Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 57 of 193
Found at i:17694884 original size:24 final size:24
Alignment explanation
Indices: 17694857--17694904 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17694847 ACATCTTTAA
17694857 AACTTTAATTCCCCATTTAATGAC
1 AACTTTAATTCCCCATTTAATGAC
*
17694881 AACTTTAATTCCCCATTTTATGAC
1 AACTTTAATTCCCCATTTAATGAC
17694905 CACACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (24 bp):
AACTTTAATTCCCCATTTAATGAC
Found at i:17694914 original size:24 final size:24
Alignment explanation
Indices: 17694863--17694915 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17694853 TTAAAACTTT
***
17694863 AATTCCCCATTTAATGACAACTTT
1 AATTCCCCATTTAATGACAACACA
* *
17694887 AATTCCCCATTTTATGACCACACA
1 AATTCCCCATTTAATGACAACACA
17694911 AATTC
1 AATTC
17694916 TCATGATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (24 bp):
AATTCCCCATTTAATGACAACACA
Found at i:17709472 original size:2 final size:2
Alignment explanation
Indices: 17709460--17709542 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
17709450 ACCATCTATC
*
17709460 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17709502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17709543 TACTCTATAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17715147 original size:21 final size:21
Alignment explanation
Indices: 17715123--17715173 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
17715113 GTGAAATTTT
17715123 TACCGATACAAGTCATGCATC
1 TACCGATACAAGTCATGCATC
17715144 TACCGATACAAGTCATGCATC
1 TACCGATACAAGTCATGCATC
17715165 TACCGATAC
1 TACCGATAC
17715174 TTTTATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
TACCGATACAAGTCATGCATC
Found at i:17715901 original size:51 final size:51
Alignment explanation
Indices: 17715841--17716013 Score: 274
Period size: 51 Copynumber: 3.4 Consensus size: 51
17715831 TTTAATTCGT
** * *
17715841 CACTTAGTCATCGGACCTTTAATTTGTAAAGGATTCATTTGCTCAAGATGA
1 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGA
*
17715892 CACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGA
1 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGA
*
17715943 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATAA
1 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGA
* *
17715994 CACTTAGTCACCGAACCTTT
1 CACTTAGTCATCGGACCTTT
17716014 CGTTTATAGA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 113 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGA
Found at i:17722998 original size:51 final size:51
Alignment explanation
Indices: 17722892--17723025 Score: 198
Period size: 51 Copynumber: 2.6 Consensus size: 51
17722882 TTTCATTTAA
* * * *
17722892 TACTCACGATGACATATTA-TCATCGAACCATTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGAACC-TTTAATCCGTAAAGGATTCATT
17722944 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
*
17722995 TACTCACGATGACACTTAGTCATCGGACCTT
1 TACTCACGATGACACTTAGTCATCGAACCTT
17723026 CGTGACACTT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 52 0.68
52 24 0.32
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
Found at i:17723031 original size:24 final size:24
Alignment explanation
Indices: 17723004--17723049 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
17722994 TTACTCACGA
17723004 TGACACTTAGTCATCGGACCTTCG
1 TGACACTTAGTCATCGGACCTTCG
17723028 TGACACTTAGTCATCGGACCTT
1 TGACACTTAGTCATCGGACCTT
17723050 TAATCCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (24 bp):
TGACACTTAGTCATCGGACCTTCG
Found at i:17723076 original size:75 final size:75
Alignment explanation
Indices: 17722953--17723100 Score: 253
Period size: 75 Copynumber: 2.0 Consensus size: 75
17722943 TTACTCACGA
*
17722953 TGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATTTACTCAC-GATGACACTTAGTCA
1 TGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATTTACTCACAG-TGACACTTAGTCA
17723017 TCGGACCTTCG
65 TCGGACCTTCG
* *
17723028 TGACACTTAGTCATCGGACCTTTAATCCATAAAGTATTCATTTACTCACAGTGACACTTAGTCAT
1 TGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATTTACTCACAGTGACACTTAGTCAT
17723093 CGGACCTT
66 CGGACCTT
17723101 TAATCCGTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 68 0.99
76 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (75 bp):
TGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATTTACTCACAGTGACACTTAGTCAT
CGGACCTTCG
Found at i:17723103 original size:51 final size:50
Alignment explanation
Indices: 17723026--17723152 Score: 200
Period size: 51 Copynumber: 2.5 Consensus size: 50
17723016 ATCGGACCTT
*
17723026 CGTGACACTTAGTCATCGGACCTTTAATCCATAAAGTATTCATTTACTCA
1 CGTGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCA
*
17723076 CAGTGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCA
1 C-GTGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCA
* *
17723127 CGATGACATTTAGTCACCGGACCTTT
1 CG-TGACACTTAGTCATCGGACCTTT
17723153 TGTTTATAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
50 2 0.03
51 69 0.97
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (50 bp):
CGTGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCA
Found at i:17725331 original size:99 final size:98
Alignment explanation
Indices: 17725146--17725333 Score: 227
Period size: 99 Copynumber: 1.9 Consensus size: 98
17725136 CTTTTACTTA
* * ** *
17725146 CTTATGAAAATTGATTAATTGTTTGAATTGATATAGAGATATGTTCAAGAGATTATTTTAATTTC
1 CTTATGAAAATTGATTAATCGTTTGAATTGACATAGAGATATGTTCAAGAGATTAAATGAATTTC
* *
17725211 ATAAGTATGTATGTGCATTAGTTAATGCATTTT
66 ATAAGTAAGTATATGCATTAGTTAATGCATTTT
* * *
17725244 CTTATTAAAATTTATTTAATCGTTTGAATTGACATAGAGATATAG-TCAAGAGA-TAAATGAGTT
1 CTTATGAAAATTGA-TTAATCGTTTGAATTGACATAGAGATAT-GTTCAAGAGATTAAATGAATT
* *
17725307 TTAGTAGGTAAGTATATGCATTAGTTA
64 TCA-TAAGTAAGTATATGCATTAGTTA
17725334 GCAAATTGCC
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
98 20 0.27
99 54 0.72
100 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (98 bp):
CTTATGAAAATTGATTAATCGTTTGAATTGACATAGAGATATGTTCAAGAGATTAAATGAATTTC
ATAAGTAAGTATATGCATTAGTTAATGCATTTT
Found at i:17730106 original size:13 final size:13
Alignment explanation
Indices: 17730088--17730112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17730078 ATTCAAAATA
17730088 ATAATTAATTAAC
1 ATAATTAATTAAC
17730101 ATAATTAATTAA
1 ATAATTAATTAA
17730113 TATTAAGATT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATTAATTAAC
Found at i:17730239 original size:18 final size:18
Alignment explanation
Indices: 17730216--17730254 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17730206 ATATCAAAAT
*
17730216 ATTT-AATTAATAATTGTA
1 ATTTAAATT-ATAATTATA
17730234 ATTTAAATTATAATTATA
1 ATTTAAATTATAATTATA
17730252 ATT
1 ATT
17730255 ATATTATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTAAATTATAATTATA
Found at i:17730385 original size:18 final size:17
Alignment explanation
Indices: 17730354--17730387 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17730344 TAATTGTAAA
*
17730354 TTAAAATATTATTATTT
1 TTAAAATATAATTATTT
17730371 TTAAATATATAATTATT
1 TTAAA-ATATAATTATT
17730388 GCAACTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAATATAATTATTT
Found at i:17731049 original size:30 final size:30
Alignment explanation
Indices: 17730990--17731047 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
17730980 TAATTAGGGC
17730990 AAAACTGCGTCCACGTAGACGCTTTTTTCA
1 AAAACTGCGTCCACGTAGACGCTTTTTTCA
*
17731020 AAAAC-GCTTCCACGTCAGCACGCTTTTT
1 AAAACTGCGTCCACGT-AG-ACGCTTTTT
17731048 CACGACACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 7 0.28
31 9 0.36
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAACTGCGTCCACGTAGACGCTTTTTTCA
Found at i:17731989 original size:21 final size:21
Alignment explanation
Indices: 17731947--17731987 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17731937 CCTTTTAATT
17731947 TTAAATATAATTATAGAAAAA
1 TTAAATATAATTATAGAAAAA
17731968 TTAAA-ATAATTA-AGATAAAA
1 TTAAATATAATTATAGA-AAAA
17731988 ATATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TTAAATATAATTATAGAAAAA
Found at i:17746597 original size:23 final size:22
Alignment explanation
Indices: 17746561--17746604 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17746551 TAGATATTTC
*
17746561 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
17746584 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
17746605 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:17749304 original size:192 final size:191
Alignment explanation
Indices: 17748914--17749354 Score: 554
Period size: 192 Copynumber: 2.3 Consensus size: 191
17748904 GAAATCGACG
*
17748914 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCA
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCA
* *
17748979 AGAAATGAGAAATGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAGT
66 AGAAATGAGAAATGAATACAAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAAT
* * * * * *
17749044 GCATATTCTCGACAGCTCGTGTAAGCAGCATTGTTTGAGAAATAGTTATATGCATACTATAT
131 GCATATTCTCGACAGCTCATGTAAGCAGCATCGTTGGAGAAATA-TTAGATGCACACTATAC
*
17749106 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTC-
* * * * *
17749171 AA-AAAGTG-G-TATGAATACTA-AATGGATTATAGGCTCTACGATGGCT-AGGATTTATGCTTA
65 AAGAAA-TGAGAAATGAATACAAGAATGGATTACAGGCCCTACGATGGCTGA-GATTTATGCATA
* * *
17749231 AATGCATATTCTCGATAGCTCATGTGAGCAGCATCGTTAGGGGACAAT-TTACAGATAG-ACACT
128 AATGCATATTCTCGACAGCTCATGTAAGCAGCATCGTT-GGAGA-AATATT--AGAT-GCACACT
*
17749294 GTAC
188 ATAC
* * *
17749298 CGATGGCTGGGGTACTGTATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
17749355 ATGTACTGGC
Statistics
Matches: 218, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
189 1 0.00
190 70 0.32
191 11 0.05
192 131 0.60
193 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (191 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCA
AGAAATGAGAAATGAATACAAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAAT
GCATATTCTCGACAGCTCATGTAAGCAGCATCGTTGGAGAAATATTAGATGCACACTATAC
Found at i:17757322 original size:331 final size:331
Alignment explanation
Indices: 17756709--17757332 Score: 1133
Period size: 331 Copynumber: 1.9 Consensus size: 331
17756699 GGTGAGGAGT
*
17756709 ATCTTGCTTAGTGTAGGGATGACTGCATGAATTTGAGGCAGGGTGACATGTCCGTTAACGATTAT
1 ATCTCGCTTAGTGTAGGGATGACTGCATGAATTTGAGGCAGGGTGACATGTCCGTTAACGATTAT
17756774 GAGATTGAGTTCCTGAGGTTGGTCCATTATGCATTTGGGTTGGTGACTAATGAGAAGGAAAAATG
66 GAGATTGAGTTCCTGAGGTTGGTCCATTATGCATTTGGGTTGGTGACTAATGAGAAGGAAAAATG
*
17756839 TGATTGGTTTAGGAAATGACTTTGACTCTCGCTACAAGACAAAGTCTACATGCATCATGATAGAG
131 AGATTGGTTTAGGAAATGACTTTGACTCTCGCTACAAGACAAAGTCTACATGCATCATGATAGAG
*
17756904 TGTTCAGTGACTTGGTTTGCCAAGCTAGGACTGCTAAGAGTTTGAAGGCTTGTAAGAAGGCTCAG
196 TGTTCAGTGACTTGGTTTGCCAAGCTAGGACTGCTAAGAGTTTGAAGGCTCGTAAGAAGGCTCAG
*
17756969 AGGGCTTAAGACAGATAGCGTGGTAAAAAGCAAACATTTGGGTTGACTTCATGAATTTGAGACAG
261 AGGGCTTAAGACAGAGAGCGTGGTAAAAAGCAAACATTTGGGTTGACTTCATGAATTTGAGACAG
17757034 GGTGAC
326 GGTGAC
* *
17757040 ATCTCGCTTAGTGTAGGGATGACTTCATGAATTTGAGGCAGGGTGACATGTTCGTTAACGATTAT
1 ATCTCGCTTAGTGTAGGGATGACTGCATGAATTTGAGGCAGGGTGACATGTCCGTTAACGATTAT
** *
17757105 GAGATTGAGTTCCTGAGGTTGGTCTGTTATGCATTTTGGTTGGTGACTAATGAGAAGGAAAAATG
66 GAGATTGAGTTCCTGAGGTTGGTCCATTATGCATTTGGGTTGGTGACTAATGAGAAGGAAAAATG
* *
17757170 AGATTGGTTTAGGAAATGACTTTGACTCTCGCTACAAGATAAAGTCTACATGCATCATGATAGGG
131 AGATTGGTTTAGGAAATGACTTTGACTCTCGCTACAAGACAAAGTCTACATGCATCATGATAGAG
17757235 TGTTCAGTGACTTGGTTTGCCAAGCTAGGACTGCTAAGAGTTT-AGAGGCTCGTAAGAAGGCTCA
196 TGTTCAGTGACTTGGTTTGCCAAGCTAGGACTGCTAAGAGTTTGA-AGGCTCGTAAGAAGGCTCA
17757299 GAGGGCTTAAGACAGAGAGCGTGGTAAAAAGCAA
260 GAGGGCTTAAGACAGAGAGCGTGGTAAAAAGCAA
17757333 GCATGCATAA
Statistics
Matches: 281, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
330 1 0.00
331 280 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (331 bp):
ATCTCGCTTAGTGTAGGGATGACTGCATGAATTTGAGGCAGGGTGACATGTCCGTTAACGATTAT
GAGATTGAGTTCCTGAGGTTGGTCCATTATGCATTTGGGTTGGTGACTAATGAGAAGGAAAAATG
AGATTGGTTTAGGAAATGACTTTGACTCTCGCTACAAGACAAAGTCTACATGCATCATGATAGAG
TGTTCAGTGACTTGGTTTGCCAAGCTAGGACTGCTAAGAGTTTGAAGGCTCGTAAGAAGGCTCAG
AGGGCTTAAGACAGAGAGCGTGGTAAAAAGCAAACATTTGGGTTGACTTCATGAATTTGAGACAG
GGTGAC
Found at i:17774347 original size:17 final size:17
Alignment explanation
Indices: 17774310--17774360 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
17774300 GGAGACATTC
* *
17774310 ATTTATTTATATAACATA
1 ATTTATTT-TAGAAAATA
17774328 ATTTATTTTAGAAAATA
1 ATTTATTTTAGAAAATA
*
17774345 ATTCT-TTTTCGAAAAT
1 ATT-TATTTTAGAAAAT
17774361 TTTGATGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTTATTTTAGAAAATA
Found at i:17783216 original size:15 final size:16
Alignment explanation
Indices: 17783183--17783228 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
17783173 TCGTAGGGTC
17783183 CTTCATGTCGTTC-TCTT
1 CTTCAT-TC-TTCTTCTT
*
17783200 CTTCCTTC-TCTTCTT
1 CTTCATTCTTCTTCTT
17783215 CTTCATTCTTCTTC
1 CTTCATTCTTCTTC
17783229 ATCTGGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 7 0.28
17 5 0.20
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.57
Consensus pattern (16 bp):
CTTCATTCTTCTTCTT
Found at i:17805742 original size:15 final size:16
Alignment explanation
Indices: 17805693--17805735 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
17805683 CCCTACCAAG
* *
17805693 ATTTTTTCTTTTTATA
1 ATTTTTTCTTTTAACA
*
17805709 TTTTTTTCTTTTAACA
1 ATTTTTTCTTTTAACA
17805725 ATTTTTTCTTT
1 ATTTTTTCTTT
17805736 AAGAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTTCTTTTAACA
Found at i:17811956 original size:26 final size:26
Alignment explanation
Indices: 17811873--17811976 Score: 77
Period size: 26 Copynumber: 4.0 Consensus size: 26
17811863 ACTACTAATA
* * *
17811873 TCGCTACATGAGCATGTCCAGAATTG
1 TCGCTGCATGAACATGTCCAGAGTTG
* * *
17811899 TCGCTGCA-GAAACTTGTCCAAAAG-TA
1 TCGCTGCATG-AACATGTCC-AGAGTTG
* * *
17811925 TAGCTGCATGAATATGTCTAGAGTTG
1 TCGCTGCATGAACATGTCCAGAGTTG
* *
17811951 TCGCTGTATGAGCATGTCCAGAGTTG
1 TCGCTGCATGAACATGTCCAGAGTTG
17811977 CACTAAGAAT
Statistics
Matches: 57, Mismatches: 17, Indels: 8
0.70 0.21 0.10
Matches are distributed among these distances:
25 4 0.07
26 50 0.88
27 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (26 bp):
TCGCTGCATGAACATGTCCAGAGTTG
Found at i:17822670 original size:38 final size:39
Alignment explanation
Indices: 17822609--17822691 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 39
17822599 ATTATTAATC
* *
17822609 AATAAAAGTTAAAAAATGAATAGTAAATGCAACTATAAA
1 AATAAAAGTTAAAAAAGGAATAGTAAATGCAACTACAAA
*
17822648 AATAAAA-TTAGAAAAGGAATAGTAAATGCAACTACAAA
1 AATAAAAGTTAAAAAAGGAATAGTAAATGCAACTACAAA
*
17822686 AGTAAA
1 AATAAA
17822692 CATCAAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 33 0.82
39 7 0.17
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.20
Consensus pattern (39 bp):
AATAAAAGTTAAAAAAGGAATAGTAAATGCAACTACAAA
Found at i:17830073 original size:25 final size:26
Alignment explanation
Indices: 17830045--17830107 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
17830035 CTTAATTTAC
*
17830045 ACAACTAAATAAAAA-AAATTAAATA
1 ACAACTAAATAAAAATAAATTAAACA
*
17830070 ACAAATCAAATAAAAATTAAATTAAACA
1 ACAACT-AAATAAAAA-TAAATTAAACA
17830098 A-AAC-AAATAA
1 ACAACTAAATAA
17830108 CTTAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 11 0.34
26 9 0.28
27 2 0.06
28 10 0.31
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (26 bp):
ACAACTAAATAAAAATAAATTAAACA
Found at i:17836012 original size:104 final size:104
Alignment explanation
Indices: 17835858--17836139 Score: 496
Period size: 104 Copynumber: 2.7 Consensus size: 104
17835848 TATGTTGACC
*
17835858 CTTTT-GACGCGAAATGAAATGACAACCCAAGCACCCTATCCCGGTTACTCAGCCCAACACACTC
1 CTTTTCGACGCGAAATGGAATGACAACCCAAGCACCCTATCCCGGTTACTCAGCCCAACACACTC
17835922 CCAATTTATTATCATTTTTTTACTTAAGAATGTATTGGT
66 CCAATTTATTATCATTTTTTTACTTAAGAATGTATTGGT
17835961 CTTTTCGACGCGAAATGGAATGACAACCCAAGCACCCTATCCCGGTTACTCAGCCCAACACACTC
1 CTTTTCGACGCGAAATGGAATGACAACCCAAGCACCCTATCCCGGTTACTCAGCCCAACACACTC
17836026 CCAATTTATTATCATTTTTTTACTTAAGAATGTATTGGT
66 CCAATTTATTATCATTTTTTTACTTAAGAATGTATTGGT
* **
17836065 CTTTTCGACGCGAAATGGAATGACAACCCAAGCACTCC-ATCCCGATTACTCAGTTCAACACACT
1 CTTTTCGACGCGAAATGGAATGACAACCCAAGCAC-CCTATCCCGGTTACTCAGCCCAACACACT
*
17836129 CCTAATTTATT
65 CCCAATTTATT
17836140 TTTTTTATTT
Statistics
Matches: 172, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
103 5 0.03
104 165 0.96
105 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (104 bp):
CTTTTCGACGCGAAATGGAATGACAACCCAAGCACCCTATCCCGGTTACTCAGCCCAACACACTC
CCAATTTATTATCATTTTTTTACTTAAGAATGTATTGGT
Found at i:17836889 original size:9 final size:9
Alignment explanation
Indices: 17836875--17836910 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
17836865 ACTAAAATTA
17836875 AAAATAAAT
1 AAAATAAAT
17836884 AAAATAAAT
1 AAAATAAAT
17836893 AAAATAAAT
1 AAAATAAAT
17836902 AAAAATAAA
1 -AAAATAAA
17836911 ATTGGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:17859562 original size:16 final size:16
Alignment explanation
Indices: 17859529--17859572 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
17859519 AATGAAAAAG
* *
17859529 AAAGAAAAA-ATGTTA
1 AAAGAAAAATTTGTAA
17859544 AAAGAAAAATTTGTAA
1 AAAGAAAAATTTGTAA
17859560 AAAGAAAATATTT
1 AAAGAAAA-ATTT
17859573 TTTTAGGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.36
16 12 0.48
17 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (16 bp):
AAAGAAAAATTTGTAA
Found at i:17872023 original size:15 final size:16
Alignment explanation
Indices: 17872003--17872043 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17871993 CTAAAAAAAT
17872003 ATTTTTCTTTT-ACAA
1 ATTTTTCTTTTAACAA
*
17872018 ATTTTTCTTTTAACAT
1 ATTTTTCTTTTAACAA
*
17872034 TTTTTTCTTT
1 ATTTTTCTTT
17872044 CTTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTCTTTTAACAA
Found at i:17898088 original size:23 final size:22
Alignment explanation
Indices: 17898057--17898100 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17898047 AAAGAAATAA
*
17898057 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
17898079 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
17898101 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:17909033 original size:23 final size:22
Alignment explanation
Indices: 17909002--17909045 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17908992 AAAGAAATAA
*
17909002 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
17909024 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
17909046 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:17910540 original size:12 final size:13
Alignment explanation
Indices: 17910516--17910558 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
17910506 GTAGAACATG
*
17910516 AGGAAATAGAGGA
1 AGGAAAGAGAGGA
17910529 AGGAAA-AGAGGA
1 AGGAAAGAGAGGA
*
17910541 A-GAAAGAAAGGA
1 AGGAAAGAGAGGA
17910553 AGGAAA
1 AGGAAA
17910559 AGAAGTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 13 0.48
