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
243223 AGCCTTAGGGT
66 AGCCTTAGGGT
*
243234 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
243299 A-CCTTCGGGC
66 AGCCTTAGGGT
*
243309 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
243374 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
243385 CATCTGTAAGTCCTGCAGTGCATTATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
243450 AA-CCTTCGGGT
65 AAGCCTTAGGGT
* *
243461 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
243491 TTAAGACCTC
Statistics
Matches: 241, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
75 71 0.29
76 137 0.57
77 33 0.14
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:243404 original size:151 final size:152
Alignment explanation
Indices: 243158--243490 Score: 596
Period size: 151 Copynumber: 2.2 Consensus size: 152
243148 CTATTTCCCA
*
243158 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
*
243223 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
243287 TGATGTTTTCAAACCTTCGGGC
131 TGATGTTTTCAAACCTTCGGGC
243309 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
* *
243374 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATTATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
*
243439 TGATGTTTTCAAACCTTCGGGT
131 TGATGTTTTCAAACCTTCGGGC
* *
243461 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
243491 TTAAGACCTC
Statistics
Matches: 174, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
151 105 0.60
152 69 0.40
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAACCTTCGGGC
Found at i:243654 original size:12 final size:12
Alignment explanation
Indices: 243637--243706 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
243627 TTTTTCGTTT
243637 ATTATTATTAAA
1 ATTATTATTAAA
243649 ATTATTATT---
1 ATTATTATTAAA
243658 ATTATTA-TAAA
1 ATTATTATTAAA
**
243669 TATTATTATTATT
1 -ATTATTATTAAA
243682 ATTATTATTATTAA
1 ATTATTATTA--AA
243696 ATATATTATTA
1 AT-TATTATTA
243707 CAAGCCCAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
12 26 0.57
13 2 0.04
14 2 0.04
15 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:243702 original size:18 final size:16
Alignment explanation
Indices: 243635--243706 Score: 78
Period size: 15 Copynumber: 4.6 Consensus size: 16
243625 AATTTTTCGT
*
243635 TTATTATTATTA-AAA
1 TTATTATTATTATATA
243650 TTATTATTATTATTATAA
1 TTATTATTATTA-TAT-A
*
243668 ATATTATTATTAT-TA
1 TTATTATTATTATATA
*
243683 TTATTATTATTAAATA
1 TTATTATTATTATATA
243699 -TATTATTA
1 TTATTATTA
243707 CAAGCCCAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
15 32 0.65
16 3 0.06
17 2 0.04
18 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTATTATATA
Found at i:243706 original size:3 final size:3
Alignment explanation
Indices: 243635--243694 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
243625 AATTTTTCGT
** * *
243635 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
243683 TTA TTA TTA TTA
1 TTA TTA TTA TTA
243695 AATATATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:243961 original size:18 final size:18
Alignment explanation
Indices: 243938--243975 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
243928 GCCGCCCCAC
243938 CCAACGGTCCAGCAGCAG
1 CCAACGGTCCAGCAGCAG
*
243956 CCAACGGTCTAGCAGCAG
1 CCAACGGTCCAGCAGCAG
243974 CC
1 CC
243976 GACGCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.08
Consensus pattern (18 bp):
CCAACGGTCCAGCAGCAG
Found at i:245185 original size:27 final size:26
Alignment explanation
Indices: 245152--245223 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
245142 ATATAGTTCT
*
245152 AATTTTATTTTTATTATTGTTTATTTA
1 AATTTTATTTTTATTATT-TATATTTA
** * *
245179 TGTTTTAATTTTACTTGTTTATATTTA
1 AATTTTATTTTTA-TTATTTATATTTA
*
245206 AATATTATTTTTATTATT
1 AATTTTATTTTTATTATT
245224 ATAGTCATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
26 4 0.12
27 26 0.76
28 4 0.12
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (26 bp):
AATTTTATTTTTATTATTTATATTTA
Found at i:251326 original size:48 final size:48
Alignment explanation
Indices: 251274--251378 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
