Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009177.1 Hibiscus syriacus cultivar Beakdansim tig00112742_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: 392072
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:3635 original size:3 final size:3
Alignment explanation
Indices: 3627--3652 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3617 ACACCGATCT
3627 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3653 CACTCTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5853 original size:21 final size:22
Alignment explanation
Indices: 5813--5854 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5803 TTAACTGATC
5813 GAATTATTATAAAATAATTATT
1 GAATTATTATAAAATAATTATT
5835 GAATT-TTATTAAAAT-ATTAT
1 GAATTATTA-TAAAATAATTAT
5855 AAAATAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
GAATTATTATAAAATAATTATT
Found at i:5881 original size:32 final size:32
Alignment explanation
Indices: 5817--5881 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
5807 CTGATCGAAT
* * *
5817 TATTATAAAATAATTATTGAATTTTATTAAAA
1 TATTATAAAATAATCATTGAAATTTATAAAAA
5849 TATTATAAAATAATCATT-AAATTTATCAAAAA
1 TATTATAAAATAATCATTGAAATTTAT-AAAAA
5881 T
1 T
5882 TTAGTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (32 bp):
TATTATAAAATAATCATTGAAATTTATAAAAA
Found at i:10595 original size:21 final size:21
Alignment explanation
Indices: 10549--10596 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
10539 GGTGTATAGA
*
10549 GAACTGGCGGTGGTGTTAAAC
1 GAACTGGCGATGGTGTTAAAC
* *
10570 AAACTGGCGATGGTAG-TAAGC
1 GAACTGGCGATGGT-GTTAAAC
10591 GAACTG
1 GAACTG
10597 ATGGTGATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (21 bp):
GAACTGGCGATGGTGTTAAAC
Found at i:16507 original size:30 final size:31
Alignment explanation
Indices: 16450--16508 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
16440 TGATTTTAAA
16450 AAATTGAAAGTTTAGATACTAAAACGTACTG
1 AAATTGAAAGTTTAGATACTAAAACGTACTG
* *
16481 AAATTGATAGTTTAGGTACT-AAACGTAC
1 AAATTGAAAGTTTAGATACTAAAACGTAC
16509 AATCTATCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (31 bp):
AAATTGAAAGTTTAGATACTAAAACGTACTG
Found at i:26239 original size:66 final size:66
Alignment explanation
Indices: 26133--26257 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
26123 GATGAAATCG
* * *
26133 CCTCTTGCGAGGTCAAAACATGTAAGTTGCTTAGCAAACAAGTGTTGGATGGAACTACCTTCATC
1 CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACCTTCATC
26198 A
66 A
*
26199 CCTCTTGCGGGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACC
1 CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACC
26258 GGGCCAATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (66 bp):
CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACCTTCATC
A
Found at i:35633 original size:7 final size:7
Alignment explanation
Indices: 35621--35672 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
35611 TATAAATTTT
35621 ATTTAAA
1 ATTTAAA
35628 ATTTAAA
1 ATTTAAA
35635 ATTTAAA
1 ATTTAAA
*
35642 A-TCACAA
1 ATTTA-AA
*
35649 ACCTTAAA
1 A-TTTAAA
35657 ATATTAAA
1 AT-TTAAA
35665 ATTTAAA
1 ATTTAAA
35672 A
1 A
35673 GTATAAACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 2 0.05
7 24 0.63
8 10 0.26
9 2 0.05
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (7 bp):
ATTTAAA
Found at i:35666 original size:30 final size:30
Alignment explanation
Indices: 35623--35692 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
35613 TAAATTTTAT
35623 TTAAAAT-TTAAAATTTAAAA-TCACAAACC
1 TTAAAATATTAAAATTTAAAAGT-ACAAACC
*
35652 TTAAAATATTAAAATTTAAAAGTATAAACC
1 TTAAAATATTAAAATTTAAAAGTACAAACC
35682 TTAAAATATTA
1 TTAAAATATTA
35693 CACTCTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 7 0.18
30 30 0.79
31 1 0.03
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (30 bp):
TTAAAATATTAAAATTTAAAAGTACAAACC
Found at i:35670 original size:15 final size:15
Alignment explanation
Indices: 35621--35692 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
35611 TATAAATTTT
35621 ATTTAAAAT-TTAAA
1 ATTTAAAATATTAAA
*
35635 ATTTAAAATCA-CAAA
1 ATTTAAAAT-ATTAAA
**
35650 CCTTAAAATATTAAA
1 ATTTAAAATATTAAA
35665 ATTTAAAAGTA-TAAA
1 ATTTAAAA-TATTAAA
**
35680 CCTTAAAATATTA
1 ATTTAAAATATTA
35693 CACTCTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
14 12 0.27
15 31 0.69
16 2 0.04
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.35
Consensus pattern (15 bp):
ATTTAAAATATTAAA
Found at i:36888 original size:18 final size:19
Alignment explanation
Indices: 36853--36889 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36843 CACGGAATGT
36853 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
36873 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
36890 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:38208 original size:20 final size:20
Alignment explanation
Indices: 38183--38241 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
38173 TTCTTTGAAA
38183 TTTTAAAATTATTATATATT
1 TTTTAAAATTATTATATATT
** * *
38203 TTTTAAGTTTATT-TTTGTT
1 TTTTAAAATTATTATATATT
*
38222 TTTTAAAATT-TTATAAATT
1 TTTTAAAATTATTATATATT
38241 T
1 T
38242 AAATTCACGT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
18 2 0.07
19 16 0.55
20 11 0.38
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTATTATATATT
Found at i:57077 original size:21 final size:23
Alignment explanation
Indices: 57030--57081 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
57020 TAATATAATT
57030 AATAATAAATGATTTTACAACATC
1 AATAATAAATGATTTTACAACA-C
57054 AATAATAAACT-ATTTTA-AAC-C
1 AATAATAAA-TGATTTTACAACAC
57075 AATAATA
1 AATAATA
57082 TTGTTGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.30
23 3 0.11
24 15 0.56
25 1 0.04
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAATAAATGATTTTACAACAC
Found at i:57121 original size:19 final size:19
Alignment explanation
Indices: 57078--57115 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57068 TTAAACCAAT
57078 AATATTGTTGAAGTGCATA
1 AATATTGTTGAAGTGCATA
* *
57097 AATATTGTTTAAGTTCATA
1 AATATTGTTGAAGTGCATA
57116 CTTATTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
AATATTGTTGAAGTGCATA
Found at i:57969 original size:32 final size:31
Alignment explanation
Indices: 57843--58008 Score: 156
Period size: 32 Copynumber: 5.3 Consensus size: 31
57833 TTTTAATACA
* * * *
57843 CAACAAACTTAAAACATAATACTCTCAATAGC
1 CAACAAACAT-AAACATAATAATTTCAATATC
* *
57875 TAACAAACTTATAACATAATAATTTCAATATC
1 CAACAAACATA-AACATAATAATTTCAATATC
* *
57907 CAACAAACATAAAGCATAACAATTTCAATATT
1 CAACAAACATAAA-CATAATAATTTCAATATC
*
57939 CATCAAACATCAAACATAATAATTTCAATATC
1 CAACAAACAT-AAACATAATAATTTCAATATC
* * **
57971 AAAGAAACATAAGAC--AATCGTTTCAATATC
1 CAACAAACATAA-ACATAATAATTTCAATATC
58001 CAACAAAC
1 CAACAAAC
58009 TCACAACATT
Statistics
Matches: 112, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
30 19 0.17
31 5 0.04
32 85 0.76
33 3 0.03
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.25
Consensus pattern (31 bp):
CAACAAACATAAACATAATAATTTCAATATC
Found at i:58387 original size:30 final size:30
Alignment explanation
Indices: 58353--58423 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
58343 TTTGCTATTG
58353 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
1 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
* *
58383 TTCCAGCTTTTCAACTGTTTTGCATGTGAT
1 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
*
58413 TTCCAACTTTT
1 TTCCAGCTTTT
58424 TCAATTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (30 bp):
TTCCAGCTTTTCAACTGCTCTGCATGTGAT
Found at i:64470 original size:20 final size:22
Alignment explanation
Indices: 64431--64473 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
64421 AAACGAGGAT
64431 AATAGTTTAAAAATTAAATTAA
1 AATAGTTTAAAAATTAAATTAA
*
64453 AATA-TTTAAAAATTAATTTAA
1 AATAGTTTAAAAATTAAATTAA
64474 GATACAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAGTTTAAAAATTAAATTAA
Found at i:79184 original size:95 final size:97
Alignment explanation
Indices: 79020--79211 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 97
79010 GACGACAACA
* * **
79020 ATGGGTGAAATTAGAGATTTAGTATTTAAGGCTTTGAGTTTTGGGGGAATTTGGGAATTTTGAAA
1 ATGGGTGAAATTAGAGATTTAGTATTTAAGGCTCTGAGTTTTGGGGGAATTTGGAAATTTCAAAA
*
79085 ATTTTAGGTGCTTTTTGAAAAATTATT-TTTT
