Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_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: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:611714 original size:207 final size:207
Alignment explanation
Indices: 611346--612115 Score: 1035
Period size: 207 Copynumber: 3.7 Consensus size: 207
611336 GGTCATGTTT
* * * ** * *
611346 AAAGATATTTGAGATAATACGGTTCCTTCGTGATGAGGACATCTGGCTACCAAAAGATGATTGAG
1 AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGCTATCAAAAGATGATTGAG
* * ** *
611411 ATAACACGGTTCCTTCGTGATGATGATGTTTACCTATCTAAGGATGATTGGAGATAACACGGTTC
66 ATAACACGGTTCCTTCGTGATGAGGATATTTGGCTATCTAAGGATGATTTGAGATAACACGGTTC
* * * *
611476 CTTCGTGATAAGGACATCTGGCTACCTAAGGATGATTTTAGATAACTCGGTTCCTTCATGATGAG
131 CTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTCCTTAATGATGAG
611541 GACATCTGGTCA
196 GACATCTGGTCA
* *
611553 AAAGATAATTGAGATAACACAATTCCTTTACGATGAGGACTTCTGGCTATCAAAAGATGATTGAG
1 AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGCTATCAAAAGATGATTGAG
* * * * * *
611618 ATAAAATGGTTCCTTCGTGATAAAGATATTTGGCTATCTAATGATGATTTGAGATAACACAGTTC
66 ATAACACGGTTCCTTCGTGATGAGGATATTTGGCTATCTAAGGATGATTTGAGATAACACGGTTC
* * * **
611683 CTTCGTGATGAGGATATCTAGTTATCTAAGGATGATTTGAGATAACTCAATTCCTTAATGATGAG
131 CTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTCCTTAATGATGAG
611748 GACATCTGGTCA
196 GACATCTGGTCA
*
611760 AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGGTATCAAAAGATGATTGAG
1 AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGCTATCAAAAGATGATTGAG
* * * *
611825 ATAACACGGTTCCTTCGTGATGAGGACATTTGGCTATCTAAGGATGATTTAAGATTACACGATTC
66 ATAACACGGTTCCTTCGTGATGAGGATATTTGGCTATCTAAGGATGATTTGAGATAACACGGTTC
* *
611890 CATT-GTTATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTCCTTTATGATGA
131 C-TTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTCCTTAATGATGA
* *
611954 GGAC-TTTGGTTA
195 GGACATCTGGTCA
* * * * * * *
611966 AAAGATAATTGAGATAACATGGTTCCTTCGCGATGA-GACTTATTGCTATCTAAGGATGATTTGA
1 AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGCTATCAAAAGATGA-TTGA
* * * * *
612030 GATAACACGGTTCCTTCATGATGGGGAAATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTT
65 GATAACACGGTTCCTTCGTGATGAGGATATTTGGCTATCTAAGGATGATTTGAGATAACACGGTT
*
612095 CCTTCATGATGAGG-CATCTGG
130 CCTTCGTGATGAGGACATCTGG
612116 TCAAAATATA
Statistics
Matches: 492, Mismatches: 68, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
205 27 0.05
206 109 0.22
207 354 0.72
208 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (207 bp):
AAAGATAATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGCTATCAAAAGATGATTGAG
ATAACACGGTTCCTTCGTGATGAGGATATTTGGCTATCTAAGGATGATTTGAGATAACACGGTTC
CTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTCCTTAATGATGAG
GACATCTGGTCA
Found at i:612069 original size:153 final size:153
Alignment explanation
Indices: 611346--612228 Score: 705
Period size: 153 Copynumber: 5.7 Consensus size: 153
611336 GGTCATGTTT
* * * * * * * *
611346 AAAGATATTTGAGATAATACGGTTCCTTCGTGATGAGGACATCTGGCTACCAAAAGATGA-TTGA
1 AAAGATAATTGAGATAACACGGTTCCTTCGCGATGAGGAC-TTTTGCTATCTAAGGATGATTTGA
* * * ** * ** * *
611410 GATAACACGGTTCCTTCGTGATGATGATGTTTACCTATCTAAGGATGATTGGAGATAACACGGTT
65 GATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTT
* * * *
611475 CCTTCGTGATAAGGACATCTGGCTA
