Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 99 of 161
Found at i:31234160 original size:14 final size:14
Alignment explanation
Indices: 31234141--31234169 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31234131 GTTCTTCGTG
31234141 AAAATCTTAAGGGA
1 AAAATCTTAAGGGA
31234155 AAAATCTTAAGGGA
1 AAAATCTTAAGGGA
31234169 A
1 A
31234170 TTCTATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAATCTTAAGGGA
Found at i:31238517 original size:30 final size:29
Alignment explanation
Indices: 31238475--31238548 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
31238465 ATATCAAAAC
*
31238475 TATAC-TTAAAATTTGACCTAATGTGCAATTT
1 TATACATT-AAATTTGA--TAATGTACAATTT
**
31238506 TATACA-TAAATTGTGATTTTGTACAATTT
1 TATACATTAAATT-TGATAATGTACAATTT
31238535 TATACATTAAATTT
1 TATACATTAAATTT
31238549 TGATTTGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 17 0.46
30 11 0.30
31 9 0.24
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (29 bp):
TATACATTAAATTTGATAATGTACAATTT
Found at i:31241031 original size:76 final size:76
Alignment explanation
Indices: 31240907--31241053 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
31240897 TCGAAACATT
* * * * *
31240907 TGAAGTATATATATTGCGCCCAACACTTATAGGTGTAACCGAAGTAAAATGTATGCCCA-ACACT
1 TGAAGTATATAAATTGCGCCCAACACCTATAGGTATAACCGAAGTAAAAGGTATACCCAGA-ACT
31240971 CATCAGAGCGTC
65 CATCAGAGCGTC
** ** *
31240983 TGAAGTATATAAATTGCGCCCAATGCCTATCA-GTATAATTGAATTAAAAGGTATACCCAGAACT
1 TGAAGTATATAAATTGCGCCCAACACCTAT-AGGTATAACCGAAGTAAAAGGTATACCCAGAACT
31241047 CATCAGA
65 CATCAGA
31241054 ATGTCAAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
76 57 0.97
77 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (76 bp):
TGAAGTATATAAATTGCGCCCAACACCTATAGGTATAACCGAAGTAAAAGGTATACCCAGAACTC
ATCAGAGCGTC
Found at i:31241823 original size:43 final size:42
Alignment explanation
Indices: 31241753--31241851 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 42
31241743 CTGTAAGGGT
*
31241753 CACACGACCGTGTAGCTAAGCCATGTAACTCACATGGCTGAGA
1 CACACG-CCGTGTAGCTAAGCCATGTAACTCACACGGCTGAGA
* ** *
31241796 CACACAGCCGTGTAGCTAGGCTGTGTAAGTCACACGGCTGAGA
1 CACAC-GCCGTGTAGCTAAGCCATGTAACTCACACGGCTGAGA
31241839 CACACGCTCGTGT
1 CACACGC-CGTGT
31241852 CTCAGGCCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 46 0.94
44 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (42 bp):
CACACGCCGTGTAGCTAAGCCATGTAACTCACACGGCTGAGA
Found at i:31242255 original size:20 final size:20
Alignment explanation
Indices: 31242230--31242277 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
31242220 AAAACATGAA
31242230 CATAACTTACCATTTCAATG
1 CATAACTTACCATTTCAATG
31242250 CATAACTTACCATTTCAATG
1 CATAACTTACCATTTCAATG
31242270 CATAACTT
1 CATAACTT
31242278 TAATACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (20 bp):
CATAACTTACCATTTCAATG
Found at i:31248684 original size:26 final size:27
Alignment explanation
Indices: 31248640--31248703 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
31248630 TACAAATTTT
*
31248640 GCCACAAAGGCATTCCTTTCATATTCC
1 GCCACAAAGGCATTCCTTTCATATTAC
* *
31248667 GCCACAAGGGC-TTTCTTTCATATTAC
1 GCCACAAAGGCATTCCTTTCATATTAC
31248693 GCCACAAAGGC
1 GCCACAAAGGC
31248704 CTTTTTCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (27 bp):
GCCACAAAGGCATTCCTTTCATATTAC
Found at i:31257970 original size:28 final size:28
Alignment explanation
Indices: 31257927--31257987 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
31257917 CTAGGTGTGG
* *
31257927 GAATGGAAAAGGCTAAGAGAAAAAGTGA
1 GAATGGAAAAGCCTAAGAGAAAAAGAGA
31257955 GAATGGAAAAGCCTAAGAGAAAAAGAGA
1 GAATGGAAAAGCCTAAGAGAAAAAGAGA
31257983 GAATG
1 GAATG
31257988 ATGCTTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.54, C:0.05, G:0.31, T:0.10
Consensus pattern (28 bp):
GAATGGAAAAGCCTAAGAGAAAAAGAGA
Found at i:31261791 original size:130 final size:130
Alignment explanation
Indices: 31261614--31261877 Score: 465
Period size: 130 Copynumber: 2.0 Consensus size: 130
31261604 TCTTTGATCT
* *
31261614 TTCTTTACTCATTTTGGCATTCTCATAGGAAAACAACCTCAGCTCTTCCAACTCATCAAGTTGTA
1 TTCTTTACACATTTTCGCATTCTCATAGGAAAACAACCTCAGCTCTTCCAACTCATCAAGTTGTA
*
31261679 ACATCCTTCTCTGACCCACTTGCTTAAGATCAAAGTTCAATTGCTTCAAAGTCCAATGAGCTTTA
66 ACATCCTTCTCTGACCCACTTGCTTAAGATCAAAGTTCAATTGCTTCAAAGCCCAATGAGCTTTA
* *
31261744 TTCTTTACACATTTTCGCATTCTCATTGGAAAACAACCTCAGTTCTTCCAACTCATCAAGTTGTA
1 TTCTTTACACATTTTCGCATTCTCATAGGAAAACAACCTCAGCTCTTCCAACTCATCAAGTTGTA
* *
31261809 ACATCCTTCTCTGACCCACTTTCTTAAGATCAAAGTTCAATTGCTTCAAAGCCCAATGATCTTTA
66 ACATCCTTCTCTGACCCACTTGCTTAAGATCAAAGTTCAATTGCTTCAAAGCCCAATGAGCTTTA
31261874 TTCT
1 TTCT
31261878 CTAACTCTAA
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (130 bp):
TTCTTTACACATTTTCGCATTCTCATAGGAAAACAACCTCAGCTCTTCCAACTCATCAAGTTGTA
ACATCCTTCTCTGACCCACTTGCTTAAGATCAAAGTTCAATTGCTTCAAAGCCCAATGAGCTTTA
Found at i:31273628 original size:43 final size:43
Alignment explanation
Indices: 31273515--31273629 Score: 101
Period size: 43 Copynumber: 2.7 Consensus size: 43
31273505 TGAGATTTAG
* * * *
31273515 TGTAAGACCACGTCTGGGATGTTGGCATCGATTGGAAACTTTCG
1 TGTAAGACCACATCTGGGACGTTGGCATCGATTGG-AACTTACA
* ** *
31273559 TGTAAGACC-CTATCTCGGACAATGGCATCGATATTTG-A-TTACA
1 TGTAAGACCAC-ATCTGGGACGTTGGCATCG--ATTGGAACTTACA
31273602 TGTAAGACCACATCTGGGACGTTGGCAT
1 TGTAAGACCACATCTGGGACGTTGGCAT
31273630 TGTACGAGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
43 27 0.48
44 25 0.45
46 4 0.07
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACATCTGGGACGTTGGCATCGATTGGAACTTACA
Found at i:31281197 original size:15 final size:15
Alignment explanation
Indices: 31281177--31281206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31281167 AAAAAATGGG
*
31281177 GAAAAAGAAAGAATA
1 GAAAAAAAAAGAATA
31281192 GAAAAAAAAAGAATA
1 GAAAAAAAAAGAATA
31281207 AACATATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
GAAAAAAAAAGAATA
Found at i:31286003 original size:14 final size:14
Alignment explanation
Indices: 31285984--31286016 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
31285974 CATTCTTATT
31285984 CTTTGTCGTAGTAA
1 CTTTGTCGTAGTAA
31285998 CTTTGTCGTAGTAA
1 CTTTGTCGTAGTAA
31286012 CTTTG
1 CTTTG
31286017 CCATAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (14 bp):
CTTTGTCGTAGTAA
Found at i:31289596 original size:9 final size:9
Alignment explanation
Indices: 31289581--31289620 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
31289571 AGGAAATTCC
31289581 ATTAGGTTA
1 ATTAGGTTA
*
31289590 GTTAGGTTA
1 ATTAGGTTA
*
31289599 ATTAAGTTA
1 ATTAGGTTA
*
31289608 ATTAGTTTA
1 ATTAGGTTA
31289617 ATTA
1 ATTA
31289621 ATATTTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
ATTAGGTTA
Found at i:31290239 original size:21 final size:21
Alignment explanation
Indices: 31290204--31290244 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31290194 ATTAAGCGGC
*
31290204 CAATATCCGAACGATTGGAGA
1 CAATATCCGAACGATGGGAGA
31290225 CAATATCC-AATCGATGGGAG
1 CAATATCCGAA-CGATGGGAG
31290245 GTTATGTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
CAATATCCGAACGATGGGAGA
Found at i:31290493 original size:18 final size:18
Alignment explanation
Indices: 31290466--31290500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31290456 ACAATTCATA
31290466 TAGAGCTAGACGTAGCAG
1 TAGAGCTAGACGTAGCAG
* *
31290484 TAGAGGTAGAGGTAGCA
1 TAGAGCTAGACGTAGCA
31290501 TTGATAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.37, T:0.17
Consensus pattern (18 bp):
TAGAGCTAGACGTAGCAG
Found at i:31293629 original size:17 final size:18
Alignment explanation
Indices: 31293609--31293642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31293599 TAGAATTTGG
31293609 TTGA-AAAAATAATTTAA
1 TTGACAAAAATAATTTAA
*
31293626 TTGACAAAATTAATTTA
1 TTGACAAAAATAATTTA
31293643 GTTAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
TTGACAAAAATAATTTAA
Found at i:31297657 original size:13 final size:13
Alignment explanation
Indices: 31297635--31297665 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31297625 TGACTTAGGT
31297635 CACACAGCCAAGC
1 CACACAGCCAAGC
*
31297648 CACACGGCCAAGC
1 CACACAGCCAAGC
31297661 CACAC
1 CACAC
31297666 CCTTGTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (13 bp):
CACACAGCCAAGC
Found at i:31298717 original size:29 final size:29
Alignment explanation
Indices: 31298674--31298918 Score: 242
Period size: 29 Copynumber: 8.4 Consensus size: 29
31298664 AGTGTGCTAA
*
31298674 CGATGGTCGTAACCATCCCTTTTCATATT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* *
31298703 CGATGGCCGTCACCATCCCTTTTCATTAAT
1 CGATGGTCGTCACCATCCCTTTTCA-TATT
31298733 CGATGGTCGTCACCATCCCTTTTCATATT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* * ** * * *
31298762 TGATAGTCGAAACTATCTCTTTTCATATA
1 CGATGGTCGTCACCATCCCTTTTCATATT
31298791 CGATGGTCGTCACCATCCCTTTTCATAATT
1 CGATGGTCGTCACCATCCCTTTTCAT-ATT
*
31298821 -GATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* *** * *
31298849 CGATAGTCAAAACTATCCCTTTTCATAGT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* ** *
31298878 CAATGGTC-AAATCCATCCCTTTTCATTAAT
1 CGATGGTCGTCA-CCATCCCTTTTCA-TATT
*
31298908 CGATGATCGTC
1 CGATGGTCGTC
31298919 GATACACCGT
Statistics
Matches: 176, Mismatches: 34, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
28 5 0.03
29 133 0.76
30 38 0.22
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
CGATGGTCGTCACCATCCCTTTTCATATT
Found at i:31298862 original size:87 final size:87
Alignment explanation
Indices: 31298688--31298918 Score: 322
