Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 151 of 160
Found at i:29719001 original size:4 final size:4
Alignment explanation
Indices: 29718988--29719017 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
29718978 TAGGAGAAGG
29718988 AGGC -GGC AGGC AGGC AGGC AGGC AGGC AGG
1 AGGC AGGC AGGC AGGC AGGC AGGC AGGC AGG
29719018 TTGCGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.23, G:0.53, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:29721088 original size:24 final size:24
Alignment explanation
Indices: 29721056--29721106 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
29721046 ATATGCCTGG
29721056 CAATGATCCCCATAAGGTTTGAAA
1 CAATGATCCCCATAAGGTTTGAAA
29721080 CAATGATCCCCATAAGGTTTGAAA
1 CAATGATCCCCATAAGGTTTGAAA
29721104 CAA
1 CAA
29721107 GAAGGGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
CAATGATCCCCATAAGGTTTGAAA
Found at i:29724363 original size:2 final size:2
Alignment explanation
Indices: 29724356--29724391 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29724346 TCAAATTCTG
*
29724356 AT AT AT AT GT 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 AT AT
29724392 TCCATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29731368 original size:44 final size:45
Alignment explanation
Indices: 29731313--29731397 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
29731303 CAAAGAAAAA
* * *
29731313 CAGCGACAACAAAATT-AAAAGGAAAATTTTTACCATCTCTGTCT
1 CAGCGAAAACAAAATTAAAAAAGAAAATCTTTACCATCTCTGTCT
29731357 CAGCGAAAACAAAATTAAAAAAGAAAATCTTTACCATCTCT
1 CAGCGAAAACAAAATTAAAAAAGAAAATCTTTACCATCTCT
29731398 TGTTGTTGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 15 0.41
45 22 0.59
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (45 bp):
CAGCGAAAACAAAATTAAAAAAGAAAATCTTTACCATCTCTGTCT
Found at i:29749408 original size:2 final size:2
Alignment explanation
Indices: 29749401--29749439 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29749391 ATGGGCAAAA
29749401 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29749440 TGTTAACTTA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29757617 original size:39 final size:40
Alignment explanation
Indices: 29757573--29757657 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
29757563 GATTGGGTGT
*
29757573 GGATTGGGTGTGGTAGGG-TGTT-GGGAGGAAGGTGGGGAG
1 GGATTGGGTGTGGT-GGGATGTTGGGGAGGAAGGTGGAGAG
*
29757612 GGATTGGGTGTGGTGGGATGTTGGGGGGGAAGGTGGAGAG
1 GGATTGGGTGTGGTGGGATGTTGGGGAGGAAGGTGGAGAG
29757652 GGATTG
1 GGATTG
29757658 ATGGGGGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
38 3 0.07
39 18 0.43
40 21 0.50
ACGTcount: A:0.15, C:0.00, G:0.61, T:0.24
Consensus pattern (40 bp):
GGATTGGGTGTGGTGGGATGTTGGGGAGGAAGGTGGAGAG
Found at i:29757929 original size:20 final size:20
Alignment explanation
Indices: 29757891--29757928 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29757881 GATTGTGTTA
*
29757891 TATATTAATTTATAATTTTG
1 TATATGAATTTATAATTTTG
29757911 TATATGAATTT-TAATTTT
1 TATATGAATTTATAATTTT
29757929 TTTTGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATGAATTTATAATTTTG
Found at i:29758182 original size:26 final size:26
Alignment explanation
Indices: 29758154--29758202 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
29758144 TAAAAAGTAA
*
29758154 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
29758179 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
29758203 ATTTTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:29762011 original size:18 final size:18
Alignment explanation
Indices: 29761988--29762112 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
29761978 ATGGTTATTA
29761988 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
29762006 TCCACCTCTTCAAATATATCC
1 TCCA-C-C-TCAAATGTATCC
*
29762027 TCCACCTCAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
29762046 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* *
29762063 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
29762081 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
*
29762096 TCAACCTCAAATGTATC
1 TCCACCTCAAATGTATC
29762113 AAGAACAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 52 0.61
19 3 0.04
20 2 0.02
21 15 0.18
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.28
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:29762020 original size:21 final size:21
Alignment explanation
Indices: 29761994--29762034 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29761984 ATTATCCACC
*
29761994 TCAAATGTATCCTCCACCTCT
1 TCAAATATATCCTCCACCTCT
29762015 TCAAATATATCCTCCACCTC
1 TCAAATATATCCTCCACCTC
29762035 AAATGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.39, G:0.02, T:0.32
Consensus pattern (21 bp):
TCAAATATATCCTCCACCTCT
Found at i:29762056 original size:36 final size:33
Alignment explanation
Indices: 29762016--29762113 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
29762006 TCCACCTCTT
29762016 CAAATATATCCTCCACCTCAAATGTATCAGTTACCA
1 CAAATATATCCTCCACCTCAAATGTATCA--T-CCA
* * * *
29762052 CAAATGTACCCTCCACCACAAATGTATCATCCT
1 CAAATATATCCTCCACCTCAAATGTATCATCCA
*
29762085 CAAATATATCCTCAACCTCAAATGTATCA
1 CAAATATATCCTCCACCTCAAATGTATCA
29762114 AGAACAAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 27 0.50
34 1 0.02
36 26 0.48
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.27
Consensus pattern (33 bp):
CAAATATATCCTCCACCTCAAATGTATCATCCA
Found at i:29762837 original size:2 final size:2
Alignment explanation
Indices: 29762832--29762862 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29762822 GTGTGTGTGT
29762832 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29762863 AATTGCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29769464 original size:75 final size:74
Alignment explanation
Indices: 29769370--29769519 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 74
29769360 ATAACCAGAT
* * * * *
29769370 TGATTTTGCATGCGTGTGGTCTTCAGACTGAAGTAAATAGGAAAGTAACCAAGTTAAATTCCACA
1 TGATTTTGCAAGCATGTGGTCTTCACACTGAAGCAAAAAGGAAAGTAACCAAGTTAAATTCCACA
29769435 TAATTAGGCA
66 TAA-TAGGCA
* *
29769445 TGATTTTGCAAGCATGTGGTCTTCACACTGAAGCAAAAAGGAATGTAACCAAGTTAAATTCCATA
1 TGATTTTGCAAGCATGTGGTCTTCACACTGAAGCAAAAAGGAAAGTAACCAAGTTAAATTCCACA
29769510 TAATAGGCA
66 TAATAGGCA
29769519 T
1 T
29769520 CAAATGATTC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 7 0.10
75 61 0.90
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (74 bp):
TGATTTTGCAAGCATGTGGTCTTCACACTGAAGCAAAAAGGAAAGTAACCAAGTTAAATTCCACA
TAATAGGCA
Found at i:29805760 original size:2 final size:2
Alignment explanation
Indices: 29805753--29805779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29805743 GTTCTTTATT
29805753 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
29805780 TTCCTTATGA
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:29807937 original size:19 final size:18
Alignment explanation
Indices: 29807897--29807958 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
29807887 AAACATATAT
* *
29807897 ATAAAATATATATAATTAA
1 ATAAATTATAAATAA-TAA
*
29807916 ATATATTCATAAATAATAA
1 ATAAATT-ATAAATAATAA
*
29807935 ATAAATTATAACTAAATAA
1 ATAAATTATAAAT-AATAA
29807954 ATAAA
1 ATAAA
29807959 CAAATAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.14
19 24 0.67
20 7 0.19
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATTATAAATAATAA
Found at i:29807940 original size:11 final size:11
Alignment explanation
Indices: 29807924--29807966 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
29807914 AAATATATTC
29807924 ATAAATAATAA
1 ATAAATAATAA
*
29807935 ATAAATTATAA
1 ATAAATAATAA
*
29807946 CTAAATAAATAA
1 ATAAAT-AATAA
*
29807958 ACAAATAAT
1 ATAAATAAT
29807967 TATAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:29818225 original size:11 final size:11
Alignment explanation
Indices: 29818209--29818242 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
29818199 AGCAGATTGA
29818209 TTTTTTTTCCT
1 TTTTTTTTCCT
*
29818220 TTTTTTTTCTT
1 TTTTTTTTCCT
29818231 TTTTTTTTCCT
1 TTTTTTTTCCT
29818242 T
1 T
29818243 CGATCCGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCCT
Found at i:29828109 original size:23 final size:24
Alignment explanation
Indices: 29828058--29828101 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29828048 GTAAACAATT