130 CCTTCATGATGAGGAC-TTTGGTTA
* * * * ** * * * * * *
611500 CCTAAGGATGATTTTAGATAACTCGGTTCCTTCATGATGAGGACATCTG--GTCAAAAGAT-AAT
1 ---AAAGAT-AATTGAGATAACACGGTTCCTTCGCGATGAGGACTTTTGCTATCTAAGGATGATT
* * * * * * *
611562 TGAGATAACACAATTCCTTTACGATGAGGACTTCTGGCTATCAAAAGATGA-TTGAGATAAAAT-
62 TGAGATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGAT-AACTC
* * * * *
611625 GGTTCCTTCGTGATAAAGATATTTGGCTATCT
126 GGTTCCTTCATGATGAGGA-CTTTGG-T-T-A
* * * * * *
611657 AATGATGATTTGAGATAACACAGTTCCTTCGTGATGAGGA-TATCTAGTTATCTAAGGATGATTT
1 AAAGAT-AATTGAGATAACACGGTTCCTTCGCGATGAGGACT-T-TTGCTATCTAAGGATGATTT
* * * * * * * *
611721 GAGATAACTCAATTCCTTAATGATGAGGACATCTGG---TCAAAAGAT-AATTGAGATAACACGA
63 GAGATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGG
*
611782 TTCCTTCACGATGAGGACTTCTGGGTATCA
128 TTCCTTCATGATGAGGACTT-T-GGT-T-A
* * * *
611812 AAAGATGATTGAGATAACACGGTTCCTTCGTGATGAGGACATTTGGCTATCTAAGGATGATTTAA
1 AAAGATAATTGAGATAACACGGTTCCTTCGCGATGAGGAC-TTTTGCTATCTAAGGATGATTTGA
* * *
611877 GATTACACGATTCCATT-GTTATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGT
65 GATAACACGATTCC-TTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGT
*
611941 TCCTTTATGATGAGGACTTTGGTTA
129 TCCTTCATGATGAGGACTTTGGTTA
*
611966 AAAGATAATTGAGATAACATGGTTCCTTCGCGATGA-GACTTATTGCTATCTAAGGATGATTTGA
1 AAAGATAATTGAGATAACACGGTTCCTTCGCGATGAGGACTT-TTGCTATCTAAGGATGATTTGA
* * *
612030 GATAACACGGTTCCTTCATGATGGGGAAATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTT
65 GATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTT
* *
612095 CCTTCATGATGAGG-CATCTGGTCA
130 CCTTCATGATGAGGAC-TTTGGTTA
* * * * *
612119 AAATATAATTGAGATAACACGATTCCTTTGCAATGAGGACTTCTGCTATCTAAGGATGATTTGAG
1 AAAGATAATTGAGATAACACGGTTCCTTCGCGATGAGGACTTTTGCTATCTAAGGATGATTTGAG
** * * *
612184 ATAACTTGGTTACTTCATGATGAGGACGTCTGGCTATCTAAGGAT
66 ATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGAT
612229 TTTTGTTTCT
Statistics
Matches: 597, Mismatches: 102, Indels: 58
0.79 0.13 0.08
Matches are distributed among these distances:
152 5 0.01
153 190 0.32
154 184 0.31
155 94 0.16
156 7 0.01
157 21 0.04
158 96 0.16
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (153 bp):
AAAGATAATTGAGATAACACGGTTCCTTCGCGATGAGGACTTTTGCTATCTAAGGATGATTTGAG
ATAACACGATTCCTTCATGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACTCGGTTC
CTTCATGATGAGGACTTTGGTTA
Found at i:613454 original size:37 final size:37
Alignment explanation
Indices: 613411--613621 Score: 99
Period size: 37 Copynumber: 5.4 Consensus size: 37
613401 CGAGTCTTAA
613411 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTT
1 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTT
** * * *
613448 AAAATGCCCC-ACATGGATCATTTCTG-TCTGAAATGGGCTTT
1 AAAATGCCCCAACAT-TTTCA-TACTGATGTG--A--GCCTTT
* * *
613489 CAAAATGCCCCAACATTTTCATACTAATGTAAGCCTTC
1 -AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTT
** * * * *
613527 AAAATGTTCC-ACATGGATT-ATTTCTG-TTTGAAATGGGCTTT
1 AAAATGCCCCAACAT--TTTCA-TACTGATGTG--A--GCCTTT
*
613568 CAAAATGCCCCAACATTTTCATACTGATGTGAGCCTTC
1 -AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTT
* *
613606 AAGATGTCCCAACATT
1 AAAATGCCCCAACATT
613622 ATAAGTTTCA
Statistics
Matches: 123, Mismatches: 31, Indels: 40
0.63 0.16 0.21
Matches are distributed among these distances:
36 8 0.07