Period size: 87 Copynumber: 2.6 Consensus size: 87
31298678 GGTCGTAACC
*
31298688 ATCCCTTTTCATATTCGATGGCCGTCACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCT
1 ATCCCTTTTCATA-TCGATGGTCGTCACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCT
* * *
31298753 TTTCATATTTGATAGTCGAAACT
65 TTTCATAATCGATAGTCAAAACT
* *
31298776 ATCTCTTTTCATATACGATGGTCGTCACCATCCCTTTTCA-TAATTGATGGTCGTCACCATCCCT
1 ATCCCTTTTCATAT-CGATGGTCGTCACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCT
31298840 TTTCATAATCGATAGTCAAAACT
65 TTTCATAATCGATAGTCAAAACT
* ** *
31298863 ATCCCTTTTCATAGTCAATGGTC-AAATCCATCCCTTTTCATTAATCGATGATCGTC
1 ATCCCTTTTCATA-TCGATGGTCGTCA-CCATCCCTTTTCATTAATCGATGGTCGTC
31298919 GATACACCGT
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
86 1 0.01
87 76 0.60
88 50 0.39
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (87 bp):
ATCCCTTTTCATATCGATGGTCGTCACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTT
TTCATAATCGATAGTCAAAACT
Found at i:31301899 original size:29 final size:29
Alignment explanation
Indices: 31301811--31301900 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
31301801 GTGTGCTAAG
* *
31301811 GATGGTCGTAACCATCCCA-TTTCATATTC
1 GATGGTCGTCACCAT-CCATTTTCATATTT
* *
31301840 GATGGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCATTTTCATATTT
*
31301869 GATGGTCGTCACCATCCATTTTTATATTT
1 GATGGTCGTCACCATCCATTTTCATATTT
31301898 GAT
1 GAT
31301901 TGTCAAAACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
28 2 0.04
29 51 0.96
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (29 bp):
GATGGTCGTCACCATCCATTTTCATATTT
Found at i:31301968 original size:29 final size:29
Alignment explanation
Indices: 31301934--31302005 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
31301924 ATGGCCGTTA
31301934 CCATCCCTTTTCATAATCGATAGTTGAAA-
1 CCATCCCTTTTCATAATCGATAGTT-AAAT
* * *
31301963 CTATCCCTTTTCATAGTCGATGGTTAAAT
1 CCATCCCTTTTCATAATCGATAGTTAAAT
*
31301992 CCATCCATTTTCAT
1 CCATCCCTTTTCAT
31302006 TCATCGATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (29 bp):
CCATCCCTTTTCATAATCGATAGTTAAAT
Found at i:31307018 original size:14 final size:13
Alignment explanation
Indices: 31306995--31307024 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
31306985 TTTGAGTGAT
31306995 GATTATTTAACTA
1 GATTATTTAACTA
31307008 GATTAATTTAACTA
1 GATT-ATTTAACTA
31307022 GAT
1 GAT
31307025 GCAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (13 bp):
GATTATTTAACTA
Found at i:31309226 original size:28 final size:27
Alignment explanation
Indices: 31309195--31309248 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
31309185 CGATTACTTG
*
31309195 AATTTAACAACTCATAATTAATTAATTT
1 AATTTAACAACTCAT-ACTAATTAATTT
* *
31309223 AATTTGATAACTCATACTAATTAATT
1 AATTTAACAACTCATACTAATTAATT
31309249 GAGTCTGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (27 bp):
AATTTAACAACTCATACTAATTAATTT
Found at i:31309348 original size:141 final size:143
Alignment explanation
Indices: 31309151--31309445 Score: 396
Period size: 145 Copynumber: 2.1 Consensus size: 143
31309141 TAAATAATTT
* * * * *
31309151 TACTATGAATTTGAAACATCATAAATTTACAAATCGATTACTTGAATTTAACAACTC-AT-AATT
1 TACTATGAACTCGGAACATCATAAACTTACAAATCGATTACTTGAATTCAACAACTCAATAAATT
* * *
31309214 AATTAATTTAATTTGATAACTCATACTAATTAATTGAGTCTGTTAGATCTATGATTGATCATGTG
66 AATTAATTTAATTTGATAACTCATACTAATTAATTGAGCCTGTTAGATCTAAGATTAATCATGTG
31309279 TAAGAATCTATTA
131 TAAGAATCTATTA
* * * * *
31309292 TTCTATGAACTCGGAACATCATAAACTTATAAATTGATTATTTGAATTCAATAACTCATGATAAA
1 TACTATGAACTCGGAACATCATAAACTTACAAATCGATTACTTGAATTCAACAACTCA--ATAAA
* * *
31309357 TTAATTAATTTAATTTGATAACTCATATTGATTAATTGAGCCTGTTAGATTTAAGATTAATCATG
64 TTAATTAATTTAATTTGATAACTCATACTAATTAATTGAGCCTGTTAGATCTAAGATTAATCATG
* *
31309422 TGTAAGAATGTATTC
129 TGTAAGAATCTATTA
31309437 TACTATGAA
1 TACTATGAA
31309446 TTCACTGCAG
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
141 47 0.36
144 2 0.02
145 82 0.63
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (143 bp):
TACTATGAACTCGGAACATCATAAACTTACAAATCGATTACTTGAATTCAACAACTCAATAAATT
AATTAATTTAATTTGATAACTCATACTAATTAATTGAGCCTGTTAGATCTAAGATTAATCATGTG
TAAGAATCTATTA
Found at i:31309356 original size:32 final size:32
Alignment explanation
Indices: 31309320--31309382 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
31309310 TCATAAACTT
*
31309320 ATAAATTGATT-ATTTGAATTCAATAACTCATG
1 ATAAATTAATTAATTT-AATTCAATAACTCATG
**
31309352 ATAAATTAATTAATTTAATTTGATAACTCAT
1 ATAAATTAATTAATTTAATTCAATAACTCAT
31309383 ATTGATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTTAATTCAATAACTCATG
Found at i:31309667 original size:43 final size:43
Alignment explanation
Indices: 31309620--31309807 Score: 214
Period size: 43 Copynumber: 4.4 Consensus size: 43
31309610 ACACTATACC
* * * *
31309620 CACAAATGCCATTAAAGAACATAATCTTTAGCGACGCTTTTAT
1 CACAAACGCCACTAAAGAACATAACCTTTAGCGACACTTTTAT
* * * *
31309663 CACAAACACCGCTAAAGAGCATAACCTTTAGCTACACTTTTAT
1 CACAAACGCCACTAAAGAACATAACCTTTAGCGACACTTTTAT
* * ***
31309706 CACAAACGCCACTAAAGAACATAACATTTAGCAATGTTTTTAT
1 CACAAACGCCACTAAAGAACATAACCTTTAGCGACACTTTTAT
* * *
31309749 CACAAACGCCGCTAAAGAACATAACCTTTAACGGCACTTTTAT
1 CACAAACGCCACTAAAGAACATAACCTTTAGCGACACTTTTAT
* *
31309792 TACAAACGCCGCTAAA
1 CACAAACGCCACTAAA
31309808 AGTACCAAAT
Statistics
Matches: 120, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 120 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (43 bp):
CACAAACGCCACTAAAGAACATAACCTTTAGCGACACTTTTAT
Found at i:31309710 original size:86 final size:86
Alignment explanation
Indices: 31309585--31309807 Score: 254
Period size: 86 Copynumber: 2.6 Consensus size: 86
31309575 GACAAAAATG
* * * * * *
31309585 CCGCTATAGAGCATGACCTTTAG-TAACAC-TATACCCACAAATGCCATTAAAGAACATAATC-T
1 CCGCTAAAGAGCATAACCTTTAGCT-ACACTTTTA-TCACAAACGCCACTAAAGAACATAA-CAT
*
31309647 TTAGCGACGCTTTTATCACAAACA
63 TTAGCAACGCTTTTATCACAAACA
31309671 CCGCTAAAGAGCATAACCTTTAGCTACACTTTTATCACAAACGCCACTAAAGAACATAACATTTA
1 CCGCTAAAGAGCATAACCTTTAGCTACACTTTTATCACAAACGCCACTAAAGAACATAACATTTA
* * *
31309736 GCAATGTTTTTATCACAAACG
66 GCAACGCTTTTATCACAAACA
* * ** * *
31309757 CCGCTAAAGAACATAACCTTTAACGGCACTTTTATTACAAACGCCGCTAAA
1 CCGCTAAAGAGCATAACCTTTAGCTACACTTTTATCACAAACGCCACTAAA
31309808 AGTACCAAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
85 1 0.01
86 113 0.96
87 4 0.03
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (86 bp):
CCGCTAAAGAGCATAACCTTTAGCTACACTTTTATCACAAACGCCACTAAAGAACATAACATTTA
GCAACGCTTTTATCACAAACA
Found at i:31311328 original size:98 final size:98
Alignment explanation
Indices: 31311149--31311345 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
31311139 ATACAATAAA
* *
31311149 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACGTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
31311214 CCTCTAGAATCCCAAACTCGGAATATTTTCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
31311247 ACTTTAAAAGAACATCCACGTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACGTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
31311312 CCTTTAAAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
31311345 A
1 A
31311346 TTATTTTAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACGTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:31312701 original size:19 final size:19
Alignment explanation
Indices: 31312677--31312749 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
31312667 AATTATATAT
31312677 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
31312696 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
31312715 TCTAAGATTGCATATTATA
1 TCTAAGATTGCATATCATA
*
31312734 TCTAAGATTGTATATC
1 TCTAAGATTGCATATC
31312750 CTCAAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:31312723 original size:38 final size:37
Alignment explanation
Indices: 31312670--31312749 Score: 126
Period size: 38 Copynumber: 2.2 Consensus size: 37
31312660 ATTACAAAAT
31312670 TATAT-ATTCTAAGATTGCATATCATATCTAAGATTA
1 TATATCATTCTAAGATTGCATATCATATCTAAGATTA
* *
31312706 TATATCATATCTAAGATTGCATATTATATCTAAGATTG
1 TATATCAT-TCTAAGATTGCATATCATATCTAAGATTA
31312744 TATATC
1 TATATC
31312750 CTCAAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 5 0.12
37 2 0.05
38 33 0.82
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (37 bp):
TATATCATTCTAAGATTGCATATCATATCTAAGATTA
Found at i:31315379 original size:19 final size:19
Alignment explanation
Indices: 31315355--31315403 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
31315345 TAACATTATA
*
31315355 ATTTTTAGTTTTTGTATTTT
1 ATTTTTA-TTTTTGCATTTT
31315375 ATTTTTATTTTTGCATTTT
1 ATTTTTATTTTTGCATTTT
*
31315394 ATTTTCATTT
1 ATTTTTATTT
31315404 GTTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGCATTTT
Found at i:31315805 original size:7 final size:7
Alignment explanation
Indices: 31315795--31315871 Score: 57
Period size: 7 Copynumber: 10.9 Consensus size: 7
31315785 TTATAAAACA
31315795 TAAACCC
1 TAAACCC
31315802 TAAACCC
1 TAAACCC
*
31315809 TAAACTC
1 TAAACCC
*
31315816 TTAACCC
1 TAAACCC
*
31315823 TTAACCCC
1 -TAAACCC
*
31315831 TAAACCT
1 TAAACCC
31315838 TAAACCC
1 TAAACCC
*
31315845 -CAACCC
1 TAAACCC
* *
31315851 TTACACCA
1 -TAAACCC
*
31315859 TAAACCA
1 TAAACCC
31315866 TAAACC
1 TAAACC
31315872 ATAATCTCTA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
6 5 0.09
7 41 0.76
8 8 0.15
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:31315821 original size:21 final size:21
Alignment explanation
Indices: 31315797--31315840 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