*
29828058 CAAATTTTGCTTATTAATTGTTAC
1 CAAATCTTGCTTATTAATTGTTAC
29828082 CAAATCTT-CTTATT-ATTGTT
1 CAAATCTTGCTTATTAATTGTT
29828102 TTCCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (24 bp):
CAAATCTTGCTTATTAATTGTTAC
Found at i:29832670 original size:21 final size:20
Alignment explanation
Indices: 29832641--29832683 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
29832631 TAATTAATAC
*
29832641 ATAAATTAAAATATAATTAA
1 ATAAATTAAAATAAAATTAA
*
29832661 ATAAATTTAACATAAAATTAA
1 ATAAA-TTAAAATAAAATTAA
29832682 AT
1 AT
29832684 TAAGTTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATTAAAATAAAATTAA
Found at i:29832694 original size:21 final size:21
Alignment explanation
Indices: 29832641--29832694 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
29832631 TAATTAATAC
* *
29832641 ATAAA-TTAAAATATAATTAA
1 ATAAAGTTAACATAAAATTAA
*
29832661 ATAAATTTAACATAAAATTAA
1 ATAAAGTTAACATAAAATTAA
* *
29832682 ATTAAGTTCACAT
1 ATAAAGTTAACAT
29832695 GCAATAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAAGTTAACATAAAATTAA
Found at i:29834986 original size:83 final size:82
Alignment explanation
Indices: 29834847--29835009 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 82
29834837 CTTTCAGAAG
* * * * *
29834847 TTGGTTTTTGAAGGTTAGACTTAGAATTGCTACCATTCATGGCCTCTTGCTCTTAACCCTTTTTC
1 TTGGTTTTTGAAGGTTAGACATAGAACTACTAACATTCATGGCCTCTTGCTCTTAACCCTTTGTC
29834912 TTAAAATAATAAGATGTT
66 -TAAAATAATAAGATGTT
* * *
29834930 TTGGTTTTTGAAGGTTAGGCATAGAACTACTAACATTCATTGCCTTTTGCTCTTAACCCTTTGTC
1 TTGGTTTTTGAAGGTTAGACATAGAACTACTAACATTCATGGCCTCTTGCTCTTAACCCTTTGTC
*
29834995 TAAAATAGTAAGATG
66 TAAAATAATAAGATG
29835010 GTAGTATGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 14 0.20
83 57 0.80
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (82 bp):
TTGGTTTTTGAAGGTTAGACATAGAACTACTAACATTCATGGCCTCTTGCTCTTAACCCTTTGTC
TAAAATAATAAGATGTT
Found at i:29839936 original size:18 final size:18
Alignment explanation
Indices: 29839915--29839954 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29839905 TTTAATTATT
29839915 TATTTAATTATATATATA
1 TATTTAATTATATATATA
* *
29839933 TATTTAATTTTATATTTA
1 TATTTAATTATATATATA
29839951 TATT
1 TATT
29839955 AAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAATTATATATATA
Found at i:29839941 original size:30 final size:31
Alignment explanation
Indices: 29839905--29839972 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
29839895 TCTATTATTT
* *
29839905 TTTAATTATT-TATTTA-ATTATATATATATA
1 TTTAATTATTATATTTATATTAAAAATA-ATA
29839935 TTTAATT-TTATATTTATATTAAAAATAATA
1 TTTAATTATTATATTTATATTAAAAATAATA
*
29839965 TTTTATTA
1 TTTAATTA
29839973 ATTTTAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.06
30 22 0.69
31 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTAATTATTATATTTATATTAAAAATAATA
Found at i:29839963 original size:23 final size:23
Alignment explanation
Indices: 29839937--29839980 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29839927 TATATATATT
*
29839937 TAAT-TTTATATTTATATTAAAAA
1 TAATATTT-TATTAATATTAAAAA
*
29839960 TAATATTTTATTAATTTTAAA
1 TAATATTTTATTAATATTAAA
29839981 TCGAATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATATTTTATTAATATTAAAAA
Found at i:29840107 original size:27 final size:27
Alignment explanation
Indices: 29840051--29840109 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
29840041 TTATTAAATT
* * * *
29840051 AAATTAAATTTAAATTTTATATATTTA
1 AAATTAAATTCAAATTTTAAATAATAA
29840078 AAATTAAA-TCAAATTTTAAATGAATAA
1 AAATTAAATTCAAATTTTAAAT-AATAA
29840105 AAATT
1 AAATT
29840110 TATATCGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATTAAATTCAAATTTTAAATAATAA
Found at i:29842609 original size:24 final size:24
Alignment explanation
Indices: 29842559--29842611 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
29842549 TGCCGCTGAT
* *
29842559 TTGTTGTTGTGGTGGTTGTTATCA
1 TTGTTGCTGTGGTGGTGGTTATCA
* *
29842583 TTGTTGCTGTGGTGGTGGTTGTTA
1 TTGTTGCTGTGGTGGTGGTTATCA
29842607 TTGTT
1 TTGTT
29842612 ATGATTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.04, G:0.36, T:0.55
Consensus pattern (24 bp):
TTGTTGCTGTGGTGGTGGTTATCA
Found at i:29879087 original size:22 final size:24
Alignment explanation
Indices: 29879036--29879080 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29879026 TAAGATATTT
29879036 CATTTTGATATATATAAAAATATA
1 CATTTTGATATATATAAAAATATA
* *
29879060 CATTTTTATATA-ATTAAAATA
1 CATTTTGATATATATAAAAATA
29879081 ATATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
CATTTTGATATATATAAAAATATA
Found at i:29881053 original size:16 final size:16
Alignment explanation
Indices: 29881020--29881053 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29881010 AATCTTTGAT
*
29881020 AGATAAAAACAAGGAA
1 AGATAAAAACAAGAAA
*
29881036 AGATAAAAACGAGAAA
1 AGATAAAAACAAGAAA
29881052 AG
1 AG
29881054 CAGCATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.06
Consensus pattern (16 bp):
AGATAAAAACAAGAAA
Found at i:29883609 original size:36 final size:36
Alignment explanation
Indices: 29883562--29883634 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
29883552 GGCAAGAAAC
29883562 TCATAGTTAAAAGTACGTTATCTATCCAATATCCAA
1 TCATAGTTAAAAGTACGTTATCTATCCAATATCCAA
29883598 TCATAGTTAAAAGTACGTTATCTATCCAATATCCAA
1 TCATAGTTAAAAGTACGTTATCTATCCAATATCCAA
29883634 T
1 T
29883635 TGATGCATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.34
Consensus pattern (36 bp):
TCATAGTTAAAAGTACGTTATCTATCCAATATCCAA
Found at i:29887886 original size:18 final size:18
Alignment explanation
Indices: 29887865--29887906 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29887855 TTTAATTAAA
29887865 TTAA-TAGATTAAATTGAT
1 TTAATTAGATT-AATTGAT
*
29887883 TTAATTTGATTAATTGA-
1 TTAATTAGATTAATTGAT
29887900 TTAATTA
1 TTAATTA
29887907 TTGAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (18 bp):
TTAATTAGATTAATTGAT
Found at i:29887901 original size:8 final size:8
Alignment explanation
Indices: 29887864--29887928 Score: 51
Period size: 8 Copynumber: 7.5 Consensus size: 8
29887854 TTTTAATTAA
*
29887864 ATTAATAG
1 ATTAATTG
29887872 ATTAAATTG
1 ATT-AATTG
29887881 ATTTAATTTG
1 A-TTAA-TTG
29887891 ATTAATTG
1 ATTAATTG
29887899 ATTAATT-
1 ATTAATTG
*
29887906 ATTGAATTA
1 ATT-AATTG
29887915 ATTTTAATTG
1 A--TTAATTG
29887925 ATTA
1 ATTA
29887929 TTAAAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.06
8 20 0.42
9 12 0.25
10 11 0.23
11 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (8 bp):
ATTAATTG
Found at i:29887931 original size:29 final size:29
Alignment explanation
Indices: 29887856--29887932 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 29
29887846 AAATTTGATT
* * *
29887856 TTAATTAAATTAATAGATTAA--ATTGAT
1 TTAATTTAATTAATTGATTAATTATTGAA
*
29887883 TTAATTTGATTAATTGATTAATTATTGAA
1 TTAATTTAATTAATTGATTAATTATTGAA
*
29887912 TTAATTTTAATTGATT-ATTAA
1 TTAA-TTTAATTAATTGATTAA
29887933 AAATAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 18 0.44
29 14 0.34
30 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (29 bp):
TTAATTTAATTAATTGATTAATTATTGAA
Found at i:29888113 original size:13 final size:13
Alignment explanation
Indices: 29888071--29888122 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
29888061 AAATTATTAA
*
29888071 AATTTTAATTTAAT
1 AATTTT-ATTGAAT
29888085 AATTTGATATTTGAAT
1 AATTT--TA-TTGAAT
*
29888101 ATTTTTATTGAAT
1 AATTTTATTGAAT
29888114 AATTTTATT
1 AATTTTATT
29888123 TAATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 14 0.44
14 7 0.22
15 1 0.03
16 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (13 bp):
AATTTTATTGAAT
Found at i:29889211 original size:54 final size:54
Alignment explanation
Indices: 29889148--29889255 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
29889138 TCAAGAGACT
29889148 TTATATTCAAAACCATCTTAATAATCTCCATCTACATGGCATTTCGCCAGAGAA
1 TTATATTCAAAACCATCTTAATAATCTCCATCTACATGGCATTTCGCCAGAGAA
*
29889202 TTATATTCAAAACCATCTTAATAATCTCCATCTATATGGCATTTCGCCAGAGAA
1 TTATATTCAAAACCATCTTAATAATCTCCATCTACATGGCATTTCGCCAGAGAA
29889256 CTGATTTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (54 bp):
TTATATTCAAAACCATCTTAATAATCTCCATCTACATGGCATTTCGCCAGAGAA
Found at i:29907625 original size:13 final size:13
Alignment explanation