251264 GTCAAATCTA
* * * *
251274 AAAAATGGAATCTACTCAGCTGCTCTTCAGGGTTGGTTAGATTTAGAT
1 AAAAAGGGAATATACTCAGCTGCTCTTCAGGGTAGGTTAGATTTAGAG
* * ** * *
251322 AAAAAGGGGATATGCTTTGTTGCTCTTCAGGGTAGGTTAGATTTTGAG
1 AAAAAGGGAATATACTCAGCTGCTCTTCAGGGTAGGTTAGATTTAGAG
251370 AAAAAGGGA
1 AAAAAGGGA
251379 TATGCTGCTC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31
Consensus pattern (48 bp):
AAAAAGGGAATATACTCAGCTGCTCTTCAGGGTAGGTTAGATTTAGAG
Found at i:253215 original size:49 final size:48
Alignment explanation
Indices: 253137--253252 Score: 130
Period size: 47 Copynumber: 2.4 Consensus size: 48
253127 TGCTCCACTG
* * *
253137 CTATTTAGGGTAGGTCA-AATCTAATGAAAAAGTGGAATATGCTTCGCTA
1 CTATTTAGGGTAGGTTAGATTCTAATGAAAAA-TGG-ATATACTTCGCTA
*
253186 CTATTTAGGGTAGGTTAGATTC-AGA-GAAAAATGGATCTACTTCGCTA
1 CTATTTAGGGTAGGTTAGATTCTA-ATGAAAAATGGATATACTTCGCTA
* *
253233 CTCTTTAGGGTAAGTTAGAT
1 CTATTTAGGGTAGGTTAGAT
253253 CAAGATAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
47 29 0.49
48 3 0.05
49 23 0.39
50 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (48 bp):
CTATTTAGGGTAGGTTAGATTCTAATGAAAAATGGATATACTTCGCTA
Found at i:253371 original size:134 final size:135
Alignment explanation
Indices: 253114--253436 Score: 345
Period size: 134 Copynumber: 2.4 Consensus size: 135
253104 AGTAGGTCCA
* * * * *
253114 ATCAAGATAGATTTGCTCCACTGCT-ATTTAGGGTAGGTCAAATCTAATGAAAAAGTGGAATATG
1 ATCAAGATAGATTTGTTCCACTACTCA-TCAAGGTAGGTCAAATCTAA--AAAAAGTGAAATATG
* * * * *
253178 CTTCGCTACTATTTAGGGTAGGTTAGATTCAGAGAAAAATGGATCTACTTCGCTACTCTTTAGGG
63 CTTCACTACTATTCAGGGTAGGTTAGATTCAGAGAAAAATGGATCTACTCCACTACTCTTCAGGG
*
253243 TAAGTTAG
128 TAAGTCAG
* *
253251 ATCAAGATAGATTTGTTCCACTCCTCATCAAGGTAGGTCAAATCTAAAAAAA-TGAAATCT-CTT
1 ATCAAGATAGATTTGTTCCACTACTCATCAAGGTAGGTCAAATCTAAAAAAAGTGAAATATGC-T
* *
253314 TCACTAC-AGTTCAGGGCT-GGTTAGATTCAGAGAAAAGTGGATCTACTCCACTGCTCTTCAGGG
65 TCACTACTA-TTCAGGG-TAGGTTAGATTCAGAGAAAAATGGATCTACTCCACTACTCTTCAGGG
* *
253377 TAGGTCGG
128 TAAGTCAG
* * **
253385 ATCAAGATAGATTTGCTT-CATTACTCTTC-AGGTTTGTCAAATCTAAAAAAAG
1 ATCAAGATAGATTTG-TTCCACTACTCATCAAGGTAGGTCAAATCTAAAAAAAG
253437 GGGATTTTCT
Statistics
Matches: 159, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
133 22 0.14
134 87 0.55
135 8 0.05
137 41 0.26
138 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (135 bp):
ATCAAGATAGATTTGTTCCACTACTCATCAAGGTAGGTCAAATCTAAAAAAAGTGAAATATGCTT
CACTACTATTCAGGGTAGGTTAGATTCAGAGAAAAATGGATCTACTCCACTACTCTTCAGGGTAA
GTCAG
Found at i:259006 original size:20 final size:20
Alignment explanation
Indices: 258981--259038 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
258971 TTTGGTTCAC
*
258981 AGAATATAAGATTACCAGTG
1 AGAATAAAAGATTACCAGTG
*
259001 AGAATAAAAGATTACCAATG
1 AGAATAAAAGATTACCAGTG
259021 AGAATAAAAGATTACCAG
1 AGAATAAAAGATTACCAG
259039 GAAATATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (20 bp):
AGAATAAAAGATTACCAGTG
Found at i:259473 original size:16 final size:17
Alignment explanation
Indices: 259452--259483 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
259442 AGGGGAATTT
259452 TAATCCAA-AATACCAG
1 TAATCCAACAATACCAG
259468 TAATCCAACAATACCA
1 TAATCCAACAATACCA
259484 AAGGAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (17 bp):
TAATCCAACAATACCAG
Found at i:259666 original size:26 final size:26
Alignment explanation
Indices: 259630--259679 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
259620 CCCACCAAAC
259630 ACACCCTAAGGGTAAACTTGAGTGAT
1 ACACCCTAAGGGTAAACTTGAGTGAT
259656 ACACCCTAAGGGTAAACTTGAGTG
1 ACACCCTAAGGGTAAACTTGAGTG
259680 TGTCACTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (26 bp):
ACACCCTAAGGGTAAACTTGAGTGAT
Found at i:259727 original size:23 final size:23
Alignment explanation
Indices: 259699--259751 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
259689 CTTGCTGAAG
259699 GATGATTCCATTGACTTGCTAGA
1 GATGATTCCATTGACTTGCTAGA
* *
259722 GATGATGCCATTGACTTGCTGGA
1 GATGATTCCATTGACTTGCTAGA
259745 GATGATT
1 GATGATT
259752 GAGTTGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (23 bp):
GATGATTCCATTGACTTGCTAGA
Done.