Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:862428 original size:60 final size:59
Alignment explanation
Indices: 862335--862517 Score: 206
Period size: 60 Copynumber: 3.1 Consensus size: 59
862325 TTATGGTCTC
*
862335 AAACTATGATCCC-CATTTTAAATTGGTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
1 AAACTATGA-CCCTCATTCTAAATT-GTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
** * *
862395 AAACTATGACTTTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCC
1 AAACTATGACCCTCATTCTAAATT-GTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
* * ** * * **
862455 AAACTGTGTCCCTCATTCTAAATTGATCCCCATACTTTTGAATCTTTTAATTTCATCCCT
1 AAACTATGACCCTCATTCTAAATTG-TCCTTAAACTTTTGAATATTCCAATTTCATCCCT
862515 AAA
1 AAA
862518 GTCATCCAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
59 2 0.02
60 101 0.98
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (59 bp):
AAACTATGACCCTCATTCTAAATTGTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
Found at i:879173 original size:34 final size:35
Alignment explanation
Indices: 879123--879188 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
879113 TTTTTCGAAT
879123 TATAATTTAATAAATATATAA-TTA-TAAATATTA
1 TATAATTTAATAAATATATAATTTATTAAATATTA
* *
879156 TATAATTTTAATTAATATTTAATTTATTAAATA
1 TATAA-TTTAATAAATATATAATTTATTAAATA
879189 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.18
34 14 0.50
35 3 0.11
36 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
TATAATTTAATAAATATATAATTTATTAAATATTA
Found at i:879178 original size:17 final size:17
Alignment explanation
Indices: 879123--879180 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
879113 TTTTTCGAAT
*
879123 TATAA-TTTAATAAATA
1 TATAATTTTAATTAATA
* * *
879139 TATAATTATAAATATTA
1 TATAATTTTAATTAATA
879156 TATAATTTTAATTAATA
1 TATAATTTTAATTAATA
*
879173 TTTAATTT
1 TATAATTT
879181 ATTAAATACT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 5 0.15
17 28 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAATTTTAATTAATA
Found at i:888121 original size:82 final size:81
Alignment explanation
Indices: 887972--888276 Score: 341
Period size: 82 Copynumber: 3.8 Consensus size: 81
887962 AGTTTTTCCT
* *
887972 ATTATACAATTA-AAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACCGCAA
1 ATTAAACAATTATAAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACAGCAA
888036 AATGAACTCTGAAATG
66 AATGAACTCTGAAATG
** * *
888052 A-TAGAACCCTT-TCGAAAAACCAAGTTTATGAAATAGGGTAGTTCAGATTTGGCTCAAGAACAG
1 ATTA-AACAATTAT--AAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACAG
* *
888115 CAAAATGAACTCCGAAACG
63 CAAAATGAACTCTGAAATG
* * * * *
888134 ATTAAATAATTATAAAAAACAAGTTTATAAAAAAGGGTACTTCAGATTTTGCTCAAGAACTGCAA
1 ATTAAACAATTATAAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACAGCAA
* *
888199 AATGAACCCTGAAATA
66 AATGAACTCTGAAATG
* * * **
888215 ATAAAACAATTATTAAAAAAACCAAGTTCA--AAAAGGGGTCCTTCAGATTTTGCTCAAGAACA
1 ATTAAACAATTA-T--AAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACA
888277 ACCAGAGTGA
Statistics
Matches: 188, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.01
80 5 0.03
81 68 0.36
82 98 0.52
83 3 0.02
84 12 0.06
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (81 bp):
ATTAAACAATTATAAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACAGCAA
AATGAACTCTGAAATG
Found at i:888262 original size:163 final size:163
Alignment explanation
Indices: 887982--888276 Score: 407
Period size: 163 Copynumber: 1.8 Consensus size: 163
887972 ATTATACAAT
* * *
887982 TAAAAAACCAAGTTTATGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACCGCAAAATGAACTCTG
1 TAAAAAACCAAGTTTATAAAAAAGGGTACTTCAGATTTTGCTCAAGAACCGCAAAATGAACCCTG
* * * ** * *
888047 AAATGATAGAACCCTTTCGAAAAACCAAGTTTATGAAATAGGGTAGTTCAGATTTGGCTCAAGAA
66 AAATAATAAAACACTTTAAAAAAACCAAGTTCA-GAAATAGGGTACTTCAGATTTGGCTCAAGAA
888112 CAGCAAAATGAACTCCGAAACGATTAAATAATTA
130 CAGCAAAATGAACTCCGAAACGATTAAATAATTA
*
888146 TAAAAAA-CAAGTTTATAAAAAAGGGTACTTCAGATTTTGCTCAAGAACTGCAAAATGAACCCTG
1 TAAAAAACCAAGTTTATAAAAAAGGGTACTTCAGATTTTGCTCAAGAACCGCAAAATGAACCCTG
* * *
888210 AAATAATAAAACAATTATTAAAAAAACCAAGTTCA-AAA-AGGGGTCCTTCAGATTTTGCTCAAG
66 AAATAATAAAAC-ACT-TTAAAAAAACCAAGTTCAGAAATA-GGGTACTTCAGATTTGGCTCAAG
888273 AACA
128 AACA
888277 ACCAGAGTGA
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
162 1 0.01
163 90 0.79
164 8 0.07
165 15 0.13
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.24
Consensus pattern (163 bp):
TAAAAAACCAAGTTTATAAAAAAGGGTACTTCAGATTTTGCTCAAGAACCGCAAAATGAACCCTG
AAATAATAAAACACTTTAAAAAAACCAAGTTCAGAAATAGGGTACTTCAGATTTGGCTCAAGAAC
AGCAAAATGAACTCCGAAACGATTAAATAATTA
Found at i:891848 original size:20 final size:18
Alignment explanation
Indices: 891825--891864 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
891815 TTTTCCTTTA
891825 TTTCTTATATTACATATTTT
1 TTTCTT-TATTA-ATATTTT
*
891845 TTTCTTTATTATTATTTT
1 TTTCTTTATTAATATTTT
891863 TT
1 TT
891865 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTATTAATATTTT
Found at i:892494 original size:19 final size:20
Alignment explanation
Indices: 892458--892499 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
892448 TATTTATTCT
*
892458 ATTTATTTTCTTCTTTCTCC
1 ATTTATTTTCTTCCTTCTCC
* *
892478 ATTT-TTTTGTTCCTTCTTC
1 ATTTATTTTCTTCCTTCTCC
892497 ATT
1 ATT
892500 CAACAAGCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTATTTTCTTCCTTCTCC
Found at i:892561 original size:18 final size:18
Alignment explanation
Indices: 892546--892584 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
892536 ATATTTCATG
892546 TTCCTCTTAGATTTCAAA
1 TTCCTCTTAGATTTCAAA
892564 TTCCTCTTAGATTTCAAA
1 TTCCTCTTAGATTTCAAA
892582 TTC
1 TTC
892585 ATCCTTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (18 bp):
TTCCTCTTAGATTTCAAA
Found at i:893295 original size:21 final size:20
Alignment explanation
Indices: 893262--893302 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
893252 TATTTATAGA
*
893262 GAAAGTTTGGTATCCATACT
1 GAAAGTTTAGTATCCATACT
893282 GAAAGGTTTAGTATCCATACT
1 GAAA-GTTTAGTATCCATACT
893303 AGAGGCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
GAAAGTTTAGTATCCATACT
Found at i:895342 original size:14 final size:14
Alignment explanation
Indices: 895323--895349 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
895313 ACAATTAATA
895323 TTATTATTATTATC
1 TTATTATTATTATC
895337 TTATTATTATTAT
1 TTATTATTATTAT
895350 TATAAGTATT
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:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATC
Found at i:897479 original size:40 final size:40
Alignment explanation
Indices: 897434--897590 Score: 269
Period size: 40 Copynumber: 3.9 Consensus size: 40
897424 TGTAGGTTTA
* *
897434 TAATACACTTTGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
897474 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
897514 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
897554 TAAAACACTTCGGTGTATATGGTGGGCATGACCTTAT
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTAT
897591 ATATAGCACT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 111 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:902064 original size:33 final size:32
Alignment explanation
Indices: 902027--902104 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
902017 TTTTCACCCT
902027 AAACCCGAACCCGACCCGAATATCACACTTTAA
1 AAACCCG-ACCCGACCCGAATATCACACTTTAA
*
902060 AAACCCGACCCAACCCGAATATCACACTTTAA
1 AAACCCGACCCGACCCGAATATCACACTTTAA
902092 AAACCCGACCCGA
1 AAACCCGACCCGA
902105 ACAAAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 36 0.84
33 7 0.16
ACGTcount: A:0.40, C:0.38, G:0.09, T:0.13
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTTAA
Found at i:902106 original size:179 final size:186
Alignment explanation
Indices: 901796--902167 Score: 560
Period size: 179 Copynumber: 2.0 Consensus size: 186
901786 TATAAGGTAA
* * *
901796 AATTATATATTTTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACTCGACCCGACCCGACCCGA
1 AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGA--C-ACCCGACCCGA
* *
901861 ATATCACACTTAAAAAAACCCGACCTAACTCGACCCGAATATCATACTTAAAAAACCCGACCCGA
63 ATATCACACTTAAAAAAACCCGACC--ACTCAACCCGAATATCACACTTAAAAAACCCGACCCGA
*
901926 ACAAAATAAAGTTTCATCCGACCCGATCCGAATATATGAATTAGAAATCCAACCCGACCCG
126 ACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCG
901987 AATTATATA-TATTTTCGGGTCGGTCCAG-TTTTTTCACCCTAAACCCGA-ACCCGACCCGAATA
1 AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGACACCCGACCCGAATA
* *
902049 TCACACTT-TAAAAACCCGA-C-C-CAACCCGAATATCACACTTTAAAAACCCGACCCGAACAAA
66 TCACACTTAAAAAAACCCGACCACTCAACCCGAATATCACACTTAAAAAACCCGACCCGAACAAA
* *
902110 ATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCG
131 ATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCG
902166 AA
1 AA
902168 ATAATAAAAA
Statistics
Matches: 171, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
179 92 0.54
180 1 0.01
183 1 0.01
184 10 0.06
185 22 0.13
189 19 0.11
190 17 0.10
191 9 0.05
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (186 bp):
AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGACACCCGACCCGAATA
TCACACTTAAAAAAACCCGACCACTCAACCCGAATATCACACTTAAAAAACCCGACCCGAACAAA
ATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCG
Found at i:910965 original size:6 final size:6
Alignment explanation
Indices: 910926--910965 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
910916 AATGAGAGTT
*
910926 GAAAAT GAAAAA -AAAAA -AAAAA -AAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
910966 GAGAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 15 0.47
6 17 0.53
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:910965 original size:12 final size:11
Alignment explanation
Indices: 910927--910965 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
910917 ATGAGAGTTG
*
910927 AAAATGAAAAA
1 AAAAAGAAAAA
910938 AAAAA-AAAAA
1 AAAAAGAAAAA
910948 AAAAAGAAAAA
1 AAAAAGAAAAA
910959 GAAAAAG
1 -AAAAAG
910966 GAGAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 10 0.40
11 9 0.36
12 6 0.24
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:912086 original size:2 final size:2
Alignment explanation
Indices: 912081--912118 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
912071 GTAGTAATTA
912081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
912119 GTAGAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:912283 original size:16 final size:17
Alignment explanation
Indices: 912251--912286 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
912241 TAAATCACTA
*
912251 TTTTAGGTATTCAAAAT
1 TTTTAGATATTCAAAAT
912268 TTTTAGATATTC-AAAT
1 TTTTAGATATTCAAAAT
912284 TTT
1 TTT
912287 GGGATTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTTAGATATTCAAAAT
Found at i:912584 original size:20 final size:21
Alignment explanation
Indices: 912559--912603 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
912549 TCAACTCCCT
912559 TTTTTCCCTTCACTT-TTTTC
1 TTTTTCCCTTCACTTATTTTC
** *
912579 TTTTTCTTTTCAGTTATTTTC
1 TTTTTCCCTTCACTTATTTTC
912600 TTTT
1 TTTT
912604 CGAATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTCCCTTCACTTATTTTC
Found at i:925422 original size:72 final size:72
Alignment explanation
Indices: 925301--925521 Score: 318
Period size: 72 Copynumber: 3.1 Consensus size: 72
925291 CTTCCAACTC
* *
925301 ATTTTGCCCAATATCTAGCGTTCCTAAATTTTTCAACTGCCCAAAACTTGGAAGAAGAGGACCAT
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAAGAAGAGGACCAT
925366 TTAATTG
66 TTAATTG
* * * *
925373 ATTTTGCCAAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAGACTTGGAGGAAAAGGACCAT
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAAGAAGAGGACCAT
925438 TTAATTG
66 TTAATTG
** * * * *
925445 ATTTTGCCCAATATCTAGAGTTTCTAAATTTGCCAATTTCCCAAAATTTGG-AGACAGAGTACCA
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAAGA-AGAGGACCA
925509 TTTAATTG
65 TTTAATTG
925517 ATTTT
1 ATTTT
925522 CTGAAACATC
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
71 2 0.02
72 130 0.98
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (72 bp):
ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAAGAAGAGGACCAT
TTAATTG
Found at i:927030 original size:14 final size:14
Alignment explanation
Indices: 927013--927043 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
927003 GGTCAAGGAG
*
927013 GTCAAGTCAACTAA
1 GTCAAGTAAACTAA
927027 GTCAAGTAAACTAA
1 GTCAAGTAAACTAA
927041 GTC
1 GTC
927044 TACGGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (14 bp):
GTCAAGTAAACTAA
Found at i:929760 original size:15 final size:16
Alignment explanation
Indices: 929740--929780 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
929730 CCAAATTTCC
*
929740 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
929755 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
929771 GAATGATTCA
1 GAATGATTCA
929781 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:936927 original size:13 final size:13
Alignment explanation
Indices: 936909--936934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
936899 CGGTCCCAAC
936909 TTTAAGTAAATTA
1 TTTAAGTAAATTA
936922 TTTAAGTAAATTA
1 TTTAAGTAAATTA
936935 GTGTTGGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTAAGTAAATTA
Found at i:941904 original size:12 final size:11
Alignment explanation
Indices: 941887--941943 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
941877 GGGCAAAAAG
941887 AAAAGAAGCAAA
1 AAAAGAA-CAAA
941899 AAAAGAA-AAA
1 AAAAGAACAAA
*
941909 ACAAGAAC-AA
1 AAAAGAACAAA
941919 AAAAG--CAAA
1 AAAAGAACAAA
*
941928 AAAAAAACAAA
1 AAAAGAACAAA
941939 TAAAA
1 -AAAA
941944 AAAAGGACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
8 1 0.03
9 6 0.16
10 15 0.41
11 4 0.11
12 11 0.30
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.02
Consensus pattern (11 bp):
AAAAGAACAAA
Found at i:941914 original size:22 final size:21
Alignment explanation
Indices: 941867--941938 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 21
941857 AGATTCAATC
* *
941867 AGAACAAAAAGGGCAAAAAGAAA
1 AGAACAAAAA-AGCAAAAA-ACA
941890 AGAAGCAAAAAAAG-AAAAAACA
1 AGAA-C-AAAAAAGCAAAAAACA
941912 AGAACAAAAAAGCAAAAAA-A
1 AGAACAAAAAAGCAAAAAACA
941932 A-AACAAA
1 AGAACAAA
941939 TAAAAAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 6 0.14
20 9 0.20
21 7 0.16
22 6 0.14
23 9 0.20
24 2 0.05
25 5 0.11
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (21 bp):
AGAACAAAAAAGCAAAAAACA
Found at i:941931 original size:11 final size:10
Alignment explanation
Indices: 941881--941933 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
941871 CAAAAAGGGC
941881 AAAAAGAAAAG
1 AAAAA-AAAAG
941892 AAGCAAAAAAAG
1 AA--AAAAAAAG
*
941904 AAAAAACAAG
1 AAAAAAAAAG
*
941914 AACAAAAAAG
1 AAAAAAAAAG
941924 CAAAAAAAAA
1 -AAAAAAAAA
941934 ACAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 15 0.43
11 10 0.29
12 7 0.20
13 3 0.09
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:941932 original size:10 final size:9
Alignment explanation
Indices: 941881--941958 Score: 54
Period size: 9 Copynumber: 8.8 Consensus size: 9
941871 CAAAAAGGGC
941881 AAAAAG-AA
1 AAAAAGAAA
* *
941889 AAGAAGCAA
1 AAAAAGAAA
941898 AAAAAGAAA
1 AAAAAGAAA
941907 AAACAAGAACA
1 AAA-AAGAA-A
*
941918 AAAAAG-CA
1 AAAAAGAAA
941926 AAAAA-AAA
1 AAAAAGAAA
* *
941934 ACAAATAAA
1 AAAAAGAAA
* *
941943 AAAAAGGAC
1 AAAAAGAAA
941952 AAAAAGA
1 AAAAAGA
941959 TTCCCTAAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
8 16 0.30
9 26 0.48
10 8 0.15
11 4 0.07
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:941944 original size:12 final size:11
Alignment explanation
Indices: 941899--941946 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 11
941889 AAGAAGCAAA
941899 AAAAGAAAAAAC
1 AAAA-AAAAAAC
941911 AAGAACAAAAAAGC
1 AA-AA-AAAAAA-C
941925 AAAAAAAAAAC
1 AAAAAAAAAAC
941936 AAATAAAAAAA
1 AAA-AAAAAAA
941947 AGGACAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.12
12 15 0.47
13 10 0.31
14 3 0.09
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:941945 original size:25 final size:26
Alignment explanation
Indices: 941899--941948 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
941889 AAGAAGCAAA
*
941899 AAAAGAAAAAACAAGAACAAAAAAGC
1 AAAAGAAAAAACAAGAAAAAAAAAGC
941925 AAAA-AAAAAACAA-ATAAAAAAAAG
1 AAAAGAAAAAACAAGA-AAAAAAAAG
941949 GACAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 17 0.77
26 4 0.18
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAAACAAGAAAAAAAAAGC
Found at i:942594 original size:22 final size:22
Alignment explanation
Indices: 942566--942608 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
942556 GCTACCCCAG
*
942566 CAAACCTTTGAGCATCCAATGC
1 CAAACCTTTGAGCATCAAATGC
942588 CAAACCTTTGAGCATCAAATG
1 CAAACCTTTGAGCATCAAATG
942609 AACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:944104 original size:106 final size:106
Alignment explanation
Indices: 943157--944089 Score: 1486
Period size: 106 Copynumber: 8.9 Consensus size: 106
943147 TTTTTGCAGT
* * *
943157 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCTAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
943222 ATTTCAACTTCACAGCG-AGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
943262 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
943327 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
943368 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
943433 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
943474 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
943539 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
943580 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
943645 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
943686 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCGGATCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
943751 ATTTCAACTTCACGGCGAAGGATATTGGACTCGAGACAGCA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
943792 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTG-------ACAACTTCCCAATTTCAGATCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