66 ATTTTAAGTGCTTTTTGAAAAATTATTGTTTT
* * *
79116 ATGGGTGAAATTA-AGATTTAGTATTTAGGGCTCTGGGTTTTGGTGGAATTTGGAAATTTCAAAA
1 ATGGGTGAAATTAGAGATTTAGTATTTAAGGCTCTGAGTTTTGGGGGAATTTGGAAATTTCAAAA
*
79180 ATTTTAAGTGTTTTTTGAAAAATTATTGTTTT
66 ATTTTAAGTGCTTTTTGAAAAATTATTGTTTT
79212 TAAGAATATA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 69 0.80
96 17 0.20
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (97 bp):
ATGGGTGAAATTAGAGATTTAGTATTTAAGGCTCTGAGTTTTGGGGGAATTTGGAAATTTCAAAA
ATTTTAAGTGCTTTTTGAAAAATTATTGTTTT
Found at i:80438 original size:24 final size:24
Alignment explanation
Indices: 80405--80513 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
80395 ATGTTTATTT
80405 ATTGTGTTCGTTTACGTTC-TTTC
1 ATTGTGTTCGTTTACGTTCGTTTC
* *
80428 ATTTATGTTCGTTTACATTCGTTT-
1 A-TTGTGTTCGTTTACGTTCGTTTC
*
80452 ATTGTGTTCGTTTATGTTCGTTTAC
1 ATTGTGTTCGTTTACGTTCGTTT-C
** * *
80477 A-TCCGTTCGTTTATGTTTG-TTC
1 ATTGTGTTCGTTTACGTTCGTTTC
80499 ATTTGTGTTCGTTTA
1 A-TTGTGTTCGTTTA
80514 TCATTTAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 22 0.31
24 42 0.60
25 4 0.06
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (24 bp):
ATTGTGTTCGTTTACGTTCGTTTC
Found at i:80485 original size:47 final size:46
Alignment explanation
Indices: 80402--80514 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 46
80392 TTTATGTTTA
* *
80402 TTTATTGTGTTCGTTTACGTTCTTTCATTTATGTTCGTTTACATTCG
1 TTTATTGTGTTCGTTTATGTTCTTTCA-TTACGTTCGTTTACATTCG
* ** *
80449 TTTATTGTGTTCGTTTATGTTCGTTTACA-TCCGTTCGTTTATGTTTG
1 TTTATTGTGTTCGTTTATGTTC-TTT-CATTACGTTCGTTTACATTCG
*
80496 TTCATTTGTGTTCGTTTAT
1 TTTA-TTGTGTTCGTTTAT
80515 CATTTAAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
47 37 0.66
48 17 0.30
49 2 0.04
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.58
Consensus pattern (46 bp):
TTTATTGTGTTCGTTTATGTTCTTTCATTACGTTCGTTTACATTCG
Found at i:82482 original size:20 final size:20
Alignment explanation
Indices: 82457--82506 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
82447 TAGAACCTTG
82457 GTATCGATACTGGC-CTTACA
1 GTATCGATACTGGCTCTTA-A
* *
82477 GTATCGATATTGTCTCTTAA
1 GTATCGATACTGGCTCTTAA
82497 GTATCGATAC
1 GTATCGATAC
82507 CCTACCCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
GTATCGATACTGGCTCTTAA
Found at i:84089 original size:24 final size:24
Alignment explanation
Indices: 84062--84118 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
84052 CACCACAACT
* *
84062 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCAAAGTGCCA
* * *
84086 CGTAGAATTTGCATCAAAGTGCCG
1 CGTAGAAATTGCACCAAAGTGCCA
84110 CGTAGAAAT
1 CGTAGAAAT
84119 ATACCGTAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (24 bp):
CGTAGAAATTGCACCAAAGTGCCA
Found at i:84276 original size:23 final size:23
Alignment explanation
Indices: 84245--84288 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
84235 AATACATATA
*
84245 TGTCTCGAATGACCACGTAGAAT
1 TGTCCCGAATGACCACGTAGAAT
*
84268 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAATGACCACGTAGA
84289 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
TGTCCCGAATGACCACGTAGAAT
Found at i:84980 original size:22 final size:22
Alignment explanation
Indices: 84955--84997 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
84945 ACTATACGGT
84955 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
84977 ATGAACAATACCGTGAACAGT
1 ATGAACAATACCGTGAACAGT
84998 GCTACAGTGC
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:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:85021 original size:21 final size:21
Alignment explanation
Indices: 84997--85059 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
84987 CCGTGAACAG
* * *
84997 TGCTACAGTGCACCGACGCAC
1 TGCTACAATGTACCGATGCAC
*
85018 TGCTATAATGTACCGATGCAC
1 TGCTACAATGTACCGATGCAC
85039 TGCTACAATGTACCGATGCAC
1 TGCTACAATGTACCGATGCAC
85060 AAAAACATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCTACAATGTACCGATGCAC
Found at i:85110 original size:21 final size:21
Alignment explanation
Indices: 85081--85140 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
85071 ATATAAATTG
*
85081 TGTATCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
*
85102 TGTACCGATGCACTGCTACAG
1 TGTACCGATGCACTGCTACAA
85123 TGTACCGATGCACTGCTA
1 TGTACCGATGCACTGCTA
85141 TAGTAACTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
TGTACCGATGCACTGCTACAA
Found at i:87530 original size:31 final size:30
Alignment explanation
Indices: 87492--87579 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
87482 CGCTACATTG
*
87492 GTGCTTTGAACACATAGGATATGTCACATCT
1 GTGCTTTGAACACATA-GATATGTCACATCA
* * * * *
87523 GTTCTTTGGACATATA-AGATGTACTATATCA
1 GTGCTTTGAACACATAGATATGT-C-ACATCA
87554 GTGCTTTGAACACATATGATATGTCA
1 GTGCTTTGAACACATA-GATATGTCA
87580 TGACAATAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
29 5 0.12
30 1 0.02
31 31 0.72
32 1 0.02
33 5 0.12
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (30 bp):
GTGCTTTGAACACATAGATATGTCACATCA
Found at i:88431 original size:31 final size:31
Alignment explanation
Indices: 88393--88458 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
88383 TTTTTATTGG
* *
88393 TTTTGAATCTTACTACGAAAAGTAGTAATCA
1 TTTTGAATCTTAATAAGAAAAGTAGTAATCA
88424 TTTTGAATCTTAATAAGAAAAGTAGTAATCA
1 TTTTGAATCTTAATAAGAAAAGTAGTAATCA
88455 TTTT
1 TTTT
88459 ACCAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTTGAATCTTAATAAGAAAAGTAGTAATCA
Found at i:96566 original size:2 final size:2
Alignment explanation
Indices: 96553--96586 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
96543 GGTAGGATCC
*
96553 AT AT AC 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
96587 GTCTATACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:108824 original size:24 final size:24
Alignment explanation
Indices: 108797--108877 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
108787 GCATGGGTAG
108797 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
108821 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
*
108845 TGCATCGATGCAC-TG-T--ATAA
1 TGCATCGATGCACATGTTAAAGAA
108865 TGCATCGATGCAC
1 TGCATCGATGCAC
108878 TTCAAGGGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
20 16 0.29
22 1 0.02
23 2 0.04
24 37 0.66
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:109676 original size:18 final size:18
Alignment explanation
Indices: 109653--109704 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
109643 GGGTCTACGC
109653 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
109671 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
109689 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
109705 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:110806 original size:31 final size:31
Alignment explanation
Indices: 110768--110862 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
110758 GAACCTCGAC
* *
110768 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
110799 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
110830 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
110861 AA
1 AA
110863 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:111028 original size:17 final size:19
Alignment explanation
Indices: 110996--111031 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
110986 CATATATCTC
110996 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
111015 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
111032 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:111709 original size:64 final size:63
Alignment explanation
Indices: 111611--111771 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
111601 TAATGAAGTT
* *
111611 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
111674 GG
62 GC
*
111676 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
111740 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
111772 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:115287 original size:20 final size:20
Alignment explanation
Indices: 115242--115319 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 20
115232 GCATGGGTAG
115242 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
115266 TGGATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
115286 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