13 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.02
Consensus pattern (13 bp):
AGGAAAGAGAGGA
Found at i:17916583 original size:27 final size:27
Alignment explanation
Indices: 17916553--17916607 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
17916543 AAACTTAGAG
*
17916553 TCTGCATTGTCCTCAATGCACTGACAT
1 TCTGCATTGTCCTCAATGCACTAACAT
*
17916580 TCTGCATTGTCCTCAATGCCCTAACAT
1 TCTGCATTGTCCTCAATGCACTAACAT
17916607 T
1 T
17916608 AATGTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.35
Consensus pattern (27 bp):
TCTGCATTGTCCTCAATGCACTAACAT
Found at i:17923407 original size:13 final size:13
Alignment explanation
Indices: 17923391--17923417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17923381 AACTTGAAAA
17923391 TGAAAATGAATTG
1 TGAAAATGAATTG
17923404 TGAAAATGAATTG
1 TGAAAATGAATTG
17923417 T
1 T
17923418 CGAAGAAATA
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:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (13 bp):
TGAAAATGAATTG
Found at i:17931121 original size:17 final size:18
Alignment explanation
Indices: 17931091--17931137 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
17931081 ACATATTAGT
* *
17931091 AACAAAATAAAAGTTAGAT
1 AACAAAA-ATAAGTTAGAA
*
17931110 AA-AAAAATAAGTTCGAA
1 AACAAAAATAAGTTAGAA
17931127 AACAAAAATAA
1 AACAAAAATAA
17931138 ACATCAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 12 0.50
19 2 0.08
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.17
Consensus pattern (18 bp):
AACAAAAATAAGTTAGAA
Found at i:17932338 original size:26 final size:26
Alignment explanation
Indices: 17932309--17932374 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
17932299 TTCCTGCACC
*
17932309 GACAATTCTGGGCATGC-TCATGTAGT
1 GACAATTCTGGGCAT-CATCATGCAGT
* *
17932335 GACATTTCTGGACATCATCATGCAGT
1 GACAATTCTGGGCATCATCATGCAGT
*
17932361 GACAATTTTGGGCA
1 GACAATTCTGGGCA
17932375 CAATTCTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (26 bp):
GACAATTCTGGGCATCATCATGCAGT
Found at i:17951993 original size:13 final size:13
Alignment explanation
Indices: 17951975--17951999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17951965 CCCATTTTAT
17951975 CATTTTTAGCATG
1 CATTTTTAGCATG
17951988 CATTTTTAGCAT
1 CATTTTTAGCAT
17952000 TTTTAACTTA
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:17959208 original size:29 final size:32
Alignment explanation
Indices: 17959148--17959209 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 32
17959138 CGTTTGTTTG
* * *
17959148 TGTTTATTTTTGTAGTTGCATTTACTATTCTT
1 TGTTTAATTTTGTAGTTGCATTAACTAATCTT
17959180 TGTTTAATTTT-TA-TTG-ATTAACTAATCTT
1 TGTTTAATTTTGTAGTTGCATTAACTAATCTT
17959209 T
1 T
17959210 TGTTGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 3 0.11
31 2 0.07
32 10 0.37
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.61
Consensus pattern (32 bp):
TGTTTAATTTTGTAGTTGCATTAACTAATCTT
Found at i:17960546 original size:18 final size:18
Alignment explanation
Indices: 17960525--17960562 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17960515 CAAATGCGAT
*
17960525 CATAGAATCAGATGTAGC
1 CATAGAATCAGATGCAGC
*
17960543 CATATAATCAGATGCAGC
1 CATAGAATCAGATGCAGC
17960561 CA
1 CA
17960563 CAAGTTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (18 bp):
CATAGAATCAGATGCAGC
Found at i:17966160 original size:16 final size:14
Alignment explanation
Indices: 17966134--17966176 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
17966124 TGTTCCTAAA
*
17966134 AACAATTTTCTTTT
1 AACATTTTTCTTTT
*
17966148 TACAATTTTTTCTTTT
1 AAC-A-TTTTTCTTTT
17966164 AACATTTTTCTTT
1 AACATTTTTCTTT
17966177 CTTTTGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 11 0.46
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (14 bp):
AACATTTTTCTTTT
Found at i:17976029 original size:21 final size:21
Alignment explanation
Indices: 17975977--17976032 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
17975967 CGGTAGGTTC
*
17975977 CTTCATT-TCATTCTCTTCTT
1 CTTCATTCTCCTTCTCTTCTT
*
17975997 CTT-TTTCTTCCTTCTCTTCTT
1 CTTCATTC-TCCTTCTCTTCTT
17976018 CTTCATTCTCCTTCT
1 CTTCATTCTCCTTCT
17976033 ACTGGTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.07
20 3 0.10
21 22 0.73
22 3 0.10
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTCATTCTCCTTCTCTTCTT
Found at i:17988710 original size:2 final size:2
Alignment explanation
Indices: 17988703--17988732 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17988693 AGATCATCTC
*
17988703 AT AT AT AT AA 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
17988733 CACAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17989596 original size:20 final size:18
Alignment explanation
Indices: 17989549--17989597 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
17989539 CAATATAAAC
17989549 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17989566 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
17989586 ATTAAATTAATA
1 ATTAAATTAATA
17989598 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:17989648 original size:37 final size:36
Alignment explanation
Indices: 17989581--17989656 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
17989571 GATAATCACT
*
17989581 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTACTAAAATAA-TA
*
17989618 TTAA-ATTAAATTTAATATCAA-ACTACTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTACTAAAATAATA
17989654 TTA
1 TTA
17989657 TTTTTTGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 11 0.31
37 22 0.63
38 2 0.06
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTACTAAAATAATA
Found at i:17999455 original size:9 final size:9
Alignment explanation
Indices: 17999441--17999468 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17999431 TCGAATTAGT
17999441 ATTAATCAA
1 ATTAATCAA
17999450 ATTAATCAA
1 ATTAATCAA
17999459 ATTAATCAA
1 ATTAATCAA
17999468 A
1 A
17999469 CTTTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAATCAA
Found at i:18004977 original size:25 final size:25
Alignment explanation
Indices: 18004943--18004993 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
18004933 TAATATGCTG
18004943 CTAAAGTTACAAGAACCTACAAGGT
1 CTAAAGTTACAAGAACCTACAAGGT
18004968 CTAAAGTTACAAGAACCTACAAGGT
1 CTAAAGTTACAAGAACCTACAAGGT
18004993 C
1 C
18004994 ACACCCTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (25 bp):
CTAAAGTTACAAGAACCTACAAGGT
Found at i:18005385 original size:123 final size:123
Alignment explanation
Indices: 18005234--18005845 Score: 874
Period size: 123 Copynumber: 5.0 Consensus size: 123
18005224 GTTTTCATTA
* * * *
18005234 AATATT-AAAATATAAAAGTTAATATCCTTTTGGAAATGATATAATGTTTTAATAAATCTTCCAT
1 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* *
18005298 ATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAATGAAATTC
66 ATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
18005356 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACC-TCTCA
1 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC-CA
*
18005420 TATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
65 TATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* *
18005479 AATATTAAAAATATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* * *
18005544 ATATTTCTCTAAGAGAATATTTTCATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * * * *
18005602 AATACTAAAAACATGGAAA-TTAGTATCCTTTTAGAAAGGATATAATATTTTCATAAACCTTACA
1 AATATTAAAAACAT-GAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCA
* *
18005666 TATATTTCTCT-AAGGAAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
65 TATATTTCTTTAAAAG-AATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * * * *
18005725 GATATTAAAAATAATGGAAGCTAATATCCTTTTGGAAAGGATATAATATTTTAATTAACCTTCCA
1 AATATTAAAAA-CATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCA
* * * *
18005790 TATATTTC-TCAAAAGGAATATTTCCATTTTAATATGAGATGTTAAATAAAAAGAAA
65 TATATTTCTTTAAAA-GAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
18005846 AGATAGAAGA
Statistics
Matches: 441, Mismatches: 40, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
122 10 0.02
123 337 0.76
124 93 0.21
125 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (123 bp):
AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAAGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:18016198 original size:15 final size:15
Alignment explanation
Indices: 18016152--18016201 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
18016142 GTTAGCAATG
*
18016152 TGAGTGATCATAGCA
1 TGAGTGTTCATAGCA
* ** *
18016167 TCAGTGTTCGCAACA
1 TGAGTGTTCATAGCA
18016182 TGAGTGTTCATAGCA
1 TGAGTGTTCATAGCA
18016197 TGAGT
1 TGAGT
18016202 TCTCGCATCT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (15 bp):
TGAGTGTTCATAGCA
Found at i:18016208 original size:30 final size:30
Alignment explanation
Indices: 18016136--18016197 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
18016126 TGCTCGCAAT
* **
18016136 ATCAGTGTTAGCAATGTGAGTGATCATAGC
1 ATCAGTGTTCGCAACATGAGTGATCATAGC
*
18016166 ATCAGTGTTCGCAACATGAGTGTTCATAGC
1 ATCAGTGTTCGCAACATGAGTGATCATAGC
18016196 AT
1 AT
18016198 GAGTTCTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (30 bp):
ATCAGTGTTCGCAACATGAGTGATCATAGC
Found at i:18021123 original size:11 final size:11
Alignment explanation
Indices: 18021109--18021134 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18021099 AAATCAAACA
18021109 AAAAGAAAAAG
1 AAAAGAAAAAG
18021120 AAAAGAAAAAG
1 AAAAGAAAAAG
18021131 AAAA