943850 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * *
943891 CAAGTTCAACTTCACGACGAAGGGACCACTGATTGTCAACAAACAATTTCCCAATTTCGGATCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
943956 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * *
943997 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAGACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
944062 ATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAACTTCACAGCGAAGGATATTGG
944090 CCTCAAAACA
Statistics
Matches: 766, Mismatches: 54, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
99 87 0.11
105 77 0.10
106 602 0.79
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:946058 original size:23 final size:24
Alignment explanation
Indices: 946000--946058 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
945990 TTATATTCAC
946000 TTTATTT-TTTATTACTTTCCTTA
1 TTTATTTATTTATTACTTTCCTTA
946023 TTTCATTTA--TATTAC-TTCCTT-
1 TTT-ATTTATTTATTACTTTCCTTA
946044 TATTATTTATTTATT
1 T-TTATTTATTTATT
946059 TCATCTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 6 0.19
22 8 0.26
23 13 0.42
24 4 0.13
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTATTTATTACTTTCCTTA
Found at i:946704 original size:58 final size:57
Alignment explanation
Indices: 946632--946802 Score: 157
Period size: 58 Copynumber: 2.9 Consensus size: 57
946622 AACTATAATT
* *
946632 CTCATTTTAAATTAGTCTTCTAAGTTTTTAATATTTCAATTTCATCCCTAAATTATGA-
1 CTCATTCTAAATTAGTC-TCTAA-TTTTTAATATTTCAATTTCATCCCCAAATTATGAC
* * * * *
946690 CTCATTCTATATTAGTC-CTAAATTTTTTGAACATTCCAATTCCATCCCCAAACTATGACC
1 CTCATTCTAAATTAGTCTCT-AA-TTTTT-AATATTTCAATTTCATCCCCAAATTATGA-C
* * * * *
946750 CTCATTCTAAATTGGTCCTCGAACTTTTGATATTTCAACTTCATCCCCAAATT
1 CTCATTCTAAATTAGT-CTCTAATTTTTAATATTTCAATTTCATCCCCAAATT
946803 CATCCAAATG
Statistics
Matches: 89, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
56 2 0.02
57 7 0.08
58 39 0.44
59 19 0.21
60 18 0.20
61 3 0.03
62 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (57 bp):
CTCATTCTAAATTAGTCTCTAATTTTTAATATTTCAATTTCATCCCCAAATTATGAC
Found at i:949425 original size:21 final size:21
Alignment explanation
Indices: 949409--949462 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
949399 GCGTTGCATT
*
949409 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGCAAA
*
949430 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGCAAA
*
949451 TCGTGTTGCGAT
1 TCGCGTTGCGAT
949463 GGTATACAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGCAAA
Found at i:950168 original size:19 final size:19
Alignment explanation
Indices: 950144--950194 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
950134 GCAACGAGAT
*
950144 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAACAAA
* *
950163 AATCGCAACGCGAAACCAA
1 AATCGCAATGCGAAACAAA
*
950182 AATCGCATTGCGA
1 AATCGCAATGCGA
950195 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAACAAA
Found at i:950206 original size:19 final size:19
Alignment explanation
Indices: 950184--950335 Score: 152
Period size: 20 Copynumber: 8.1 Consensus size: 19
950174 GAAACCAAAA
*
950184 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
950203 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
950222 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
**
950242 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
950261 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
950275 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
950294 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
950314 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
950334 TC
1 TC
950336 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 2 0.02
19 48 0.43
20 49 0.44
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:950243 original size:39 final size:38
Alignment explanation
Indices: 950184--950335 Score: 152
Period size: 39 Copynumber: 4.1 Consensus size: 38
950174 GAAACCAAAA
* ** *
950184 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATT
950222 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATAGTCATT
1 TCGC-GTTGCGATTTTCATTTCGCGTTGCGATAGTCATT
*
950261 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATT
* * * **
950294 TCCACGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATAGTCATT
950334 TC
1 TC
950336 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
33 19 0.20
34 9 0.09
36 5 0.05
38 11 0.11
39 35 0.36
40 18 0.19
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATT
Found at i:950287 original size:33 final size:34
Alignment explanation
Indices: 950245--950310 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
950235 TTTCATTTCG
*
950245 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCACGTTGCGATTCTCT
950278 CGTTGCGATAGTCATTTCCACGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCACGTTGCGATTCTC
950311 ATTATCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCACGTTGCGATTCTCT
Found at i:952396 original size:42 final size:42
Alignment explanation
Indices: 952336--952458 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
952326 GCCCGACTCG
* * *
952336 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
952378 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
952420 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
952459 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:952416 original size:21 final size:21
Alignment explanation
Indices: 952392--952458 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
952382 TCATTCCTCG
952392 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
952413 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
952434 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
952455 AGAG
1 AGAG
952459 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:953838 original size:14 final size:14
Alignment explanation
Indices: 953819--953854 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
953809 ATTGTTTAAT
953819 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
953833 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
953847 TGATTTGT
1 TGATTTGT
953855 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:953985 original size:19 final size:19
Alignment explanation
Indices: 953961--954038 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
953951 AAAAAGTACT
*
953961 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
953980 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
953994 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
*
954014 ATCGCAACGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
*
954033 TTCGCA
1 ATCGCA
954039 TTGCGATTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
19 20 0.41
20 14 0.29
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:954075 original size:33 final size:32
Alignment explanation
Indices: 954033--954144 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 32
954023 CGAAATTAAA
954033 TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATT-CCTCGTTGCGATTTTCAT
**
954066 TTCGCATTGCGAAATT-AGCGTTGCGATTTTCAT
1 TTCGCATTGCG--ATTCCTCGTTGCGATTTTCAT
954099 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTC-CTCGTTGCGATTTTCAT
954132 TTCGCATTGCGAT
1 TTCGCATTGCGAT
954145 AGTAATTTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
31 3 0.04
33 65 0.92
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
TTCGCATTGCGATTCCTCGTTGCGATTTTCAT
Found at i:954077 original size:19 final size:19
Alignment explanation
Indices: 954053--954144 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
954043 GATTCCCTCG
954053 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
954072 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
954086 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
954105 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
954119 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
954138 TTGCGAT
1 TTGCGAT
954145 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 17 0.31
16 7 0.13
17 7 0.13
19 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:956454 original size:12 final size:12
Alignment explanation
Indices: 956437--956461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
956427 TCTTCGGGGA
956437 CTTTTTCTTCTT
1 CTTTTTCTTCTT
956449 CTTTTTCTTCTT
1 CTTTTTCTTCTT
956461 C
1 C
956462 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:956670 original size:24 final size:24
Alignment explanation
Indices: 956636--956689 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
956626 CTGAAACATC
* *
956636 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
956660 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
956684 ATCAAA
1 ATCAAA
956690 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:957774 original size:20 final size:20
Alignment explanation
Indices: 957749--957806 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
957739 ATTCATTTGA
957749 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
957769 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