115306 TGCATCGATGCACT
1 TGCATCGATGCACT
115320 TCAAGGGGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 37 0.71
22 1 0.02
23 2 0.04
24 12 0.23
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:116066 original size:18 final size:18
Alignment explanation
Indices: 116043--116090 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
116033 GGGTCTACGC
116043 GGTCCTTCGGGATATAGT
1 GGTCCTTCGGGATATAGT
*
116061 GGTCCTTTGGGATATAGT
1 GGTCCTTCGGGATATAGT
*
116079 GGTCATTCGGGA
1 GGTCCTTCGGGA
116091 CATATGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (18 bp):
GGTCCTTCGGGATATAGT
Found at i:126867 original size:31 final size:31
Alignment explanation
Indices: 126791--126875 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
126781 GATTATCCAC
* *
126791 CACAGCAAAT-CAAAGAAAACATAAACCCAT
1 CACAACAAATACAAAGAAAACAAAAACCCAT
**
126821 CACAGA-AAA-AGCAAAGAAAACAAAAATTCAT
1 CACA-ACAAATA-CAAAGAAAACAAAAACCCAT
*
126852 CACAACAAATACAAAGGAAACAAA
1 CACAACAAATACAAAGAAAACAAA
126876 GATAGGGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 8 0.18
31 36 0.80
32 1 0.02
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.08
Consensus pattern (31 bp):
CACAACAAATACAAAGAAAACAAAAACCCAT
Found at i:127832 original size:179 final size:175
Alignment explanation
Indices: 127533--127858 Score: 458
Period size: 179 Copynumber: 1.8 Consensus size: 175
127523 ACTAAAATGA
* * ** *
127533 AATAAAAACTAAATGTTAGGTATGATTTTGAAAAAAAAAAATTAGGTACTGAAATGAACTAAAAC
1 AATAAAAACCAAATGTTAGGTATAATTTAAAAAAAAAAAAATTAGGTACTAAAATGAACTAAAAC
** ** *
127598 TGATAGCTTAAATACTAAACGCGTAGTTTACTTATAAATAGTTGACTTCCATGTTTCTTATTAAA
66 TGATAGCTTAAATACTAAACGCGTAGTTTACCCATAAATAAATGACTTCCATGTTTCTTACTAAA
127663 GACCAATCGTGGCCGTCCAGTTGTAAAAGACCCTATGAGTTGACT
131 GACCAATCGTGGCCGTCCAGTTGTAAAAGACCCTATGAGTTGACT
127708 AATAAAAACCAAATGTT-GAGTATAATTTAAAAAAAAATTAAAAGTTTAGGTACTAAAACT-AAC
1 AATAAAAACCAAATGTTAG-GTATAATTTAAAAAAAAA--AAAA--TTAGGTACTAAAA-TGAAC
* ** *
127771 TAAAACTTATAGCTTAAATACTAAACTTGTAGTTTACCCATAAATAAATGACTTTCATGTTTCTT
60 TAAAACTGATAGCTTAAATACTAAACGCGTAGTTTACCCATAAATAAATGACTTCCATGTTTCTT
127836 ACTAAAGACCAATCGTGGCCGTC
125 ACTAAAGACCAATCGTGGCCGTC
127859 TAGTCCTAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
174 1 0.01
175 31 0.24
177 4 0.03
179 94 0.72
180 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (175 bp):
AATAAAAACCAAATGTTAGGTATAATTTAAAAAAAAAAAAATTAGGTACTAAAATGAACTAAAAC
TGATAGCTTAAATACTAAACGCGTAGTTTACCCATAAATAAATGACTTCCATGTTTCTTACTAAA
GACCAATCGTGGCCGTCCAGTTGTAAAAGACCCTATGAGTTGACT
Found at i:137995 original size:30 final size:30
Alignment explanation
Indices: 137954--138026 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
137944 GTCTGTTTTA
* *
137954 ATACTTAAACTTTTATTTTTTTTCAAAATC
1 ATACTTAAACTTTCATTTTTTTTCAAAACC
*
137984 ATACCTAAACTTTCATTTTTTTTCAAAACC
1 ATACTTAAACTTTCATTTTTTTTCAAAACC
138014 ATACTTAAACTTT
1 ATACTTAAACTTT
138027 AGCTTTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (30 bp):
ATACTTAAACTTTCATTTTTTTTCAAAACC
Found at i:146209 original size:22 final size:22
Alignment explanation
Indices: 146183--146228 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
146173 CGTACACATT
*
146183 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
146205 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
146227 AA
1 AA
146229 CATATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:150493 original size:161 final size:161
Alignment explanation
Indices: 150308--150604 Score: 450
Period size: 161 Copynumber: 1.8 Consensus size: 161
150298 AACACAATAA
* * * * *
150308 AATACCTATGTAACTTCAATTCTTAATTTTTTACTAAAAATGTAGTCTCTCTTTTTATTTAGTCC
1 AATACCTATGTAACTTCAATTCTTAATTTTTTACTAAAAATATACTCTCTCTTTTAATTCAATCC
* *
150373 CTTAACTTTGTATTTTACTCAATATGATCTCTTGACTATAATTGTTTACAGATTCTTTCTTTCCA
66 CTTAAATTTGTATTTTACTCAATATGATCTCTTGACTATAATTGTTTACAGATTCTTTCTTCCCA
150438 CCAATTTCTTGACTCCTCTATACACCACAAG
131 CCAATTTCTTGACTCCTCTATACACCACAAG
* *
150469 AATACCTATGTAACTTCGATTCTTACTTTTTTACTAAAAATATACTCTCTCTTTTAATTCAATCC
1 AATACCTATGTAACTTCAATTCTTAATTTTTTACTAAAAATATACTCTCTCTTTTAATTCAATCC
* * * * * *
150534 CTTAAATTTTTATTTTACTCAATTTGGTCTTTTGACTATAATTGTTTGCATATTCTTTCTTCCCA
66 CTTAAATTTGTATTTTACTCAATATGATCTCTTGACTATAATTGTTTACAGATTCTTTCTTCCCA
*
150599 TCAATT
131 CCAATT
150605 CCTAATAAAG
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
161 120 1.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (161 bp):
AATACCTATGTAACTTCAATTCTTAATTTTTTACTAAAAATATACTCTCTCTTTTAATTCAATCC
CTTAAATTTGTATTTTACTCAATATGATCTCTTGACTATAATTGTTTACAGATTCTTTCTTCCCA
CCAATTTCTTGACTCCTCTATACACCACAAG
Found at i:155353 original size:16 final size:17
Alignment explanation
Indices: 155313--155366 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 17
155303 TATATATATA
155313 TTATAATATTACAT-ATT
1 TTAT-ATATTACATAATT
*
155330 TAAT-TATTA-ATAATT
1 TTATATATTACATAATT
*
155345 TTATATATTATATAAGTT
1 TTATATATTACATAA-TT
155363 TTAT
1 TTAT
155367 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.35
16 5 0.16
17 7 0.23
18 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATATTACATAATT
Found at i:161582 original size:46 final size:47
Alignment explanation
Indices: 161521--161613 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 47
161511 TTCTCCCATT
*
161521 TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGCTGACATGTGTA
1 TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
161568 TTTTT-GTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
1 TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
161614 ATAGATAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 40 0.89
47 5 0.11
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (47 bp):
TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
Found at i:162988 original size:35 final size:35
Alignment explanation
Indices: 162942--163013 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
162932 CAAAAAAAGA
* *
162942 AGAGTTTGATTAGGACTCAAATACTAATCTAAAAT
1 AGAGTTGGATTAAGACTCAAATACTAATCTAAAAT
*
162977 AGAGTTGGATTAAGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAAGACTCAAATACTAATCTAAAAT
163012 AG
1 AG
163014 GATTTTTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAAGACTCAAATACTAATCTAAAAT
Found at i:163621 original size:86 final size:81
Alignment explanation
Indices: 163478--163635 Score: 194
Period size: 86 Copynumber: 1.9 Consensus size: 81
163468 TTTTACTATA
* * *
163478 TTTTATTATTATTATATATATATATATATTTCTTTAATATTTTACTTATAAGTCTATTATTACTA
1 TTTTATTATTATTATATATATATATATATTTCTTTAATAGTTTACTTATAAGCCTATTATTAATA
163543 TATATATTGTAATTAT
66 TATATATTGTAATTAT
* *
163559 TTTTATCTAGTTA-TATATATATATATATTTTTATACTTTTAATAGTTTATTTATATA-CCTATT
1 TTTTAT-TA-TTATTATATATATATATA-TATT-T-C-TTTAATAGTTTACTTATA-AGCCTATT
163622 ATTAATATATATAT
59 ATTAATATATATAT
163636 ATATTCTTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
81 6 0.09
82 16 0.25
83 6 0.09
84 1 0.02
85 1 0.02
86 34 0.52
87 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (81 bp):
TTTTATTATTATTATATATATATATATATTTCTTTAATAGTTTACTTATAAGCCTATTATTAATA
TATATATTGTAATTAT
Found at i:163751 original size:38 final size:38
Alignment explanation
Indices: 163709--163792 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
163699 TATATATATA
** *
163709 TATATTATTTTTTATTATTTTTAT-TTTTTATTCATTAT
1 TATATTATTTTTTAAAATTTTTATGTCTTTA-TCATTAT
*
163747 TATATTATTTTTTAAAATTTTTGTGTCTTTATCATTAT
1 TATATTATTTTTTAAAATTTTTATGTCTTTATCATTAT
163785 TATTATTA
1 TA-TATTA
163793 AACATTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 30 0.75
39 10 0.25
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (38 bp):
TATATTATTTTTTAAAATTTTTATGTCTTTATCATTAT
Found at i:163992 original size:2 final size:2
Alignment explanation
Indices: 163985--164046 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
163975 TAATACTTTG
163985 AT AT AT AT 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 AT AT AT AT
164027 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
164047 TTTCCTTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:164121 original size:13 final size:13
Alignment explanation
Indices: 164100--164137 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
164090 TTTATTTTCC