1 AAAA
18021135 AAATATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:18025010 original size:123 final size:123
Alignment explanation
Indices: 18024865--18025471 Score: 946
Period size: 123 Copynumber: 4.9 Consensus size: 123
18024855 GATTTCGTTA
18024865 AATATT-AAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*
18024929 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAATGAAATTG
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * *
18024987 AATATTAAAAACATGAAAGTTAATATCCATTTGGAAAGGATATAATGTTTTAATAAACCTCCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*
18025052 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
*
18025110 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* *
18025175 ATATTTCTCTAAGGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * *
18025233 AATATTAAAAACATGAAAGTTAATATCTTTTTGGAAAGGATATAATATTTTAATAAATCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* * * ** * *
18025298 ATGTTTCTCTGAAGGGAATATTTTTATTTTAATATAAGATTTTATATAAAAGGAAATTG
66 ATATTTCT-TTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* **
18025357 AATATTAAAAACATGGAAGTTAATATCTTTTTGGAAAGGGCATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*** * * *
18025422 ATATTTCGCAAAAGGAATATTTTCATTTTAATATAAGATATTAAATAAAA
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAA
18025472 AAAGAAAAGA
Statistics
Matches: 446, Mismatches: 37, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
122 6 0.01
123 330 0.74
124 110 0.25
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:18026586 original size:22 final size:23
Alignment explanation
Indices: 18026560--18026607 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
18026550 GCCAAGAAAG
* *
18026560 AGAAAATTAGTGGAAA-ACAAAA
1 AGAAAATGAGTAGAAACACAAAA
18026582 AGAAAATGAGTAGAAACACAAAA
1 AGAAAATGAGTAGAAACACAAAA
18026605 AGA
1 AGA
18026608 GAAGGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.65, C:0.06, G:0.19, T:0.10
Consensus pattern (23 bp):
AGAAAATGAGTAGAAACACAAAA
Found at i:18037872 original size:24 final size:25
Alignment explanation
Indices: 18037827--18037878 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
18037817 TATATAATTT
*
18037827 TTATTATCTTTATCTTTGTTTTGAA
1 TTATTATCTTTATCTTTGTTTTAAA
18037852 TTATTAT-TTTATCTTAT-TTTTAAA
1 TTATTATCTTTATCTT-TGTTTTAAA
18037876 TTA
1 TTA
18037879 ATGGTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (25 bp):
TTATTATCTTTATCTTTGTTTTAAA
Found at i:18048975 original size:33 final size:33
Alignment explanation
Indices: 18048933--18049000 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
18048923 CTGCCACTAT
*
18048933 TTATCATGCTTATTTGATATCTTTTTACACTTA
1 TTATCATGCTTATTTGATATCCTTTTACACTTA
18048966 TTATCATGCTTATTTGATATCCTTTTACACTTA
1 TTATCATGCTTATTTGATATCCTTTTACACTTA
18048999 TT
1 TT
18049001 TTAGCATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.54
Consensus pattern (33 bp):
TTATCATGCTTATTTGATATCCTTTTACACTTA
Found at i:18050958 original size:64 final size:64
Alignment explanation
Indices: 18050852--18050981 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 64
18050842 AATAGATATG
* * * * *
18050852 AAAAGTAAGCATATATGAAATTCAATAAATAAATCTAAGACTTATAAATGTCATGCATTTAAAC
1 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTATAAATGTAATGCATTTAAAC
* *
18050916 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTATAGATTTAATGCATTTAAAC
1 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTATAAATGTAATGCATTTAAAC
18050980 AA
1 AA
18050982 TGTGTAACAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (64 bp):
AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTATAAATGTAATGCATTTAAAC
Found at i:18052056 original size:38 final size:38
Alignment explanation
Indices: 18052005--18052093 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
18051995 TGATTGATTG
* *
18052005 CATGTTCAGCATGCCCACTGATATTATTGAATCGAATA
1 CATGTTAAGCATGCCCACTGATACTATTGAATCGAATA
* * * * *
18052043 CATGTTAAGCATGCCTACTGCTACTGTTGAATTGAGTA
1 CATGTTAAGCATGCCCACTGATACTATTGAATCGAATA
*
18052081 CATGTTAAACATG
1 CATGTTAAGCATG
18052094 TCTACTGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (38 bp):
CATGTTAAGCATGCCCACTGATACTATTGAATCGAATA
Found at i:18052099 original size:38 final size:38
Alignment explanation
Indices: 18052031--18052152 Score: 172
Period size: 38 Copynumber: 3.2 Consensus size: 38
18052021 ACTGATATTA
* * * * *
18052031 TTGAATCGAATACATGTTAAGCATGCCTACTGCTACTG
1 TTGAATTGAGTACATGTTAAACATGTCTACTGCTAGTG
*
18052069 TTGAATTGAGTACATGTTAAACATGTCTACTGTTAGTG
1 TTGAATTGAGTACATGTTAAACATGTCTACTGCTAGTG
* *
18052107 ATGAATTGCGTACATGTTAAACATGTCTACTGCTAGTG
1 TTGAATTGAGTACATGTTAAACATGTCTACTGCTAGTG
18052145 TTGAATTG
1 TTGAATTG
18052153 TTCTATTACA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (38 bp):
TTGAATTGAGTACATGTTAAACATGTCTACTGCTAGTG
Found at i:18055801 original size:25 final size:25
Alignment explanation
Indices: 18055759--18056135 Score: 328
Period size: 25 Copynumber: 14.8 Consensus size: 25
18055749 AGTTTAGCTA
*
18055759 TTACGAGCCCAGACAGAATATCGCTC
1 TTACGAG-CCAGTCAGAATATCGCTC
*
18055785 TTACGAGCCAGTCAGAATATGGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* *
18055810 TTACAAGCCAGAT-AAAATATCGCTC
1 TTACGAGCCAG-TCAGAATATCGCTC
* *
18055835 CTACGAGCCAGTCAGAATATTGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* **
18055860 TTACGAGCTAGAT-AGAATATTTCTC
1 TTACGAGCCAG-TCAGAATATCGCTC
* * * *
18055885 TCATGAGCTAGACAGAATATCGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* *
18055910 TTTCGAGCCAGAATCAGAATATCACTC
1 TTACGAGCCAG--TCAGAATATCGCTC
* * * *
18055937 TTTCGAGCGAGAATCAAAATATCACTC
1 TTACGAGCCAG--TCAGAATATCGCTC
* *
18055964 TTACGAGCCAGACAAAATATCGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* *
18055989 CTATGAGCCAGTCAGAATATCGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
*
18056014 TTACGAGCCCGAT-AGAATATCGCTC
1 TTACGAGCCAG-TCAGAATATCGCTC
* * *
18056039 TTATGAGCCAGACAGAATATTGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* * *
18056064 TCATGAGCCAGACAGAATATCGCTC
1 TTACGAGCCAGTCAGAATATCGCTC
* * *
18056089 TTTCGAGCCAGAATCATAATATCACTC
1 TTACGAGCCAG--TCAGAATATCGCTC
* *
18056116 TCACGAGCCAGACAGAATAT
1 TTACGAGCCAGTCAGAATAT
18056136 TACTTCTATA
Statistics
Matches: 289, Mismatches: 52, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.00
25 212 0.73
26 10 0.03
27 66 0.23
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (25 bp):
TTACGAGCCAGTCAGAATATCGCTC
Found at i:18055829 original size:50 final size:50
Alignment explanation
Indices: 18055759--18056135 Score: 376
Period size: 50 Copynumber: 7.4 Consensus size: 50
18055749 AGTTTAGCTA
* *
18055759 TTACGAGCCCAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATGGCTC
1 TTACGAG-CCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
* * * *
18055810 TTACAAGCCAGATAAAATATCGCTCCTACGAGCCAGTCAGAATATTGCTC
1 TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
* ** * * * *
18055860 TTACGAGCTAGATAGAATATTTCTCTCATGAGCTAGACAGAATATCGCTC
1 TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
* * * * * *
18055910 TTTCGAGCCAGAATCAGAATATCACTCTTTCGAGCGAGAATCAAAATATCACTC
1 TTACGAGCCAG-AT-AGAATATCGCTCTTACGAGCCAG--TCAGAATATCGCTC
* * * *
18055964 TTACGAGCCAGACAAAATATCGCTCCTATGAGCCAGTCAGAATATCGCTC
1 TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
* * * *
18056014 TTACGAGCCCGATAGAATATCGCTCTTATGAGCCAGACAGAATATTGCTC
1 TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
* * * * * *
18056064 TCATGAGCCAGACAGAATATCGCTCTTTCGAGCCAGAATCATAATATCACTC
1 TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAG--TCAGAATATCGCTC
* *
18056116 TCACGAGCCAGACAGAATAT
1 TTACGAGCCAGATAGAATAT
18056136 TACTTCTATA
Statistics
Matches: 266, Mismatches: 54, Indels: 11
0.80 0.16 0.03
Matches are distributed among these distances:
50 173 0.65
51 8 0.03
52 63 0.24
53 1 0.00
54 21 0.08
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (50 bp):
TTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGTCAGAATATCGCTC
Found at i:18055862 original size:75 final size:75
Alignment explanation
Indices: 18055760--18056159 Score: 381
Period size: 75 Copynumber: 5.2 Consensus size: 75
18055750 GTTTAGCTAT
* * * *
18055760 TACGAGCCCAGACAGAATATCGCTCTTACGAGCCAG-TCAGAATATGGCTCTTACAAGCCAGATA
1 TACGAG-CCAGTCAGAATATCGCTCTTACGAGCCAGAT-AGAATATCGCTCTTACGAGCCAGACA
18055824 AAATATCGCTCC
64 AAATATCGCTCC
* * ** * * * *
18055836 TACGAGCCAGTCAGAATATTGCTCTTACGAGCTAGATAGAATATTTCTCTCATGAGCTAGACAGA
1 TACGAGCCAGTCAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGACAAA
*
18055901 ATATCGCTCT
66 ATATCGCTCC
* * * * * *
18055911 TTCGAGCCAGAATCAGAATATCACTCTTTCGAGCGAGAATCAAAATATCACTCTTACGAGCCAGA
1 TACGAGCCAG--TCAGAATATCGCTCTTACGAGCCAG-AT-AGAATATCGCTCTTACGAGCCAGA
18055976 CAAAATATCGCTCC
62 CAAAATATCGCTCC
* * * *
18055990 TATGAGCCAGTCAGAATATCGCTCTTACGAGCCCGATAGAATATCGCTCTTATGAGCCAGACAGA
1 TACGAGCCAGTCAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGACAAA
*
18056055 ATATTGCT-C
66 ATATCGCTCC
* * * * * *
18056064 TCATGAGCCAGACAGAATATCGCTCTTTCGAGCCAGAATCATAATATCACTCTCACGAGCCAGAC
1 T-ACGAGCCAGTCAGAATATCGCTCTTACGAGCCAG-AT-AGAATATCGCTCTTACGAGCCAGAC
* ** *
18056129 AGAATATTACTTC
63 AAAATATCGCTCC
**
18056142 TATAAGCCAGTCAGAATA
1 TACGAGCCAGTCAGAATA
18056160 ACATTCATTC
Statistics
Matches: 269, Mismatches: 46, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
74 2 0.01
75 126 0.47
76 11 0.04
77 88 0.33
78 4 0.01
79 38 0.14