957789 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
957807 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:957849 original size:14 final size:16
Alignment explanation
Indices: 957829--957902 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
957819 TGAAAATCGC
957829 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
957844 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
957861 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
957880 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
957896 -TTGCGAT
1 ATTGCGAT
957903 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:957866 original size:19 final size:19
Alignment explanation
Indices: 957825--957892 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
957815 GAAATGAAAA
957825 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
957841 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
957858 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
957877 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
957893 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:958028 original size:14 final size:14
Alignment explanation
Indices: 958009--958045 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
957999 CATCAATTAA
958009 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
958023 ACAAATCATCTTTT
1 ACAAATCAACATTT
958037 ACAAATCAA
1 ACAAATCAA
958046 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:959944 original size:20 final size:19
Alignment explanation
Indices: 959909--959975 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
959899 GAAACTTAAA
959909 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
959928 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
959948 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
959967 ATCGCAACG
1 ATCGCAACG
959976 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:959983 original size:14 final size:14
Alignment explanation
Indices: 959964--960021 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
959954 ATGCGAAATG
959964 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
959978 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
959994 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
960010 AAAATCACAACG
1 AAAATCGCAACG
960022 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:960006 original size:32 final size:33
Alignment explanation
Indices: 959948--960026 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
959938 GGAAATGGCT
*
959948 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
959981 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
960013 ATCACAACGCGAAA
1 ATCGCAACGCGAAA
960027 CACAAATCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:960074 original size:14 final size:14
Alignment explanation
Indices: 960055--960144 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
960045 TTTCATTTCG
960055 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
960069 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
960085 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
960101 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
960117 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
960133 CGTTGCGATTTT
1 CGTTGCGATTTT
960145 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:960085 original size:32 final size:33
Alignment explanation
Indices: 960038--960160 Score: 223
Period size: 32 Copynumber: 3.8 Consensus size: 33
960028 ACAAATCGTA
*
960038 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
960071 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
960103 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
960135 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
960161 AGCCATTTCC
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
32 63 0.72
33 25 0.28
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:960196 original size:20 final size:20
Alignment explanation
Indices: 960145--960188 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
960135 TTGCGATTTT
*
960145 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
960164 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
960184 CATTT
1 CATTT
960189 TCGTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:960707 original size:18 final size:18
Alignment explanation
Indices: 960681--960725 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
960671 GTCGATCAGA
*
960681 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
960699 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
960717 TGATGGCTC
1 TGATGGCTC
960726 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:962069 original size:20 final size:20
Alignment explanation
Indices: 962044--962081 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
962034 AATAGTTTCT
962044 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
962064 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
962082 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:962586 original size:21 final size:22
Alignment explanation
Indices: 962556--962651 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 22
962546 CGCTTTGAAA
*
962556 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* *
962577 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGTAAGT
* * * *
962597 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGATTATGTAAGT
*
962618 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGTAAGT
962638 ATCGCATTGCGATT
1 ATCGCATTGCGATT
962652 TTCCCAATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.08
20 28 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:962619 original size:41 final size:41
Alignment explanation
Indices: 962556--962653 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
962546 CGCTTTGAAA
* *
962556 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * * *
962597 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
962638 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
962654 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:962668 original size:21 final size:21
Alignment explanation
Indices: 962639--962694 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
962629 ATAGTCAGTA
*
962639 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
962660 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
962681 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
962695 ACTTATTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:962669 original size:41 final size:41
Alignment explanation
Indices: 962556--962671 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
962546 CGCTTTGAAA
* ** * *
962556 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
962597 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
962638 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
962672 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
41 60 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:962704 original size:20 final size:21
Alignment explanation
Indices: 962639--962711 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
962629 ATAGTCAGTA
* *
962639 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
*
962660 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
962681 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
*
962701 TCGCATTGCGA
1 TCGCGTTGCGA
962712 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACCAAT
Found at i:962782 original size:21 final size:21
Alignment explanation
Indices: 962742--962782 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
962732 ACTGTATACC
**
962742 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
962763 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
962783 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:963068 original size:11 final size:11
Alignment explanation
Indices: 963052--963111 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 11
963042 TAAAATTATA
963052 ATTTTAAAATT
1 ATTTTAAAATT
*
963063 ATTTT---ATA
1 ATTTTAAAATT
963071 ATTTTAAAATT
1 ATTTTAAAATT
*
963082 ATTTT---ATA
1 ATTTTAAAATT
963090 ATTTTAAAATT
1 ATTTTAAAATT
*
963101 ATTTTATAATT
1 ATTTTAAAATT
963112 TTGAAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
8 14 0.37
11 24 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:963071 original size:19 final size:19
Alignment explanation
Indices: 963047--963118 Score: 135
Period size: 19 Copynumber: 3.7 Consensus size: 19
963037 AATTATAAAA
963047 TTATAATTTTAAAATTATT
1 TTATAATTTTAAAATTATT
963066 TTATAATTTTAAAATTATT
1 TTATAATTTTAAAATTATT
963085 TTATAATTTTAAAATTATT
1 TTATAATTTTAAAATTATT
963104 TTATAATTTTGAAAA
1 TTATAATTTT-AAAA
963119 ACAAAATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 48 0.92
20 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (19 bp):
TTATAATTTTAAAATTATT
Found at i:963780 original size:2 final size:2
Alignment explanation
Indices: 963773--963804 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
963763 ATATGAAGAA