*
164100 TTATCTTATTTAT
1 TTATTTTATTTAT
164113 TTATTTTATTTAT
1 TTATTTTATTTAT
164126 TTCATTTTATTT
1 TT-ATTTTATTT
164138 TATTCTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:168614 original size:15 final size:16
Alignment explanation
Indices: 168557--168589 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
168547 AGATTCAATC
168557 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
*
168572 AATAAGCAAAAAAGAA
1 AAGAAGCAAAAAAGAA
168588 AA
1 AA
168590 AAAACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:169368 original size:39 final size:37
Alignment explanation
Indices: 169293--169381 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
169283 ACCGACCCGA
*
169293 TCGGGTCGGATTTTTTTTAAAATATTTCGGGTTCGGG
1 TCGGGTCGGGTTTTTTTTAAAATATTTCGGGTTCGGG
*
169330 TCGGGTCGGGTTTTTTTTAAATGTACTGTTCGGG-TCGGG
1 TCGGGTCGGGTTTTTTTTAAA-ATA-T-TTCGGGTTCGGG
*
169369 TCGAGTCGGGTTT
1 TCGGGTCGGGTTT
169382 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
37 20 0.43
38 2 0.04
39 18 0.39
40 6 0.13
ACGTcount: A:0.12, C:0.12, G:0.34, T:0.42
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTTTAAAATATTTCGGGTTCGGG
Found at i:170934 original size:37 final size:37
Alignment explanation
Indices: 170864--170935 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
170854 TGGAACTAAG
* * * *
170864 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
170901 TTTTGCCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAA
170936 CAGATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (37 bp):
TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:171708 original size:106 final size:106
Alignment explanation
Indices: 171520--172273 Score: 881
Period size: 106 Copynumber: 7.3 Consensus size: 106
171510 CACATCCACG
* * * * *
171520 ATTTCAACTCCACAACGGAGGATATTGCGCCACCCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAGCGAAGGATATTG-G--ACTCAAGACAACACAAGTTCAACTTCACAACGAA
* * *
171585 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
171629 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
171694 ACGGTTGGTTGTCAACAAACAATTTCCCAATTTCATAGTCA
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
*
171735 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTT-----C------
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
171789 ACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C-
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
* *
171828 ----CAA--T---AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
171884 ACGGCTAGTTGTCAACAAATAATTTCCCAATTTCAGGGTCA
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
* * * *
171925 ATTTTAACTTCACATCGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAACAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
171988 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
* * * * *
172029 ATTTCAACTTCACAGTGAATGATATTGGACTCGAGACGACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
172094 ACGACTGGATGTCAACAAATAATTTCCCAATTTCAGGGTCA
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
* * * * *
172135 ATTTCAACTTCACATCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * * *
172200 GCGGTTGGCTGTCAACAAATAATTTTCCAGTTCCATAGCCA
66 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
** *
172241 ATTTCAACTTCATGGCGGAGGATATTGGACTCA
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCA
172274 GAACAATACA
Statistics
Matches: 559, Mismatches: 62, Indels: 51
0.83 0.09 0.08
Matches are distributed among these distances:
84 37 0.07
87 1 0.00
89 4 0.01
94 1 0.00
95 69 0.12
96 1 0.00
101 3 0.01
103 1 0.00
104 96 0.17
106 321 0.57
108 1 0.00
109 24 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
Found at i:173194 original size:17 final size:18
Alignment explanation
Indices: 173168--173207 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
173158 ATTATATGGA
173168 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
173184 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
173202 TATTAT
1 TATTAT
173208 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:173272 original size:2 final size:2
Alignment explanation
Indices: 173265--173299 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
173255 TATTTTATTT
173265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
173300 TTATTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:173674 original size:41 final size:39
Alignment explanation
Indices: 173612--173688 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
173602 GAGGGCCCAT
* *
173612 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
* *
173653 TTTTTGTCTTATTTTTTACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
173689 GGTGAAACGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.31
40 1 0.03
41 21 0.66
ACGTcount: A:0.17, C:0.27, G:0.05, T:0.51
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:175163 original size:13 final size:13
Alignment explanation
Indices: 175145--175170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175135 GATAAAAATG
175145 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
175158 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
175171 TGATATGGAT
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:176151 original size:21 final size:21
Alignment explanation
Indices: 176125--176167 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
176115 TCGGTGATTT
176125 GGGAGGCGTGGAAGGAGAGGA
1 GGGAGGCGTGGAAGGAGAGGA
176146 GGGAGGCGTGGAAGGAGAGGA
1 GGGAGGCGTGGAAGGAGAGGA
176167 G
1 G
176168 TAATGCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.63, T:0.05
Consensus pattern (21 bp):
GGGAGGCGTGGAAGGAGAGGA
Found at i:178733 original size:21 final size:22
Alignment explanation
Indices: 178703--178744 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
178693 CGATATTTTT
178703 TATTGTCTATTTT-TTTATATTG
1 TATTGTCTATTTTCTTT-TATTG
178725 TATT-TCTATTTTCTTTTATT
1 TATTGTCTATTTTCTTTTATT
178745 TTTTAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TATTGTCTATTTTCTTTTATTG
Found at i:178800 original size:23 final size:23
Alignment explanation
Indices: 178770--178839 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
178760 AGTCTATATG
178770 TATGACACATTTTCATATGTTTT
1 TATGACACATTTTCATATGTTTT
178793 TATGACACATTTTCATATGTTTT
1 TATGACACATTTTCATATGTTTT
*
178816 TATGACACATTTTCTTATGTTTT
1 TATGACACATTTTCATATGTTTT
178839 T
1 T
178840 TGGCATGTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (23 bp):
TATGACACATTTTCATATGTTTT
Found at i:181256 original size:13 final size:13
Alignment explanation
Indices: 181238--181264 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
181228 AGAGATCACT
181238 CATCTTAGTATTA
1 CATCTTAGTATTA
181251 CATCTTAGTATTA
1 CATCTTAGTATTA
181264 C
1 C
181265 GAGATCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (13 bp):
CATCTTAGTATTA
Found at i:186342 original size:32 final size:32
Alignment explanation
Indices: 186306--186471 Score: 314
Period size: 32 Copynumber: 5.2 Consensus size: 32
186296 TATAATATTT
*
186306 CATTAACAAAGGAAGCACAACAATAGGGGCGA
1 CATTAACAAAGGAAGCACAACAATAGGGGCAA
186338 CATTAACAAAGGAAGCACAACAATAGGGGCAA
1 CATTAACAAAGGAAGCACAACAATAGGGGCAA
186370 CATTAACAAAGGAAGCACAACAATAGGGGCAA
1 CATTAACAAAGGAAGCACAACAATAGGGGCAA
*
186402 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
1 CATTAACAAAGGAAGCACAACAATAGGGGCAA
186434 CATTAACAAAGGAAGCACAACAATAGGGGCAA
1 CATTAACAAAGGAAGCACAACAATAGGGGCAA
186466 CATTAA
1 CATTAA
186472 GGACGACAAT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 131 1.00
ACGTcount: A:0.50, C:0.18, G:0.22, T:0.10
Consensus pattern (32 bp):
CATTAACAAAGGAAGCACAACAATAGGGGCAA
Found at i:195003 original size:19 final size:19
Alignment explanation
Indices: 194970--195017 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
194960 ATTAGTAATT
*
194970 TTTATCTTTATATTACTAAA
1 TTTA-CTTTAGATTACTAAA
194990 TTTACTTTAGATTACTAAA
1 TTTACTTTAGATTACTAAA
195009 TTTACTTTA
1 TTTACTTTA
195018 TATAGTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTACTTTAGATTACTAAA
Found at i:200119 original size:23 final size:23
Alignment explanation
Indices: 200073--200133 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
200063 AGCTCGTATC
* *
200073 ATTGCACCGAAGTG-CACGTAGA