Indices: 29907607--29907632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29907597 AAAAGAAAAT
29907607 AATTTAAATTTTA
1 AATTTAAATTTTA
29907620 AATTTAAATTTTA
1 AATTTAAATTTTA
29907633 TCCACAATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:29930909 original size:136 final size:136
Alignment explanation
Indices: 29930665--29930940 Score: 471
Period size: 136 Copynumber: 2.0 Consensus size: 136
29930655 GCACTGAAGC
* * *
29930665 ATGTAACTTAACTATATTCAGCTAAAGCATATCATAAATGCAAAAGCAAACTAAAGATCATATTT
1 ATGTAACTTAACTATATTCAGCTAAAGCATATCATAAATACAAAACCAAACTAAAAATCATATTT
* * * *
29930730 GAAGTCAAGTAGCAAGTAATATTTAATTTTTGAACAGCATAGCAGCAAAAATTTCTTTATGATCA
66 GAAATCAAGTAGCAAGAAATATTTAAGTTTTGAACAGCATAGCAGCAAAAACTTCTTTATGATCA
29930795 GACATA
131 GACATA
*
29930801 ATGTACCTTAACTATATTCAGCTAAAGCATATCATAAATACAAAACCAAACTAAAAATCATATTT
1 ATGTAACTTAACTATATTCAGCTAAAGCATATCATAAATACAAAACCAAACTAAAAATCATATTT
*
29930866 GAAATCAAGTAGCAGGAAATATTTAAGTTTTGAACAGCATAGCAGCAAAAACTTCTTTATGATCA
66 GAAATCAAGTAGCAAGAAATATTTAAGTTTTGAACAGCATAGCAGCAAAAACTTCTTTATGATCA
29930931 GACATA
131 GACATA
29930937 ATGT
1 ATGT
29930941 GAAATGATGC
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 131 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (136 bp):
ATGTAACTTAACTATATTCAGCTAAAGCATATCATAAATACAAAACCAAACTAAAAATCATATTT
GAAATCAAGTAGCAAGAAATATTTAAGTTTTGAACAGCATAGCAGCAAAAACTTCTTTATGATCA
GACATA
Found at i:29931025 original size:30 final size:30
Alignment explanation
Indices: 29930991--29931048 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29930981 TTTGATTAAC
* **
29930991 TTAAATATAACTTGTGAAACCTCAGTGACT
1 TTAAAGATAACTCATGAAACCTCAGTGACT
*
29931021 TTAAAGATAACTCATGCAACCTCAGTGA
1 TTAAAGATAACTCATGAAACCTCAGTGA
29931049 GCTCAGATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (30 bp):
TTAAAGATAACTCATGAAACCTCAGTGACT
Found at i:29933319 original size:20 final size:20
Alignment explanation
Indices: 29933277--29933320 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29933267 TATTTATATA
* *
29933277 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTAT
29933297 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAATTTAT
29933317 TATT
1 TATT
29933321 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:29940288 original size:16 final size:18
Alignment explanation
Indices: 29940258--29940300 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
29940248 TATTTATAAA
29940258 TATAATATTTGATTAT-AT
1 TATAAT-TTTGATTATGAT
*
29940276 TATAATTTT-ATTATGTT
1 TATAATTTTGATTATGAT
29940293 TATAATTT
1 TATAATTT
29940301 CAAAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATAATTTTGATTATGAT
Found at i:29940714 original size:23 final size:23
Alignment explanation
Indices: 29940673--29940716 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
29940663 ATAAATATAT
29940673 ATATAAAATAATAATAATTAAAA
1 ATATAAAATAATAATAATTAAAA
29940696 ATATACAAATAATAA-AATTAA
1 ATATA-AAATAATAATAATTAA
29940717 TTTACCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATAAAATAATAATAATTAAAA
Found at i:29941109 original size:21 final size:20
Alignment explanation
Indices: 29941073--29941132 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
29941063 CGATAAATAT
29941073 TTATTTTAATAAATAATTAA
1 TTATTTTAATAAATAATTAA
*
29941093 TTATTTATAACAAATAATTAA
1 TTATTT-TAATAAATAATTAA
29941114 TT-TTTTAATAATATAATTA
1 TTATTTTAATAA-ATAATTA
29941133 TATGACACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.14
20 16 0.44
21 15 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTTTAATAAATAATTAA
Found at i:29941783 original size:22 final size:21
Alignment explanation
Indices: 29941717--29941783 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 21
29941707 TTAAAAAAAT
29941717 TTCAAATATAAAAAT-TCG-A
1 TTCAAATATAAAAATCTCGAA
** *
29941736 TT-AAATTTATAAACTTCTTGAA
1 TTCAAA--TATAAAAATCTCGAA
29941758 -TCAAATATAAAAATACTCGAA
1 TTCAAATATAAAAAT-CTCGAA
29941779 TTCAA
1 TTCAA
29941784 CTCGATCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 11
0.67 0.12 0.21
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 14 0.40
21 8 0.23
22 8 0.23
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.34
Consensus pattern (21 bp):
TTCAAATATAAAAATCTCGAA
Found at i:29942364 original size:18 final size:19
Alignment explanation
Indices: 29942337--29942377 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
29942327 TTATTCAAAT
29942337 ATTT-TATTTTTT-AATTA
1 ATTTATATTTTTTAAATTA
29942354 ATTTATATTTTTTAAATTA
1 ATTTATATTTTTTAAATTA
29942373 ATTTA
1 ATTTA
29942378 AAATCATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTATATTTTTTAAATTA
Found at i:29949171 original size:19 final size:19
Alignment explanation
Indices: 29949121--29949172 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
29949111 TGATAAAAAT
* *
29949121 TTAAATTATTTAATATTTA
1 TTAAATTATTAAATAATTA
* *
29949140 TAAAATTAATAAATAATTA
1 TTAAATTATTAAATAATTA
*
29949159 TTAAAGTATTAAAT
1 TTAAATTATTAAAT
29949173 TATTTTTATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAAATTATTAAATAATTA
Found at i:29953778 original size:16 final size:15
Alignment explanation
Indices: 29953750--29953791 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29953740 AGACTATTTA
*
29953750 TTTTCTTTTTTCT-T
1 TTTTTTTTTTTCTGT
29953764 TCTTTTTTTTCTTCTGT
1 T-TTTTTTTT-TTCTGT
29953781 TTTTTTTTTTT
1 TTTTTTTTTTT
29953792 TTTCCCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 12 0.50
17 2 0.08
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTCTGT
Found at i:29953783 original size:23 final size:21
Alignment explanation
Indices: 29953752--29953795 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29953742 ACTATTTATT
*
29953752 TTCTTTTTTCTTTCTTTTTTTTC
1 TTCTGTTTT-TTT-TTTTTTTTC
29953775 TTCTGTTTTTTTTTTTTTTTC
1 TTCTGTTTTTTTTTTTTTTTC
29953796 CCTTTTGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (21 bp):
TTCTGTTTTTTTTTTTTTTTC
Found at i:29961763 original size:16 final size:16
Alignment explanation
Indices: 29961742--29961772 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29961732 TTTTTGTGAT
29961742 TAAAAAATAATAAAAA
1 TAAAAAATAATAAAAA
29961758 TAAAAAATAATAAAA
1 TAAAAAATAATAAAA
29961773 CTCATATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAATAATAAAAA
Found at i:29962077 original size:31 final size:30
Alignment explanation
Indices: 29962042--29962102 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
29962032 GAGGGTTATC
*
29962042 AATATTAATAATTACATTTTAACTCTTTAAT
1 AATATCAATAATTACATTTTAA-TCTTTAAT
* *
29962073 AATATCAATAATTGCATTTTAATTTTTAAT
1 AATATCAATAATTACATTTTAATCTTTAAT
29962103 TTTTTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (30 bp):
AATATCAATAATTACATTTTAATCTTTAAT
Found at i:29962399 original size:19 final size:19
Alignment explanation
Indices: 29962372--29962414 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
29962362 TTAAATAAAT
29962372 ATAA-ATATAAAAATTTTAA
1 ATAATATATAAAAA-TTTAA
29962391 GATAATATATAAAAATTTAA
1 -ATAATATATAAAAATTTAA
29962411 ATAA
1 ATAA
29962415 CTCCCGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 9 0.41
21 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAATATATAAAAATTTAA
Found at i:29964510 original size:52 final size:51
Alignment explanation
Indices: 29964431--29964576 Score: 161
Period size: 52 Copynumber: 2.8 Consensus size: 51
29964421 CAAACAATCC
* * *
29964431 ATTAAGAATCC-TTCTCTTCTTATAATTCTTCTCCTGTAAGTCAAACTTGCCT
1 ATTAAGAATCCTTTC-CTT-TTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
*
29964483 ATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAAT-CCTTTCCTTTTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
* * **
29964535 ATTAAGAATTTTCTTT-CTCTTAGAATTCTTCTTTTGCAAGTC
1 ATTAAGAA--TCCTTTCCTTTTAGAATTCTTCTCCTGCAAGTC
29964577 TTCTTGTCCA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
52 70 0.84
53 9 0.11
54 4 0.05
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (51 bp):
ATTAAGAATCCTTTCCTTTTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
Found at i:29964617 original size:11 final size:11
Alignment explanation
Indices: 29964601--29964642 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
29964591 GTAATAACTG
29964601 ACAAATCTCAA
1 ACAAATCTCAA
*
29964612 ACAAATCTCTA
1 ACAAATCTCAA
29964623 ACAAATCTCAA