31315787 ATAAAACATA
31315797 AACCC-TAAACCCTAAACTCTT
1 AACCCTTAAACCCTAAAC-CTT
*
31315818 AACCCTTAACCCCTAAACCTT
1 AACCCTTAAACCCTAAACCTT
31315839 AA
1 AA
31315841 ACCCCAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTTAAACCCTAAACCTT
Found at i:31315871 original size:28 final size:28
Alignment explanation
Indices: 31315818--31315871 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
31315808 CTAAACTCTT
* *
31315818 AACCCTTAACCCCTAAACCTTAAACCCC
1 AACCCTTAACCCATAAACCATAAACCCC
31315846 AACCCTT-ACACCATAAACCATAAACC
1 AACCCTTAAC-CCATAAACCATAAACC
31315872 ATAATCTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.17
Consensus pattern (28 bp):
AACCCTTAACCCATAAACCATAAACCCC
Found at i:31315905 original size:7 final size:7
Alignment explanation
Indices: 31315795--31315905 Score: 53
Period size: 7 Copynumber: 15.6 Consensus size: 7
31315785 TTATAAAACA
*
31315795 TAAACCC
1 TAAACCT
*
31315802 TAAACCC
1 TAAACCT
31315809 TAAACTCT
1 TAAAC-CT
*
31315817 TAACCCT
1 TAAACCT
* *
31315824 TAACCCC
1 TAAACCT
31315831 TAAACCT
1 TAAACCT
*
31315838 TAAACCC
1 TAAACCT
* *
31315845 CAACCCT
1 TAAACCT
* *
31315852 TACACCA
1 TAAACCT
*
31315859 TAAACCA
1 TAAACCT
*
31315866 TAAACCA
1 TAAACCT
*
31315873 T-AATCT
1 TAAACCT
31315879 CTAAACTCT
1 -TAAAC-CT
* *
31315888 TAATCCA
1 TAAACCT
31315895 TAAACCT
1 TAAACCT
31315902 TAAA
1 TAAA
31315906 ATAGTAACTC
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
6 3 0.04
7 63 0.80
8 11 0.14
9 2 0.03
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:31316042 original size:7 final size:7
Alignment explanation
Indices: 31316030--31316146 Score: 60
Period size: 7 Copynumber: 16.6 Consensus size: 7
31316020 AAACACTAAT
31316030 TAAACCC
1 TAAACCC
31316037 TAAACCC
1 TAAACCC
* *
31316044 TTATCTCC
1 TAAAC-CC
31316052 TAAACCC
1 TAAACCC
* *
31316059 TAAATCA
1 TAAACCC
*
31316066 TAAACCA
1 TAAACCC
*
31316073 TAAAACC
1 TAAACCC
31316080 TAAACCCC
1 TAAA-CCC
*
31316088 T-AATCC
1 TAAACCC
*
31316094 TAACCCC
1 TAAACCC
31316101 TAAATCCC
1 TAAA-CCC
31316109 --AACCC
1 TAAACCC
*
31316114 TTAAACCA
1 -TAAACCC
*
31316122 TAAACCA
1 TAAACCC
* *
31316129 TAATCCT
1 TAAACCC
*
31316136 TAAACCA
1 TAAACCC
31316143 TAAA
1 TAAA
31316147 ACTCGATCTA
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
5 3 0.04
6 5 0.06
7 61 0.73
8 15 0.18
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:31316071 original size:14 final size:14
Alignment explanation
Indices: 31316030--31316146 Score: 71
Period size: 14 Copynumber: 8.3 Consensus size: 14
31316020 AAACACTAAT
*
31316030 TAAACCCTAAACCC
1 TAAATCCTAAACCC
**
31316044 TTATCTCCTAAACCC
1 -TAAATCCTAAACCC
* *
31316059 TAAATCATAAACCA
1 TAAATCCTAAACCC
*
31316073 TAAAACCTAAACCCC
1 TAAATCCTAAA-CCC
*
31316088 T-AATCCTAACCCC
1 TAAATCCTAAACCC
*
31316101 TAAATCC-CAACCC
1 TAAATCCTAAACCC
*
31316114 TTAAA-CCATAAACCA
1 -TAAATCC-TAAACCC
*
31316129 T-AATCCTTAAACCA
1 TAAATCC-TAAACCC
31316143 TAAA
1 TAAA
31316147 ACTCGATCTA
Statistics
Matches: 78, Mismatches: 17, Indels: 14
0.72 0.16 0.13
Matches are distributed among these distances:
13 12 0.15
14 46 0.59
15 20 0.26
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAATCCTAAACCC
Found at i:31321552 original size:64 final size:64
Alignment explanation
Indices: 31321447--31321566 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 64
31321437 CCTATATTGG
* * * *
31321447 GACGCTCATAAAGAGCTGCGGTATGTCCGCAATATAAGCAGGATCAATACCGATCATATAACAA
1 GACGCTCACAAAGAGCTGCGGTATATCCGCAACACAAGCAGGATCAATACCGATCATATAACAA
*
31321511 GACGCTCACAAAGAGCTGCGGTATATCCGCAACACATGCAGGATCAATACCGATCA
1 GACGCTCACAAAGAGCTGCGGTATATCCGCAACACAAGCAGGATCAATACCGATCA
31321567 GGATGCTCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (64 bp):
GACGCTCACAAAGAGCTGCGGTATATCCGCAACACAAGCAGGATCAATACCGATCATATAACAA
Found at i:31324179 original size:51 final size:51
Alignment explanation
Indices: 31324057--31324295 Score: 252
Period size: 51 Copynumber: 4.7 Consensus size: 51
31324047 TATCATTCAA
* * * *
31324057 TACACGTAGTAGCCTTCACTTAGTACTACACACGTGATCA-AACTTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATCCGG
* *
31324107 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TAACTATCCGG
* * * *
31324158 TACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATCCGG
* * * * * **
31324209 TGCGCATAGTAGCCTGCACATAGTACTACACATGAGACC-TTTC-ATTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTA-TCCGG
* * *
31324259 TACACGTAGTAGCCTTCACATAGTACTGCACATGTGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA
31324296 TCATCACTTT
Statistics
Matches: 156, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 74 0.47
51 79 0.51
52 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATCCGG
Found at i:31324268 original size:101 final size:102
Alignment explanation
Indices: 31324056--31324298 Score: 337
Period size: 101 Copynumber: 2.4 Consensus size: 102
31324046 TTATCATTCA
* * * *
31324056 ATACACGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAACTTTCCGGTTCACGTAGTAGC
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAACTATCCGGTGCACATAGTAGC
*
31324120 CTGCACATAGTACTACACACGTGACCATTAATATCCG
66 CTGCACATAGTACTACACACGAGACCATTAATATCCG
* * * *
31324157 ATACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCTGGTGCGCATAGTAGC
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAACTATCCGGTGCACATAGTAGC
* * *
31324222 CTGCACATAGTACTACACATGAGACCTTTCAT-TCCG
66 CTGCACATAGTACTACACACGAGACCATTAATATCCG
* * *
31324258 GTACACGTAGTAGCCTTCACATAGTACTGCACATGTGATCA
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA
31324299 TCACTTTCAC
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
101 77 0.62
102 47 0.38
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (102 bp):
ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAACTATCCGGTGCACATAGTAGC
CTGCACATAGTACTACACACGAGACCATTAATATCCG
Found at i:31329970 original size:144 final size:144
Alignment explanation
Indices: 31329784--31330045 Score: 327
Period size: 144 Copynumber: 1.8 Consensus size: 144
31329774 TGAAATGTAG
* * ** *
31329784 AAAGTGAAGAATTCAGTTTCAACCAAAACCCTGGTTTTCTTTTTCTATTAAAAA-TGA-GCAACC
1 AAAGTGAAGAATTCAGTTACAACCAAAACCCTGATTCACTTTTTCTAGTAAAAAGT-ATGC-ACC
* * * *
31329847 A-TCTATATCA-TATTCAAATCAAAATCTTTTTTTCTGATGAAAATATAGTCCAACAATCTACAT
64 ACTCTAGAT-AGTATTCAAATCAAAAT-ATTTTTTATGATGAAAATAAAGTCCAACAATCTACAT
31329910 AGGCTATTCAAAACATGA
127 AGGCTATTCAAAACATGA
* * *
31329928 AAAGTGAAGAATTCAGTTACAACTAAAACCCAT-ATTCACTTTTTCTAGTAACAAGTATGCATCA
1 AAAGTGAAGAATTCAGTTACAACCAAAACCC-TGATTCACTTTTTCTAGTAAAAAGTATGCACCA
*
31329992 CTCTAGATAGTATTCAAATCCAAATATTTTTTATGATGAAAATAAAGTCCAACA
65 CTCTAGATAGTATTCAAATCAAAATATTTTTTATGATGAAAATAAAGTCCAACA
31330046 GTTTTTACAG
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
144 76 0.76
145 24 0.24
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (144 bp):
AAAGTGAAGAATTCAGTTACAACCAAAACCCTGATTCACTTTTTCTAGTAAAAAGTATGCACCAC
TCTAGATAGTATTCAAATCAAAATATTTTTTATGATGAAAATAAAGTCCAACAATCTACATAGGC
TATTCAAAACATGA
Found at i:31333719 original size:28 final size:29
Alignment explanation
Indices: 31333679--31333733 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
31333669 TTTATTTAAA
31333679 GTTTAAGAATTTT-AAAAAATAAATTAGG
1 GTTTAAGAATTTTCAAAAAATAAATTAGG
* *
31333707 GTTT-AGAATTTTTCTAAAAATTAATTA
1 GTTTAAGAA-TTTTCAAAAAATAAATTA
31333734 AATTAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (29 bp):
GTTTAAGAATTTTCAAAAAATAAATTAGG
Found at i:31333737 original size:34 final size:34
Alignment explanation
Indices: 31333698--31333814 Score: 130
Period size: 34 Copynumber: 3.4 Consensus size: 34
31333688 TTTTAAAAAA
** *
31333698 TAAATTAGGGTTTAGAATTTTTCTAA-AAATTAAT
1 TAAATTAGGGTTTAGAGGTTTT-AAATAAATTAAT
*
31333732 TAAATTAGGTTTTA-AGGGTTTTAAATAAATTAAT
1 TAAATTAGGGTTTAGA-GGTTTTAAATAAATTAAT
** * *
31333766 TAAATTAGATTTTAGGGGTTTTAAATAAATAAAT
1 TAAATTAGGGTTTAGAGGTTTTAAATAAATTAAT
31333800 TAAATTAGGGTTTAG
1 TAAATTAGGGTTTAG
31333815 TTTTTTAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
33 3 0.04
34 68 0.96
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (34 bp):
TAAATTAGGGTTTAGAGGTTTTAAATAAATTAAT
Found at i:31333827 original size:34 final size:33
Alignment explanation
Indices: 31333691--31333823 Score: 119
Period size: 34 Copynumber: 4.0 Consensus size: 33
31333681 TTAAGAATTT
** *
31333691 TAAA-AAA-TAAATTAGGGTTTAGAATTTTTCTAA
1 TAAATAAATTAAATTAGGGTTTAG-GGTTTT-AAA
* *
31333724 -AAATTAATTAAATTAGGTTTTAAGGGTTTTAAA
1 TAAATAAATTAAATTAGGGTTT-AGGGTTTTAAA
* **
31333757 TAAATTAATTAAATTAGATTTTAGGGGTTTTAAA
1 TAAATAAATTAAATTAGGGTTTA-GGGTTTTAAA
**
31333791 TAAATAAATTAAATTAGGGTTTAGTTTTTTAAA
1 TAAATAAATTAAATTAGGGTTTAGGGTTTTAAA
31333824 ATAATTTTTG
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.04
33 13 0.15
34 66 0.79
35 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.43
Consensus pattern (33 bp):
TAAATAAATTAAATTAGGGTTTAGGGTTTTAAA
Found at i:31334138 original size:126 final size:126
Alignment explanation
Indices: 31333908--31334431 Score: 692
Period size: 126 Copynumber: 4.2 Consensus size: 126
31333898 AAGAAAGATT
* * * * *
31333908 TTTTTCTATAGTAGTTTCAGAAAAATTAATTTTGAGAAGACAGTTCTGAAAAGATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTCAAAA
* * * * *
31333973 ACGCTTTAAGTAGGATGCACCATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTA
66 ACGCTTCAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * *
31334034 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTCAAAA
* * * * *
31334099 ACGCTTTAAGCAAGATGCACTATCAGCAAAATTAATGAAAAAAGCTCCTACGTGGATGCTC