1 ATTGCACCGTAGTGCCGCGTAGA
*
200095 ATTGCATCGTAGTGCCGCGTAGA
1 ATTGCACCGTAGTGCCGCGTAGA
200118 ATTGCACCGTAGTGCC
1 ATTGCACCGTAGTGCC
200134 CTATAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
ATTGCACCGTAGTGCCGCGTAGA
Found at i:201914 original size:64 final size:64
Alignment explanation
Indices: 201760--201916 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 64
201750 TAATGAAGGT
* * * ** *
201760 ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCAATGTTGTATTATTATTGGG
1 ATGCATCGATGCATTACTAATGCATCGATGCACAAAATGCATTCAATGTTCTATTATTAAAGAG
* * * * *
201824 ATGCATCGATGCATGACTTATACATCGATGCACAAATTGCATTCGATGTTTCTATT-TTAAA-AG
1 ATGCATCGATGCATTACTAATGCATCGATGCACAAAATGCATTCAATG-TTCTATTATTAAAGAG
*
201887 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCATTACTAATGCATCGAT
201917 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 2 0.03
64 68 0.89
65 6 0.08
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCATTACTAATGCATCGATGCACAAAATGCATTCAATGTTCTATTATTAAAGAG
Found at i:206679 original size:20 final size:20
Alignment explanation
Indices: 206656--206744 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
206646 CTCAGTTTCC
* * *
206656 AAAATCGCAGCGTGAATTGG
1 AAAATCGCAACGCGAATTAG
206676 AAAATCGCAACGCGAATTAG
1 AAAATCGCAACGCGAATTAG
*
206696 AAAATCACAACGCGAATTTAG
1 AAAATCGCAACGCGAA-TTAG
*
206717 AAAATCACAACGCGAATTTAG
1 AAAATCGCAACGCGAA-TTAG
206738 AAAATCG
1 AAAATCG
206745 TAAAATCGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
20 32 0.51
21 31 0.49
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGAATTAG
Found at i:206718 original size:21 final size:21
Alignment explanation
Indices: 206675--206743 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
206665 GCGTGAATTG
*
206675 GAAAATCGCAACGCGAA-TTA
1 GAAAATCACAACGCGAATTTA
206695 GAAAATCACAACGCGAATTTA
1 GAAAATCACAACGCGAATTTA
206716 GAAAATCACAACGCGAATTTA
1 GAAAATCACAACGCGAATTTA
206737 GAAAATC
1 GAAAATC
206744 GTAAAATCGC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (21 bp):
GAAAATCACAACGCGAATTTA
Found at i:210017 original size:52 final size:52
Alignment explanation
Indices: 209955--210057 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
209945 TTATAATATT
209955 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
210007 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
210058 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:214607 original size:52 final size:52
Alignment explanation
Indices: 214545--214647 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
214535 TTATAATATT
214545 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
214597 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
214648 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:215930 original size:21 final size:22
Alignment explanation
Indices: 215899--215941 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
215889 CTAAAAAGAT
*
215899 GAGAAGAGAAGTAGCTGCCATG
1 GAGAAGAGAAGTAGCCGCCATG
*
215921 GAGAA-AGAAGTTGCCGCCATG
1 GAGAAGAGAAGTAGCCGCCATG
215942 CGGGTGGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.14
Consensus pattern (22 bp):
GAGAAGAGAAGTAGCCGCCATG
Found at i:230032 original size:28 final size:29
Alignment explanation
Indices: 229973--230032 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
229963 CATGGTTGGT
* ** *
229973 GGGTTAAATTGTATTTTTTTCAAGTTCGA
1 GGGTCAAATTGTATTTTTTAAAAGTTCAA
*
230002 GGGTCAAATTG-ATTTTTTAAAAGTTTAA
1 GGGTCAAATTGTATTTTTTAAAAGTTCAA
230030 GGG
1 GGG
230033 CTTATTTGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.43
Consensus pattern (29 bp):
GGGTCAAATTGTATTTTTTAAAAGTTCAA
Found at i:230099 original size:21 final size:21
Alignment explanation
Indices: 230073--230140 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
230063 AATTCAAAAT
230073 ATATAAAAATTTAAAAATTAA
1 ATATAAAAATTTAAAAATTAA
**
230094 ATAT-AAAATACAAAAA-TAA
1 ATATAAAAATTTAAAAATTAA
* * *
230113 AAATTAAATTATTAAAAAGTTAA
1 ATATAAAAAT-TTAAAAA-TTAA
230136 ATATA
1 ATATA
230141 TATTATTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 6 0.17
20 14 0.40
21 9 0.26
23 6 0.17
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (21 bp):
ATATAAAAATTTAAAAATTAA
Found at i:230809 original size:104 final size:104
Alignment explanation
Indices: 230700--230928 Score: 350
Period size: 104 Copynumber: 2.2 Consensus size: 104
230690 GTCAAGTGAA
* * *
230700 ATAAACGAATTTAGATTTATAAAAAAATAGTGAAATAGAATTTAAAAATACACTTAGAATTTAAG
1 ATAAACGAATTTAGATTTATAAAAAAATAGTGAAATAGAATTTAAAAAGAAACTTAAAATTTAAG
*
230765 ATAATTGGATGTAAATATATAAAATAAAATTTGAATAGG
66 ATAATTGAATGTAAATATATAAAATAAAATTTGAATAGG
** * *
230804 ATAAACGAATTTAGATTTATAAAAATTTAGTGGAATATAATTTAAAAAGAAACTTAAAATTTAAG
1 ATAAACGAATTTAGATTTATAAAAAAATAGTGAAATAGAATTTAAAAAGAAACTTAAAATTTAAG
* **
230869 ATAATTGAATGTGAATATATAAAATAAAATTTGTGTAGG
66 ATAATTGAATGTAAATATATAAAATAAAATTTGAATAGG
*
230908 ATAAACGAATTTATATTTATA
1 ATAAACGAATTTAGATTTATA
230929 TAAATAAAAG
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 113 1.00
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (104 bp):
ATAAACGAATTTAGATTTATAAAAAAATAGTGAAATAGAATTTAAAAAGAAACTTAAAATTTAAG
ATAATTGAATGTAAATATATAAAATAAAATTTGAATAGG
Found at i:231043 original size:24 final size:23
Alignment explanation
Indices: 231016--231073 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
231006 TTTGGTGTTA
*
231016 TTATATTTAAATTTTTGAATATTT
1 TTATATTTAAA-TTTAGAATATTT
231040 TTATATTTTAAATTTAGAATATTT
1 TTATA-TTTAAATTTAGAATATTT
231064 TTAT-TTTAAA
1 TTATATTTAAA
231074 AAAAATCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.19
24 20 0.62
25 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
TTATATTTAAATTTAGAATATTT
Found at i:231071 original size:22 final size:24
Alignment explanation
Indices: 231016--231073 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 24
231006 TTTGGTGTTA
*
231016 TTATATTTAAATTTTTGAATATTTT
1 TTAT-TTTAAATTTTAGAATATTTT
231041 TATATTTTAAA-TTTAGAATA-TTT
1 T-TATTTTAAATTTTAGAATATTTT
231064 TTATTTTAAA
1 TTATTTTAAA
231074 AAAAATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 9 0.29
23 4 0.13
24 8 0.26
25 7 0.23
26 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
TTATTTTAAATTTTAGAATATTTT
Found at i:231128 original size:27 final size:28
Alignment explanation
Indices: 231093--231146 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
231083 ATAAGTCCTT
*
231093 AAACTTTAAAAAAATCAATTTGGCCCAA
1 AAACTTTAAAAAAATCAATTTAGCCCAA
231121 AAAC-TTAAAAAAATCAATTTAGCCCA
1 AAACTTTAAAAAAATCAATTTAGCCCA
231147 TTTGTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.24
Consensus pattern (28 bp):
AAACTTTAAAAAAATCAATTTAGCCCAA
Found at i:246816 original size:20 final size:20
Alignment explanation
Indices: 246752--246862 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
246742 GTTTCTAGAT
*
246752 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * * *
246772 TCGTAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
246792 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
**
246812 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
246833 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
246853 TCGCAACGCG
1 TCGCAACGCG
246863 TTAATACATA
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.04
20 49 0.70
21 16 0.23
22 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:246837 original size:21 final size:21
Alignment explanation
Indices: 246811--246885 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
246801 GATTCTGACT
246811 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
246832 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
246852 ATCGCAACGCGTTAATACATA
1 ATCGCAACGCGATAATACATA
246873 ATCGCAACGCGAT
1 ATCGCAACGCGAT
246886 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:246839 original size:41 final size:41
Alignment explanation
Indices: 246752--246886 Score: 184
Period size: 41 Copynumber: 3.3 Consensus size: 41
246742 GTTTCTAGAT
* * * **
246752 TCGCAACGCGATTTTGACTATCGTAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT-AA
*
246792 TCGCAACGTGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
246833 TCGCAACGCGATTCTGACTATCGCAACGCGTTAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
246874 TCGCAACGCGATT