37 41 0.33
38 17 0.14
39 2 0.02
40 2 0.02
41 18 0.15
42 27 0.22
43 8 0.07
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (37 bp):
AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTT
Found at i:613495 original size:42 final size:42
Alignment explanation
Indices: 613444--613579 Score: 115
Period size: 42 Copynumber: 3.4 Consensus size: 42
613434 TGATGTGAGC
*
613444 CTTT-AAAATGCCCCACATGGATCATTTCTGTCTGAAATGGG
1 CTTTCAAAATGCCCCACATGGATCATTTCTGTATGAAATGGG
** * * *
613485 CTTTCAAAATGCCCCAACAT-TTTCA-TACT-AATGTAA---G
1 CTTTCAAAATGCCCC-ACATGGATCATTTCTGTATGAAATGGG
* ** * *
613522 CCTTCAAAATGTTCCACATGGATTATTTCTGTTTGAAATGGG
1 CTTTCAAAATGCCCCACATGGATCATTTCTGTATGAAATGGG
613564 CTTTCAAAATGCCCCA
1 CTTTCAAAATGCCCCA
613580 ACATTTTCAT
Statistics
Matches: 68, Mismatches: 19, Indels: 15
0.67 0.19 0.15
Matches are distributed among these distances:
36 4 0.06
37 15 0.22
38 3 0.04
39 4 0.06
40 4 0.06
41 7 0.10
42 27 0.40
43 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (42 bp):
CTTTCAAAATGCCCCACATGGATCATTTCTGTATGAAATGGG
Found at i:613501 original size:79 final size:79
Alignment explanation
Indices: 613411--613616 Score: 331
Period size: 79 Copynumber: 2.6 Consensus size: 79
613401 CGAGTCTTAA
*
613411 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTTAAAATGCCCCACATGGATCATTTCTGTC
1 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTCAAAATGCCCCACATGGATCATTTCTGTC
613476 TGAAATGGGCTTTC
66 TGAAATGGGCTTTC
* * ** * *
613490 AAAATGCCCCAACATTTTCATACTAATGTAAGCCTTCAAAATGTTCCACATGGATTATTTCTGTT
1 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTCAAAATGCCCCACATGGATCATTTCTGTC
613555 TGAAATGGGCTTTC
66 TGAAATGGGCTTTC
* *
613569 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTCAAGATGTCCCA
1 AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTCAAAATGCCCCA
613617 ACATTATAAG
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 116 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (79 bp):
AAAATGCCCCAACATTTTCATACTGATGTGAGCCTTCAAAATGCCCCACATGGATCATTTCTGTC
TGAAATGGGCTTTC
Found at i:619784 original size:15 final size:16
Alignment explanation
Indices: 619759--619788 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
619749 AACTAAAAGT
619759 AATATTAAAAATTAAA
1 AATATTAAAAATTAAA
619775 AATA-TAAAAATTAA
1 AATATTAAAAATTAA
619789 GGGATTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATTAAAAATTAAA
Found at i:620194 original size:13 final size:14
Alignment explanation
Indices: 620165--620201 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
620155 CTCTTTTCAT
*
620165 TTCTCTCTTTGAGC
1 TTCTCTCTCTGAGC
620179 TTCTCTCTCT-AGC
1 TTCTCTCTCTGAGC
620192 TTCTCTCTCT
1 TTCTCTCTCT
620202 TAGAGAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.05, C:0.35, G:0.08, T:0.51
Consensus pattern (14 bp):
TTCTCTCTCTGAGC
Found at i:621104 original size:5 final size:5
Alignment explanation
Indices: 621088--621123 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
621078 TTATTTATTA
621088 ATAAT AATAAT ATAAT ATAAT ATAATT ATAAT ATAA
1 ATAAT -ATAAT ATAAT ATAAT ATAA-T ATAAT ATAA
621124 AACGTAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:621109 original size:16 final size:16
Alignment explanation
Indices: 621088--621123 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
621078 TTATTTATTA