963773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
963805 TGATTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:964164 original size:23 final size:23
Alignment explanation
Indices: 964138--964196 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
964128 TCTTGATCAG
*
964138 GTTTGAG-TTTAAACTGAGTTCGA
1 GTTTGAGATTTAAAC-GAGCTCGA
* *
964161 GTTTGAGCTTTAATCGAGCTCGA
1 GTTTGAGATTTAAACGAGCTCGA
*
964184 GTTTAAGATTTAA
1 GTTTGAGATTTAA
964197 TAGAGTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (23 bp):
GTTTGAGATTTAAACGAGCTCGA
Found at i:966801 original size:6 final size:6
Alignment explanation
Indices: 966790--967041 Score: 414
Period size: 6 Copynumber: 41.5 Consensus size: 6
966780 CAATGCACAC
966790 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
966838 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
966886 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
966934 ATACAT ATACAT ATACAT ATACAT ATACAT AATGTATAT GTACAT ATATAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT -A--TACAT ATACAT ATACAT
* * * *
966985 ATACAT ATACAT GTACAT GTATAT GTACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
967033 ATACAT ATA
1 ATACAT ATA
967042 TATCATGAGA
Statistics
Matches: 233, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
6 228 0.98
7 1 0.00
9 4 0.02
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (6 bp):
ATACAT
Found at i:969155 original size:3 final size:3
Alignment explanation
Indices: 969109--969136 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
969099 TACCCTACTC
969109 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
969137 AAATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:969165 original size:12 final size:13
Alignment explanation
Indices: 969109--969166 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
969099 TACCCTACTC
*
969109 TTATTATT-ATTA
1 TTATTATTAAATA
*
969121 TTATTATT-ATTA
1 TTATTATTAAATA
* *
969133 TTATAAATAAAATA
1 TTAT-TATTAAATA
969147 TTATTATTAAATA
1 TTATTATTAAATA
969160 -TATTATT
1 TTATTATT
969167 TATATTTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 23 0.59
13 9 0.23
14 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTAAATA
Found at i:975043 original size:25 final size:25
Alignment explanation
Indices: 975001--975077 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
974991 GAGATAAGGG
975001 AAAGA-AACAAAAAGAAGAAAAGAAA
1 AAAGACAA-AAAAAGAAGAAAAGAAA
**
975026 AAATTCAAAAAAAGAAGAATAAGAAA
1 AAAGACAAAAAAAGAAGAA-AAGAAA
* *
975052 AAAGAGAAAAAAATAAGAGAAAGAAA
1 AAAGACAAAAAAAGAAGA-AAAGAAA
975078 TAATGAAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 14 0.33
26 28 0.65
27 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAGACAAAAAAAGAAGAAAAGAAA
Found at i:975078 original size:13 final size:13
Alignment explanation
Indices: 975046--975080 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
975036 AAAGAAGAAT
*
975046 AAGAAAAAAGAGA
1 AAGAAATAAGAGA
*
975059 AAAAAATAAGAGA
1 AAGAAATAAGAGA
975072 AAGAAATAA
1 AAGAAATAA
975081 TGAAAGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (13 bp):
AAGAAATAAGAGA
Found at i:976283 original size:26 final size:26
Alignment explanation
Indices: 976253--976357 Score: 192
Period size: 26 Copynumber: 4.0 Consensus size: 26
976243 CGACGAGGGA
976253 GAAGAAGTTCCTAATGAGAAGAACTT
1 GAAGAAGTTCCTAATGAGAAGAACTT
976279 GAAGAAGTTCCTAATGAGAAGAACTT
1 GAAGAAGTTCCTAATGAGAAGAACTT
976305 GAAGAAGTTCCTAATGAGAAGAACTT
1 GAAGAAGTTCCTAATGAGAAGAACTT
* *
976331 GAAGAAGTTCTTAATGAGAAAAACTT
1 GAAGAAGTTCCTAATGAGAAGAACTT
976357 G
1 G
976358 TTCAATCTCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (26 bp):
GAAGAAGTTCCTAATGAGAAGAACTT
Found at i:976818 original size:38 final size:38
Alignment explanation
Indices: 976776--976874 Score: 171
Period size: 38 Copynumber: 2.6 Consensus size: 38
976766 CCCAAAGAAT
*
976776 AGTTCATAATGAGAAGAGCTTGTCCAATGAGAGTGAAG
1 AGTTCATAATGAGAAGAGCTTGTCCAAGGAGAGTGAAG
*
976814 AGTTCATAATGAGAAGAGCTCGTCCAAGGAGAGTGAAG
1 AGTTCATAATGAGAAGAGCTTGTCCAAGGAGAGTGAAG
*
976852 AGTTCATAATGAGAAGAACTTGT
1 AGTTCATAATGAGAAGAGCTTGT
976875 AGCTCAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.23
Consensus pattern (38 bp):
AGTTCATAATGAGAAGAGCTTGTCCAAGGAGAGTGAAG
Found at i:976826 original size:20 final size:20
Alignment explanation
Indices: 976801--976865 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
976791 GAGCTTGTCC
976801 AATGAGAGTGAAGAGTTCAT
1 AATGAGAGTGAAGAGTTCAT
* *
976821 AAT--GA--GAAGAGCTCGT
1 AATGAGAGTGAAGAGTTCAT
*
976837 CCAAGGAGAGTGAAGAGTTCAT
1 --AATGAGAGTGAAGAGTTCAT
976859 AATGAGA
1 AATGAGA
976866 AGAACTTGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 9 0.27
18 4 0.12
20 11 0.33
22 9 0.27
ACGTcount: A:0.40, C:0.09, G:0.31, T:0.20
Consensus pattern (20 bp):
AATGAGAGTGAAGAGTTCAT
Found at i:977004 original size:3 final size:3
Alignment explanation
Indices: 976996--977022 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
976986 CCTAACCCTC
976996 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
977023 TACATTGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:980944 original size:2 final size:2
Alignment explanation
Indices: 980937--980964 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
980927 CTTATAGAAA
980937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
980965 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:981445 original size:16 final size:16
Alignment explanation
Indices: 981421--981452 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
981411 ATGTCGAGTT
*
981421 AGGTGCGAGTTTTATC
1 AGGTCCGAGTTTTATC
981437 AGGTCCGAGTTTTATC
1 AGGTCCGAGTTTTATC
981453 TCAAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (16 bp):
AGGTCCGAGTTTTATC
Found at i:981757 original size:12 final size:12
Alignment explanation
Indices: 981740--981764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
981730 GCCTATAGCT
981740 TATTTTTTATTA
1 TATTTTTTATTA
981752 TATTTTTTATTA
1 TATTTTTTATTA
981764 T
1 T
981765 GTATTAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTTATTA
Found at i:985411 original size:17 final size:18
Alignment explanation
Indices: 985371--985414 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
985361 TTAATAGTAA
985371 AATTTGATAAAATATTTT
1 AATTTGATAAAATATTTT
**
985389 AA-TTGATTCAAT-TTTT
1 AATTTGATAAAATATTTT
985405 AATTTGATAA
1 AATTTGATAA
985415 CTTAATTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTTGATAAAATATTTT
Found at i:986141 original size:2 final size:2
Alignment explanation
Indices: 986134--986166 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
986124 CAACCCTTGA
986134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
986167 GCAATACATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:991548 original size:21 final size:21
Alignment explanation
Indices: 991505--991548 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
991495 TTTGTTGCCT
*
991505 TTTTCTAAACAAATATTATTA
1 TTTTCTAAACAAATATTAATA
991526 TTTTCTAAAC-AATATCTAATA
1 TTTTCTAAACAAATAT-TAATA
991547 TT
1 TT
991549 AGGAGAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTCTAAACAAATATTAATA
Found at i:994601 original size:49 final size:49
Alignment explanation
Indices: 994508--994601 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
994498 AACATTATTA
* ** ***
994508 TTTCTACCGATTTTGTTATTATTGGACGTTTTACCGGTTTTGTTATTTT
1 TTTCTACCGATTTTATTATTATTGGACACTTTACCGGAAATGTTATTTT
*
994557 TTTCTACCGATTTTATTATTATTGGACACTTTATCGGAAATGTTA
1 TTTCTACCGATTTTATTATTATTGGACACTTTACCGGAAATGTTA
994602 AAAAACATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (49 bp):
TTTCTACCGATTTTATTATTATTGGACACTTTACCGGAAATGTTATTTT
Found at i:998620 original size:21 final size:21
Alignment explanation
Indices: 998594--998674 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
998584 CAGAACCCCA
*
998594 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
998615 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * * *
998635 CAAAGGGGGAATCGGTTCCCTTAT
1 ---GGGGGGAATCGATTCCCCTGT
998659 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
998675 TCTGCACAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 10 0.20
21 22 0.44
23 17 0.34
24 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:998664 original size:22 final size:23
Alignment explanation
Indices: 998615--998674 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
998605 ATTCCCCTGT
998615 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
998638 AGGGGGAATCGGTT-CCCTT-AT
1 GGGGGGAATCGGTTCCCCTTCAA
*
998659 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
998675 TCTGCACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1008944 original size:20 final size:19
Alignment explanation
Indices: 1008884--1008945 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1008874 TAGATATTTA
*
1008884 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1008903 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1008921 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1008941 ATTTT