1 TCGCAACGCGATT
246887 TTCAAAGCGC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 26 0.31
41 54 0.64
42 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
Found at i:247050 original size:22 final size:22
Alignment explanation
Indices: 247025--247080 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
247015 ACTCTCTACA
*
247025 ACGACATCCGTCCCCATCTCCG
1 ACGAAATCCGTCCCCATCTCCG
*
247047 ACGAAATCCGTCCCCATCTTCG
1 ACGAAATCCGTCCCCATCTCCG
*
247069 GCGAAATCCGTC
1 ACGAAATCCGTC
247081 TATCTCCATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
ACGAAATCCGTCCCCATCTCCG
Found at i:247481 original size:20 final size:18
Alignment explanation
Indices: 247456--247546 Score: 65
Period size: 20 Copynumber: 4.7 Consensus size: 18
247446 AAAATCGCAA
247456 CGATAGTCAAATTTGCGTTG
1 CGATAGTC--ATTTGCGTTG
*
247476 CGATAGTCATTTTCGTGTAG
1 CGATAGTCATTTGCGT-T-G
** *
247496 CGATTTTCATTTCTCGTTG
1 CGATAGTCATTT-GCGTTG
*
247515 TGATAGTCAAATTTGCGTTG
1 CGATAGTC--ATTTGCGTTG
*
247535 CGATAGTTATTT
1 CGATAGTCATTT
247547 TCGTGTTGCG
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 11 0.19
19 7 0.12
20 31 0.54
21 8 0.14
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (18 bp):
CGATAGTCATTTGCGTTG
Found at i:249444 original size:20 final size:20
Alignment explanation
Indices: 249419--249467 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
249409 CGAAACTTAA
249419 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
* *
249439 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATAACT
249459 ATCGCAACG
1 ATCGCAACG
249468 AGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:249621 original size:20 final size:19
Alignment explanation
Indices: 249596--249663 Score: 100
Period size: 20 Copynumber: 3.5 Consensus size: 19
249586 ACGATTATCC
*
249596 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
249616 CGTTGCGATAGTCATTTCCT
1 CGTTGCGATAGTCATTT-CG
249636 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
249655 CGTTGCGAT
1 CGTTGCGAT
249664 TTAAGTTTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:249672 original size:19 final size:20
Alignment explanation
Indices: 249650--249692 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
249640 GCGATAGTCA
249650 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
249669 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
249689 TTTC
1 TTTC
249693 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:250262 original size:21 final size:21
Alignment explanation
Indices: 250171--250267 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
250161 GACTCACCTG
*
250171 TCATCGTTCAAGAGGCCTCT-
1 TCATCGTTCAAGAGGCCCCTA
*
250191 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTA
** *
250213 TCATCCCTCAAG-GGTCCCCTC
1 TCATCGTTCAAGAGG-CCCCTA
* *
250234 CCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
*
250255 TCATCGTTGAAGA
1 TCATCGTTCAAGA
250268 TTTCCCACCC
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:250279 original size:42 final size:42
Alignment explanation
Indices: 250196--250289 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
250186 CCTCTCCTAT
* *
250196 CGTTCAAGAGGCCCCTATCATCCCTCAAGGGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCACCCAC
** * * *
250238 CGTTCAAGAGGCCCCTATCATCGTTGAAGATTTCCCACCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCACCCAC
*
250280 CATTCAAGAG
1 CGTTCAAGAG
250290 CCCGATTCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCACCCAC
Found at i:251856 original size:20 final size:20
Alignment explanation
Indices: 251831--251884 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
251821 AGGTACACTT
*
251831 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
251851 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
251871 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
251885 TCAATTCACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:251952 original size:20 final size:20
Alignment explanation
Indices: 251927--252111 Score: 178
Period size: 20 Copynumber: 9.8 Consensus size: 20
251917 GCGATTTTCT
* *
251927 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
251947 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
251967 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
251987 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
252007 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
252021 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
252041 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
252061 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
252075 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
252095 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
252112 GAATGTGTAA
Statistics
Matches: 134, Mismatches: 19, Indels: 24
0.76 0.11 0.14
Matches are distributed among these distances:
14 22 0.16
16 2 0.01
18 2 0.01
20 108 0.81
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:251982 original size:40 final size:39
Alignment explanation
Indices: 251887--252111 Score: 151
Period size: 34 Copynumber: 6.1 Consensus size: 39
251877 CGCGAAAGTC
* *
251887 AATTCACGTTGCGATAGTCTAATACGCTTTGCGAT-T--
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATATCA
* *
251923 --TTCTCGTTGCGATAGTCAAATACCCGTTGCGATAATCA
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGAT-ATCA
* *
251961 AATTCACGTTGCGATAGTCAAATTCGTGTTGCGATAGTCA
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATA-TCA
* **
252001 AATTCGCGTTGCGAT--T----TTTGCGTTGCGATAGTCA
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATA-TCA
* * *
252035 TATTCGA-GTTGCGATAGTCAAATTCGCATTGCGAT-T--
1 AATTC-ACGTTGCGATAGTCAAATACGCGTTGCGATATCA
* * *
252071 -TTTGA-GTTGCGATAGTCAAATTCGCGTTGCGATATTCA
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATA-TCA
252109 AAT
1 AAT
252112 GAATGTGTAA
Statistics
Matches: 151, Mismatches: 19, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
34 85 0.56
35 2 0.01
36 3 0.02
38 2 0.01
39 2 0.01
40 57 0.38
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (39 bp):
AATTCACGTTGCGATAGTCAAATACGCGTTGCGATATCA
Found at i:252025 original size:54 final size:54
Alignment explanation
Indices: 251967--252111 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
251957 ATCAAATTCA
* *
251967 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
*
252021 CGTTGCGATAGTCATATTCGAGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
* * *
252075 AGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAAT
252112 GAATGTGTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
Found at i:252334 original size:140 final size:140
Alignment explanation
Indices: 252082--252364 Score: 548
Period size: 140 Copynumber: 2.0 Consensus size: 140
252072 TTGAGTTGCG
* *
252082 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATTA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGGAATAAGTGATAACAACTGAACAGATCA
252147 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
252212 AATACACATA
131 AATACACATA
252222 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGGAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGGAATAAGTGATAACAACTGAACAGATCA
252287 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
252352 AATACACATA
131 AATACACATA
252362 ATA
1 ATA
252365 CAACGTTTTC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGGAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:252445 original size:18 final size:18
Alignment explanation
Indices: 252422--252456 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
252412 AAGCCGGTTG
*
252422 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
252440 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
252457 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:254099 original size:39 final size:39
Alignment explanation
Indices: 254045--254119 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
254035 TGAACCGAGC
254045 ATTCATGTCAGTCATAATTTCATGTCCCCGATATACAAA
1 ATTCATGTCAGTCATAATTTCATGTCCCCGATATACAAA
254084 ATTCATGTCAGTCATAATTTCATGTCCCCGATATAC
1 ATTCATGTCAGTCATAATTTCATGTCCCCGATATAC
254120 CCTGCCATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (39 bp):
ATTCATGTCAGTCATAATTTCATGTCCCCGATATACAAA
Found at i:254774 original size:24 final size:24