1 ACAAATCTCAA
29964634 ACAAATCTC
1 ACAAATCTC
29964643 TTATGGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:29964626 original size:22 final size:22
Alignment explanation
Indices: 29964601--29964643 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
29964591 GTAATAACTG
29964601 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
29964623 ACAAATCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
29964644 TATGGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:29964959 original size:25 final size:25
Alignment explanation
Indices: 29964880--29964984 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
29964870 TCTTAAACCA
* *
29964880 AGCTCTTCTCACATCTTAAACCTTT
1 AGCTCTTCTCACATCTTGAACCTTC
* * ** *
29964905 AGCTTTTC-CACGTCTCAAACTTTC
1 AGCTCTTCTCACATCTTGAACCTTC
* *
29964929 AGCTCTTTTCACATCTTGAATCTTC
1 AGCTCTTCTCACATCTTGAACCTTC
* * *
29964954 AACTCTTCTCACGTTTTGAACCTTC
1 AGCTCTTCTCACATCTTGAACCTTC
29964979 AGCTCT
1 AGCTCT
29964985 GATACCATTT
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
24 18 0.30
25 43 0.70
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (25 bp):
AGCTCTTCTCACATCTTGAACCTTC
Found at i:29965016 original size:31 final size:30
Alignment explanation
Indices: 29964978--29965062 Score: 125
Period size: 31 Copynumber: 2.8 Consensus size: 30
29964968 TTTGAACCTT
*
29964978 CAGCTCTGATACCATTTGTTGGGGATCACCA
1 CAGCTCTGATACCATTTGTTGGGAAT-ACCA
* *
29965009 CAGCTCTGATACCACTTGTTGGAAAATACCA
1 CAGCTCTGATACCATTTGTTGG-GAATACCA
29965040 CAGCTCTGATACCATTTGTTGGG
1 CAGCTCTGATACCATTTGTTGGG
29965063 CTAAAAGCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 46 0.96
32 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (30 bp):
CAGCTCTGATACCATTTGTTGGGAATACCA
Found at i:29965636 original size:52 final size:51
Alignment explanation
Indices: 29965546--29965702 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 51
29965536 TATAACCATA
* * *
29965546 CAAACTTGTCC-ATTAAGAAT-CATTCTCTTCTTATAATTCTTCTCCTGTAAGT
1 CAAACTTG-CCTATTAAGAATCCTTTC-CTT-TTAGAATTCTTCTCCTGCAAGT
*
29965598 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* * **
29965650 CAAACTTACCTATTAAGAATCTTCTTT-CTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC--CTTTCCTTTTAGAATTCTTCTCCTGCAAGT
29965702 C
1 C
29965703 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
51 3 0.03
52 79 0.85
53 7 0.08
54 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
Found at i:29965743 original size:11 final size:11
Alignment explanation
Indices: 29965727--29965768 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
29965717 GCAATAACTG
29965727 ACAAATCTCAA
1 ACAAATCTCAA
*
29965738 ACAAATCTCTA
1 ACAAATCTCAA
29965749 ACAAATCTCAA
1 ACAAATCTCAA
29965760 ACAAATCTC
1 ACAAATCTC
29965769 TTATGGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:29965752 original size:22 final size:22
Alignment explanation
Indices: 29965727--29965769 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
29965717 GCAATAACTG
29965727 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
29965749 ACAAATCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
29965770 TATGGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:29973104 original size:2 final size:2
Alignment explanation
Indices: 29973099--29973128 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29973089 AAATTGTCTA
29973099 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
29973129 GGTTGTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29973198 original size:21 final size:22
Alignment explanation
Indices: 29973160--29973202 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
29973150 GAATATCTAA
*
29973160 AAAATTAAGCATTTTTTGTGGG
1 AAAATAAAGCATTTTTTGTGGG
29973182 AAAATAAAGCA-TTTTTGTGGG
1 AAAATAAAGCATTTTTTGTGGG
29973203 CTTCAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (22 bp):
AAAATAAAGCATTTTTTGTGGG
Found at i:29975476 original size:2 final size:2
Alignment explanation
Indices: 29975471--29975504 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29975461 ATCATAGCTA
29975471 AT 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 AT
29975505 TCTTAAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29979226 original size:21 final size:21
Alignment explanation
Indices: 29979157--29979227 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
29979147 TTTTTCTATC
*
29979157 TATTTTTTTATGTTTTAAAAT
1 TATTTTTTTATATTTTAAAAT
**
29979178 TATATTTTTTA-ACACTT-AAAT
1 TAT-TTTTTTATA-TTTTAAAAT
**
29979199 CCCTTTTTTTATATTTTAAAAT
1 -TATTTTTTTATATTTTAAAAT
29979221 TATTTTT
1 TATTTTT
29979228 CATAATTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (21 bp):
TATTTTTTTATATTTTAAAAT
Found at i:29986723 original size:18 final size:15
Alignment explanation
Indices: 29986685--29986731 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
29986675 ATTTAATCCT
29986685 ACAAAATATAAATAA
1 ACAAAATATAAATAA
*
29986700 ATAAAATAATAACATGAA
1 ACAAAAT-ATAA-AT-AA
29986718 ACAAAA-ATAAATAA
1 ACAAAATATAAATAA
29986732 GTAAAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.07
15 8 0.30
16 8 0.30
17 2 0.07
18 7 0.26
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (15 bp):
ACAAAATATAAATAA
Found at i:29986764 original size:13 final size:13
Alignment explanation
Indices: 29986698--29986765 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 13
29986688 AAATATAAAT
29986698 AAATAAAATAATA
1 AAATAAAATAATA
* * *
29986711 ACATGAAA-CA-A
1 AAATAAAATAATA
29986722 AAAT-AAATAAGTA
1 AAATAAAATAA-TA
*
29986735 AAACCAAAA-AATA
1 AAA-TAAAATAATA
29986748 AAATAAAATAATA
1 AAATAAAATAATA
29986761 AAATA
1 AAATA
29986766 TCAAATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 5 0.12
13 24 0.57
14 2 0.05
15 3 0.07
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:29987565 original size:35 final size:35
Alignment explanation
Indices: 29987519--29987587 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
29987509 CGCAATTCAA
* *
29987519 AGATTCACAAAACTTGTAGATTCA-TAATAATTTTT
1 AGATTCACAAAAATTGTAGAATCATTAA-AATTTTT
* *
29987554 AGATTTACAAAAATTTTAGAATCATTAAAATTTT
1 AGATTCACAAAAATTGTAGAATCATTAAAATTTT
29987588 CATTCTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (35 bp):
AGATTCACAAAAATTGTAGAATCATTAAAATTTTT
Found at i:29988000 original size:64 final size:66
Alignment explanation
Indices: 29987914--29988040 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 66
29987904 TCTAAAATTT
* * *
29987914 AAAATATTCACATTCAAAAAATTTTAAAGCTTGACATTTACAAATT-AATATTCACATTCAAGTT
1 AAAATATTCACATTCAAAAAATTTTAAAGCTTCACATCTAAAAATTAAATATTCACATTCAAGTT
29987978 C
66 C
* * * *
29987979 AAAA-ATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTCAA
1 AAAATATTCACATTCAAAAAATTTTAAAGCTTCACATCTAAAAATT-AAATATTCACATTCAA
29988041 ACAATTTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 35 0.66
65 4 0.08
66 14 0.26
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.35
Consensus pattern (66 bp):
AAAATATTCACATTCAAAAAATTTTAAAGCTTCACATCTAAAAATTAAATATTCACATTCAAGTT
C
Found at i:29988071 original size:20 final size:20
Alignment explanation
Indices: 29988046--29988136 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 20
29988036 TTCAAACAAT
29988046 TTTAAAGTTTCACATCTAAA
1 TTTAAAGTTTCACATCTAAA
*
29988066 TTTAAA-TATTCACAT-TCAAG
1 TTTAAAGT-TTCACATCT-AAA
* * *
29988086 TTCAAAGATTCACATACAAGAAA
1 TTTAAAGTTTCACAT-C--TAAA
*
29988109 TTTTAAAGTTTCACATATAAA
1 -TTTAAAGTTTCACATCTAAA
*
29988130 TTCAAAG
1 TTTAAAG
29988137 GCTTACATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
19 2 0.04
20 33 0.62
21 3 0.06
23 2 0.04
24 13 0.25
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (20 bp):
TTTAAAGTTTCACATCTAAA
Found at i:29988082 original size:44 final size:45
Alignment explanation
Indices: 29987976--29988085 Score: 152
Period size: 46 Copynumber: 2.4 Consensus size: 45
29987966 CACATTCAAG
* *
29987976 TTCAAAAATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAA
1 TTCAAATATTCACATTCAAGAAATTTTAAAGTTTCACATCT-AAAA
*
29988022 TTCAAATATTTACATTCAA-ACAATTTTAAAGTTTCACATCT-AAA
1 TTCAAATATTCACATTCAAGA-AATTTTAAAGTTTCACATCTAAAA
*
29988066 TTTAAATATTCACATTCAAG
1 TTCAAATATTCACATTCAAG
29988086 TTCAAAGATT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 20 0.35
45 1 0.02
46 36 0.63