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (75 bp):
TACGAGCCAGTCAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAGACAAA
ATATCGCTCC
Found at i:18056082 original size:179 final size:179
Alignment explanation
Indices: 18055775--18056116 Score: 499
Period size: 179 Copynumber: 1.9 Consensus size: 179
18055765 GCCCAGACAG
* * * * *
18055775 AATATCGCTCTTACGAGCCAGTCAGAATATGGCTCTTACAAGCCAGATAAAATATCGCTCCTACG
1 AATATCACTCTTACGAGCCAGACAAAATATCGCTCCTACAAGCCAGATAAAATATCGCTCCTACG
* * * * *
18055840 AGCCAGTCAGAATATTGCTCTTACGAGCTAGATAGAATATTTCTCTCATGAGCTAGACAGAATAT
66 AGCCAGTCAGAATATCGCTCTTACGAGCCAGACAGAATATTGCTCTCATGAGCCAGACAGAATAT
18055905 CGCTCTTTCGAGCCAGAATCAGAATATCACTCTTTCGAGCGAGAATCAA
131 CGCTCTTTCGAGCCAGAATCAGAATATCACTCTTTCGAGCGAGAATCAA
** * *
18055954 AATATCACTCTTACGAGCCAGACAAAATATCGCTCCTATGAGCCAG-TCAGAATATCGCTCTTAC
1 AATATCACTCTTACGAGCCAGACAAAATATCGCTCCTACAAGCCAGAT-AAAATATCGCTCCTAC
* *
18056018 GAGCCCGAT-AGAATATCGCTCTTATGAGCCAGACAGAATATTGCTCTCATGAGCCAGACAGAAT
65 GAGCCAG-TCAGAATATCGCTCTTACGAGCCAGACAGAATATTGCTCTCATGAGCCAGACAGAAT
*
18056082 ATCGCTCTTTCGAGCCAGAATCATAATATCACTCT
129 ATCGCTCTTTCGAGCCAGAATCAGAATATCACTCT
18056117 CACGAGCCAG
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
178 1 0.01
179 142 0.99
180 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (179 bp):
AATATCACTCTTACGAGCCAGACAAAATATCGCTCCTACAAGCCAGATAAAATATCGCTCCTACG
AGCCAGTCAGAATATCGCTCTTACGAGCCAGACAGAATATTGCTCTCATGAGCCAGACAGAATAT
CGCTCTTTCGAGCCAGAATCAGAATATCACTCTTTCGAGCGAGAATCAA
Found at i:18057821 original size:14 final size:15
Alignment explanation
Indices: 18057802--18057835 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18057792 ACTAACTTTT
18057802 AATTCAATAATT-AA
1 AATTCAATAATTCAA
*
18057816 AATTCACTAATTCAA
1 AATTCAATAATTCAA
18057831 AATTC
1 AATTC
18057836 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:18063410 original size:26 final size:23
Alignment explanation
Indices: 18063375--18063423 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
18063365 TTATCTAGTA
*
18063375 GTTATTTATTTTCATGTCATTTTATT
1 GTTATCTATTTT-AT-T-ATTTTATT
18063401 GTTATCTATTTTATTATTTTATT
1 GTTATCTATTTTATTATTTTATT
18063424 ATTTAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
25 2 0.09
26 11 0.50
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.67
Consensus pattern (23 bp):
GTTATCTATTTTATTATTTTATT
Found at i:18063616 original size:16 final size:16
Alignment explanation
Indices: 18063563--18063619 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 16
18063553 GCATTGCATA
18063563 TATTTGTTATTA-TTT
1 TATTTGTTATTATTTT
* *
18063578 TATTTATTA-TATATT
1 TATTTGTTATTATTTT
*
18063593 CATTTGTTATTATTTT
1 TATTTGTTATTATTTT
*
18063609 TTTTTGTTATT
1 TATTTGTTATT
18063620 TACATTCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 2 0.06
15 17 0.52
16 14 0.42
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (16 bp):
TATTTGTTATTATTTT
Found at i:18063668 original size:15 final size:15
Alignment explanation
Indices: 18063563--18063673 Score: 57
Period size: 15 Copynumber: 7.2 Consensus size: 15
18063553 GCATTGCATA
18063563 TATTTGTTA-TTATTT
1 TATTTGTTATTTA-TT
* *
18063578 TATTTATTATATATT
1 TATTTGTTATTTATT
* *
18063593 CATTTGTTATTATTTT
1 TATTTGTTATT-TATT
* *
18063609 TTTTTGTTATTTACAT
1 TATTTGTTATTTA-TT
* *
18063625 TCTTGCTTTTATTTAATT
1 TATT--TGTTATTT-ATT
* *
18063643 TAATT-TAATTTATT
1 TATTTGTTATTTATT
18063657 TATTTGTTATTT-TT
1 TATTTGTTATTTATT
18063671 TAT
1 TAT
18063674 GCTATTTATA
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
14 12 0.17
15 29 0.41
16 19 0.27
18 10 0.14
19 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.69
Consensus pattern (15 bp):
TATTTGTTATTTATT
Found at i:18067414 original size:3 final size:3
Alignment explanation
Indices: 18067408--18067470 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
18067398 AAAAATCATA
18067408 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18067454 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
18067471 AGATCCTCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18100390 original size:15 final size:15
Alignment explanation
Indices: 18100372--18100433 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
18100362 CCTTCATCCA
18100372 TGTTCGCAACATCAG
1 TGTTCGCAACATCAG
*
18100387 TGTTCGCAGC-TCCAG
1 TGTTCGCAACAT-CAG
* *
18100402 TGTCCGCAACATGAG
1 TGTTCGCAACATCAG
* *
18100417 TGCTCGCAACACCAG
1 TGTTCGCAACATCAG
18100432 TG
1 TG
18100434 CTCACATCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (15 bp):
TGTTCGCAACATCAG
Found at i:18100410 original size:30 final size:30
Alignment explanation
Indices: 18100368--18100433 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
18100358 TTATCCTTCA
* * *
18100368 TCCA-TGTTCGCAACATCAGTGTTCGCAGC
1 TCCAGTGTCCGCAACATCAGTGCTCGCAAC
*
18100397 TCCAGTGTCCGCAACATGAGTGCTCGCAAC
1 TCCAGTGTCCGCAACATCAGTGCTCGCAAC
*
18100427 ACCAGTG
1 TCCAGTG
18100434 CTCACATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGTGTCCGCAACATCAGTGCTCGCAAC
Found at i:18103479 original size:17 final size:17
Alignment explanation
Indices: 18103459--18103502 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
18103449 TTCAATTTAT
*
18103459 TTGTCATTGCATTTGCA
1 TTGTCATTGCATTTCCA
*
18103476 TTGTCATTACATTTCCA
1 TTGTCATTGCATTTCCA
18103493 TGTGTCATTG
1 T-TGTCATTG
18103503 TAAATTAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (17 bp):
TTGTCATTGCATTTCCA
Found at i:18106071 original size:45 final size:44
Alignment explanation
Indices: 18106020--18106768 Score: 780
Period size: 45 Copynumber: 16.6 Consensus size: 44
18106010 CACCAAATTG
* *
18106020 AATCTTTTACCCCTAATCTAGAGGCCCAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCCAGAGG-GCAGATTGAAGCCACCATCC
* ** * *
18106065 AGTCTTTTACCCCTAATCTGGAGAGACAGATTGAAGCCACCATCT
1 AATCTTTTACCCCTAATCCAGAG-GGCAGATTGAAGCCACCATCC
* * * *
18106110 AATCTTTTACCCCTAATCTAGAGAGGCAGTTTAAAGCCACCATCT
1 AATCTTTTACCCCTAATCCAGAG-GGCAGATTGAAGCCACCATCC
* * * * * *
18106155 AATCTTTCACCTCTAATCCAGAGAGGCAAATTGAACCCATCATTC
1 AATCTTTTACCCCTAATCCAGAG-GGCAGATTGAAGCCACCATCC
* * *
18106200 AATCTTTTACCCCTAATCCAGAGAGGCAAATTAAACCCACCATCC
1 AATCTTTTACCCCTAATCCAGAG-GGCAGATTGAAGCCACCATCC
*
18106245 AATCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGTCACCATCC
1 AATCTTTTACCCCTAATCCAGA-GGGCAGATTGAAGCCACCATCC
* *
18106290 AATATTTTACCCCTAAATCCAGAGGGGCAGATTAAAGCCACCATCC
1 AATCTTTTACCCCT-AATCCAGA-GGGCAGATTGAAGCCACCATCC
* * * * *
18106336 AATCTTTTACCCTTAAATCCAAAAAGGCAGATTGAGGTCACCATCC
1 AATCTTTTACCCCT-AATCC-AGAGGGCAGATTGAAGCCACCATCC
* * *
18106382 AATCTTTTACCCCTAATCTAGAAGGGTAGATTAAAGCCACCATCC
1 AATCTTTTACCCCTAATCCAG-AGGGCAGATTGAAGCCACCATCC
* * * * *
18106427 AAACTTTTACCCCTAATCTAGAGGGGCAAATCGAAGCAACCATCC
1 AATCTTTTACCCCTAATCCAGA-GGGCAGATTGAAGCCACCATCC
* * * *
18106472 AATCTTTTACCCCTAAATCCAAAGGGCATACTGAAGCCATCAT-C
1 AATCTTTTACCCCT-AATCCAGAGGGCAGATTGAAGCCACCATCC
*
18106516 AATCTTTTACCCTTAAATCCAGAGGGACAGATTGAAGCCACCATCC
1 AATCTTTTACCCCT-AATCCAGAGGG-CAGATTGAAGCCACCATCC
* * * * * *
18106562 AATCTTATACCTCTAAATCTAGAAGGACATATTGAAGCTACCATCC
1 AATCTTTTACCCCT-AATCCAG-AGGGCAGATTGAAGCCACCATCC
* * * *
18106608 AATCTATTACCCCAAATCTAGAGTGACAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCCAGAG-GGCAGATTGAAGCCACCATCC
* *
18106653 AATCTTTTACCCCTAATCCAGAGGGTAGAGTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCCAGAGGGCAGATTGAAGCCACCATCC
* *
18106697 AATCTTTTACCCCTAAATCCAGAGAGCCAGATTAAAGCCACCATCC
1 AATCTTTTACCCCT-AATCCAGAG-GGCAGATTGAAGCCACCATCC
* * *
18106743 AATCTTATACCCTTAAATCTAGAGGG
1 AATCTTTTACCCCT-AATCCAGAGGG
18106769 GCGGATTAAA
Statistics
Matches: 599, Mismatches: 92, Indels: 26
0.84 0.13 0.04
Matches are distributed among these distances:
44 61 0.10
45 363 0.61
46 170 0.28
47 5 0.01
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (44 bp):
AATCTTTTACCCCTAATCCAGAGGGCAGATTGAAGCCACCATCC
Found at i:18107680 original size:20 final size:20
Alignment explanation
Indices: 18107655--18107692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18107645 ATTATTATTT
18107655 ATATTTAGTTGTTTATTTTG
1 ATATTTAGTTGTTTATTTTG
**
18107675 ATATTTTTTTGTTTATTT
1 ATATTTAGTTGTTTATTT
18107693 ATTTATTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (20 bp):
ATATTTAGTTGTTTATTTTG
Found at i:18107699 original size:20 final size:21
Alignment explanation
Indices: 18107649--18107700 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
18107639 TTTATTATTA
18107649 TTATTTATATTTAGTTGTTTAT
1 TTATTTAT-TTTAGTTGTTTAT
* *
18107671 TT-TGATATTTT-TTTGTTTAT
1 TTAT-TTATTTTAGTTGTTTAT
18107691 TTATTTATTT
1 TTATTTATTT
18107701 GTTATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 15 0.60
21 5 0.20
22 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (21 bp):
TTATTTATTTTAGTTGTTTAT
Found at i:18107707 original size:15 final size:16
Alignment explanation
Indices: 18107676--18107711 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
18107666 TTTATTTTGA
*
18107676 TATTTTTTTGTTTATT
1 TATTTATTTGTTTATT
18107692 TATTTATTTG-TTATT
1 TATTTATTTGTTTATT
18107707 TATTT
1 TATTT
18107712 TCATGCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TATTTATTTGTTTATT
Found at i:18107792 original size:12 final size:12
Alignment explanation
Indices: 18107733--18107792 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
18107723 CCTAATTATT
*
18107733 TTTATTGTTTATA
1 TTTATTTTTTA-A
*
18107746 TTTATTTGTTTAC
1 TTTATTT-TTTAA
* *
18107759 TTTAGTATTTAA
1 TTTATTTTTTAA