621088 ATAATAATAA-TATAAT
1 ATAAT-ATAATTATAAT
621104 ATAATATAATTATAAT
1 ATAATATAATTATAAT
621120 ATAA
1 ATAA
621124 AACGTAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATAATTATAAT
Found at i:625001 original size:2 final size:2
Alignment explanation
Indices: 624994--625036 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
624984 TATGGCATAG
624994 TA TA TA 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
625036 T
1 T
625037 TAAATAACGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:628926 original size:32 final size:31
Alignment explanation
Indices: 628881--628970 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 31
628871 CAAAATATAT
*
628881 AACTTTTAAAAAATTAA-ATTTTTGGTCCCCTA
1 AACTTTTAAAAAATTAATA-TTTTGGTCACC-A
* *
628913 AACTTTTACAAAATTTATATTTTGGTCACCA
1 AACTTTTAAAAAATTAATATTTTGGTCACCA
* * *
628944 AAC-TTTCAAAACTT-ATATTTTAGTCAC
1 AACTTTTAAAAAATTAATATTTTGGTCAC
628971 TAACCAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 12 0.24
30 8 0.16
31 4 0.08
32 25 0.50
33 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (31 bp):
AACTTTTAAAAAATTAATATTTTGGTCACCA
Found at i:628959 original size:29 final size:32
Alignment explanation
Indices: 628881--628970 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 32
628871 CAAAATATAT
* * *
628881 AACTTTTA-AAAAATTAAATTTTTGGTCCCCTA
1 AACTTTTACAAAACTTATA-TTTTGGTCACCTA
*
628913 AACTTTTACAAAATTTATATTTTGGTCACC-A
1 AACTTTTACAAAACTTATATTTTGGTCACCTA
*
628944 AAC-TTT-CAAAACTTATATTTTAGTCAC
1 AACTTTTACAAAACTTATATTTTGGTCAC
628971 TAACCAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 19 0.37
30 3 0.06
31 4 0.08
32 18 0.35
33 8 0.15
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (32 bp):
AACTTTTACAAAACTTATATTTTGGTCACCTA
Found at i:636740 original size:6 final size:6
Alignment explanation
Indices: 636729--636769 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
636719 CTGAAGCAAC
* *
636729 TCTATT TCTATT TCTATA TCTATT T-TATT TC-ATT TCAATT T
1 TCTATT TCTATT TCTATT TCTATT TCTATT TCTATT TCTATT T
636770 ACTTATCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (6 bp):
TCTATT
Found at i:640821 original size:25 final size:25
Alignment explanation
Indices: 640772--640821 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
640762 ATTCCTTTAT
* *
640772 CATCTTCCATTATCATTCTTTCAAC
1 CATCTTCCATTATCATTCATACAAC
* *
640797 CATCTTCCATTGTCGTTCATACAAC
1 CATCTTCCATTATCATTCATACAAC
640822 AACATCAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (25 bp):
CATCTTCCATTATCATTCATACAAC
Found at i:652597 original size:19 final size:21
Alignment explanation
Indices: 652551--652599 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
652541 AGTAATAATG
652551 TATAATATATATTTTCAATAAA
1 TATAATATATATTTT-AATAAA
*
652573 -ACAATATATA-TTT-ATAAA
1 TATAATATATATTTTAATAAA
652591 TATAATATA
1 TATAATATA
652600 CATATAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 3 0.12
21 9 0.38
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATATATATTTTAATAAA
Found at i:657449 original size:22 final size:21
Alignment explanation
Indices: 657419--657459 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
657409 AGCCTTCATC
657419 TCTTATGATAGTCTTCATCTGG
1 TCTTATGATAGTCTT-ATCTGG
* *
657441 TCTTCTGATTGTCTTATCT
1 TCTTATGATAGTCTTATCT