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.37
Consensus pattern (45 bp):
TTCAAATATTCACATTCAAGAAATTTTAAAGTTTCACATCTAAAA
Found at i:29988097 original size:110 final size:109
Alignment explanation
Indices: 29987870--29988188 Score: 351
Period size: 110 Copynumber: 2.9 Consensus size: 109
29987860 CCAAGATTTT
** * * * *
29987870 AAAGATT-ATTATTCAA-AAATTTTAGTGTTTTACATCTAAAATTTAAAATATTCACATTCAAAA
1 AAAGATTCA-TATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTC-AAA
* * *
29987933 AATTTTAAAGCTTGACATTTACAAATT-AATATTCACATTCAAGTTC
64 AATTTTAAAGCTTCACATCTA-AATTTAAATATTCACATTCAAGTTC
*
29987979 AAAAATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTCAAACA
1 AAAGATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTCAAA-A
*
29988044 ATTTTAAAGTTTCACATCTAAATTTAAATATTCACATTCAAGTTC
65 ATTTTAAAGCTTCACATCTAAATTTAAATATTCACATTCAAGTTC
* * * *** **
29988089 AAAGATTCACATACAAGAAATTTTAAAGTTTCACA--TATAAATTCAAAGGCTTACATTTGAAAA
1 AAAGATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTCAAAAA
* * * *
29988152 TTTTAAGGGTTCACATCCAACATTTAAAGATTCACAT
66 TTTTAAAGCTTCACATCTAA-ATTTAAATATTCACAT
29988189 AAAAAAAACT
Statistics
Matches: 181, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
107 19 0.10
108 35 0.19
109 20 0.11
110 107 0.59
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (109 bp):
AAAGATTCATATTCAAGAAATTTTAAAGTTTCACATCTAAAAATTCAAATATTTACATTCAAAAA
TTTTAAAGCTTCACATCTAAATTTAAATATTCACATTCAAGTTC
Found at i:29988888 original size:8 final size:9
Alignment explanation
Indices: 29988874--29988900 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
29988864 TTTTGGGGAT
29988874 TTTTTTTAA
1 TTTTTTTAA
29988883 TTTTTTTAA
1 TTTTTTTAA
29988892 TTTTTTTAA
1 TTTTTTTAA
29988901 AAATTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:29989332 original size:4 final size:4
Alignment explanation
Indices: 29989325--29989354 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
29989315 TTTTTTCATT
29989325 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
29989355 GTAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:29989425 original size:20 final size:20
Alignment explanation
Indices: 29989402--29989451 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
29989392 TTTTGAGAGA
*
29989402 AAAAAAATAT-TAAAATTTT
1 AAAAAAATATAAAAAATTTT
*
29989421 TAAAAAATAATAAAAAATTTT
1 AAAAAAAT-ATAAAAAATTTT
29989442 AAAAATAATA
1 AAAAA-AATA
29989452 CTATTCGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 13 0.52
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAAATATAAAAAATTTT
Found at i:29989427 original size:19 final size:20
Alignment explanation
Indices: 29989403--29989451 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
29989393 TTTGAGAGAA
* *
29989403 AAAAAAT-ATTAAAATTTTT
1 AAAAAATAATAAAAAATTTT
29989422 AAAAAATAATAAAAAATTTT
1 AAAAAATAATAAAAAATTTT
29989442 -AAAAATAATA
1 AAAAAATAATA
29989452 CTATTCGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATAATAAAAAATTTT
Found at i:29989649 original size:55 final size:55
Alignment explanation
Indices: 29989570--29989696 Score: 177
Period size: 55 Copynumber: 2.3 Consensus size: 55
29989560 ATTTTCCCTT
* * * * *
29989570 AAAA-AAAATTTCAAAAGAATGATTTAAGGAAAGTCGAAGTATTAA-TTTTTAAA
1 AAAATAAAATTTCAAAAAAAAGATTTAAAGAAAGTCAAAGTATCAATTTTTTAAA
29989623 AAAATAAATATTTCAAAAAAAAGATTTAAAGAAAGTCAAAGTATCAATTTTTTAAA
1 AAAATAAA-ATTTCAAAAAAAAGATTTAAAGAAAGTCAAAGTATCAATTTTTTAAA
29989679 AAAATAAAAATTTCAAAA
1 AAAAT-AAAATTTCAAAA
29989697 GATGTATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
53 4 0.06
54 3 0.05
55 33 0.51
56 22 0.34
57 3 0.05
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (55 bp):
AAAATAAAATTTCAAAAAAAAGATTTAAAGAAAGTCAAAGTATCAATTTTTTAAA
Found at i:29991562 original size:86 final size:86
Alignment explanation
Indices: 29991390--29992170 Score: 373
Period size: 86 Copynumber: 9.1 Consensus size: 86
29991380 TTTTTTACTC
* * * * ** * * *
29991390 TTAGACTTTAATTCAA-TCTAGGTCATTTTGTTTT-GGATTTCAACTTATGCTAGATCCTTCATC
1 TTAGACTTTGATTCAATTC-AAGTCATTTTATTTTCAGATTTTGACTTATGCCAGATCTTTCTTC
* * *
29991453 GGA-TTAGGCCAAGGTATTTATT
65 -GACTTAGTCCAAGTTATTCATT
* *
29991475 TTAGATTTTGATTCAATTCAAGTCATTTTATTTTCGGATTTTGACTTATGCCAGATCTTTCTTCG
1 TTAGACTTTGATTCAATTCAAGTCATTTTATTTTCAGATTTTGACTTATGCCAGATCTTTCTTCG
*
29991540 ACTTAGTTCAAGTTATTCATT
66 ACTTAGTCCAAGTTATTCATT
* * ** * * * * * * * * *
29991561 TTAAACTTTGTTTTGATCCAGGTTA-TTTAGTTATCAGATTTTGGCCTATGCTAGATCCTTATTC
1 TTAGACTTTGATTCAATTCAAGTCATTTTA-TTTTCAGATTTTGACTTATGCCAGATCTTTCTTC
* * *
29991625 -AGCTTAGACTAAGTTATTTATT
65 GA-CTTAGTCCAAGTTATTCATT
* * * * *
29991647 TTAGACTTTGGTTCAA-TCTAGGTCATTTTATTTTCATA-TTTAATCTTATGCCAAATCTTT-TT
1 TTAGACTTTGATTCAATTC-AAGTCATTTTATTTTCAGATTTTGA-CTTATGCCAGATCTTTCTT
* *
29991709 CCGACTTAGTCTAAGTTATTTATTT
64 -CGACTTAGTCCAAGTTATTCA-TT
* * * * * * * **
29991734 TTCAAACTTTGGTTCAATTTAGGTCATTTTGTTTTTAAATTTTGACTTATGTTTA-ATCTTTCTT
1 TT-AGACTTTGATTCAATTCAAGTCATTTTATTTTCAGATTTTGACTTATG-CCAGATCTTTCTT
*
29991798 -TAGCTTAGTCCAAGTTATTCATTCT
64 CGA-CTTAGTCCAAGTTATTCA-T-T
* * * * * * *
29991823 TTAGACTTTGATTTAATTC-AGATCATTTTATTTTTAGATTTTAACCTATGCCATATCCTTCTTT
1 TTAGACTTTGATTCAATTCAAG-TCATTTTATTTTCAGATTTTGACTTATGCCAGATCTTTCTTC
* **
29991887 GATTTAGTTTAAGTTATTCATTCT
65 GACTTAGTCCAAGTTATTCA-T-T
* * * * * * *
29991911 TTAAAC-TTCAGTTCAATGCAAGTCA-TTTAGTTTTCAAATTTT-AGCCTATGCCAAATCTTTTT
1 TTAGACTTTGA-TTCAATTCAAGTCATTTTA-TTTTCAGATTTTGA-CTTATGCCAGATCTTTCT
* *
29991973 TC-AGCTTAGTCGAAATTATTCATTTT
63 TCGA-CTTAGTCCAAGTTATTCA--TT
* * * * * * * * *
29991999 TTAGAGTTTGA-TC----CAGGCCATTTTGTTTT-TGAATTTTGACTTGTGTCTGATCCTTCTTC
1 TTAGACTTTGATTCAATTCAAGTCATTTTATTTTCAG-ATTTTGACTTATGCCAGATCTTTCTTC
*
29992058 AACTTAGTCCAAGTTATTCATT
65 GACTTAGTCCAAGTTATTCATT
* * ** * * ** * * * * *
29992080 TTAAAC-TTAAGTTTGATCCAAGTCATTATATTTTTGGATTTTGGCTTATGCTAAATCTTTTTTT
1 TTAGACTTTGA-TTCAATTCAAGTCATTTTATTTTCAGATTTTGACTTATGCCAGATCTTTCTTC
*
29992144 GACTTAGTCCAAGTTGTTCATT
65 GACTTAGTCCAAGTTATTCATT
29992166 TTAGA
1 TTAGA
29992171 AAATAGAGTT
Statistics
Matches: 531, Mismatches: 126, Indels: 77
0.72 0.17 0.10
Matches are distributed among these distances:
80 3 0.01
81 6 0.01
82 1 0.00
83 43 0.08
84 5 0.01
85 40 0.08
86 208 0.39
87 24 0.05
88 182 0.34
89 19 0.04
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (86 bp):
TTAGACTTTGATTCAATTCAAGTCATTTTATTTTCAGATTTTGACTTATGCCAGATCTTTCTTCG
ACTTAGTCCAAGTTATTCATT
Found at i:29991783 original size:88 final size:86
Alignment explanation
Indices: 29991481--29992167 Score: 333
Period size: 88 Copynumber: 7.9 Consensus size: 86
29991471 TATTTTAGAT
* * * * ** * *
29991481 TTTGATTCAATTCAAGTCATTTTATTTTCGGATTTTGACTTATGCCAGATCTTTCTTCGACTTAG
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAATCTTT-TTCGACTTAG
29991546 T-TCAAGTTATTCA-TTTTAAAC
65 TCT-AAGTTATTCATTTTTAAAC
* ** * * * * * * * *
29991567 TTTGTTTTGATCCAGGTTATTTAGTTATCAGATTTTGGCCTATGCTAGATCCTTATTC-AGCTTA
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAAT-CTTTTTCGA-CTTA
* * *
29991631 GACTAAGTTATTTA-TTTTAGAC
64 GTCTAAGTTATTCATTTTTAAAC
* * * * *
29991653 TTTGGTTCAATCTAGGTCATTTTATTTTCATA-TTTAATCTTATGCCAAATCTTTTTCCGACTTA
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGA-CCTATGCCAAATCTTTTT-CGACTTA
*
29991717 GTCTAAGTTATTTATTTTTCAAAC
64 GTCTAAGTTATTCATTTTT-AAAC
** * * *** *
29991741 TTTGGTTCAATTTAGGTCATTTTGTTTTTAAATTTTGACTTATGTTTAATCTTTCTT-TAGCTTA
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAATCTTT-TTCGA-CTTA
* *
29991805 GTCCAAGTTATTCATTCTTTAGAC
64 GTCTAAGTTATTCATT-TTTAAAC
* * * * * * * * * *
29991829 TTTGATTTAATTCAGATCATTTTATTTTTAGATTTTAACCTATGCCATATCCTTCTTT-GATTTA
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAAT-CTT-TTTCGACTTA
*
29991893 GTTTAAGTTATTCATTCTTTAAAC
64 GTCTAAGTTATTCATT-TTTAAAC
** * * *
29991917 TTCAGTTCAATGCAAGTCATTTAGTTTTCAAATTTT-AGCCTATGCCAAATCTTTTTTC-AGCTT
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGA-CCTATGCCAAATC-TTTTTCGA-CTT
* * * *
29991980 AGTCGAAATTATTCATTTTTTAGAG
63 AGTCTAAGTTATTCA-TTTTTAAAC
* ** * * * ** * *
29992005 TTT-G----ATCCAGGCCATTTTGTTTTTGAATTTTGACTTGTGTCTGATCCTTCTTCAACTTAG
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAAT-CTTTTTCGACTTAG
*
29992065 TCCAAGTTATTCA-TTTTAAAC
65 TCTAAGTTATTCATTTTTAAAC