66 ACGCTTCAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * *
31334160 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTCAAAA
* * * *
31334225 AAGCTTCAAGCAGGATGCATTATCAGCAAAATTACTGAAAAAAACTCCCACGT-GAACGCTC
66 ACGCTTCAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAG-ACGCTC
* * *
31334286 TTTTTCTACAGTAGTT-CTTATAAAAATAATTTTGAGAAGGCAGTTCTGAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGA-AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTCAAA
** * * * * * *
31334350 AATACTTCAAGCAATATGCACTGTTAGCAAAATTACTGAAAAAGGCTCCCACATAGACGTTC
65 AACGCTTCAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
31334412 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
31334432 TTTGGCCTTA
Statistics
Matches: 352, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
125 3 0.01
126 346 0.98
127 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTCAAAA
ACGCTTCAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
Found at i:31337949 original size:18 final size:18
Alignment explanation
Indices: 31337928--31337963 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31337918 AAAATGAAAT
*
31337928 ATATAAGGGTTATGATAC
1 ATATAAGGGTTAGGATAC
31337946 ATATAAGGGTTAGGATAC
1 ATATAAGGGTTAGGATAC
31337964 GCACCTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (18 bp):
ATATAAGGGTTAGGATAC
Found at i:31338670 original size:11 final size:11
Alignment explanation
Indices: 31338656--31338693 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
31338646 ATTCTATTCT
31338656 ATTAGTATTAG
1 ATTAGTATTAG
31338667 ATTAGTATTAG
1 ATTAGTATTAG
*
31338678 -TTAG-ATTAT
1 ATTAGTATTAG
31338687 ATTAGTA
1 ATTAGTA
31338694 GTGATCCCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 4 0.17
10 8 0.33
11 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:31338683 original size:15 final size:14
Alignment explanation
Indices: 31338663--31338692 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
31338653 TCTATTAGTA
31338663 TTAGATTAGTATTAG
1 TTAGATTA-TATTAG
31338678 TTAGATTATATTAG
1 TTAGATTATATTAG
31338692 T
1 T
31338693 AGTGATCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TTAGATTATATTAG
Found at i:31339440 original size:53 final size:53
Alignment explanation
Indices: 31339353--31339456 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
31339343 GCAACCTCCA
* *
31339353 ATTTTGGCTTTATTTGGTGGTGTCACCCCGCACATCTCTCGGTACAATGTTGG
1 ATTTTGGCTTTATTTGGTGGTGTCACCCCACACATCTCTCGATACAATGTTGG
*
31339406 ATTTTGGCTTTATTTGGTGGTGTCGCCCCACACATCTCTCGATACAATGTT
1 ATTTTGGCTTTATTTGGTGGTGTCACCCCACACATCTCTCGATACAATGTT
31339457 TCCAATACGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.38
Consensus pattern (53 bp):
ATTTTGGCTTTATTTGGTGGTGTCACCCCACACATCTCTCGATACAATGTTGG
Found at i:31340487 original size:19 final size:19
Alignment explanation
Indices: 31340439--31340487 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
31340429 AGCGATTTTG
* *
31340439 CCACATCAACAAAGCGCGT
1 CCACATCAGCAAAGCGCAT
* *
31340458 CCACATTAGCAAAGTGCAT
1 CCACATCAGCAAAGCGCAT
31340477 CCACATCAGCA
1 CCACATCAGCA
31340488 TATTGTGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.37, C:0.35, G:0.14, T:0.14
Consensus pattern (19 bp):
CCACATCAGCAAAGCGCAT
Found at i:31347733 original size:20 final size:20
Alignment explanation
Indices: 31347702--31347752 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
31347692 AATATTTTAT
*
31347702 AATTACATTAATTTTTCAATA
1 AATTA-ATTAATTTTTAAATA
*
31347723 TATTAATTAATTTTTAAATA
1 AATTAATTAATTTTTAAATA
*
31347743 AATTTATTAA
1 AATTAATTAA
31347753 ACCTGTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAATTAATTTTTAAATA
Found at i:31353648 original size:61 final size:61
Alignment explanation
Indices: 31353579--31353700 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
31353569 ACTTCTACCA
*
31353579 ATTTGCTAATATAATCATCAAAATACATAATATCTTACTTTACAACAAAACTATATAACAT
1 ATTTGCTAATATAATAATCAAAATACATAATATCTTACTTTACAACAAAACTATATAACAT
31353640 ATTTGCTAATATAATAATCAAAATACATAATATCTTACTTTACAACAAAACTATATAACAT
1 ATTTGCTAATATAATAATCAAAATACATAATATCTTACTTTACAACAAAACTATATAACAT
31353701 CCCAAAATAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (61 bp):
ATTTGCTAATATAATAATCAAAATACATAATATCTTACTTTACAACAAAACTATATAACAT
Found at i:31354289 original size:21 final size:21
Alignment explanation
Indices: 31354231--31354314 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
31354221 CCTGATCAGT
*
31354231 ATACGACACAT-AAGTGCCTA
1 ATACGACACATAAAGTGCCTG
* ** *
31354251 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
31354272 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT--G
*
31354295 ATAAGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
31354315 AATTGGCAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 9 0.17
21 23 0.44
23 20 0.38
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:31354302 original size:23 final size:23
Alignment explanation
Indices: 31354271--31354314 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31354261 CGAGGTGCCT
*
31354271 GATACGACACATAAAGTGCCTGA
1 GATAAGACACATAAAGTGCCTGA
31354294 GATAAGACACATAAAGTGCCT
1 GATAAGACACATAAAGTGCCT
31354315 AATTGGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (23 bp):
GATAAGACACATAAAGTGCCTGA
Found at i:31355368 original size:19 final size:20
Alignment explanation
Indices: 31355346--31355383 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31355336 CCAAATCCTT
*
31355346 TTTTGTTCA-TTTTTATTTA
1 TTTTATTCATTTTTTATTTA
31355365 TTTTATTCATTTTTTATTT
1 TTTTATTCATTTTTTATTT
31355384 TGTTTTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTATTCATTTTTTATTTA
Found at i:31356166 original size:7 final size:7
Alignment explanation
Indices: 31356154--31356188 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
31356144 TACTTATATA
31356154 TATATTT
1 TATATTT
31356161 TATATTT
1 TATATTT
31356168 TATATTT
1 TATATTT
31356175 TATAATTTT
1 TAT-A-TTT
31356184 TATAT
1 TATAT
31356189 ACATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.69
8 2 0.08
9 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:31356196 original size:12 final size:12
Alignment explanation
Indices: 31356175--31356204 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31356165 TTTTATATTT
31356175 TATA-ATTTTTA
1 TATACATTTTTA
31356186 TATACATTTTTA
1 TATACATTTTTA
31356198 TATACAT
1 TATACAT
31356205 ATACGTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATACATTTTTA
Found at i:31357104 original size:108 final size:107
Alignment explanation
Indices: 31356881--31357083 Score: 286
Period size: 108 Copynumber: 1.9 Consensus size: 107
31356871 ATAATAAAGG
* * *
31356881 CAATGTTTTGCGTTTG-GAATTCGAGAAAACGCGCCCTAATGTGCTGGGTGTCGATTTTTCTCGT
1 CAATATTTTGCATTTGAAAATTCGAGAAAACGCGCCCTAATGTGCTGGGTGTCGA-TTTTCTCGT
* *
31356945 TCGACCAAATAGCCAAATATCCTTTTAAAATTTCGAAGTAAGA
65 TCGACCAAATAGCCAAATATCCTCTTAAAATCTCGAAGTAAGA
* * *
31356988 CAATATTTTGCATTTGAAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTCTCGTT
1 CAATATTTTGCATTTGAAAATTCGAGAAAACGCGCCCTAATGTGCTGGGTGTCGATTTTCTCGTT
* *
31357052 TGACCAAATAGCCAAATATTCTCTT-AAATCTC
66 CGACCAAATAGCCAAATATCCTCTTAAAATCTC
31357084 AATCCATGTC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 6 0.07
106 31 0.36
107 14 0.16
108 34 0.40
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (107 bp):
CAATATTTTGCATTTGAAAATTCGAGAAAACGCGCCCTAATGTGCTGGGTGTCGATTTTCTCGTT
CGACCAAATAGCCAAATATCCTCTTAAAATCTCGAAGTAAGA
Found at i:31361424 original size:50 final size:50
Alignment explanation
Indices: 31361356--31362439 Score: 754
Period size: 50 Copynumber: 21.7 Consensus size: 50
31361346 GTTTGCAATT
* * * * * *
31361356 AAAAGACTGAGGCCACAACGGTGAATCTTACTTCTCAGGCGGTGCAACGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * **** **
31361406 AATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGATATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * **
31361456 AAAAGGTTGAGGCCACAACGGTGAATCTTACTTCCCAGGCGGTGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * ** * **
31361506 AACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGTAATTA
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * *
31361556 AAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGTGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * ** *
31361606 AATAGATTGAAGCTACAACAGCGAATCTTGCTTCTCCA-ACATTGCAATTG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTC-CCAGGCGGTGCAATGG
** *
31361656 AAAAGATTGAAGCTACAACGGCGAATCTTACTTTACAGGCGGTGCAGT-G
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * ** * **
31361705 AAATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTACAATTA
1 AAA-AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * * **
31361756 AAAAGATTGAAGCTACAATGGTGAATCTTACATCTCAGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * ** **
31361806 AACAA-ATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTA
1 AA-AAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * *
31361856 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * ** **
31361906 AACAA-ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTA
1 AA-AAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * **
31361956 AAAAGATTGAGGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * ** **
31362006 AACAA-ATTGAAGCTACAACGGCGAATCTTGCTT-CCACGACATTGCAATTA
1 AA-AAGATTGAAGCTACAACGGCGAATCTTACTTCCCA-GGCGGTGCAATGG
* * * *
31362056 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCATGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * * ** *