Alignment explanation
Indices: 254747--254793 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
254737 ATCATTAAAA
*
254747 TCCGAGTATTTACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
254771 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
254794 TTTCGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:255473 original size:22 final size:22
Alignment explanation
Indices: 255448--255498 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
255438 GATGGGGAAG
255448 GATGTCGTTGGATATAGGAACA
1 GATGTCGTTGGATATAGGAACA
*
255470 GATGTCGTTGGATATAGGAACG
1 GATGTCGTTGGATATAGGAACA
255492 GATGTCG
1 GATGTCG
255499 CCGGAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.35, T:0.27
Consensus pattern (22 bp):
GATGTCGTTGGATATAGGAACA
Found at i:255661 original size:20 final size:20
Alignment explanation
Indices: 255644--255782 Score: 95
Period size: 20 Copynumber: 6.9 Consensus size: 20
255634 TGTTGCGACT
255644 GTCAGAATCGCATTGCGATA
1 GTCAGAATCGCATTGCGATA
*
255664 GTCAGAATCGCGTTGCGATTA
1 GTCAGAATCGCATTGCGA-TA
** *
255685 TGT-ATTATCGCGTTGCGAT-
1 -GTCAGAATCGCATTGCGATA
* * * *
255704 TTACATATTCGCGTTGCGATA
1 GT-CAGAATCGCATTGCGATA
*
255725 GTCAGAATCGCGTTGCGAT-
1 GTCAGAATCGCATTGCGATA
* * *
255744 TTACATATTCGCATTGCGATA
1 GT-CAGAATCGCATTGCGATA
* *
255765 GTCAAAATCGCGTTGCGA
1 GTCAGAATCGCATTGCGA
255783 ATCTGGAAAC
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 74 0.78
21 17 0.18
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
GTCAGAATCGCATTGCGATA
Found at i:255744 original size:40 final size:41
Alignment explanation
Indices: 255635--255782 Score: 162
Period size: 40 Copynumber: 3.7 Consensus size: 41
255625 GAAATTCAGT
* * * *
255635 GTTGCGACT-GTCAGAATCGCATTGCGATAGT-CAGAATCGC
1 GTTGCGACTAGTCAGAATCGCGTTGCGAT-TTACATATTCGC
* **
255675 GTTGCGATTATGT-ATTATCGCGTTGCGATTTACATATTCGC
1 GTTGCGACTA-GTCAGAATCGCGTTGCGATTTACATATTCGC
255716 GTTGCGA-TAGTCAGAATCGCGTTGCGATTTACATATTCGC
1 GTTGCGACTAGTCAGAATCGCGTTGCGATTTACATATTCGC
* *
255756 ATTGCGA-TAGTCAAAATCGCGTTGCGA
1 GTTGCGACTAGTCAGAATCGCGTTGCGA
255783 ATCTGGAAAC
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.02
40 62 0.67
41 27 0.29
42 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
GTTGCGACTAGTCAGAATCGCGTTGCGATTTACATATTCGC
Found at i:270438 original size:31 final size:32
Alignment explanation
Indices: 270387--270447 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 32
270377 AATTGTCATA
270387 TTTGTAGTTTATAGGTCTTTAAATAAATTGTC
1 TTTGTAGTTTATAGGTCTTTAAATAAATTGTC
270419 TTTGTAAG-TTAT-GGTCTTTAAATAAATTG
1 TTTGT-AGTTTATAGGTCTTTAAATAAATTG
270448 GGATCACCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 17 0.61
32 9 0.32
33 2 0.07
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (32 bp):
TTTGTAGTTTATAGGTCTTTAAATAAATTGTC
Found at i:274899 original size:12 final size:12
Alignment explanation
Indices: 274877--274905 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
274867 AGTTACAGAC
274877 TGTTA-GAATGT
1 TGTTAGGAATGT
274888 TGTTAGGAATGT
1 TGTTAGGAATGT
274900 TGTTAG
1 TGTTAG
274906 ACTATTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (12 bp):
TGTTAGGAATGT
Found at i:278422 original size:239 final size:232
Alignment explanation
Indices: 277982--278453 Score: 881
Period size: 239 Copynumber: 2.0 Consensus size: 232
277972 ATGACAAGCT
277982 TAAAGCCAGTTTAATTCGGCTTGGCTTTAGTGAATCTAAAGCTGATGTATCATTGTTTTAAGAAT
1 TAAAGCCAGTTTAATTCGGCTTGGCTTTAGTGAATCTAAAGCTGATGTATCATTGTTTTAAGAAT
278047 GATGCAGGTTGCTATACATATATTCTTGTTATGTGATGATATCATACTCAAGTGCTTCTTCATGT
66 GATGCAGGTTGCTATACATATATTCTTGTTATGTGATGATATCATACTCAAGTGCTTCTTCATGT
278112 GTCGTTAATGCTGTGACAAGCGTTGAATCAGGAGTTTCCTTGAAGGATCTAGGAGAATTATCCTA
131 GTCGTTAATGCTGTGACAAGCGTTGAATCAGGAGTTTCCTTGAAGGATCTAGGAGAATTATCCTA
278177 CTTCTTGGGCATTGAAGTCAAACGTAGCAAGGAGTCC
196 CTTCTTGGGCATTGAAGTCAAACGTAGCAAGGAGTCC
278214 TAAAGCCAGTTTAATTCGGCTTGGCTTTAGTGAATCTAAAGCTGATGTATCATTGTTGTTAAGAA
1 TAAAGCCAGTTTAATTCGGCTTGGCTTTAGTGAATCTAAAGCTGATGTATCATTGTT-TTAAGAA
278279 TGATGCAGGTTGCTATACATATATTCTTGTTTATGTTGATGATATCATACTCACAAGTGCTTCTT
65 TGATGCAGGTTGCTATACATATATTCTTG-TTATG-TGATGATATCATACT--CAAGTGCTTCTT
278344 CATGTGTCGTTAATGCTGTGATACAAGCGTTGAATCAGGAGTTTCCTTGAAGGATCTAGGAGAAT
126 CATGTGTCGTTAATGCTGTG--ACAAGCGTTGAATCAGGAGTTTCCTTGAAGGATCTAGGAGAAT
278409 TATCCTACTTCTTGGGCATTGAAGTCAAACGTAGCAAGGAGTCC
189 TATCCTACTTCTTGGGCATTGAAGTCAAACGTAGCAAGGAGTCC
278453 T
1 T
278454 TGGTGCTGTC
Statistics
Matches: 233, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
232 57 0.24
233 36 0.15
234 5 0.02
235 15 0.06
237 32 0.14
239 88 0.38
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (232 bp):
TAAAGCCAGTTTAATTCGGCTTGGCTTTAGTGAATCTAAAGCTGATGTATCATTGTTTTAAGAAT
GATGCAGGTTGCTATACATATATTCTTGTTATGTGATGATATCATACTCAAGTGCTTCTTCATGT
GTCGTTAATGCTGTGACAAGCGTTGAATCAGGAGTTTCCTTGAAGGATCTAGGAGAATTATCCTA
CTTCTTGGGCATTGAAGTCAAACGTAGCAAGGAGTCC
Found at i:281384 original size:26 final size:27
Alignment explanation
Indices: 281326--281384 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
281316 GATTATTTAG
* **
281326 TAATTTTAAAATTTAATAGTTATTTTAT
1 TAATTTTAAAAATT-ATAGTTATTAAAT
*
281354 AAATTTTAAAAATT-TAGTTATTAAAT
1 TAATTTTAAAAATTATAGTTATTAAAT
281380 TAATT
1 TAATT
281385 ATTTAAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
TAATTTTAAAAATTATAGTTATTAAAT
Found at i:282416 original size:36 final size:36
Alignment explanation
Indices: 282376--282487 Score: 130
Period size: 36 Copynumber: 3.2 Consensus size: 36
282366 GAATTACGGG
282376 TATTAAAATGAAACAAAAACTAATTGAAATTTTATA
1 TATTAAAATGAAACAAAAACTAATTGAAATTTTATA
* *
282412 TATTAAAAT-ATATC---AA--AATTGATAA-TTTAGA
1 TATTAAAATGA-AACAAAAACTAATTGA-AATTTTATA
*
282443 TACTAAAATGAAACAAAAACTAATTGAAATTTTATA
1 TATTAAAATGAAACAAAAACTAATTGAAATTTTATA
282479 TATTAAAAT
1 TATTAAAAT
282488 ATATTAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
31 21 0.34
32 3 0.05
33 2 0.03
34 2 0.03
35 3 0.05
36 30 0.49
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (36 bp):
TATTAAAATGAAACAAAAACTAATTGAAATTTTATA
Found at i:282432 original size:31 final size:31
Alignment explanation
Indices: 282397--282497 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 31
282387 AACAAAAACT
282397 AATTGAAATTTTATATATTAAAATATATCAA
1 AATTGAAATTTTATATATTAAAATATATCAA
* * *
282428 AATTGATAA-TTTAGATACTAAAATGA-AACAAAAA
1 AATTGA-AATTTTATATATTAAAAT-ATATC---AA
*
282462 CTAATTGAAATTTTATATATTAAAATATATTAA
1 --AATTGAAATTTTATATATTAAAATATATCAA
282495 AAT
1 AAT
282498 ATAATTTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
31 24 0.44
32 3 0.06
33 2 0.04
34 2 0.04
35 3 0.06
36 20 0.37
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (31 bp):
AATTGAAATTTTATATATTAAAATATATCAA
Found at i:282487 original size:67 final size:65
Alignment explanation
Indices: 282379--282513 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 65
282369 TTACGGGTAT
282379 TAAAATGAAACAAAAACTAATTGAAATTTTATATATTAAAATATATCAAAATTGATAATTTAGAT
1 TAAAATGAAACAAAAACTAATTGAAATTTTATATATTAAAATATATCAAAA-T-ATAATTTAGAT
282444 AC
64 AC
*
282446 TAAAATGAAACAAAAACTAATTGAAATTTTATATATTAAAATATATTAAAATATAATTTAGATAC
1 TAAAATGAAACAAAAACTAATTGAAATTTTATATATTAAAATATATCAAAATATAATTTAGATAC
282511 TAA
1 TAA
282514 CAAGTAATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 16 0.24
66 1 0.01
67 50 0.75
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (65 bp):
TAAAATGAAACAAAAACTAATTGAAATTTTATATATTAAAATATATCAAAATATAATTTAGATAC
Found at i:282499 original size:8 final size:10
Alignment explanation
Indices: 282476--282500 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
282466 TTGAAATTTT
282476 ATATATTAAA
1 ATATATTAAA
282486 ATATATTAAA
1 ATATATTAAA
282496 ATATA
1 ATATA
282501 ATTTAGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATTAAA
Found at i:282503 original size:36 final size:36
Alignment explanation
Indices: 282396--282503 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 36
282386 AAACAAAAAC
282396 TAATTGAAATTTTATATATTAAAATATATCAAAAT-
1 TAATTGAAATTTTATATATTAAAATATATCAAAATA
* * * *
282431 TGA-T--AA-TTTAGATACTAAAATGA-AACAAAA-A
1 TAATTGAAATTTTATATATTAAAAT-ATATCAAAATA
*
282462 CTAATTGAAATTTTATATATTAAAATATATTAAAATA
1 -TAATTGAAATTTTATATATTAAAATATATCAAAATA