** ** * * * *** * * * *
29992086 TTAAGTTTGATCCAAGTCATTATATTTTTGGATTTTGGCTTATGCTAAATCTTTTTTTGACTTAG
1 TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAATC-TTTTTCGACTTAG
* *
29992151 TCCAAGTTGTTCATTTT
65 TCTAAGTTATTCATTTT
29992168 AGAAAATAGA
Statistics
Matches: 458, Mismatches: 114, Indels: 57
0.73 0.18 0.09
Matches are distributed among these distances:
81 8 0.02
82 1 0.00
83 49 0.11
84 3 0.01
85 10 0.02
86 163 0.36
87 20 0.04
88 186 0.41
89 17 0.04
90 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (86 bp):
TTTGGTTCAATCCAGGTCATTTTGTTTTCAAATTTTGACCTATGCCAAATCTTTTTCGACTTAGT
CTAAGTTATTCATTTTTAAAC
Found at i:29991875 original size:176 final size:170
Alignment explanation
Indices: 29991456--29992010 Score: 487
Period size: 176 Copynumber: 3.2 Consensus size: 170
29991446 CTTCATCGGA
* * * * * *
29991456 TTAGGCCAAGGTATTTA-TTTTAGATTTTGATTCAATTCA-AGTCATTTTATTTTCGGATTTTGA
1 TTAGTCCAAGTTATTCATTTTTAGACTTTGATTCAATTCAGA-TCATTTTATTTTCAGATTTTAA
* * **
29991519 CTTATGCCAGATCTTTCTTCGACTTAGTTCAAGTTATTCA-TTTTAAACTTTGTTTTGATCCAGG
65 CTTATGCCAAATCTTT-TTCGACTTAGTT-AAGTTATTCATTTTTAAACTTTGGTTCAATCCAGG
* * * * * *
29991583 TTATTTAGTTATCAGATTTTGGCCTATGCTAGATCCTTATTCAGC
128 TCATTTAGTTTTCAAATTTTGACCTATGCTA-AT-CTTTTTTAGC
* * * * * *
29991628 TTAGACTAAGTTATTTA-TTTTAGACTTTGGTTCAA-TCTAGGTCATTTTATTTTCATA-TTTAA
1 TTAGTCCAAGTTATTCATTTTTAGACTTTGATTCAATTC-AGATCATTTTATTTTCAGATTTTAA
* **
29991690 TCTTATGCCAAATCTTTTTCCGACTTAGTCTAAGTTATTTATTTTTCAAACTTTGGTTCAATTTA
65 -CTTATGCCAAATCTTTTT-CGACTTAGT-TAAGTTATTCATTTTT-AAACTTTGGTTCAATCCA
* * * *
29991755 GGTCATTTTGTTTTTAAATTTTGACTTATGTTTAATCTTTCTTTAGC
126 GGTCATTTAGTTTTCAAATTTTGACCTATG-CTAATCTTT-TTTAGC
* *
29991802 TTAGTCCAAGTTATTCATTCTTTAGACTTTGATTTAATTCAGATCATTTTATTTTTAGATTTTAA
1 TTAGTCCAAGTTATTCATT-TTTAGACTTTGATTCAATTCAGATCATTTTATTTTCAGATTTTAA
* * * ** *
29991867 CCTATGCCATATCCTTCTTT-GATTTAGTTTAAGTTATTCATTCTTTAAACTTCAGTTCAATGCA
65 CTTATGCCAAAT-CTT-TTTCGACTTAG-TTAAGTTATTCATT-TTTAAACTTTGGTTCAATCCA
* *
29991931 AGTCATTTAGTTTTCAAATTTT-AGCCTATGCCAAATCTTTTTTCAGC
126 GGTCATTTAGTTTTCAAATTTTGA-CCTATG-CTAATCTTTTTT-AGC
* * *
29991978 TTAGTCGAAATTATTCATTTTTTAGAGTTTGAT
1 TTAGTCCAAGTTATTCA-TTTTTAGACTTTGAT
29992011 CCAGGCCATT
Statistics
Matches: 311, Mismatches: 52, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
171 8 0.03
172 78 0.25
173 8 0.03
174 57 0.18
175 7 0.02
176 134 0.43
177 16 0.05
178 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (170 bp):
TTAGTCCAAGTTATTCATTTTTAGACTTTGATTCAATTCAGATCATTTTATTTTCAGATTTTAAC
TTATGCCAAATCTTTTTCGACTTAGTTAAGTTATTCATTTTTAAACTTTGGTTCAATCCAGGTCA
TTTAGTTTTCAAATTTTGACCTATGCTAATCTTTTTTAGC
Found at i:29993263 original size:60 final size:59
Alignment explanation
Indices: 29993147--29993377 Score: 258
Period size: 60 Copynumber: 3.8 Consensus size: 59
29993137 GAAACAAAAC
* * *
29993147 TTCAAAAAAGTATTTTCTTAAG-AATGATTG-AA-TATCAATTTTCCTAAAAAAGTAAAAATT
1 TTCAAAAAA-TATTTT-TTAAGAAAAG-TTGAAAGTATCAATTTTTCT-TAAAAGTAAAAATT
29993207 TTCAAAAAATATTTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAAATT
1 TTCAAAAAATATTTTTT-AAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAAATT
*
29993267 TT-AAAAAATATTTTTTGGAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAG-ATAAAATT
1 TTCAAAAAATATTTTTT-AAG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAGTA-AAAATT
* * * *
29993326 TTTAAAATATATTTTTTAAAAAAACGTTGAAAGTATTAATTTTTCTTGAAAA
1 TTCAAAAAATATTTTTTAAGAAAA-GTTGAAAGTATCAATTTTTCTT-AAAA
29993378 CGAATATTTC
Statistics
Matches: 153, Mismatches: 8, Indels: 19
0.85 0.04 0.11
Matches are distributed among these distances:
58 7 0.05
59 63 0.41
60 68 0.44
61 15 0.10
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (59 bp):
TTCAAAAAATATTTTTTAAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAAATT
Found at i:29993599 original size:12 final size:12
Alignment explanation
Indices: 29993562--29993602 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29993552 TTTTTTTAAA
*
29993562 TAAAAATTTTTT
1 TAAAAATATTTT
*
29993574 TTAAAATATATTT
1 TAAAAATAT-TTT
29993587 TAAAAATATTTT
1 TAAAAATATTTT
29993599 TAAA
1 TAAA
29993603 GAAAAATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:29993647 original size:71 final size:71
Alignment explanation
Indices: 29993516--29993648 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 71
29993506 AAAAATAAAA
* * * ***
29993516 TAAAAAGAATTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTTAAATAAAAATTTTTTTTAAAAT
1 TAAAAAGAATTTTAAAGAAAAATTGAAAGTATCAATTTTTCTTAAATAAAAATGGGTTTTAAAAT
29993581 ATATTT
66 ATATTT
* *
29993587 TAAAAATATTTTTAAAGAAAAATTGAAAGTATCAATTTTTCTTAAATAAGAAA-GGGTTTTAA
1 TAAAAAGAATTTTAAAGAAAAATTGAAAGTATCAATTTTTCTTAAATAA-AAATGGGTTTTAA
29993649 GGAGAAGTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 50 0.94
72 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (71 bp):
TAAAAAGAATTTTAAAGAAAAATTGAAAGTATCAATTTTTCTTAAATAAAAATGGGTTTTAAAAT
ATATTT
Found at i:29993657 original size:118 final size:121
Alignment explanation
Indices: 29993525--29993757 Score: 294
Period size: 122 Copynumber: 1.9 Consensus size: 121
29993515 ATAAAAAGAA
** * * **
29993525 TTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTTA-AATAA-AAATTTTTTTTAAAATATATTT-
1 TTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA-AATAAAATTTCTCAAAAATATATTTC
* * *
29993587 TAA-AAATATTTTTAAAGAAAAATTGAAAGTATCAATTTTTCTTAAATAAGAAAGGG
65 AAAGAAACATTTTTAAAGAAAAATTAAAAGTATCAATTTTTCTTAAATAAGAAAGGG
*
29993643 TTTTAAGGAGAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAAATTTCTCAAAAATATATTTCA
1 TTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAAATTTCTCAAAAATATATTTCA
* * * *
29993708 AAGGAAACATTTTTTAGGAAAAGTTAAAAGTATCAATTTTTCTTATATAA
66 AA-GAAACATTTTTAAAGAAAAATTAAAAGTATCAATTTTTCTTAAATAA
29993758 AAACCTTCTC
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 34 0.35
119 20 0.21
120 2 0.02
122 40 0.42
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (121 bp):
TTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAAATTTCTCAAAAATATATTTCA
AAGAAACATTTTTAAAGAAAAATTAAAAGTATCAATTTTTCTTAAATAAGAAAGGG
Found at i:29995310 original size:13 final size:15
Alignment explanation
Indices: 29995290--29995323 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29995280 AGTCTTCATT
*
29995290 TTTTTTTTTTTCACA
1 TTTTTTTTTTGCACA
29995305 TTTTTTTTTTGCACA
1 TTTTTTTTTTGCACA
29995320 TTTT
1 TTTT
29995324 CACACATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTTGCACA
Found at i:29998672 original size:25 final size:24
Alignment explanation
Indices: 29998641--29998692 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
29998631 ACCGTTTGGG
29998641 TTTATTTAAAAAATTTTTTACAAGT
1 TTTATTTAAAAAATTTTTTACAA-T
***
29998666 TTTATTTTCTAAATTTTTTACAAT
1 TTTATTTAAAAAATTTTTTACAAT
29998690 TTT
1 TTT
29998693 GGGCCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATTTAAAAAATTTTTTACAAT
Found at i:30000575 original size:10 final size:10
Alignment explanation
Indices: 30000560--30000586 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30000550 AGAAAAAGGG
30000560 AAAGAAATGA
1 AAAGAAATGA
30000570 AAAGAAATGA
1 AAAGAAATGA
30000580 AAAGAAA
1 AAAGAAA
30000587 AAGACAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (10 bp):
AAAGAAATGA
Found at i:30002606 original size:10 final size:10
Alignment explanation
Indices: 30002585--30002629 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
30002575 TTAATCATAT
30002585 TTTATGATTCA
1 TTTAT-ATTCA
30002596 TTTATATTCA
1 TTTATATTCA
* *
30002606 TTTAGATTCG
1 TTTATATTCA
*
30002616 TTTATATTCG
1 TTTATATTCA
30002626 TTTA
1 TTTA
30002630 GAATTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 26 0.84
11 5 0.16
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (10 bp):
TTTATATTCA
Found at i:30002619 original size:20 final size:20
Alignment explanation
Indices: 30002585--30002641 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
30002575 TTAATCATAT
30002585 TTTATGATTCATTTATATTCA
1 TTTA-GATTCATTTATATTCA
* *
30002606 TTTAGATTCGTTTATATTCG
1 TTTAGATTCATTTATATTCA
*
30002626 TTTAGAATTTATTTAT
1 TTTAG-ATTCATTTAT
30002642 CTAGTTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTAGATTCATTTATATTCA
Found at i:30003454 original size:19 final size:20
Alignment explanation