31362106 AATAGATTGAAGCTACAACAGCGAATCTT-CTTTCCCTGACATTGCAAT-T
1 AAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGCGGTGCAATGG
* * * ** **
31362155 AAAAGATTAAAACCACAACGGCGGGTCTTACTCTCCCAGGCGGTGCTGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACT-TCCCAGGCGGTGCAATGG
* ** * **** * *
31362206 AATAGATTGAAGCTACAACAACGAATCTT-CTTTCCCCGATATTGTAAT-T
1 AAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGCGGTGCAATGG
* * *
31362255 AAAAGATTGAATCCACAACGGC-AGATCTTACTTTCCCAGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGA-ATCTTAC-TTCCCAGGCGGTGCAATGG
* * * * ** *
31362306 AACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAAT-T
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* * * *
31362355 AAAAGATTGAAGCCACAACAGAGAATCTTA-TTCCCAGGCGGTGTAATGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
* ** *
31362404 AATAGATTGAAGCTATGACGGCAAATCTTACTTCCC
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC
31362440 CGACATTACA
Statistics
Matches: 759, Mismatches: 252, Indels: 46
0.72 0.24 0.04
Matches are distributed among these distances:
48 13 0.02
49 108 0.14
50 575 0.76
51 62 0.08
52 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAATGG
Found at i:31361529 original size:100 final size:100
Alignment explanation
Indices: 31361348--31362455 Score: 1467
Period size: 100 Copynumber: 11.1 Consensus size: 100
31361338 AAACCATAGT
* * * * **
31361348 TTGCAATT-AAAAGACTGAGGCCACAACGGTGAATCTTACTTCTCAGGCGGTGCAACGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
*
31361412 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGATA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * *
31361447 TTGCAATTAAAAAGGTTGAGGCCACAACGGTGAATCTTACTTCCCAGGCGGTGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
31361512 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
31361547 TTGTAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGTGGTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
* * *
31361612 TTGAAGCTACAACAGCGAATCTTGCTTCTCCAACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * ** *
31361647 TTGCAATTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTTACAGGCGGTGCAGTGAAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
31361712 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * * * * * *
31361747 TTACAATTAAAAAGATTGAAGCTACAATGGTGAATCTTACATCTCAGGCGATGCAGCGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
*
31361812 TTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
31361847 TTGCAATTAAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
*
31361912 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * *
31361947 TTGCAATTAAAAAGATTGAGGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGCGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
*
31362012 TTGAAGCTACAACGGCGAATCTTGCTTCCACGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* *
31362047 TTGCAATTAAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCATGCGGTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
* *
31362112 TTGAAGCTACAACAGCGAATCTT-CTTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTTGC-TTCCCCGACA
* * ** *
31362147 TTGCAATT-AAAAGATTAAAACCACAACGGCGGGTCTTACTCTCCCAGGCGGTGCTGTGGAATAG
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACT-TCCCAGGCGGTGCAGTGGAATAG
** *
31362211 ATTGAAGCTACAACAACGAATCTT-CTTTCCCCGATA
65 ATTGAAGCTACAACGGCGAATCTTGC-TTCCCCGACA
* * *
31362247 TTGTAATT-AAAAGATTGAATCCACAACGGC-AGATCTTACTTTCCCAGGCGGTGCAGTGGAACA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGA-ATCTTAC-TTCCCAGGCGGTGCAGTGGAATA
31362310 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
64 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
31362347 TTGCAATT-AAAAGATTGAAGCCACAACAGAGAATCTTA-TTCCCAGGCGGTGTAATGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
** * *
31362410 TTGAAGCTATGACGGCAAATCTTACTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* *
31362445 TTACAGTTAAA
1 TTGCAATTAAA
31362456 CAGACAAAAG
Statistics
Matches: 904, Mismatches: 97, Indels: 16
0.89 0.10 0.02
Matches are distributed among these distances:
98 59 0.07
99 38 0.04
100 804 0.89
101 3 0.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
Found at i:31362674 original size:128 final size:129
Alignment explanation
Indices: 31362456--31362766 Score: 473
Period size: 128 Copynumber: 2.4 Consensus size: 129
31362446 TACAGTTAAA
* * *
31362456 CAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTACAATAGAGCGGATTAAAACCACAGATATT
1 CAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATATT
31362521 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCC-TATCTCCCTAAAGTTACAGTGGAG
66 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG-CCTTATCTCCCTAAAGTTACAGTGGAG
* *
31362585 CAGACAAAAGAATCCAATCCTATCTCCCT-AAGTTGCAGTGGAGCGGATTAAAACCACAGATCTT
1 CAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATATT
* *
31362649 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGCCTTATCTCCCTGAAGTTGCAGTGGAG
66 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGCCTTATCTCCCTAAAGTTACAGTGGAG
* * * * * * *
31362713 CGGATAGAAGAAGCTAATCCTGTCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA
1 CAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
31362767 TGATGAATTC
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
127 2 0.01
128 113 0.68
129 51 0.31
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (129 bp):
CAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATATT
ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGCCTTATCTCCCTAAAGTTACAGTGGAG
Found at i:31364299 original size:12 final size:12
Alignment explanation
Indices: 31364278--31364307 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31364268 ATATATATTT
31364278 TATA-ATTTTTA
1 TATACATTTTTA
31364289 TATACATTTTTA
1 TATACATTTTTA
31364301 TATACAT
1 TATACAT
31364308 ATACGTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATACATTTTTA
Found at i:31365206 original size:108 final size:107
Alignment explanation
Indices: 31364982--31365185 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 107
31364972 ATAATAAAGG
*
31364982 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTTCTCAT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGA-TTTTCTCAT
* *
31365047 TCGACCAAATAGCCAAATATCCTTTTAAAATTTCGAAGTAAGA
65 TCGACCAAATAGCCAAATATCCTCTTAAAATCTCGAAGTAAGA
* * *
31365090 CAATATTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTCTCGTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTCTCATT
*
31365154 TGACCAAATAGCCAAATATCCTCTT-AAATCTC
66 CGACCAAATAGCCAAATATCCTCTTAAAATCTC
31365186 AATCCATGTC
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 6 0.07
106 31 0.35
108 52 0.58
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (107 bp):
CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTCTCATT
CGACCAAATAGCCAAATATCCTCTTAAAATCTCGAAGTAAGA
Found at i:31365733 original size:15 final size:16
Alignment explanation
Indices: 31365715--31365746 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31365705 TTAATTAATA
31365715 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
31365730 TAATTTAATAATATTT
1 TAATTTAATAATATTT
31365746 T
1 T
31365747 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:31365737 original size:25 final size:26
Alignment explanation
Indices: 31365702--31365754 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
31365692 TATTATCTTA
31365702 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
31365726 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
31365753 AT
1 AT
31365755 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:31366741 original size:50 final size:50
Alignment explanation
Indices: 31366620--31366807 Score: 209
Period size: 50 Copynumber: 3.8 Consensus size: 50
31366610 ACATGGCAAA
** * * *
31366620 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * * ** *
31366669 GCTATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * *
31366719 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
*
31366769 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
31366808 ATTTCAATGA
Statistics
Matches: 116, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 32 0.28
50 83 0.72
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:31392550 original size:4 final size:4
Alignment explanation
Indices: 31392541--31392574 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
31392531 TAAGATTTCT
*
31392541 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TATA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
31392575 GCTGTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:31414896 original size:16 final size:17
Alignment explanation
Indices: 31414875--31414907 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
31414865 GATACGATTG
31414875 CTAATTTT-TAACTTAT
1 CTAATTTTCTAACTTAT
31414891 CTAATTTTCTAACTTAT
1 CTAATTTTCTAACTTAT
31414908 TCCTGTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (17 bp):
CTAATTTTCTAACTTAT
Found at i:31417958 original size:12 final size:12
Alignment explanation
Indices: 31417941--31417966 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31417931 ATGCAATTAA
31417941 ATGTACCTAAGT
1 ATGTACCTAAGT
31417953 ATGTACCTAAGT
1 ATGTACCTAAGT
31417965 AT
1 AT
31417967 AGACAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTACCTAAGT
Found at i:31419692 original size:50 final size:50
Alignment explanation
Indices: 31419563--31419804 Score: 186
Period size: 50 Copynumber: 4.7 Consensus size: 50
31419553 GATAATAACA
* * *