18107771 TTT-TTATTTTAA
1 TTTATT-TTTTAA
18107783 TTTATTTTTT
1 TTTATTTTTT
18107793 GTTTATTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
11 1 0.03
12 19 0.51
13 13 0.35
14 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:18108088 original size:22 final size:20
Alignment explanation
Indices: 18108061--18108116 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
18108051 ACATTCTTGC
18108061 TTTTATTTAATTTTATTTATT
1 TTTTATTT-ATTTTATTTATT
*
18108082 GTTTTATGTATTTTATTTATT
1 -TTTTATTTATTTTATTTATT
*
18108103 TGTTATTT-TTTTAT
1 TTTTATTTATTTTAT
18108117 ACTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 12 0.39
22 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTATTTATTTTATTTATT
Found at i:18118401 original size:9 final size:8
Alignment explanation
Indices: 18118384--18118429 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
18118374 ACGAAGAAGC
*
18118384 AAGAGAAG
1 AAGAAAAG
18118392 AAGAGAAAG
1 AAGA-AAAG
18118401 AAGAAAAGG
1 AAGAAAA-G
18118410 AAGAAAAG
1 AAGAAAAG
18118418 AAGAAAA-
1 AAGAAAAG
18118425 AAGAA
1 AAGAA
18118430 GAAAGCATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 5 0.14
8 15 0.43
9 15 0.43
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:18118404 original size:17 final size:16
Alignment explanation
Indices: 18118384--18118434 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
18118374 ACGAAGAAGC
18118384 AAGAGAAGAAGAGAAAG
1 AAGA-AAGAAGAGAAAG
18118401 AAGAAAAGGAAGA-AAAG
1 AAG-AAA-GAAGAGAAAG
*
18118418 AAGAAAAAAGAAGAAAG
1 AAGAAAGAAG-AGAAAG
18118435 CATTGCCCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 3 0.10
16 4 0.14
17 16 0.55
18 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAGAGAAAG
Found at i:18118425 original size:18 final size:17
Alignment explanation
Indices: 18118389--18118433 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
18118379 GAAGCAAGAG
18118389 AAGAAGAGAAAGAAGAAA
1 AAGAAGA-AAAGAAGAAA
*
18118407 AGGAAGAAAAGAAGAAAA
1 AAGAAGAAAAGAAG-AAA
18118425 AAGAAGAAA
1 AAGAAGAAA
18118434 GCATTGCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAGAAGAAA
Found at i:18128364 original size:20 final size:21
Alignment explanation
Indices: 18128328--18128366 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18128318 GTTTTTAGTC
18128328 ATTTTAAAGAAAAAGTTTAAA
1 ATTTTAAAGAAAAAGTTTAAA
*
18128349 ATTTTAAA-ATAAAGTTTA
1 ATTTTAAAGAAAAAGTTTA
18128367 TTTTTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (21 bp):
ATTTTAAAGAAAAAGTTTAAA
Found at i:18129139 original size:3 final size:3
Alignment explanation
Indices: 18129133--18129169 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
18129123 ATTATTATTA
18129133 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
18129170 CGTCATCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:18132310 original size:13 final size:13
Alignment explanation
Indices: 18132292--18132316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18132282 CGGGTCATAT
18132292 GGTTTGGGTTAAG
1 GGTTTGGGTTAAG
18132305 GGTTTGGGTTAA
1 GGTTTGGGTTAA
18132317 ACTGAATTGA
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:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
GGTTTGGGTTAAG
Found at i:18143386 original size:24 final size:24
Alignment explanation
Indices: 18143359--18143406 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
18143349 AAATTCATAA
18143359 GTTAAATAAATTAT-GCTAATAAAT
1 GTTAAATAAATTATAG-TAATAAAT
*
18143383 GTTAAATATATTATAGTAATAAAT
1 GTTAAATAAATTATAGTAATAAAT
18143407 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
GTTAAATAAATTATAGTAATAAAT
Found at i:18143412 original size:24 final size:24
Alignment explanation
Indices: 18143361--18143413 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18143351 ATTCATAAGT
**
18143361 TAAATAAATTATGCTAATAAATGT
1 TAAATAAATTATGCTAATAAATAC
*
18143385 TAAATATATTATAG-TAATAAATAC
1 TAAATAAATTAT-GCTAATAAATAC
18143409 TAAAT
1 TAAAT
18143414 CTTCTAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAATAAATTATGCTAATAAATAC
Found at i:18144393 original size:18 final size:21
Alignment explanation
Indices: 18144366--18144408 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18144356 AAGCAGTGGA
18144366 TTTT-TTTCAT-TT-TA-ATT
1 TTTTATTTCATATTATACATT
18144383 TTTTATTTCATATTATACATT
1 TTTTATTTCATATTATACATT
18144404 TTTTA
1 TTTTA
18144409 AAAGTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 2 0.09
20 2 0.09
21 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTTCATATTATACATT
Found at i:18151622 original size:29 final size:29
Alignment explanation
Indices: 18151570--18151625 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
18151560 TAACATCATT
* * *
18151570 TTATATTTATATATTGTAATAATAAATAA
1 TTATATTTATATAATATAAAAATAAATAA
*
18151599 TTATATTTATCTAATATAAAAATAAAT
1 TTATATTTATATAATATAAAAATAAAT
18151626 TGATGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TTATATTTATATAATATAAAAATAAATAA
Found at i:18158301 original size:31 final size:31
Alignment explanation
Indices: 18158273--18158346 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
18158263 CACCGGTATG
*
18158273 TAGTACCTT-ATATAATATGGTCATCGGTACT
1 TAGTA-CTTGATATAATATAGTCATCGGTACT
*
18158304 TAGTACTTGATATAATATAGTCA-CTGGTACA
1 TAGTACTTGATATAATATAGTCATC-GGTACT
*
18158335 TAGTATTTGATA
1 TAGTACTTGATA
18158347 CTTTCAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (31 bp):
TAGTACTTGATATAATATAGTCATCGGTACT
Found at i:18162130 original size:35 final size:35
Alignment explanation
Indices: 18162047--18162134 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
18162037 TTATAGCGTT
* *
18162047 TCTAGTGTGTTGGATGGTACTGGCTCTTACGAGCA
1 TCTAGTGTGCTGGATGGTACTAGCTCTTACGAGCA
* * * *
18162082 TCTATTGTACTGGATGGTACTATCTCTTATGAGCA
1 TCTAGTGTGCTGGATGGTACTAGCTCTTACGAGCA
* *
18162117 TTTGGTGTGCTGGATGGT
1 TCTAGTGTGCTGGATGGT
18162135 TAACCGTGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.39
Consensus pattern (35 bp):
TCTAGTGTGCTGGATGGTACTAGCTCTTACGAGCA
Found at i:18167364 original size:12 final size:11
Alignment explanation
Indices: 18167347--18167407 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 11
18167337 GAAAAGTACT
18167347 AAAAATAAACAA
1 AAAAATAAA-AA
18167359 AAAAATAAAAA
1 AAAAATAAAAA
18167370 ATAAAGATAAAATA
1 A-AAA-ATAAAA-A
18167384 AATAAATAAATAA
1 AA-AAATAAA-AA
18167397 ATAAAATAAAA
1 A-AAAATAAAA
18167408 TACAAACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.07
12 13 0.30
13 21 0.49
14 6 0.14
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:18167388 original size:4 final size:4
Alignment explanation
Indices: 18167349--18167406 Score: 57
Period size: 4 Copynumber: 14.8 Consensus size: 4
18167339 AAAGTACTAA
* * * *
18167349 AAAT AAAC AAAA AAAT AAA- AAAT AAAG ATA- AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
18167395 AAAT AAAAT AAA
1 AAAT -AAAT AAA
18167407 ATACAAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 5 0.11
4 36 0.80
5 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:18167618 original size:16 final size:16
Alignment explanation
Indices: 18167592--18167637 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
18167582 TAAGAGTGCT
18167592 AAAAA-TAAATA-ACAA
1 AAAAAGTAAATATA-AA
*
18167607 AATAAGTAAATATAAA
1 AAAAAGTAAATATAAA
18167623 AAAAAGTAAA-ATAAA
1 AAAAAGTAAATATAAA
18167638 TATGCAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
AAAAAGTAAATATAAA
Found at i:18168454 original size:14 final size:14
Alignment explanation
Indices: 18168435--18168461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18168425 AAGGTTGTTT
18168435 TATTTTTATTTTTA
1 TATTTTTATTTTTA
18168449 TATTTTTATTTTT
1 TATTTTTATTTTT
18168462 GAAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TATTTTTATTTTTA
Found at i:18175547 original size:81 final size:81
Alignment explanation
Indices: 18175390--18175558 Score: 250
Period size: 81 Copynumber: 2.1 Consensus size: 81
18175380 TCGGACCTTC
* *
18175390 TTCTTATTATTCTCACCTCTATATGCAAACTCACATTAGGCCAAACAATGTGTCGCGAGAATAAA
1 TTCTTATTATTCTCACCTCTATATGCAAACTCACATTAGGCCAAACAATGTCTCACGAGAATAAA
* *
18175455 CTCCCTTGATCTGTAT
66 CTCCATTGATCTATAT
* *
18175471 TTCTTATTGTTCTCAGCTCTATATGCAAACTCACATTAGGCCAAACAATGTCTCACGAGAATAAA
1 TTCTTATTATTCTCACCTCTATATGCAAACTCACATTAGGCCAAACAATGTCTCACGAGAATAAA
*
18175536 CT-GATTCGATCTATAT
66 CTCCATT-GATCTATAT
18175552 TATCTTA
1 T-TCTTA
18175559 GCACAAGTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 2 0.03
81 72 0.91
82 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (81 bp):
TTCTTATTATTCTCACCTCTATATGCAAACTCACATTAGGCCAAACAATGTCTCACGAGAATAAA
CTCCATTGATCTATAT
Found at i:18184530 original size:26 final size:26
Alignment explanation
Indices: 18184494--18184546 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
18184484 TATTTTCTTG
*
18184494 AAATTTTACCAAGGGCAAAATCATCA
1 AAATTCTACCAAGGGCAAAATCATCA
* *
18184520 AAATTCTACCAAGGGTAAAATCGTCA
1 AAATTCTACCAAGGGCAAAATCATCA
18184546 A
1 A
18184547 TTTTTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (26 bp):
AAATTCTACCAAGGGCAAAATCATCA
Found at i:18188376 original size:25 final size:24
Alignment explanation
Indices: 18188341--18188452 Score: 74
Period size: 25 Copynumber: 4.8 Consensus size: 24
18188331 GTTCATTTAC
*
18188341 ACATTAATCACATTAACACATATA
1 ACATTTATCACATTAACACATATA
* *
18188365 AGCATTTATCACATATAAGCATATATC
1 A-CATTTATCACAT-TAA-CACATATA
* ***
18188392 ACA-TTAACACA-TAA-GGGTAT-
1 ACATTTATCACATTAACACATATA