1 ATTTT
1008946 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1017813 original size:14 final size:16
Alignment explanation
Indices: 1017778--1017818 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
1017768 ACTAAGGTTT
1017778 TTTTTATAAATATAATA
1 TTTTTA-AAATATAATA
1017795 TTTTTAAAA-ATAA-A
1 TTTTTAAAATATAATA
1017809 TTTTTAAAAT
1 TTTTTAAAAT
1017819 TACCTTAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 3 0.13
17 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTTAAAATATAATA
Found at i:1021816 original size:87 final size:87
Alignment explanation
Indices: 1021657--1021818 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
1021647 ATGTTATATT
*
1021657 ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1 ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGATA
**
1021722 ATTCTTATATAATAAAATAGAC
66 ACGCTTATATAATAAAATAGAC
* * * *
1021744 ATTTAACCGAAAATATTATCAAGTATAATAACATATTAGGTAGCATTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGATA
*
1021809 GCGCTTATAT
66 ACGCTTATAT
1021819 TGACTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAGCACTTATATAATGTAATAGATA
ACGCTTATATAATAAAATAGAC
Found at i:1026134 original size:200 final size:194
Alignment explanation
Indices: 1025863--1027006 Score: 755
Period size: 200 Copynumber: 5.7 Consensus size: 194
1025853 GTAAATTTCA
* * *
1025863 ACCGGTTACATTGTAAATTGACCTATTACATTATAATT-TCCGGTCTCGATGTATTTGGGTTCGA
1 ACCGGTTACATTGTAAATTGA-CTATTACATTATAATTAT--GGTTTCGATGTTTTTGGGATCGA
* * * *
1025927 TACTTTTTATAAATGTATCGACACTTTATGCGTGGACATCGTTTGG-CATTTATTATAGACAAAA
63 CACTTTTTATAAATGTATCGACACTTT-TGCGTGCACATCGTTTGGAAATATATTATAGAC-AAA
1025991 AGTATCGACACAAATGTATACA-GTGTCGATACATTATGTAGAAC-TATTTTCTCATAAAACCAG
126 AGTATCGACAC--ATGT-TACATGTGTCGATACATTATGTA-AACATATTTTCTCAT-AAACCAG
*
1026054 TAAATTTA-
186 TAAATGTAG
* * *
1026062 AGTCGGTTACACTGTAAAGTGACATATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGA
1 A-CCGGTTACATTGTAAATTGAC-TATTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGA
* * * * *
1026127 CACTTTTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTGGAAAATATATTTTGGACAAAA
63 CACTTTTTATAAATGTATCGACACTTTTGCGTGCACATCGTTTGG-AAATATATTATAGACAAAA
* * * * * * * *
1026192 GTATCGACACTTGTTAGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAATCGGTATA
127 GTATCGACACATGTTACA--TGTGTCGATACATTATGTAAACATATTTTCTCATAAACCAGTAAA
1026257 TGTAG
190 TGTAG
* * * * *
1026262 ACCGGTTACATTGTTATTTTATCTATTGCATTATAATTATGTGTTTCGATGTTTTTGGGATAGAC
1 ACCGGTTACATTGTAAATTGA-CTATTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGAC
* * * * * * * * * *
1026327 ACCTGTTATAAATGTATCGAAACTTTTTCGTGCACTTGGTTTAGAAAATACATTCTGGACAAAAA
64 ACTTTTTATAAATGTATCGACACTTTTGCGTGCACATCGTTT-GGAAATATATTATAGAC-AAAA
* ** * * * ** **
1026392 GTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTGTA
127 GTATCGACACATGTT--ACATGTGTCGATACATTATGTAAACATATTTTCTCATAAACCAGTAAA
*
1026457 TTTAG
190 TGTAG
* * * * * * * *
1026462 GCCGGTTACATTGTTATTTTACCTATTACATTAT-ATCTTTGTGTTTTGATGTTTTTAGTATCGA
1 ACCGGTTACATTGTAAATTGA-CTATTACATTATAAT-TATG-GTTTCGATGTTTTTGGGATCGA
* * * * * *
1026526 CACTTGTTATAAATGTATCGACAC-TTTGTCGTGCACTTGGTTTGGAAAATACATTCTTGACAAA
63 CACTTTTTATAAATGTATCGACACTTTTG-CGTGCACATCGTTTGG-AAATATATTATAGAC-AA
* * * * * * * **
1026590 AAGTATCGATACTTGTTGA-ATTTGTGTCGATACTTTATGTATACTTGTTTTCTCAAAAACTGGT
125 AAGTATCGACACATGTT-ACA--TGTGTCGATACATTATGTAAACATATTTTCTCATAAACCAGT
* *
1026654 ATATTTAG
187 AAATGTAG
* * * * * * *
1026662 ACCGGTTATATTGTTAATTTACTTATTACATTATAATTATGTGTTTTGATGATTTTAGTATCGAC
1 ACCGGTTACATTGTAAATTGAC-TATTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGAC
* * ** * * *
1026727 ACTTGTTATAAATGTATCAACAC-TTTGTCGTGCATTTTGTTTGGAAAATACATTATGGACAAAA
64 ACTTTTTATAAATGTATCGACACTTTTG-CGTGCACATCGTTTGG-AAATATATTATAGAC-AAA
* ** * * * *** *
1026791 AGTATCGACACTTGTTGA-ATTTGTGTCGATATTTTATGTATACATGTTTTCTCAGAAATTGGTG
126 AGTATCGACACATGTT-ACA--TGTGTCGATACATTATGTAAACATATTTTCTCATAAACCAGTA
* *
1026855 TATTTAG
188 AATGTAG
* * * * * * * *
1026862 GCCGGTTACATTGTTATTTTACCTATTACATTAT-ATCTTTGTGTTTCTATGTTTTTAGTATCGA
1 ACCGGTTACATTGTAAATTGA-CTATTACATTATAAT-TATG-GTTTCGATGTTTTTGGGATCGA
* * * * * *
1026926 CACTTGTTATAAATGTATCGACAC-TTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAA
63 CACTTTTTATAAATGTATCGACACTTTTG-CGTGCACATCGTTTGG-AAATATATTATAGAC-AA
*
1026990 AAGTATCGACACTTGTT
125 AAGTATCGACACATGTT
1027007 GAATTTGTGT
Statistics
Matches: 830, Mismatches: 90, Indels: 49
0.86 0.09 0.05
Matches are distributed among these distances:
197 3 0.00
198 3 0.00
199 146 0.18
200 663 0.80
201 14 0.02
202 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (194 bp):
ACCGGTTACATTGTAAATTGACTATTACATTATAATTATGGTTTCGATGTTTTTGGGATCGACAC
TTTTTATAAATGTATCGACACTTTTGCGTGCACATCGTTTGGAAATATATTATAGACAAAAGTAT
CGACACATGTTACATGTGTCGATACATTATGTAAACATATTTTCTCATAAACCAGTAAATGTAG
Found at i:1027007 original size:200 final size:200
Alignment explanation
Indices: 1026086--1027061 Score: 1426
Period size: 200 Copynumber: 4.9 Consensus size: 200
1026076 TAAAGTGACA
* * * * *
1026086 TATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACAC
1 TATTACATTATAATTATGTGTTTCTATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACAC
* * *
1026151 TTTTTCGTGCACTTGGTTTGGAAAATATATTTTGGAC-AAAAGTATCGACACTTGTT-AGATTTG
66 TTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGA-ATTTG
*
1026214 TGTCGATACTTTATGTATACATGTTTTCTCATAAA-TCGGTATATGTAGACCGGTTACATTGTTA
130 TGTCGATACTTTATGTATACATGTTTTCTCATAAACT-GGTATATTTAGACCGGTTACATTGTTA
*
1026278 TTTTATC
194 TTTTACC
* * * * * * *
1026285 TATTGCATTATAATTATGTGTTTCGATGTTTTTGGGATAGACACCTGTTATAAATGTATCGAAAC
1 TATTACATTATAATTATGTGTTTCTATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACAC
* * *
1026350 TTTTTCGTGCACTTGGTTTAGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGT
66 TTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTTGT
* *
1026415 GTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTGTATTTAGGCCGGTTACATTGTTATT
131 GTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTATATTTAGACCGGTTACATTGTTATT
1026480 TTACC
196 TTACC
*
1026485 TATTACATTAT-ATCTTTGTGTTT-TGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGAC
1 TATTACATTATAAT-TATGTGTTTCT-ATGTTTTTAGTATCGACACTTGTTATAAATGTATCGAC
* *
1026548 ACTTTGTCGTGCACTTGGTTTGGAAAATACATTCTTGACAAAAAGTATCGATACTTGTTGAATTT
64 ACTTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTT
* * *
1026613 GTGTCGATACTTTATGTATACTTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGTTA
129 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTATATTTAGACCGGTTACATTGTTA
* *
1026678 ATTTACT
194 TTTTACC
* *
1026685 TATTACATTATAATTATGTGTTT-TGATGATTTTAGTATCGACACTTGTTATAAATGTATCAACA
1 TATTACATTATAATTATGTGTTTCT-ATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACA
* * *
1026749 CTTTGTCGTGCATTTTGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGAATTTG
65 CTTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTTG
* * * * *
1026814 TGTCGATATTTTATGTATACATGTTTTCTCAGAAATTGGTGTATTTAGGCCGGTTACATTGTTAT
130 TGTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTATATTTAGACCGGTTACATTGTTAT
1026879 TTTACC
195 TTTACC
*
1026885 TATTACATTAT-ATCTTTGTGTTTCTATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACA
1 TATTACATTATAAT-TATGTGTTTCTATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACA
1026949 CTTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTTG
65 CTTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTTG
* * * * *
1027014 TGTTGATACTTTATGTATACCTGTTTTTCTCAAAAACCGATATATTTA
130 TGTCGATACTTTATGTATACATG-TTTTCTCATAAACTGGTATATTTA
1027062 TAACAAGTGT
Statistics
Matches: 703, Mismatches: 65, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
199 97 0.14
200 583 0.83
201 23 0.03
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (200 bp):
TATTACATTATAATTATGTGTTTCTATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACAC
TTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGAATTTGT
GTCGATACTTTATGTATACATGTTTTCTCATAAACTGGTATATTTAGACCGGTTACATTGTTATT
TTACC
Found at i:1027335 original size:24 final size:24
Alignment explanation
Indices: 1027298--1027344 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1027288 ATTTACATTT
1027298 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
1027322 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
1027345 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:1028709 original size:6 final size:6
Alignment explanation
Indices: 1028702--1028735 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1028692 GTTTGAATCA
* *
1028702 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1028736 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:1029913 original size:15 final size:15
Alignment explanation
Indices: 1029889--1029930 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1029879 AGGAGATTGT
* *
1029889 GGTTAAGAAGAGTTG
1 GGTTGAGAAGAGGTG
*
1029904 GGTTGGGAAGAGGTG
1 GGTTGAGAAGAGGTG
1029919 GGTTGAGAAGAG
1 GGTTGAGAAGAG