31419563 TGCCAAAT-CCATGTCCCAGACATGGTATTACATGGGATGTT-TCTTGTAC--
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
31419612 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * * ** * *
31419662 TGCCCATGCCATGTCCTAGACATGGTCTTACAGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** *
31419712 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC---GG
* * *
31419768 TGCCAATGCCATGTTCCAAACATAGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31419805 TCTCATCACC
Statistics
Matches: 154, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
48 7 0.05
49 33 0.21
50 79 0.51
53 2 0.01
56 33 0.21
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:31420182 original size:30 final size:29
Alignment explanation
Indices: 31420143--31420199 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
31420133 CAGCCCTCGA
*
31420143 CTCTAACTTTTGCAAAATTACAATTTTAC
1 CTCTAACTTTTACAAAATTACAATTTTAC
* *
31420172 CTCTAAACTTTTACATAATTACACTTTT
1 CTCT-AACTTTTACAAAATTACAATTTT
31420200 TCCCCAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (29 bp):
CTCTAACTTTTACAAAATTACAATTTTAC
Found at i:31428816 original size:18 final size:19
Alignment explanation
Indices: 31428789--31428824 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31428779 ATGGGTTGGC
31428789 AAGTAAAATTCAA-ATCCA
1 AAGTAAAATTCAACATCCA
*
31428807 AAGTATAATTCAACATCC
1 AAGTAAAATTCAACATCC
31428825 TTTCCATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (19 bp):
AAGTAAAATTCAACATCCA
Found at i:31432202 original size:20 final size:20
Alignment explanation
Indices: 31432172--31432209 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31432162 TAAGTATTAT
31432172 TCAACTTCTCTTTCGAGTTAA
1 TCAACTTCTCTTT-GAGTTAA
31432193 TCAA-TTCTCTTTGAGTT
1 TCAACTTCTCTTTGAGTT
31432210 TTTCTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (20 bp):
TCAACTTCTCTTTGAGTTAA
Found at i:31434827 original size:23 final size:23
Alignment explanation
Indices: 31434783--31434827 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31434773 AAACAAAAAC
* *
31434783 ATTTAAACATAATATCATCCATA
1 ATTTAAACATAATATAAACCATA
* *
31434806 ATTTAATCATATTATAAACCAT
1 ATTTAAACATAATATAAACCAT
31434828 TCATACACTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAACATAATATAAACCATA
Found at i:31437860 original size:21 final size:21
Alignment explanation
Indices: 31437835--31437879 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
31437825 TAATACAACC
31437835 TTAATAACACTTCATAAATAT
1 TTAATAACACTTCATAAATAT
*
31437856 TTAATAACACTTCGTAAATAT
1 TTAATAACACTTCATAAATAT
31437877 TTA
1 TTA
31437880 GTAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATAACACTTCATAAATAT
Found at i:31438417 original size:3 final size:3
Alignment explanation
Indices: 31438409--31438449 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31438399 GGAATTGGCT
31438409 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
31438450 TATTAAAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:31443608 original size:14 final size:14
Alignment explanation
Indices: 31443589--31443624 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31443579 TGCTACCATT
31443589 TTACTATTATGTTG
1 TTACTATTATGTTG
31443603 TTACTATTATGTTG
1 TTACTATTATGTTG
*
31443617 TTATTATT
1 TTACTATT
31443625 TGGATATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:31443727 original size:27 final size:27
Alignment explanation
Indices: 31443687--31443751 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
31443677 CATTTGCTTG
*
31443687 TTAAGT-TGCATTAATCCTAGTGTTAT
1 TTAAGTCTACATTAATCCTAGTGTTAT
*
31443713 TTAAGTCTACATTAATCTTAGTGTTAT
1 TTAAGTCTACATTAATCCTAGTGTTAT
31443740 TTAAGTCTACAT
1 TTAAGTCTACAT
31443752 ATTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 6 0.17
27 30 0.83
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (27 bp):
TTAAGTCTACATTAATCCTAGTGTTAT
Found at i:31444805 original size:54 final size:54
Alignment explanation
Indices: 31444726--31444835 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
31444716 TTCAATCATG
* * * *
31444726 TTCAAGTGCGTTTTATTCTCCTATTCTATTTTATATTTTAATAGAGTTTAATTA
1 TTCAAGTGCGTTTTATCCTCCTATTCTATTTCATATTTTAATAAAGCTTAATTA
* **
31444780 TTCAAGTGTGTTTTATCCTTTTATTCTATTTCATATTTTAATAAAGCTTAATTA
1 TTCAAGTGCGTTTTATCCTCCTATTCTATTTCATATTTTAATAAAGCTTAATTA
31444834 TT
1 TT
31444836 TAACTCAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (54 bp):
TTCAAGTGCGTTTTATCCTCCTATTCTATTTCATATTTTAATAAAGCTTAATTA
Found at i:31446849 original size:21 final size:21
Alignment explanation
Indices: 31446823--31446864 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31446813 AATATGATTT
*
31446823 TTTAAATAATTACAA-AAAATA
1 TTTAAA-AATTAAAAGAAAATA
31446844 TTTAAAAATTAAAAGAAAATA
1 TTTAAAAATTAAAAGAAAATA
31446865 CAACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TTTAAAAATTAAAAGAAAATA
Found at i:31447393 original size:16 final size:16
Alignment explanation
Indices: 31447368--31447405 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
31447358 AATTTAAACC
*
31447368 TTAAACTTAAATACCA
1 TTAAAATTAAATACCA
*
31447384 TTAAAATTAAATACCC
1 TTAAAATTAAATACCA
31447400 TTAAAA
1 TTAAAA
31447406 GCCTAAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAATTAAATACCA
Found at i:31447428 original size:16 final size:16
Alignment explanation
Indices: 31447381--31447432 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
31447371 AACTTAAATA
*
31447381 CCATTAAAATTAAATAC
1 CCATTAAAATTTAA-AC
**
31447398 CC-TTAAAAGCCTAAAC
1 CCATTAAAA-TTTAAAC
31447414 CCATTAAAATTTAAAC
1 CCATTAAAATTTAAAC
31447430 CCA
1 CCA
31447433 ATATTCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (16 bp):
CCATTAAAATTTAAAC
Found at i:31450064 original size:43 final size:43
Alignment explanation
Indices: 31450016--31450113 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
31450006 TATCCCAAAT
* * *
31450016 ATGGTCTTACATGTAATCT-CGTATCGATGCCAATAG-CCCAGCC
1 ATGGTCTTACATGAAAT-TACATATCGATGCCAAT-GTCCCAGAC
* *
31450059 ATGGTCTTATACGAAATTACATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGAAATTACATATCGATGCCAATGTCCCAGAC
31450102 ATGGTCTTACAT
1 ATGGTCTTACAT
31450114 ATAGATGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.04
43 44 0.96
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACATGAAATTACATATCGATGCCAATGTCCCAGAC
Found at i:31450143 original size:32 final size:33
Alignment explanation
Indices: 31450075--31450144 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
31450065 TTATACGAAA
* *
31450075 TTACATATCGATGCCAATGTCCCAGACATGGTC
1 TTACATATAGATGCCAATATCCCAGACATGGTC
* **
31450108 TTACATATAGATGCC-ATATCTCAGGTATGGTC
1 TTACATATAGATGCCAATATCCCAGACATGGTC
31450140 TTACA
1 TTACA
31450145 CGTAATCTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (33 bp):
TTACATATAGATGCCAATATCCCAGACATGGTC
Found at i:31456122 original size:26 final size:26
Alignment explanation
Indices: 31456084--31456135 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31456074 TAAGAATTAC
31456084 CAAAACCAAAACAATGCC-TATCAAA
1 CAAAACCAAAACAATGCCATATCAAA
* *
31456109 CAAAAGCACAAACATTGCCATATCAAA
1 CAAAACCA-AAACAATGCCATATCAAA
31456136 TAGGATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.54, C:0.27, G:0.06, T:0.13
Consensus pattern (26 bp):
CAAAACCAAAACAATGCCATATCAAA
Found at i:31465341 original size:27 final size:27
Alignment explanation
Indices: 31465311--31465365 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31465301 CAAACCTACA
31465311 GTACGAAGTCTCGATACACCTTCCTAT
1 GTACGAAGTCTCGATACACCTTCCTAT
*
31465338 GTACGAAGTCTCGATACACCTTTCTAT
1 GTACGAAGTCTCGATACACCTTCCTAT
31465365 G
1 G
31465366 AGTATCGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (27 bp):
GTACGAAGTCTCGATACACCTTCCTAT
Found at i:31466290 original size:17 final size:17
Alignment explanation
Indices: 31466254--31466292 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31466244 TTTATTGTTC
*
31466254 TATTTATTTAGCTTAGT
1 TATTTATTTAGCTTAAT
**
31466271 TATTTATTTATTTTAAT
1 TATTTATTTAGCTTAAT
31466288 TATTT
1 TATTT
31466293 TATCTAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (17 bp):
TATTTATTTAGCTTAAT
Found at i:31467330 original size:2 final size:2
Alignment explanation
Indices: 31467323--31467373 Score: 59
Period size: 2 Copynumber: 25.0 Consensus size: 2
31467313 ATTTGAACCC
* *
31467323 AT AT AT AT AT AT AT AT AT AT AT AT AT GAA AT CA- AC 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
31467366 AT AT AT AT
1 AT AT AT AT
31467374 TTGTTTAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:31469769 original size:23 final size:23
Alignment explanation
Indices: 31469739--31469784 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31469729 CTCTGTCAAC
*
31469739 CTTATCATGAAA-CTTTGTAATAA
1 CTTATCATCAAACCTTT-TAATAA
31469762 CTTATCATCAAACCTTTTAATAA
1 CTTATCATCAAACCTTTTAATAA
31469785 TTTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (23 bp):
CTTATCATCAAACCTTTTAATAA
Found at i:31478840 original size:27 final size:27
Alignment explanation
Indices: 31478785--31478955 Score: 127
Period size: 27 Copynumber: 6.3 Consensus size: 27
31478775 TTCTCCATAG
* * * * *
31478785 AGGCGTTCTTTTCATATTGCGCTAAAA
1 AGGCTTTCCTTTCATATTGCACCACAA
* *
31478812 AGGCTTTCCTTTTATATTGCACCATAA
1 AGGCTTTCCTTTCATATTGCACCACAA
* * *
31478839 AGACGTTCCTTTTATAATT-CACCACAA
1 AGGCTTTCCTTTCAT-ATTGCACCACAA
* * *
31478866 CA-ACATTT-CTTTCATATTGCGCCATAA
1 -AGGC-TTTCCTTTCATATTGCACCACAA
*
31478893 AGGCTTTCCTTTCATATTACACCACAA
1 AGGCTTTCCTTTCATATTGCACCACAA
31478920 AGG-TGTTCCTTTCATAATT-CACCACAA