282499 TAATT
1 TAATT
282504 TAGATACTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
31 19 0.35
32 5 0.09
33 1 0.02
34 1 0.02
35 5 0.09
36 23 0.42
37 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (36 bp):
TAATTGAAATTTTATATATTAAAATATATCAAAATA
Found at i:285703 original size:26 final size:26
Alignment explanation
Indices: 285667--285720 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
285657 ATCATATAAG
285667 ATTGATTCTTTTCACAGTTTGAAACC
1 ATTGATTCTTTTCACAGTTTGAAACC
285693 ATTGATTCTTTTCACAGTTTGAAACC
1 ATTGATTCTTTTCACAGTTTGAAACC
285719 AT
1 AT
285721 GGCTTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (26 bp):
ATTGATTCTTTTCACAGTTTGAAACC
Found at i:290498 original size:13 final size:13
Alignment explanation
Indices: 290480--290504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290470 GATCCCATCT
290480 GTATACGTGTTCG
1 GTATACGTGTTCG
290493 GTATACGTGTTC
1 GTATACGTGTTC
290505 ATATTTTTAA
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:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (13 bp):
GTATACGTGTTCG
Found at i:299316 original size:49 final size:49
Alignment explanation
Indices: 299244--299341 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
299234 TACAGGTAAG
299244 AAAAAAAAAGGAGAGGTGAAATGCACAAAGTTGTAGTCACAGCCATTGC
1 AAAAAAAAAGGAGAGGTGAAATGCACAAAGTTGTAGTCACAGCCATTGC
299293 AAAAAAAAAGGAGAGGTGAAATGCACAAAGTTGTAGTCACAGCCATTGC
1 AAAAAAAAAGGAGAGGTGAAATGCACAAAGTTGTAGTCACAGCCATTGC
299342 TTTATATTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.16
Consensus pattern (49 bp):
AAAAAAAAAGGAGAGGTGAAATGCACAAAGTTGTAGTCACAGCCATTGC
Found at i:307177 original size:17 final size:17
Alignment explanation
Indices: 307134--307177 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
307124 TTTCACCTTG
307134 AAGAGGAAGAAGAAGAA
1 AAGAGGAAGAAGAAGAA
* * *
307151 GAGAGAAAGATGAAGAA
1 AAGAGGAAGAAGAAGAA
*
307168 AAGGGGAAGA
1 AAGAGGAAGA
307178 GTGTTTGGTG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (17 bp):
AAGAGGAAGAAGAAGAA
Found at i:315638 original size:58 final size:58
Alignment explanation
Indices: 315548--315660 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
315538 GATGCCCCTC
* * *
315548 TGCCCACATCACAATTTTCTGTAGGAAAATGATTGGTTGCATAGGGAATGATCAACTT
1 TGCCCACATCACAATTTTCTGCAGGAAAATGATTGGTTACATAGAGAATGATCAACTT
315606 TGCCCACATCACAATTTTCTGCAGGAAAATGATTGGTTACATAGAGAATGATCAA
1 TGCCCACATCACAATTTTCTGCAGGAAAATGATTGGTTACATAGAGAATGATCAA
315661 TTGTTGATCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (58 bp):
TGCCCACATCACAATTTTCTGCAGGAAAATGATTGGTTACATAGAGAATGATCAACTT
Found at i:325203 original size:33 final size:33
Alignment explanation
Indices: 325166--325228 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
325156 TTAACTTCTT
325166 GATTGACATACTGAATCTTAAGACTCGGGTCTC
1 GATTGACATACTGAATCTTAAGACTCGGGTCTC
*
325199 GATTGACATATTGAATCTTAAGACTCGGGT
1 GATTGACATACTGAATCTTAAGACTCGGGT
325229 ATCAATGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (33 bp):
GATTGACATACTGAATCTTAAGACTCGGGTCTC
Found at i:332462 original size:75 final size:75
Alignment explanation
Indices: 332249--332460 Score: 255
Period size: 75 Copynumber: 2.8 Consensus size: 75
332239 CAATTCAAAG
* * * * *
332249 CCAAAAATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTG
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGA-T-CCCCCCATAGGAGGAACCGATTCCCCCCTA
**
332314 AATGGTTTGGCT
64 AACAGTTTGGCT
* *
332326 CCAAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCCTAAA
* * *
332391 CATTTTTGTT
66 CAGTTTGGCT
* * * *
332401 CCGAGAATTCCAGTATGCTCGGAGGGAACCGATCCCCCCA-AGGGGGTACCGATTCCCCCC
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCC
332461 CTGTTCAACG
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
74 18 0.15
75 71 0.61
76 1 0.01
77 27 0.23
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (75 bp):
CCAAGAATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCCTAAA
CAGTTTGGCT
Found at i:338301 original size:21 final size:21
Alignment explanation
Indices: 338275--338314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
338265 CCCCCTTTGA
*
338275 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
338296 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
338315 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:341039 original size:74 final size:74
Alignment explanation
Indices: 340891--341074 Score: 251
Period size: 74 Copynumber: 2.5 Consensus size: 74
340881 CAAAGCCAAA
* * * * **
340891 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
340956 TTGGCTCCGAG
64 TTGGCTCCGAG
* *
340967 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACATTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
341032 TGTTCCGAG
66 GGCTCCGAG
*
341041 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
341075 CTGTTCAACG
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 71 0.74
76 25 0.26
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:350275 original size:18 final size:18
Alignment explanation
Indices: 350223--350266 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
350213 TGCAAGACTC
350223 TCTGCTTTACAATTCTTT
1 TCTGCTTTACAATTCTTT
350241 TCTGCTTTACAATTCTTT
1 TCTGCTTTACAATTCTTT
350259 TCTGCTTT
1 TCTGCTTT
350267 CTGTTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.57
Consensus pattern (18 bp):
TCTGCTTTACAATTCTTT
Found at i:356931 original size:20 final size:21
Alignment explanation
Indices: 356884--356931 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
356874 ATGAAATTTT
*
356884 TCCCGAAGGACCTCATGTATG
1 TCCCGAAGGACCTCATGTATA
* *
356905 TCTCGAAGGATCT-ATGTATA
1 TCCCGAAGGACCTCATGTATA
356925 TCCCGAA
1 TCCCGAA
356932 ACCCTATGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
TCCCGAAGGACCTCATGTATA
Found at i:358773 original size:31 final size:31
Alignment explanation
Indices: 358700--358778 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
358690 ATATAATAAG
* ** *
358700 TCGGGTTGGGTCAATATTGGATCGGTTGATT
1 TCGGGTTGGATCAATATCAGATCGATTGATT
* *
358731 TTGGGTCGGATCAA-ATCAGATCGATTGACTT
1 TCGGGTTGGATCAATATCAGATCGATTGA-TT
358762 TCGGGTTGGATCAATAT
1 TCGGGTTGGATCAATAT
358779 TCGATCAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 11 0.29
31 25 0.66
32 2 0.05
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (31 bp):
TCGGGTTGGATCAATATCAGATCGATTGATT
Found at i:359222 original size:20 final size:21
Alignment explanation
Indices: 359182--359225 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
359172 GTATAATTAA
359182 AAATTAATTAAAATTTAAAGGT
1 AAATTAATTAAAA-TTAAAGGT
*
359204 AAATTATTTAAAA-TAAAGGT
1 AAATTAATTAAAATTAAAGGT
359224 AA
1 AA
359226 GCTATATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATTAATTAAAATTAAAGGT
Found at i:359949 original size:32 final size:30
Alignment explanation
Indices: 359900--360014 Score: 88
Period size: 32 Copynumber: 3.6 Consensus size: 30
359890 CAGTACAATT
* *
359900 GTGTCGCCATCCCTTCCATGCGATACCAAAGG
1 GTGTCGCCATGCTTTCCA-GCGATACCAAA-G
* *
359932 GTGTCGCCATGCTTTCCAGCCAACACCCAAAG
1 GTGTCGCCATGCTTTCCAG-CGATA-CCAAAG
* *
359964 GTGTCGCCA-GCTGTTCCAAGCGACTCCCAACG
1 GTGTCGCCATGCT-TTCC-AGCGA-TACCAAAG
* *
359996 GTGTTGCCATGCATTCCAG
1 GTGTCGCCATGCTTTCCAG
360015 ACGAATCCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
31 6 0.09
32 52 0.78
33 9 0.13
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.22
Consensus pattern (30 bp):
GTGTCGCCATGCTTTCCAGCGATACCAAAG
Found at i:361188 original size:22 final size:22
Alignment explanation
Indices: 361163--361204 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
361153 TATATATCTT
* *
361163 TATAATGTAAAATAAGTTATAG
1 TATAATATAAAACAAGTTATAG
*
361185 TATAGTATAAAACAAGTTAT
1 TATAATATAAAACAAGTTAT
361205 TTTTTATATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (22 bp):
TATAATATAAAACAAGTTATAG
Found at i:362591 original size:23 final size:23
Alignment explanation
Indices: 362544--362591 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
362534 AATAACATAT
**
362544 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
362567 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
362590 TA
1 TA
362592 AGCATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Done.