1029931 CTTTGAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (15 bp):
GGTTGAGAAGAGGTG
Found at i:1030734 original size:199 final size:199
Alignment explanation
Indices: 1030277--1031366 Score: 1745
Period size: 199 Copynumber: 5.5 Consensus size: 199
1030267 TTTTCAAATT
* * * * * *
1030277 AAACCGGTATATTTATACCGATTACATTGTAAAATGACCTATTACATTAAAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * * * * * *
1030342 TGTTATTAGGACCAATACTTGTTATAAATGTATCGACACTTTTTCCTGCACTTGGTTTGGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* * * *
1030407 CATTATGAACCAAAAGTATCGACACTTGCTTTATTTGTGTCGATAC-TTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
1030471 TCAA
196 TCAA
** * *
1030475 AAATTGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTATAATTATGGGTTTTGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
1030540 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACAATTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* * * *
1030605 CATTCTGGACCAAAAGTATCTACACTTATTTTATTTGTGTTGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
1030670 TCAA
196 TCAA
*
1030674 AAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* *
1030739 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTCTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* *
1030804 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTTTGTTGATACTTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
*
1030869 TAAA
196 TCAA
* *
1030873 AAACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* *
1030938 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* *
1031003 CATTCTGGACTAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
*
1031068 TAAA
196 TCAA
* *
1031072 AAACCAGTATATTTAGACCGGTTACATTGTTAATTTACATATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1031137 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
*
1031202 CATTCTGGACAAAAAGTATCGACACTTGTTTTATTTGTGTCGATAC-TTTTGTACACATG-TTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
1031265 TCAA
196 TCAA
* * *
1031269 AAAACGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTTTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1031334 TGTTTTTGGGATCGACACTTATTATAAATGTAT
66 TGTTTTTGGGATCGACACTTATTATAAATGTAT
1031367 TGACTCCTAA
Statistics
Matches: 831, Mismatches: 60, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
197 100 0.12
198 163 0.20
199 568 0.68
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
TCAA
Found at i:1031765 original size:19 final size:19
Alignment explanation
Indices: 1031741--1031786 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1031731 ATTCACATAA
*
1031741 AAAATTATAAATCGTATAC
1 AAAATTAAAAATCGTATAC
*
1031760 AAAATTAAAAATCTTATAC
1 AAAATTAAAAATCGTATAC
1031779 AAAATTAA
1 AAAATTAA
1031787 CCCTACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATTAAAAATCGTATAC
Found at i:1033272 original size:18 final size:18
Alignment explanation
Indices: 1033249--1033287 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1033239 TTCTCCCCAT
*
1033249 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTATCTTC
1033267 TTCCTCCATCTTATCTTC
1 TTCCTCCATCTTATCTTC
1033285 TTC
1 TTC
1033288 AAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTATCTTC
Found at i:1035335 original size:19 final size:18
Alignment explanation
Indices: 1035311--1035363 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1035301 CTATATTTAT
1035311 TTTCTACCTAGAATATCA
1 TTTCTACCTAGAATATCA
*
1035329 CTTTCTACAT-GTAATATCA
1 -TTTCTACCTAG-AATATCA
* *
1035348 TTTTTACCTATAATAT
1 TTTCTACCTAGAATAT
1035364 TAAATAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (18 bp):
TTTCTACCTAGAATATCA
Found at i:1035363 original size:18 final size:18
Alignment explanation
Indices: 1035309--1035363 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1035299 ATCTATATTT
*
1035309 ATTTTCTACCTAGAATATC
1 ATTTT-TACCTATAATATC
* * *
1035328 ACTTTCTACATGTAATATC
1 A-TTTTTACCTATAATATC
1035347 ATTTTTACCTATAATAT
1 ATTTTTACCTATAATAT
1035364 TAAATAAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 13 0.46
19 12 0.43
20 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (18 bp):
ATTTTTACCTATAATATC
Found at i:1035392 original size:75 final size:77
Alignment explanation
Indices: 1035267--1035418 Score: 227
Period size: 75 Copynumber: 2.0 Consensus size: 77
1035257 ACAACCTAAA
* * * ***
1035267 ATCATTTTCTACCTATAATATTATATACATGTATCTATATTTATTTTCTACCTAGAATATCACTT
1 ATCATTTTCTACCTATAATATTAAATACAAGTATCGATATTTAGCATCTACCTAGAATATCACTT
*
1035332 TCTACATGTAAT
66 TCTACATATAAT
1035344 ATCATTTT-TACCTATAATATTAAATA-AAGTATCGATATTTAGCATCTACCTAGAATATCACTT
1 ATCATTTTCTACCTATAATATTAAATACAAGTATCGATATTTAGCATCTACCTAGAATATCACTT
1035407 TCTACATATAAT
66 TCTACATATAAT
1035419 CGGTCCCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 43 0.63
76 17 0.25
77 8 0.12
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (77 bp):
ATCATTTTCTACCTATAATATTAAATACAAGTATCGATATTTAGCATCTACCTAGAATATCACTT
TCTACATATAAT
Found at i:1036453 original size:182 final size:182
Alignment explanation
Indices: 1035783--1036456 Score: 950
Period size: 182 Copynumber: 3.7 Consensus size: 182
1035773 TATGCGTACT
* * *
1035783 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTATCATTTTGGGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCG
* *
1035848 GTTTTGTCATATTTTTACCTGCTATATTGTTATGGATCGATACATTTTTTA-AAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCATAAGTATCGACACT
1035912 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
1035964 TATTAAATTATCGACACTTTCAACATATCTGATATCTTTTTACC-GATTTT-TCATTTTTGAGAC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAG-TTTTGTCA-TTTTGAGAC
** * * ** **
1036027 ATGTTTTGTCATA-TTTTACTTGTTATATTGTTATGAATCGATATTTTTTTTTTGAAGTATCGAC
64 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCAT-AAGTATCGAC
1036091 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
128 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
1036146 TATTAAAGTATCGAAACTTTCAACATATACGGTAG-TTCTTTACCAGTTTTGTCATTTTGAGACC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCAGTTTTGTCATTTTGAGACC
* *
1036210 GGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACA-TTTTCATAAAGTATCGATA
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCAT-AAGTATCGACA
*
1036274 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTA
129 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* *
1036328 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCG
* * * **
1036393 GTTTTGTCATATTTTTACCTATAATATT-TCTATGGAGCGATACATTTTTCATTTGTATCGACAC
66 GTTTTGTCATATTTTTACCTGTTATATTGT-TATGGATCGATACATTTTTCATAAGTATCGACAC
1036457 AAACCAACAA
Statistics
Matches: 436, Mismatches: 45, Indels: 23
0.87 0.09 0.05
Matches are distributed among these distances:
180 37 0.08
181 66 0.15
182 294 0.67
183 39 0.09
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCATAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:1043560 original size:16 final size:17
Alignment explanation
Indices: 1043539--1043571 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1043529 CGGATATCCG
1043539 ATCCGAAATTT-CGGAT
1 ATCCGAAATTTGCGGAT
*
1043555 ATCCGAATTTTGCGGAT
1 ATCCGAAATTTGCGGAT
1043572 CGGATACGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (17 bp):
ATCCGAAATTTGCGGAT
Found at i:1056834 original size:20 final size:20
Alignment explanation
Indices: 1056787--1056967 Score: 141
Period size: 20 Copynumber: 8.8 Consensus size: 20
1056777 AATGACCAAC
* *
1056787 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
1056806 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
1056826 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
1056846 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1056867 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
**
1056888 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* *
1056909 AAGAATCGTAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
**
1056930 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
1056951 AAGAATCGCAACGCGAT
1 AA-AATCGCAACGCGAT
1056968 CTTACATAAA
Statistics
Matches: 126, Mismatches: 27, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
19 18 0.14
20 51 0.40
21 16 0.13
22 41 0.33
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1056876 original size:22 final size:22
Alignment explanation
Indices: 1056848--1056970 Score: 157
Period size: 22 Copynumber: 5.8 Consensus size: 22
1056838 TTGAAAAGAA
1056848 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATCTTCCAAG
*
1056870 AATCGCAACGCGA--TT-CAGAA
1 AATCGCAACGCGATCTTCCA-AG
1056890 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATCTTCCAAG
* ***
1056912 AATCGTAACGCGAT-TAAGAA-
1 AATCGCAACGCGATCTTCCAAG
1056932 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATCTTCCAAG
1056954 AATCGCAACGCGATCTT
1 AATCGCAACGCGATCTT
1056971 ACATAAATGA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
19 2 0.02
20 29 0.34
21 6 0.07
22 46 0.54
23 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (22 bp):