Indices: 30003424--30003465 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
30003414 TGATTTAATC
30003424 TAATACAAAATATTATTATT
1 TAATACAAAATATTATTATT
*
30003444 TAATA-AAAATATTTTTATT
1 TAATACAAAATATTATTATT
30003463 TAA
1 TAA
30003466 ATTGATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATACAAAATATTATTATT
Found at i:30003591 original size:29 final size:29
Alignment explanation
Indices: 30003559--30003619 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
30003549 CATAAATATT
* *
30003559 TTATTATTTCACTAATAAATAGTAATAAA
1 TTATTATTTCAATAATAAATAATAATAAA
* *
30003588 TTATTATTTTAATAATAAATAATAATATA
1 TTATTATTTCAATAATAAATAATAATAAA
30003617 TTA
1 TTA
30003620 AATAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (29 bp):
TTATTATTTCAATAATAAATAATAATAAA
Found at i:30003833 original size:29 final size:28
Alignment explanation
Indices: 30003796--30003863 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
30003786 TAATAGTATA
*
30003796 AATATTTTTAATATTTTAATAATAAATATT
1 AATA-TTTTAATATTATAATAATAAA-ATT
* * *
30003826 ACTATTTTATTATTATATTAATAAAATT
1 AATATTTTAATATTATAATAATAAAATT
30003854 AATATTTTAA
1 AATATTTTAA
30003864 GAATAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 11 0.34
29 18 0.56
30 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
AATATTTTAATATTATAATAATAAAATT
Found at i:30003985 original size:21 final size:23
Alignment explanation
Indices: 30003961--30004010 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
30003951 TAATATTTTG
*
30003961 ATATTAAATTTT-ATTATTAA-A
1 ATATTAAATTTTGAATATTAATA
30003982 ATA-TAAATTTTGAATATTAATA
1 ATATTAAATTTTGAATATTAATA
*
30004004 ATTTTAA
1 ATATTAA
30004011 TAATAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.33
21 10 0.42
22 3 0.12
23 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTAAATTTTGAATATTAATA
Found at i:30009634 original size:6 final size:6
Alignment explanation
Indices: 30009620--30009668 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
30009610 TATATAATTT
* *
30009620 TTTAT- TTTATA TTTATA TAT-TA TTTATA TTTAT- TTAAT- TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30009664 TTTAT
1 TTTAT
30009669 GTTAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 17 0.46
6 20 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:30009645 original size:17 final size:16
Alignment explanation
Indices: 30009623--30009668 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
30009613 ATAATTTTTT
30009623 ATTTTATATTTATATA
1 ATTTTATATTTATATA
* *
30009639 TTATTTATATTTATTTA
1 AT-TTTATATTTATATA
30009656 ATTTTATATTTAT
1 ATTTTATATTTAT
30009669 GTTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATATTTATATA
Found at i:30011657 original size:2 final size:2
Alignment explanation
Indices: 30011652--30011678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30011642 AAACCCCTAA
30011652 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
30011679 AAAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30015346 original size:50 final size:49
Alignment explanation
Indices: 30015257--30015355 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
30015247 TATTTATTTA
* * *
30015257 ACTTTCATTTTGGATTGTTGTTTCTATGATTTTCAAAGTTTGAATTTTT
1 ACTTTCATTTTGGATTGTTGTTTCAATGATTCTCAAAGTTTAAATTTTT
* * *
30015306 ACTTTCAGTTTTTGATTGTTGTTTCAATTATTCTCTAAGTTTAAATTTTT
1 ACTTTCA-TTTTGGATTGTTGTTTCAATGATTCTCAAAGTTTAAATTTTT
30015356 GGGGAAATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 7 0.16
50 36 0.84
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (49 bp):
ACTTTCATTTTGGATTGTTGTTTCAATGATTCTCAAAGTTTAAATTTTT
Found at i:30021578 original size:11 final size:11
Alignment explanation
Indices: 30021562--30021586 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30021552 AATTGTTTTA
30021562 TTTCCTTATAT
1 TTTCCTTATAT
30021573 TTTCCTTATAT
1 TTTCCTTATAT
30021584 TTT
1 TTT
30021587 TTTCTTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCCTTATAT
Found at i:30050138 original size:12 final size:12
Alignment explanation
Indices: 30050121--30050158 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
30050111 GGCTTTAGCT
*
30050121 GCAGCAGTTGCA
1 GCAGCAGCTGCA
30050133 GCAGCAGCTGCA
1 GCAGCAGCTGCA
*
30050145 GCAGCTGCTGCA
1 GCAGCAGCTGCA
30050157 GC
1 GC
30050159 GGCCGCAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (12 bp):
GCAGCAGCTGCA
Found at i:30058145 original size:6 final size:6
Alignment explanation
Indices: 30058134--30058273 Score: 64
Period size: 6 Copynumber: 23.8 Consensus size: 6
30058124 ATTTATTTAC
* * * * *
30058134 TATCTT TATCTT TATATT TAT-TT TATATT TAAT-TT TGTATT TGTCTT
1 TATCTT TATCTT TATCTT TATCTT TATCTT T-ATCTT TATCTT TATCTT
* * *
30058181 TATTTT TATTCTT TAT-TT AATTCATT TATCTT TAT-TT TATTTT TAT-TGT
1 TATCTT TA-TCTT TATCTT TA-TC-TT TATCTT TATCTT TATCTT TATCT-T
* * *
30058230 TAT-TT TAT-TT TATTTT TAT-TCT TATCTT CATTTT TA-CTT TATCT
1 TATCTT TATCTT TATCTT TATCT-T TATCTT TATCTT TATCTT TATCT
30058274 CGCTTATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
5 29 0.27
6 67 0.61
7 10 0.09
8 3 0.03
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (6 bp):
TATCTT
Found at i:30058158 original size:17 final size:17
Alignment explanation
Indices: 30058138--30058248 Score: 65
Period size: 17 Copynumber: 6.6 Consensus size: 17
30058128 ATTTACTATC
30058138 TTTATCTTTATATTTAT
1 TTTATCTTTATATTTAT
* *
30058155 TTTATATTTA-ATTTTGT
1 TTTATCTTTATA-TTTAT
* *
30058172 ATTTGTCTTTATTTTTAT
1 -TTTATCTTTATATTTAT
* *
30058190 TCTT-TATTTA-ATTCA-
1 T-TTATCTTTATATTTAT
30058205 TTTATCTTTAT-TTTATT
1 TTTATCTTTATATTTA-T
30058222 TTTAT-TGTTAT-TTTAT
1 TTTATCT-TTATATTTAT
*
30058238 TTTATTTTTAT
1 TTTATCTTTAT
30058249 TCTTATCTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.03
15 9 0.12
16 15 0.21
17 33 0.45
18 14 0.19
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTATCTTTATATTTAT
Found at i:30058168 original size:12 final size:11
Alignment explanation
Indices: 30058116--30058254 Score: 84
Period size: 11 Copynumber: 11.7 Consensus size: 11
30058106 TCTAATTTTA
*
30058116 TATTTTTTATT
1 TATTTTATATT
*
30058127 TATTTACTATCTT
1 TATTT--TATATT
30058140 TATCTTTATATT
1 TAT-TTTATATT
30058152 TATTTTATATT
1 TATTTTATATT
*
30058163 TAATTTTGTATT
1 T-ATTTTATATT
* *
30058175 TGTCTTTATTTT
1 TAT-TTTATATT
30058187 TATTCTT-TATT
1 TATT-TTATATT
*
30058198 TAATTCATTTATCTT
1 T-A-T--TTTATATT
*
30058213 TATTTTATTTT
1 TATTTTATATT
30058224 TATTGTTAT-TT
1 TATT-TTATATT
*
30058235 TATTTTATTTT
1 TATTTTATATT
30058246 TATTCTTAT
1 TATT-TTAT
30058255 CTTCATTTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
10 4 0.04
11 43 0.42
12 37 0.36
13 9 0.09
14 5 0.05
15 5 0.05
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (11 bp):
TATTTTATATT
Found at i:30058239 original size:22 final size:23
Alignment explanation
Indices: 30058206--30058263 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
30058196 TTTAATTCAT
*
30058206 TTATCTTTATTTTATTTTTATTG
1 TTATCTTTATTTTATTTTTATTC
30058229 TTAT-TTTATTTTATTTTTATTC
1 TTATCTTTATTTTATTTTTATTC
*
30058251 TTATCTTCATTTT
1 TTATCTTTATTTT
30058264 TACTTTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (23 bp):
TTATCTTTATTTTATTTTTATTC
Found at i:30059373 original size:15 final size:17
Alignment explanation
Indices: 30059353--30059384 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
30059343 ATGGTTTTAA
30059353 GAATTTT-T-AAATTAT
1 GAATTTTATCAAATTAT
30059368 GAATTTTATCAAATTAT
1 GAATTTTATCAAATTAT
30059385 TGAAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
GAATTTTATCAAATTAT
Found at i:30059725 original size:3 final size:3
Alignment explanation
Indices: 30059717--30059758 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
30059707 TAAATTTTAA
30059717 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
30059759 TTTTCAACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30059914 original size:21 final size:20
Alignment explanation
Indices: 30059867--30059914 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
30059857 TTTTTAATAT
*
30059867 AAAATTCTATTAAATGATTG
1 AAAATTCTATTAAATGATTC
* *
30059887 AAGAATTCTATTAATTGTTTTC
1 AA-AATTCTATTAAATG-ATTC
30059909 AAAATT
1 AAAATT
30059915 AATTTCTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 17 0.74