18188412 ACA--TATCACATTAACACATATA
1 ACATTTATCACATTAACACATATA
*
18188434 AGCATATATCACATTAACA
1 A-CATTTATCACATTAACA
18188453 TGATAGTTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
19 6 0.09
20 6 0.09
21 6 0.09
22 1 0.01
23 5 0.07
24 1 0.01
25 31 0.46
26 5 0.07
27 7 0.10
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (24 bp):
ACATTTATCACATTAACACATATA
Found at i:18188377 original size:17 final size:17
Alignment explanation
Indices: 18188357--18188447 Score: 73
Period size: 17 Copynumber: 5.3 Consensus size: 17
18188347 ATCACATTAA
*
18188357 CACATATAAGCATTTAT
1 CACATATAAGCATATAT
18188374 CACATATAAGCATATAT
1 CACATATAAGCATATAT
*
18188391 CACAT-TAACACATAAGGGTAT
1 CACATATAA-GCAT-A---TAT
* *
18188412 -ACATATCA-CAT-TAA
1 CACATATAAGCATATAT
18188426 CACATATAAGCATATAT
1 CACATATAAGCATATAT
18188443 CACAT
1 CACAT
18188448 TAACATGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
16 6 0.10
17 31 0.53
18 1 0.02
19 3 0.05
20 4 0.07
21 5 0.08
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.29
Consensus pattern (17 bp):
CACATATAAGCATATAT
Found at i:18188441 original size:29 final size:27
Alignment explanation
Indices: 18188387--18188441 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
18188377 ATATAAGCAT
**
18188387 ATATCACATTAACACATAAGGGTATAC
1 ATATCACATTAACACATAAGCATATAC
18188414 ATATCACATTAACACATATAAGCATATA
1 ATATCACATTAACAC--ATAAGCATATA
18188442 TCACATTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
29 9 0.38
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.27
Consensus pattern (27 bp):
ATATCACATTAACACATAAGCATATAC
Found at i:18202982 original size:40 final size:40
Alignment explanation
Indices: 18202866--18202990 Score: 181
Period size: 36 Copynumber: 3.3 Consensus size: 40
18202856 AATTTGTGAT
18202866 AAAGA-AAGACTTATGACTCAGTAGAGCATAAGATTGTTA
1 AAAGAGAAGACTTATGACTCAGTAGAGCATAAGATTGTTA
*
18202905 AAAGGGAAGACTTATGA--C--TAGAGCATAAGATTGTTA
1 AAAGAGAAGACTTATGACTCAGTAGAGCATAAGATTGTTA
* *
18202941 AAAGAGAATACTTATGACTCAGTAGAGCATAAGATTTTTA
1 AAAGAGAAGACTTATGACTCAGTAGAGCATAAGATTGTTA
18202981 AAAG-GAAGAC
1 AAAGAGAAGAC
18202991 ACATGAACCT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
36 33 0.43
38 2 0.03
39 9 0.12
40 32 0.42
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.25
Consensus pattern (40 bp):
AAAGAGAAGACTTATGACTCAGTAGAGCATAAGATTGTTA
Found at i:18204099 original size:30 final size:31
Alignment explanation
Indices: 18204042--18204111 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
18204032 GGATACGTAA
*
18204042 TACCTGATATAATATTGTCACCGGTACACAG
1 TACCTGATATAATATAGTCACCGGTACACAG
* *
18204073 TACCTGATATAAT-TAGTCATCGGTACATAG
1 TACCTGATATAATATAGTCACCGGTACACAG
*
18204103 TACTTGATA
1 TACCTGATA
18204112 CTTTATTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (31 bp):
TACCTGATATAATATAGTCACCGGTACACAG
Found at i:18223122 original size:26 final size:26
Alignment explanation
Indices: 18223057--18223126 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
18223047 AGGCATGATA
**
18223057 ATTTTACCCCCAATAAAATTATAATG
1 ATTTTACCCCTGATAAAATTATAATG
18223083 ATTTTACCCCTGATAAAATTATAATG
1 ATTTTACCCCTGATAAAATTATAATG
*
18223109 ATTTTACCCTTGATAAAA
1 ATTTTACCCCTGATAAAA
18223127 ATTCTAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (26 bp):
ATTTTACCCCTGATAAAATTATAATG
Found at i:18227351 original size:36 final size:36
Alignment explanation
Indices: 18227237--18227341 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
18227227 TTTGTAAAAG
* *
18227237 TAAATATGTGGGTATGTAATTCATGCCATGTGACAA
1 TAAATATGTGAGTATGTTATTCATGCCATGTGACAA
* *
18227273 TAAATATGTGAGTATATTATTCATGCCATGAGACAA
1 TAAATATGTGAGTATGTTATTCATGCCATGTGACAA
*
18227309 TAAATATGTGAATATGTTATTCATGCCATGTGA
1 TAAATATGTGAGTATGTTATTCATGCCATGTGA
18227342 TAGTGAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (36 bp):
TAAATATGTGAGTATGTTATTCATGCCATGTGACAA
Found at i:18228160 original size:25 final size:24
Alignment explanation
Indices: 18228107--18228162 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
18228097 TTAATTGAAA
18228107 CAAAAAGGCCATAACGTAGGCAAG
1 CAAAAAGGCCATAACGTAGGCAAG
* *
18228131 CAAAAAGGTCATAACTTAGGCAAG
1 CAAAAAGGCCATAACGTAGGCAAG
18228155 CAAAAAGG
1 CAAAAAGG
18228163 AGACTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (24 bp):
CAAAAAGGCCATAACGTAGGCAAG
Found at i:18228161 original size:70 final size:71
Alignment explanation
Indices: 18228063--18228198 Score: 229
Period size: 70 Copynumber: 1.9 Consensus size: 71
18228053 ACACAGAAGC
18228063 AAGGTCATAACTTAAAGGCAAGCAAAAAGGAGACTTAATTGAAACAAAAAGGCCATAACGTAGGC
1 AAGGTCATAACTT-AAGGCAAGCAAAAAGGAGACTTAATTGAAACAAAAAGGCCATAACGTAGGC
18228128 AAGCAAA
65 AAGCAAA
* * *
18228135 AAGGTCATAACTT-AGGCAAGCAAAAAGGAGACTTAATTGAAGCAATAAGGCCATAACTTAGGCA
1 AAGGTCATAACTTAAGGCAAGCAAAAAGGAGACTTAATTGAAACAAAAAGGCCATAACGTAGGCA
18228199 CATTTCACTT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 48 0.79
72 13 0.21
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.16
Consensus pattern (71 bp):
AAGGTCATAACTTAAGGCAAGCAAAAAGGAGACTTAATTGAAACAAAAAGGCCATAACGTAGGCA
AGCAAA
Found at i:18231445 original size:16 final size:16
Alignment explanation
Indices: 18231424--18231456 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18231414 CGGTACATAT
18231424 AGTAAGT-TGTATCACA
1 AGTAAGTATGT-TCACA
18231440 AGTAAGTATGTTCACA
1 AGTAAGTATGTTCACA
18231456 A
1 A
18231457 CTACAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (16 bp):
AGTAAGTATGTTCACA
Found at i:18239204 original size:35 final size:35
Alignment explanation
Indices: 18239130--18239196 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
18239120 AATTAACATC
* * *
18239130 AAAATCCCAAAATTATTTAATAACGCATTAATAAG
1 AAAATCCCAAAATAATTTAATAACGAAATAATAAG
18239165 AAAATCCCAAAATAATTT-ATAA-GAAATAATAA
1 AAAATCCCAAAATAATTTAATAACGAAATAATAA
18239197 ATGAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 8 0.28
34 4 0.14
35 17 0.59
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (35 bp):
AAAATCCCAAAATAATTTAATAACGAAATAATAAG
Found at i:18240261 original size:20 final size:21
Alignment explanation
Indices: 18240232--18240280 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
18240222 TTGATAAAAA
*
18240232 AAAGTTAATGGTCAA-CAGTC
1 AAAGTCAATGGTCAATCAGTC
**
18240252 AAAGTCAATGGTCAATGGGTC
1 AAAGTCAATGGTCAATCAGTC
18240273 AAAGTCAA
1 AAAGTCAA
18240281 CGATCTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (21 bp):
AAAGTCAATGGTCAATCAGTC
Found at i:18244296 original size:20 final size:20
Alignment explanation
Indices: 18244271--18244325 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
18244261 GATTGGTAAG
18244271 AAAGTCAATGGTCAATGATC
1 AAAGTCAATGGTCAATGATC
*** *
18244291 AAAGTCAACAATCAATGGTC
1 AAAGTCAATGGTCAATGATC
18244311 AAAGGT-AATGGTCAA
1 AAA-GTCAATGGTCAA
18244326 CGGGTCAAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAGTCAATGGTCAATGATC
Found at i:18244345 original size:21 final size:21
Alignment explanation
Indices: 18244307--18244346 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18244297 AACAATCAAT
*
18244307 GGTCAAAGGTAATGGTCAACG
1 GGTCAAAGGTAATAGTCAACG
18244328 GGTCAAA-GTGAATAGTCAA
1 GGTCAAAGGT-AATAGTCAA
18244347 GGTCAACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (21 bp):
GGTCAAAGGTAATAGTCAACG
Found at i:18246527 original size:26 final size:27
Alignment explanation
Indices: 18246465--18246529 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
18246455 TTTATTGAGG
*
18246465 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATATT
* *
18246492 TTATTAATTTATCGATAATTTAATA-T
1 TTATTAATTTATCGATAAATGAATATT
18246518 TTATTAATTTAT
1 TTATTAATTTAT
18246530 AGAATATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATGAATATT
Found at i:18246538 original size:26 final size:27
Alignment explanation
Indices: 18246465--18246548 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
18246455 TTTATTGAGG
* * * * *
18246465 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATAGATAATTTAATACT
*
18246492 TTATTAATTTATCGATAATTTAATA-T
1 TTATTAATTTATAGATAATTTAATACT
*
18246518 TTATTAATTTATAGA-ATATTTCATACT
1 TTATTAATTTATAGATA-ATTTAATACT
18246545 TTAT
1 TTAT
18246549 GCATGAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.02
26 22 0.44
27 27 0.54
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (27 bp):
TTATTAATTTATAGATAATTTAATACT
Found at i:18246674 original size:31 final size:33
Alignment explanation
Indices: 18246636--18246715 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 33
18246626 CATGTATCAA
18246636 AGTTAATTGGTTCATGTAA-CAAAAAG-AAAAG
1 AGTTAATTGGTTCATGTAACCAAAAAGAAAAAG
*
18246667 AGTTAATTTATTGATTCATGTAACCAAAAAGAAAAAAG
1 AGTT-A---ATTGGTTCATGTAACCAAAAAG-AAAAAG
18246705 AGTTAA-TGGTT
1 AGTTAATTGGTT
18246716 TCAAAATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
31 4 0.10
32 1 0.03
33 4 0.10
34 1 0.03
35 13 0.32
36 7 0.17
37 1 0.03
38 9 0.22
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.30
Consensus pattern (33 bp):
AGTTAATTGGTTCATGTAACCAAAAAGAAAAAG
Found at i:18246688 original size:35 final size:37
Alignment explanation
Indices: 18246641--18246711 Score: 110
Period size: 35 Copynumber: 1.9 Consensus size: 37
18246631 ATCAAAGTTA
*
18246641 ATTGGTTCATGTAA-CAAAAAG-AAAAGAGTTAATTT
1 ATTGATTCATGTAACCAAAAAGAAAAAGAGTTAATTT
18246676 ATTGATTCATGTAACCAAAAAGAAAAAAGAGTTAAT
1 ATTGATTCATGTAACCAAAAAG-AAAAAGAGTTAAT