AATCGCAACGCGATCTTCCAAG
Found at i:1056890 original size:42 final size:42
Alignment explanation
Indices: 1056843--1056967 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
1056833 CAACGTTGAA
1056843 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
* *
1056885 CAGAAAATCGCAACGCGATCTTCCAAGAATCGTAACGCGATT
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1056927 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT
1056968 CTTACATAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
Found at i:1056997 original size:84 final size:84
Alignment explanation
Indices: 1056843--1056997 Score: 197
Period size: 84 Copynumber: 1.8 Consensus size: 84
1056833 CAACGTTGAA
* * * * ***
1056843 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTC
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCACAAAATCGAAAAGCGAACGAA
*
1056908 CAAGAATCGTAACGCGATT
66 AAAGAATCGTAACGCGATT
*
1056927 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATCTTACATAAAT-GAAAAGC-AACG
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT-TCACA-AAATCGAAAAGCGAACG
1056990 AAAAAGAA
64 AAAAAGAA
1056998 AATGCAGAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
84 48 0.80
85 8 0.13
86 4 0.07
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (84 bp):
AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCACAAAATCGAAAAGCGAACGAA
AAAGAATCGTAACGCGATT
Found at i:1058197 original size:3 final size:3
Alignment explanation
Indices: 1058189--1058245 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
1058179 AAGGCTGCAA
1058189 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1058237 AAT -AT AAT A
1 AAT AAT AAT A
1058246 TATTTTTCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1058818 original size:22 final size:23
Alignment explanation
Indices: 1058770--1058818 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1058760 TTCATATTAA
* *
1058770 TAAAAAATATAGAAGTTTAATGC
1 TAAAAAAAATAGAAGTTTAAAGC
1058793 TAAAAAAAATAG-AGTTCTAAAG-
1 TAAAAAAAATAGAAGTT-TAAAGC
1058815 TAAA
1 TAAA
1058819 TGCTCTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (23 bp):
TAAAAAAAATAGAAGTTTAAAGC
Found at i:1059310 original size:16 final size:15
Alignment explanation
Indices: 1059289--1059326 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1059279 TTTTCGTCGG
1059289 TTTTAGTTGTTTATTT
1 TTTTAGTTGTTT-TTT
1059305 TTTTAG-TGTTTTTT
1 TTTTAGTTGTTTTTT
*
1059319 TCTTAGTT
1 TTTTAGTT
1059327 ATCATGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 6 0.30
16 6 0.30
ACGTcount: A:0.11, C:0.03, G:0.13, T:0.74
Consensus pattern (15 bp):
TTTTAGTTGTTTTTT
Found at i:1068792 original size:13 final size:13
Alignment explanation
Indices: 1068758--1068795 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
1068748 TTTACAGTTA
1068758 TCTTTTAATATAC
1 TCTTTTAATATAC
*
1068771 TAATTTTAATATAC
1 T-CTTTTAATATAC
1068785 TCTTTTAATAT
1 TCTTTTAATAT
1068796 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (13 bp):
TCTTTTAATATAC
Found at i:1068803 original size:13 final size:13
Alignment explanation
Indices: 1068760--1068805 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1068750 TACAGTTATC
1068760 TTTTAATATACTAA
1 TTTTAATATACT-A
*
1068774 TTTTAATATACTC
1 TTTTAATATACTA
**
1068787 TTTTAATATTTTA
1 TTTTAATATACTA
1068800 TTTTAA
1 TTTTAA
1068806 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTAATATACTA
Found at i:1068822 original size:20 final size:20
Alignment explanation
Indices: 1068794--1068838 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1068784 CTCTTTTAAT
* *
1068794 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
1068814 ATTTAATTTCATAGATAAAA
1 ATTTAATTTCAAAAATAAAA
1068834 ATTTA
1 ATTTA
1068839 TTAAAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:1069567 original size:15 final size:15
Alignment explanation
Indices: 1069558--1069588 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1069548 ATCATCGTCG
*
1069558 TCGTCGTCATCATTA
1 TCGTCGTCATCATCA
1069573 TCGTCGTCATCATCA
1 TCGTCGTCATCATCA
1069588 T
1 T
1069589 AACTTGACGT
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:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (15 bp):
TCGTCGTCATCATCA
Found at i:1069570 original size:18 final size:18
Alignment explanation
Indices: 1069547--1069588 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1069537 TCCCAACCAC
* *
1069547 CATCATCGTCGTCGTCGT
1 CATCATCATCGTCGTCAT
*
1069565 CATCATTATCGTCGTCAT
1 CATCATCATCGTCGTCAT
1069583 CATCAT
1 CATCAT
1069589 AACTTGACGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (18 bp):
CATCATCATCGTCGTCAT
Found at i:1073146 original size:23 final size:23
Alignment explanation
Indices: 1073071--1073149 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
1073061 AGCTCATATA
*
1073071 AATTGTACCGAAGT-CCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1073093 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
1073117 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
1073140 AATTGCACCG
1 AATTGCACCG
1073150 TAGTACCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
22 3 0.07
23 33 0.72
24 10 0.22
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1074253 original size:20 final size:20
Alignment explanation
Indices: 1074180--1074244 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1074170 TTTTTCATTT
1074180 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
*
1074200 AGGGGGAATCTG-T---TCCC
1 AGGGGGAATC-GATACCCCCC
*
1074217 --GGGAAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
1074235 AGGGGGAATC
1 AGGGGGAATC
1074245 TGTTCCCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
14 1 0.03
15 8 0.24
17 3 0.09
18 3 0.09
20 18 0.53
21 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.32, T:0.14
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:1076036 original size:3 final size:3
Alignment explanation
Indices: 1076023--1076075 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1076013 TTAAAAAATA
* *
1076023 TAT TA- TAT TAT TAT TAT TAT TAT TAT TACT TAT TAT TAT TAG TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1076068 TAT TAT TA
1 TAT TAT TA
1076076 ATTTATATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1076062 original size:25 final size:25
Alignment explanation
Indices: 1076028--1076075 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1076018 AAATATATTA
* *
1076028 TATTATTATTATTATTATTATTACT
1 TATTATTATTAGTAGTATTATTACT
1076053 TATTATTATTAGTAGTATTATTA
1 TATTATTATTAGTAGTATTATTA
1076076 ATTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTATTATTAGTAGTATTATTACT
Found at i:1078108 original size:13 final size:13
Alignment explanation
Indices: 1078090--1078114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1078080 GTGGGGTAGG
1078090 ATTTTTTTTGTTC
1 ATTTTTTTTGTTC
1078103 ATTTTTTTTGTT
1 ATTTTTTTTGTT
1078115 TTGATTTACC
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:0.08, C:0.04, G:0.08, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTGTTC
Found at i:1080899 original size:106 final size:106
Alignment explanation
Indices: 1080710--1081500 Score: 1280
Period size: 106 Copynumber: 7.5 Consensus size: 106
1080700 TTTTTGCAGT
* *
1080710 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGTCTCCAGACAATGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
1080775 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * *
1080816 TTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
1080881 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
*
1080922 TTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
1080987 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
*
1081028 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* *
1081093 ACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* ** * *
1081134 TTTTAGAGCCAATTTCAACTTCACAATGAATGATATTGGACACCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
1081199 ACGATGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* *
1081239 TTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
1081304 ACGACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * * * *
1081344 TTTCAGAGCCAAATTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* * *
1081409 ACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * *
1081450 TTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
1081501 ACAACTTTCA
Statistics
Matches: 641, Mismatches: 43, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
105 192 0.30
106 449 0.70
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (106 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
Found at i:1082429 original size:3 final size:3
Alignment explanation
Indices: 1082416--1082465 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1082406 TTAAAAAATA
* * *
1082416 TAT TA- TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAG TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
1082461 TAT TA
1 TAT TA
1082466 ATTTATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Done.