1 AGGCT-TTCCTTTCAT-ATTGCACCACAA
*
31478947 AGGCATTCC
1 AGGCTTTCC
31478956 ATTGCTGACA
Statistics
Matches: 117, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
26 8 0.07
27 100 0.85
28 9 0.08
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (27 bp):
AGGCTTTCCTTTCATATTGCACCACAA
Found at i:31478895 original size:81 final size:81
Alignment explanation
Indices: 31478794--31478946 Score: 234
Period size: 81 Copynumber: 1.9 Consensus size: 81
31478784 GAGGCGTTCT
* * * * *
31478794 TTTCATATTGCGCTAAAAAGGCTTTCCTTTTATATTGCACCATAAAGACGTTCCTTTTATAATTC
1 TTTCATATTGCGCCAAAAAGGCTTTCCTTTCATATTACACCACAAAGACGTTCCTTTCATAATTC
31478859 ACCACAACAACATTTC
66 ACCACAACAACATTTC
* **
31478875 TTTCATATTGCGCCATAAAGGCTTTCCTTTCATATTACACCACAAAGGTGTTCCTTTCATAATTC
1 TTTCATATTGCGCCAAAAAGGCTTTCCTTTCATATTACACCACAAAGACGTTCCTTTCATAATTC
31478940 ACCACAA
66 ACCACAA
31478947 AGGCATTCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (81 bp):
TTTCATATTGCGCCAAAAAGGCTTTCCTTTCATATTACACCACAAAGACGTTCCTTTCATAATTC
ACCACAACAACATTTC
Found at i:31478935 original size:54 final size:55
Alignment explanation
Indices: 31478816--31478919 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 55
31478806 CTAAAAAGGC
* *
31478816 TTTCCTTTTATATTGCACCATAAAGACGTTCCTTTTATAATTCACCACAACAACA
1 TTTCCTTTCATATTGCACCATAAAGACGTTCCTTTCATAATTCACCACAACAACA
* * *
31478871 TTT-CTTTCATATTGCGCCATAAAGGCTTTCCTTTCAT-ATTACACCACAA
1 TTTCCTTTCATATTGCACCATAAAGACGTTCCTTTCATAATT-CACCACAA
31478920 AGGTGTTCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.07
54 37 0.86
55 3 0.07
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.38
Consensus pattern (55 bp):
TTTCCTTTCATATTGCACCATAAAGACGTTCCTTTCATAATTCACCACAACAACA
Found at i:31480230 original size:31 final size:32
Alignment explanation
Indices: 31480192--31480254 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
31480182 CACCGAAACC
31480192 GAGGTATTACAACTCT-CCCCCTTAACAAAAT
1 GAGGTATTACAACTCTCCCCCCTTAACAAAAT
31480223 GAGGTATTACAACTCTCCCCCCTTAACAAAAT
1 GAGGTATTACAACTCTCCCCCCTTAACAAAAT
31480255 TTCATCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (32 bp):
GAGGTATTACAACTCTCCCCCCTTAACAAAAT
Found at i:31482120 original size:21 final size:21
Alignment explanation
Indices: 31482096--31482137 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31482086 TATTTAAACC
31482096 AAATT-AAATTAAATTAGATTA
1 AAATTAAAATT-AATTAGATTA
*
31482117 AAATTAAAATTAATTATATTA
1 AAATTAAAATTAATTAGATTA
31482138 TGAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATTAAAATTAATTAGATTA
Found at i:31486458 original size:50 final size:50
Alignment explanation
Indices: 31486334--31486513 Score: 175
Period size: 50 Copynumber: 3.6 Consensus size: 50
31486324 AATAATAACA
* * **
31486334 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCCTAT-AT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA-GTTCTCATATCGG
* * * *
31486383 TGCAAATGCCATATCCCAGATATGGTCTTATATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCGG
* * ** * ** *
31486433 TGCCTATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCGG
* *
31486483 TGCCAACGCAATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
31486514 GTGGGATATC
Statistics
Matches: 105, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 3 0.03
49 37 0.35
50 65 0.62
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCGG
Found at i:31507923 original size:15 final size:15
Alignment explanation
Indices: 31507905--31507935 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31507895 GTAAAAGCTG
31507905 AAAATAATTAAATAA
1 AAAATAATTAAATAA
*
31507920 AAAATAGTTAAATAA
1 AAAATAATTAAATAA
31507935 A
1 A
31507936 TCTGAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATAATTAAATAA
Found at i:31514256 original size:27 final size:27
Alignment explanation
Indices: 31514235--31514643 Score: 406
Period size: 27 Copynumber: 15.2 Consensus size: 27
31514225 AGGTATAATA
*
31514235 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * * **
31514262 ATCATTTTAGCCTA-CGGAGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * **
31514288 GTTATTCTACCCTATGAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
31514315 GTCATTTTACCCTATAGGGGTATTCTA
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
31514342 GTCATTTTATCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
31514369 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
31514396 GTTATTTTAGCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
31514423 GTTATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
31514450 ATCATTTTACCCTATAGGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
31514477 GTTATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
31514504 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
31514531 ATTATTTTACCATATGGGGGTGTTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
31514558 GTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
31514585 GTCATTCTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* **
31514612 GTGATTTTACCCTATGGAAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
31514639 GTCAT
1 GTCAT
31514644 AATAGTGTAA
Statistics
Matches: 306, Mismatches: 75, Indels: 2
0.80 0.20 0.01
Matches are distributed among these distances:
26 19 0.06
27 287 0.94
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:31518565 original size:19 final size:18
Alignment explanation
Indices: 31518541--31518585 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
31518531 ATGACTAATT
31518541 AATTTAATTCCATTT-TTAA
1 AATTTAATT--ATTTATTAA
31518560 AATTTAATTATTTAATTAA
1 AATTTAATTATTT-ATTAA
31518579 AATTTAA
1 AATTTAA
31518586 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
19 20 0.83
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAATTATTTATTAA
Found at i:31521304 original size:13 final size:13
Alignment explanation
Indices: 31521261--31521314 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
31521251 AGGTTTATCG
* *
31521261 ATTTAGTTCATTT
1 ATTTATTTCTTTT
* *
31521274 GTTTATTTCTCATT
1 ATTTATTTCT-TTT
31521288 ATTTATTTCTTTT
1 ATTTATTTCTTTT
*
31521301 ATTTATTTATTTT
1 ATTTATTTCTTTT
31521314 A
1 A
31521315 ATTCATCTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (13 bp):
ATTTATTTCTTTT
Found at i:31521609 original size:13 final size:14
Alignment explanation
Indices: 31521591--31521627 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
31521581 TGCTGGGGGG
31521591 ATTTTGACAAT-AA
1 ATTTTGACAATAAA
*
31521604 ATTTTGAAAATAAA
1 ATTTTGACAATAAA
31521618 ATTTT-ACAAT
1 ATTTTGACAAT
31521628 TAATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
ATTTTGACAATAAA
Found at i:31525434 original size:3 final size:3
Alignment explanation
Indices: 31525426--31525454 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31525416 TGCTGCAGGG
31525426 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
31525455 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:31530513 original size:14 final size:12
Alignment explanation
Indices: 31530482--31530513 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31530472 GGCCGTGTGA
31530482 GCCACACAGACT
1 GCCACACAGACT
*
31530494 GCCACACAGGCT
1 GCCACACAGACT
31530506 GCCACACA
1 GCCACACA
31530514 ACCATGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.44, G:0.19, T:0.06
Consensus pattern (12 bp):
GCCACACAGACT
Found at i:31531618 original size:16 final size:17
Alignment explanation
Indices: 31531599--31531631 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31531589 AATTTAGCCA
31531599 TTATTT-TTTTTAATTT
1 TTATTTGTTTTTAATTT
31531615 TTATTTGTTTTTAATTT
1 TTATTTGTTTTTAATTT
31531632 AATTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTGTTTTTAATTT
Found at i:31562644 original size:53 final size:53
Alignment explanation
Indices: 31562561--31562667 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
31562551 GTGAAAATTA
* *
31562561 ATGCACAATTAGCAACGAACTTACTGGAAATATGCAAAAATTAGAGATGATTC
1 ATGCACAATTAGCAACAAACTTACTAGAAATATGCAAAAATTAGAGATGATTC
*
31562614 ATGCACAATTAGCAACAAACTTATTAGAAATATGCAAAAATTAGAGATGATTC
1 ATGCACAATTAGCAACAAACTTACTAGAAATATGCAAAAATTAGAGATGATTC
31562667 A
1 A
31562668 ATTCAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (53 bp):
ATGCACAATTAGCAACAAACTTACTAGAAATATGCAAAAATTAGAGATGATTC
Found at i:31567250 original size:45 final size:45
Alignment explanation
Indices: 31567197--31567290 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
31567187 CAATGATACT
* *
31567197 CGGTGGAATCAGCACATAGCAACCACCTTCATAATCAATAGTACC
1 CGGTGGAATCAGCACACAGCAACCACCTTCAGAATCAATAGTACC
* * * *
31567242 CGGTGGAATCAGCACGCAGCAAGCACCTTTAGAATCAATGGTACC
1 CGGTGGAATCAGCACACAGCAACCACCTTCAGAATCAATAGTACC
31567287 CGGT
1 CGGT
31567291 ACACGTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (45 bp):
CGGTGGAATCAGCACACAGCAACCACCTTCAGAATCAATAGTACC
Found at i:31572063 original size:45 final size:43
Alignment explanation
Indices: 31571968--31572099 Score: 124
Period size: 45 Copynumber: 3.0 Consensus size: 43
31571958 ACAGATACAC
** *
31571968 GGTGG-ATCAGCACATAGC-ACCACCCTTATGGTCAATGATACTT
1 GGTGGAATCAGCACATAGCAACCA-CCTTATAATCAATG-TACCT
*
31572011 GGTGGAATCAGCACATAGCAATCACCTTCATAATCAATAGTACCT
1 GGTGGAATCAGCACATAGCAACCACCTT-ATAATCAAT-GTACCT
* * * *
31572056 GGTGGAATCAACATACAACAACCACCTTTATAATCAATGGTACC
1 GGTGGAATCAGCACATAGCAACCACC-TTATAATCAAT-GTACC
31572100 CGATACACGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 5 0.07
44 17 0.23
45 49 0.66
46 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (43 bp):