18246712 GGTTTCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
38 12 0.38
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.28
Consensus pattern (37 bp):
ATTGATTCATGTAACCAAAAAGAAAAAGAGTTAATTT
Found at i:18248613 original size:15 final size:15
Alignment explanation
Indices: 18248590--18248633 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
18248580 TAACCGAGAT
*
18248590 TATTAATTTATCGAA
1 TATTCATTTATCGAA
*
18248605 TATTCATTTATTGAA
1 TATTCATTTATCGAA
18248620 TATTCATTTATCGA
1 TATTCATTTATCGA
18248634 TGTTTTAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (15 bp):
TATTCATTTATCGAA
Found at i:18250008 original size:24 final size:25
Alignment explanation
Indices: 18249963--18250093 Score: 184
Period size: 24 Copynumber: 5.5 Consensus size: 25
18249953 CTAGACTAAT
* *
18249963 AAGAGTTTAACT-AAAAAAATAAAC
1 AAGAGTTTAATTGAAACAAATAAAC
18249987 AAG-GTTTAATTGAAACAAATAAAC
1 AAGAGTTTAATTGAAACAAATAAAC
18250011 -AGAGTTTAATTGAAACAAATAAAC
1 AAGAGTTTAATTGAAACAAATAAAC
18250035 -AGAGTTTAATTGAAACAAATAAAC
1 AAGAGTTTAATTGAAACAAATAAAC
*
18250059 AA-ACTTTAATTGAAACAAATAAAC
1 AAGAGTTTAATTGAAACAAATAAAC
*
18250083 -AGACTTTAATT
1 AAGAGTTTAATT
18250094 CGAAGATTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
23 10 0.10
24 89 0.89
25 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (25 bp):
AAGAGTTTAATTGAAACAAATAAAC
Found at i:18251599 original size:24 final size:24
Alignment explanation
Indices: 18251542--18251601 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
18251532 TAGACTAATA
*
18251542 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
18251566 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
18251590 AGAGTTTAATTG
1 AGAGTTTAATTG
18251602 GAAGATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:18252201 original size:23 final size:24
Alignment explanation
Indices: 18252170--18252228 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
18252160 TGTAAATCAA
18252170 AAAAT-ATCTCT-AGAA-ACTTTCT
1 AAAATAATCTCTCA-AAGACTTTCT
18252192 AAAATAATCTCTTCAAAGACTTTCT
1 AAAATAATCTC-TCAAAGACTTTCT
*
18252217 GAAATAATCTCT
1 AAAATAATCTCT
18252229 TCTTCAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 4 0.12
25 18 0.56
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.36
Consensus pattern (24 bp):
AAAATAATCTCTCAAAGACTTTCT
Found at i:18254668 original size:194 final size:193
Alignment explanation
Indices: 18254339--18254961 Score: 649
Period size: 194 Copynumber: 3.3 Consensus size: 193
18254329 TACCAGTACC
* *
18254339 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCAGTACGAT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGGTACGAT
* * * * ** *
18254404 GTCTATCTATAAACTATCTCCTAACGATGCTGCTCACATGAGCTCCCGGGTGTATGCACCTATGC
66 GTCTGTCTATAAACTGTCTCCTAACGATGCTGTTCACAAGAGCTATCGGGTGTATGCACTTATGC
*
18254469 ATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTCTAGGATTCATATCTCTTTTTTTGACTCA
131 ATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATT-TAGGATTCATATCTCTTTTTTCGACTCA
* * * ** *
18254533 CGATGCTGCTCACATGAGCTATCGAGGATTCGCAACATATGTAGTACCTCAGTCATCGGTACGAT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGGTACGAT
18254598 GTCTGTCTATAAACTGTCTCCTAACGATGCTGTTCACAAGAGCTATCGGGTGTATGCACTTATGC
66 GTCTGTCTATAAACTGTCTCCTAACGATGCTGTTCACAAGAGCTATCGGGTGTATGCACTTATGC
* * * *
18254663 ATAAGTCCCAACCA---T------TG---T--A---GGGATTCATATCTATTGTTTCGACTCA
131 ATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTTAGGATTCATATCTCTTTTTTCGACTCA
* * * * * * *
18254709 CAATGTTGCTCACACGAGCTGTCGAGGACTCGTAATATATGCGGTACCTTAGCCATCGATACGGT
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGGTACGAT
* * * * ** * *
18254774 ATCTGTGC-ATATAACTGT-TCCCTAACGATGCTGCTT-ACACGAGCTGTCGAGAATATGCAGTC
66 GTCTGT-CTATA-AACTGTCT-CCTAACGATGCTG-TTCACAAGAGCTATCGGGTGTATGCACTT
* *
18254836 AAGCATAAATCCCAGCCATCGTAGGGCCTGTAATCCATTTTAGGATTTCATATCTC-TTTTTCGA
127 ATGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCA-TTTAGGA-TTCATATCTCTTTTTTCGA
18254900 CTCA
190 CTCA
* *** * *
18254904 CGATGCTACTCACACGAGCTATCGAGGACTCACCACATATGCGGTACCACAACCATCG
1 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCG
18254962 CGTCGGTTTC
Statistics
Matches: 348, Mismatches: 58, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
176 84 0.24
177 54 0.16
178 2 0.01
180 2 0.01
182 1 0.00
185 2 0.01
186 2 0.01
189 1 0.00
191 2 0.01
194 128 0.37
195 61 0.18
196 9 0.03
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (193 bp):
CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGGTACGAT
GTCTGTCTATAAACTGTCTCCTAACGATGCTGTTCACAAGAGCTATCGGGTGTATGCACTTATGC
ATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTTAGGATTCATATCTCTTTTTTCGACTCA
Found at i:18260253 original size:25 final size:24
Alignment explanation
Indices: 18260201--18260254 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
18260191 TCACGTTCAC
* *
18260201 ATTTTTTTCTCAATGCTTCCCTAG
1 ATTTTTTTCTCAATGCTTCACTAA
18260225 ATTTGTTTTCTCAATGCTTTCAC-AA
1 ATTT-TTTTCTCAATGC-TTCACTAA
18260250 ATTTT
1 ATTTT
18260255 CTCAATGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.52
Consensus pattern (24 bp):
ATTTTTTTCTCAATGCTTCACTAA
Found at i:18263046 original size:423 final size:413
Alignment explanation
Indices: 18262205--18263047 Score: 1172
Period size: 415 Copynumber: 2.0 Consensus size: 413
18262195 TGTCTTCAGT
* * * * *
18262205 TCGTGTTCAGTTAATAAAGGTTATAAAAATTGAACTTGTTTAACGATGGTTGATATGAAATGTCA
1 TCGTGTTCAGCTAATAAAGGTTATAAAAATAGAACTTGCTTAACAATGATTGATATGAAATGTCA
* *
18262270 TTTGAAAATGAAATATTTTGCATGCATATGAAATGTGATAATTGACAACATATGAAAGATTTCAA
66 TTTGAAAATGAAATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGATTGCAA
* *
18262335 ACTGGTTAAAAATGAGCCATGGGGGCTGATTTAAATATGAATAAGTCAGTAGTGTAACACCCTAT
131 AATGGTTAAAAATGAGCCATGGGGGCTAATTTAAATATGAATAAGTCAGTAGTGTAACACCCTAT
** * * * *
18262400 ACTTGACCTGATTGCTAGGTCCAAGCTATAGGATGTCATATTATTTGTCGGAGCAAGTATGAAAA
196 ACTTGACCCAATTGCTAGGTCCAAGCTATAGGATGCCATATTAGTTGTCGGAGCAACTACGAAAA
18262465 CAATTCCATTCATTCATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTA
261 CAATTCCATTCATTCATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTA
* * * * *
18262530 TCTTATTTGGGGCTTATACGAGCTAACAATAGCTGTTACGATAACCTGAGACCAATTAAGGACCT
326 TCTTATCTAGGGCTTATACGAACTAACAATAGCTCTTACGATAACATGAGACCAATTAAGGACCT
18262595 AACTGCAAAGTTTTCAAAGTAAA
391 AACTGCAAAGTTTTCAAAGTAAA
*
18262618 TCGTGTTCAGCTAATAAGGGTTATAAAACA-AGAACTTGCTTAACAATGATTGATATGAAATGTC
1 TCGTGTTCAGCTAATAAAGGTTATAAAA-ATAGAACTTGCTTAACAATGATTGATATGAAATGTC
* *
18262682 ATTTGAACATGAAATATTTTGCATGCATATGAAAAGTGATAATTGACAACATGTGAAAGATGATG
65 ATTTGAAAATGAAATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGAT--TG
* * *
18262747 CAAAATGGTTAAAAATGAGCCTTGGGGG-TCAATTTGAATATGAATGAGTCAGTAGTGTAACA-C
128 CAAAATGGTTAAAAATGAGCCATGGGGGCT-AATTTAAATATGAATAAGTCAGTAGTGTAACACC
* * * *
18262810 CTAATACTTGACCCAATTGCTGGGTCTAAGCTACTA-TATGCCATATTCGTTGTCGGAGCAACTA
192 CT-ATACTTGACCCAATTGCTAGGTCCAAGCTA-TAGGATGCCATATTAGTTGTCGGAGCAACTA
* * *
18262874 CGAAAACAATTCCAATTCATTCATTCATTAATTAAAACAAATTTTAATAATTAATACATCATTAT
255 CGAAAACAATT-C----CATTCATTCATTAATTAAAAC-AAGTTT--TAATTAATAAATCAATAT
* ** *
18262939 AACATGTTATATTATCTTATCTAGGGCTTATATGAACTTTCAATAGCTCTTATGATAACATGAGA
312 AACATGTTATATTATCTTATCTAGGGCTTATACGAACTAACAATAGCTCTTACGATAACATGAGA
* * *
18263004 CCATTTAAGGACCTAATTGCAAAGTTTTCAAAGTAGA
377 CCAATTAAGGACCTAACTGCAAAGTTTTCAAAGTAAA
18263041 TCGTGTT
1 TCGTGTT
18263048 GGCGACACGA
Statistics
Matches: 376, Mismatches: 40, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
413 114 0.30
414 5 0.01
415 115 0.31
416 3 0.01
420 21 0.06
421 5 0.01
423 113 0.30
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (413 bp):
TCGTGTTCAGCTAATAAAGGTTATAAAAATAGAACTTGCTTAACAATGATTGATATGAAATGTCA
TTTGAAAATGAAATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGATTGCAA
AATGGTTAAAAATGAGCCATGGGGGCTAATTTAAATATGAATAAGTCAGTAGTGTAACACCCTAT
ACTTGACCCAATTGCTAGGTCCAAGCTATAGGATGCCATATTAGTTGTCGGAGCAACTACGAAAA
CAATTCCATTCATTCATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTA
TCTTATCTAGGGCTTATACGAACTAACAATAGCTCTTACGATAACATGAGACCAATTAAGGACCT
AACTGCAAAGTTTTCAAAGTAAA
Found at i:18278746 original size:21 final size:21
Alignment explanation
Indices: 18278700--18278754 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
18278690 GTGACCAAGA
*
18278700 GAAGGATAAAGAAAAAGAAAAT
1 GAAGGA-AAAGAAAAAGAAAAG
* *
18278722 GAAGGAAAAGAAGAAGAGAAG
1 GAAGGAAAAGAAAAAGAAAAG
18278743 GAA-GAAACAGAA
1 GAAGGAAA-AGAA
18278755 CCTGCCGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 19 0.66
22 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.29, T:0.04
Consensus pattern (21 bp):
GAAGGAAAAGAAAAAGAAAAG
Found at i:18279215 original size:18 final size:17
Alignment explanation
Indices: 18279175--18279217 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
18279165 AGTTAACTGT
18279175 CTTGCATTTTTATTATG
1 CTTGCATTTTTATTATG
*
18279192 CCTGCATTTTTAATTAT-
1 CTTGCATTTTT-ATTATG
18279209 CGTTGCATT
1 C-TTGCATT
18279218 CAATCTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (17 bp):
CTTGCATTTTTATTATG
Found at i:18283150 original size:20 final size:20
Alignment explanation
Indices: 18283122--18283159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18283112 ATCACTCTAT
*
18283122 TTTTCTTTTTTTTTTCTTCA
1 TTTTCTTTTTCTTTTCTTCA
*
18283142 TTTTGTTTTTCTTTTCTT
1 TTTTCTTTTTCTTTTCTT
18283160 TCTTCCATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTCTTCA
Done.