22 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (20 bp):
AAAATTCTATTAAATGATTC
Found at i:30065881 original size:2 final size:2
Alignment explanation
Indices: 30065876--30065905 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30065866 CTCTCCCCGC
30065876 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
30065906 TCAATTACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30078602 original size:15 final size:15
Alignment explanation
Indices: 30078582--30078620 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
30078572 ATTTAGAATG
*
30078582 GTTATAGAAGGACCA
1 GTTATAGAAGGACAA
30078597 GTTATAG-AGGACAA
1 GTTATAGAAGGACAA
30078611 GTTATAGAAG
1 GTTATAGAAG
30078621 ATATGATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (15 bp):
GTTATAGAAGGACAA
Found at i:30090592 original size:34 final size:33
Alignment explanation
Indices: 30090554--30090629 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 33
30090544 TATTGAATTT
30090554 TAATTAAAAAATTATTTAAATATTTATTT-TATTA
1 TAATTAAAAAATT-TTT-AATATTTATTTATATTA
* *
30090588 TAATTAATTAATATTTTTAGTATTTATTTATATTA
1 TAATTAA--AAAATTTTTAATATTTATTTATATTA
30090623 -AATTAAA
1 TAATTAAA
30090630 TTTTTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 1 0.03
34 23 0.62
35 8 0.22
36 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (33 bp):
TAATTAAAAAATTTTTAATATTTATTTATATTA
Found at i:30090598 original size:26 final size:25
Alignment explanation
Indices: 30090563--30090638 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 25
30090553 TTAATTAAAA
* *
30090563 AATTATTTAAATATTTATTTTATTAT
1 AATTAATTAAATTTTTATTTTATT-T
30090589 AATTAATTAATATTTTTAGTATTTATTT
1 AATTAATTAA-ATTTTTA-T-TTTATTT
30090617 ATATTAAATTAAATTTTTATTT
1 A-ATT-AATTAAATTTTTATTT
30090639 AGACGAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 9 0.21
27 8 0.19
28 4 0.09
29 16 0.37
30 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (25 bp):
AATTAATTAAATTTTTATTTTATTT
Found at i:30092444 original size:27 final size:28
Alignment explanation
Indices: 30092382--30092435 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
30092372 TATTTTATTA
* **
30092382 AAATCATATATTATATTTTAATATTTAG
1 AAATAATATATTATATTTTAATAAATAG
30092410 AAATAATAT-TTATATTTTAATAAATA
1 AAATAATATATTATATTTTAATAAATA
30092436 TAATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
AAATAATATATTATATTTTAATAAATAG
Found at i:30092763 original size:25 final size:22
Alignment explanation
Indices: 30092723--30092767 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
30092713 ATTTTTATCA
*
30092723 ATATTTTATTTTTTATTAATTGT
1 ATATATTATTTTTTA-TAATTGT
30092746 ATATATTATTATTGTTATAATT
1 ATATATTATT-TT-TTATAATT
30092768 ATTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 7 0.37
25 3 0.16
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
ATATATTATTTTTTATAATTGT
Found at i:30092838 original size:18 final size:18
Alignment explanation
Indices: 30092797--30092839 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30092787 ATTAATAAAA
* *
30092797 TTTTTTGTTAGATTATCC
1 TTTTTTTTTAAATTATCC
30092815 TTTTTTTTTAAATTA-CC
1 TTTTTTTTTAAATTATCC
30092832 TTTTTTTT
1 TTTTTTTT
30092840 ATACATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTTTTTAAATTATCC
Found at i:30104686 original size:13 final size:14
Alignment explanation
Indices: 30104659--30104688 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
30104649 AAGTTTGAAT
30104659 TTTATTAATAATTA
1 TTTATTAATAATTA
30104673 TTTATTAA-AATTA
1 TTTATTAATAATTA
30104686 TTT
1 TTT
30104689 TAAACTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTAATAATTA
Found at i:30104690 original size:14 final size:15
Alignment explanation
Indices: 30104657--30104690 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
30104647 TTAAGTTTGA
30104657 ATTTTATTAATAATT
1 ATTTTATTAATAATT
30104672 A-TTTATTAA-AATT
1 ATTTTATTAATAATT
30104685 ATTTTA
1 ATTTTA
30104691 AACTCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTATTAATAATT
Found at i:30106045 original size:23 final size:25
Alignment explanation
Indices: 30106015--30106068 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
30106005 TTTTAAATTA
*
30106015 ATAAAATATTGTTTTTAA-A-AAAT
1 ATAAAATATTATTTTTAATATAAAT
30106038 ATAAAATATTATTTTTAATATAAAT
1 ATAAAATATTATTTTTAATATAAAT
30106063 ATAAAA
1 ATAAAA
30106069 AATAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATAAAATATTATTTTTAATATAAAT
Found at i:30110268 original size:2 final size:2
Alignment explanation
Indices: 30110261--30110294 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30110251 AATATAAGTT
30110261 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
30110295 CACACATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30112450 original size:18 final size:19
Alignment explanation
Indices: 30112408--30112451 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
30112398 TAACTGGTTA
*
30112408 TTAATTTACTTTTAATTTT
1 TTAATTTACATTTAATTTT
*
30112427 AT-ATTTA-ATTTAATTTT
1 TTAATTTACATTTAATTTT
30112444 TTAATTTA
1 TTAATTTA
30112452 TTTTGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTTACATTTAATTTT
Found at i:30155311 original size:44 final size:44
Alignment explanation
Indices: 30155262--30155347 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
30155252 TACACACAGC
30155262 GGCAGGTAGTACGGTCAAGGCTCTGGCAACTGACACGGCTTCGT
1 GGCAGGTAGTACGGTCAAGGCTCTGGCAACTGACACGGCTTCGT
30155306 GGCAGGTAGTACGGTCAAGGCTCTGGCAACTGACACGGCTTC
1 GGCAGGTAGTACGGTCAAGGCTCTGGCAACTGACACGGCTTC
30155348 AGTTCCGGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.20
Consensus pattern (44 bp):
GGCAGGTAGTACGGTCAAGGCTCTGGCAACTGACACGGCTTCGT
Found at i:30156030 original size:21 final size:22
Alignment explanation
Indices: 30156001--30156044 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30155991 ACTAAAGGAC
*
30156001 ATGAGTCATAAC-TAAGGTACA
1 ATGACTCATAACTTAAGGTACA
* *
30156022 ATGACTCATGACTTATGGTACA
1 ATGACTCATAACTTAAGGTACA
30156044 A
1 A
30156045 AGGTCCATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (22 bp):
ATGACTCATAACTTAAGGTACA
Found at i:30159675 original size:22 final size:21
Alignment explanation
Indices: 30159625--30159675 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
30159615 GATAAGACTA
*
30159625 AAGG-ACAATGAGTCATAACT
1 AAGGTACAATGACTCATAACT
*
30159645 AAGGTACAATGACTCATGACTT
1 AAGGTACAATGACTCATAAC-T
*
30159667 ATGGTACAA
1 AAGGTACAA
30159676 AGGTTCATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 13 0.50
22 9 0.35
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGGTACAATGACTCATAACT
Found at i:30166924 original size:20 final size:20
Alignment explanation
Indices: 30166888--30166949 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
30166878 GATATATATA
* *
30166888 AATT-ATTTTTTAATTATTT
1 AATTAATTTTATATTTATTT
*
30166907 AATTAATTTTATATTTATAT
1 AATTAATTTTATATTTATTT
30166927 -ATATAATTTTATATTTATATT
1 AAT-TAATTTTATATTTAT-TT
30166948 AA
1 AA
30166950 AAATAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 6 0.17
20 27 0.77
21 1 0.03
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTAATTTTATATTTATTT
Found at i:30166974 original size:22 final size:25
Alignment explanation
Indices: 30166932--30166985 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
30166922 TATATATATA
*
30166932 ATTTTATATTTATATTAAAAATAAT
1 ATTTTATATTTATATTAAAAAAAAT
30166957 ATTTTATA-TT-T-TTAAAAAAAAT
1 ATTTTATATTTATATTAAAAAAAAT
30166979 ATTTTAT
1 ATTTTAT
30166986 TAATTTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
23 1 0.04
24 2 0.07
25 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTATATTTATATTAAAAAAAAT
Found at i:30190088 original size:49 final size:51
Alignment explanation
Indices: 30190028--30190123 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
30190018 TCAACCGTAC
*
30190028 TTGAGAAATTTTTA-GATTTAATTCCA-AATCAATTCATATTAAAATGATG
1 TTGAGAAATTTTTAGGATTTAATTCCAGAATCAATTCACATTAAAATGATG
* * *
30190077 TTGAGAGATTTTTAGGATTTAATTCTAGAATCAATTCACGTTAAAAT
1 TTGAGAAATTTTTAGGATTTAATTCCAGAATCAATTCACATTAAAAT
30190124 AAAATCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 13 0.32
50 11 0.27
51 17 0.41
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (51 bp):
TTGAGAAATTTTTAGGATTTAATTCCAGAATCAATTCACATTAAAATGATG
Done.