GGTGGAATCAGCACATAGCAACCACCTTATAATCAATGTACCT
Found at i:31578255 original size:42 final size:42
Alignment explanation
Indices: 31578185--31578291 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
31578175 TAGGCAGAAC
* * * **
31578185 ACATGGGCATGTGCCCATGCCATGTGAGTCACACGGGTAAGG
1 ACATGGGCATGTGTCCAGGCCATATGAGTCACACGGACAAGG
** * *
31578227 ACATGGGCATGTGTCCAGGCTGTATGAGTCATATGGACAAGG
1 ACATGGGCATGTGTCCAGGCCATATGAGTCACACGGACAAGG
*
31578269 ACATGGGCGTGTGTCCAGGCCAT
1 ACATGGGCATGTGTCCAGGCCAT
31578292 GTGGCATATA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (42 bp):
ACATGGGCATGTGTCCAGGCCATATGAGTCACACGGACAAGG
Found at i:31583585 original size:40 final size:40
Alignment explanation
Indices: 31583525--31583958 Score: 852
Period size: 40 Copynumber: 10.9 Consensus size: 40
31583515 TGAGCATTGG
*
31583525 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583565 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583605 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583645 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583685 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583725 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583765 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583805 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583845 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583885 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
31583925 GATATATCCGGGCTATGACCCGAAGGCAA-TATGC
1 GATATATCCGGGCTATGACCCGAAGGCAATTATGC
31583959 TTGACCAACC
Statistics
Matches: 393, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
39 5 0.01
40 388 0.99
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
GATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
Found at i:31590730 original size:50 final size:50
Alignment explanation
Indices: 31590655--31590897 Score: 317
Period size: 50 Copynumber: 4.9 Consensus size: 50
31590645 CATTTGGGTA
* *
31590655 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAC
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* *
31590705 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTTGCACTGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * *
31590755 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* *** * * *
31590805 GAGAGGCCCCCCATAAGACCATGTTTGGGACAT-GCATGGGCACCGATAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** *
31590854 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31590898 TGTTATTATC
Statistics
Matches: 163, Mismatches: 28, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
49 16 0.10
50 140 0.86
51 7 0.04
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:31593950 original size:13 final size:13
Alignment explanation
Indices: 31593932--31593956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31593922 TCAAATGACC
31593932 AAATTTTCACACG
1 AAATTTTCACACG
31593945 AAATTTTCACAC
1 AAATTTTCACAC
31593957 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:31598785 original size:30 final size:30
Alignment explanation
Indices: 31598746--31598815 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
31598736 ACTGTATTTG
*
31598746 CACTATTACTGTATTAGACTAAGGCCCACA
1 CACTGTTACTGTATTAGACTAAGGCCCACA
* * * *
31598776 CTCTGTTACTGTATTGGGCTATGGCCCACA
1 CACTGTTACTGTATTAGACTAAGGCCCACA
*
31598806 CACTGCTACT
1 CACTGTTACT
31598816 ATATATGGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (30 bp):
CACTGTTACTGTATTAGACTAAGGCCCACA
Found at i:31598832 original size:30 final size:29
Alignment explanation
Indices: 31598767--31598833 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
31598757 TATTAGACTA
* * *
31598767 AGGCCCACACTCTGTTACTGTATTGGGCT
1 AGGCCCACACACTGCTACTATATTGGGCT
31598796 ATGGCCCACACACTGCTACTATATAT-GGCT
1 A-GGCCCACACACTGCTACTATAT-TGGGCT
31598826 CAGGCCCA
1 -AGGCCCA
31598834 GACTGATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.03
30 29 0.91
31 2 0.06
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (29 bp):
AGGCCCACACACTGCTACTATATTGGGCT
Found at i:31600249 original size:27 final size:27
Alignment explanation
Indices: 31600219--31600396 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31600209 ATATTGAGTC
* * * *
31600219 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31600246 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31600273 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31600301 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31600328 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31600355 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31600382 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31600397 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31600358 original size:82 final size:81
Alignment explanation
Indices: 31600240--31600395 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31600230 TGCTATATAA
* *
31600240 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31600305 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31600322 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31600386 CACTTAGTGC
65 CACTTAGTGC
31600396 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31617771 original size:29 final size:29
Alignment explanation
Indices: 31617729--31617807 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
31617719 CGACAGTCGT
* * * *
31617729 AACCGTCCCATTTCATATTCGATGGTTGA
1 AACCATCCCTTTTCATAATCCATGGTTGA
*
31617758 AACCATCCCTTTTCATTAATCCATGGTTGT
1 AACCATCCCTTTTCA-TAATCCATGGTTGA
* *
31617788 CACCATCCCTATTCATAATC
1 AACCATCCCTTTTCATAATC
31617808 AATAGCCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.35
Consensus pattern (29 bp):
AACCATCCCTTTTCATAATCCATGGTTGA
Found at i:31623837 original size:40 final size:40
Alignment explanation
Indices: 31623793--31624056 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
31623783 GCTCCTCGTT
* *
31623793 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
31623833 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
31623873 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
31623913 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
31623953 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
31623992 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
31624033 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31624057 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:31631971 original size:79 final size:82
Alignment explanation
Indices: 31631860--31632044 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
31631850 GCTACTCGTT
* *
31631860 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
31631923 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
31631940 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
31632003 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
31632020 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31632045 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:31632044 original size:40 final size:40
Alignment explanation
Indices: 31631841--31632044 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
31631831 CGGAATTTAA
** *
31631841 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31631881 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
31631921 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31631960 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
31632000 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31632040 CCGGA
1 CCGGA
31632045 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31636103 original size:25 final size:25
Alignment explanation
Indices: 31636069--31636205 Score: 132
Period size: 25 Copynumber: 5.5 Consensus size: 25
31636059 TACCGATTTA
* *
31636069 AGCTCTTATGAGCTTACCGTTACTC
1 AGCTCGTATGAGCTTACCGTTATTC
31636094 AGCTCGTATGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* ** * *
31636119 AACTCAAAAGAGCTTACTGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
31636144 AGCTCGTAGGAGCTTAGCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * * * *
31636169 AACTTGAAGGAGCTTACCGTT-TAC
1 AGCTCGTATGAGCTTACCGTTATTC
*
31636193 AGCTCATATGAGC
1 AGCTCGTATGAGC
31636206 ATACATGTAT
Statistics
Matches: 89, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
24 10 0.11
25 79 0.89
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:31636146 original size:50 final size:50
Alignment explanation
Indices: 31636078--31636205 Score: 168
Period size: 50 Copynumber: 2.6 Consensus size: 50
31636068 AAGCTCTTAT
*
31636078 GAGCTTACCGTTACTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
1 GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
* * * ** *
31636128 GAGCTTACTGTTATTCAGCTCGTAGGAGCTTAGCGTTATTCAACTTGAAG
1 GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
* *
31636178 GAGCTTACCGTT-TACAGCTCATATGAGC
1 GAGCTTACCGTTATTCAGCTCGTATGAGC
31636206 ATACATGTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 13 0.19
50 54 0.81
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
Found at i:31646711 original size:40 final size:40
Alignment explanation
Indices: 31646655--31646742 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
31646645 ATTGGTACTC
31646655 TCTGTCTGGTGCGTTTC-AGTTGGATTAG-TTCTTATGAGCT
1 TCTGTCTGGTGCGTTTCGA-TTGGATTAGCTT-TTATGAGCT
* *
31646695 TCTGTCTGGTGTGTTTCGATTGGATTAGCTTTTATGTGCT
1 TCTGTCTGGTGCGTTTCGATTGGATTAGCTTTTATGAGCT
31646735 TCTGTCTG
1 TCTGTCTG
31646743 TCGTCTTCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (40 bp):
TCTGTCTGGTGCGTTTCGATTGGATTAGCTTTTATGAGCT
Done.