657460 TTTCCTCCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.51
Consensus pattern (21 bp):
TCTTATGATAGTCTTATCTGG
Found at i:659969 original size:358 final size:358
Alignment explanation
Indices: 659102--660178 Score: 1929
Period size: 358 Copynumber: 3.0 Consensus size: 358
659092 GGATAAATTC
659102 TCACAAGTCTTCACTTTCACCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAAA
1 TCACAAGTCTTCACTTTCACCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAAA
* * *
659167 GCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTATAAATATTTATCTGGGAAAAAAAA
66 GCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTACAACTATTTATCTGGGAAAAAATA
*
659232 TTCAAATGTAAATAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTAAAGAA
131 TTCAAATGTAAATAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGAA
*
659297 GACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCACA
196 GACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCGCA
* * * * **
659362 ACGGCCCCTTCAGGTGGCCCCAGATTTGCATTCCGGCTTTGAATCCTGATAGAGTTTCCACCGAT
261 ACGGCCCCTTCAGGTGG-CCCGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCACCACCGAT
*
659427 CATTTTGTATGAGATAGATAGGACACCTTGATTT
325 CATTTTGTATGAGATAGATCGGACACCTTGATTT
659461 TCACAAGTCTTCACTTTCACCCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAA
1 TCACAAGTCTTCACTTTCA-CCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAA
* *
659526 AGCCTTTAAAAAATCTAAAAACACTAAAAGAAGACATTATTACAACTATTTATTTGGGAAAAAAT
65 AGCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTACAACTATTTATCTGGGAAAAAAT
*
659591 ATTCAAATGTAAAAAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGA
130 ATTCAAATGTAAATAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGA
* *
659656 AGACAACCGATTAATCGATTTTGTCATGACTCTCAATGTCCCCAATAGAATCACCAAGCTATCGC
195 AGACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCGC
* *
659721 AACAGCCCCTTCAGGTGGCCTGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCACCACCGAT
260 AACGGCCCCTTCAGGTGGCCCGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCACCACCGAT
659786 CATTTTGTATGAGATAGATCGGACACCTTGATTT
325 CATTTTGTATGAGATAGATCGGACACCTTGATTT
659820 TCACAAGTCTTCACTTTCACCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAAA
1 TCACAAGTCTTCACTTTCACCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAAA
659885 GCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTACAACTATTTATCTGGGAAAAAATA
66 GCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTACAACTATTTATCTGGGAAAAAATA
*
659950 TTCAAATGTAAATAAAGTTGATTGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGAA
131 TTCAAATGTAAATAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGAA
660015 GACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCGCA
196 GACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCGCA
*
660080 ACGGCCCCTTCAGGTGGCCCGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCGCCACCGATC
261 ACGGCCCCTTCAGGTGGCCCGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCACCACCGATC
* *
660145 ATTTTGTAGGAGGTAGATCGGACACCTTGATTT
326 ATTTTGTATGAGATAGATCGGACACCTTGATTT
660178 T
1 T
660179 GCCTATTTTA
Statistics
Matches: 687, Mismatches: 30, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
358 329 0.48
359 111 0.16
360 247 0.36
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (358 bp):
TCACAAGTCTTCACTTTCACCCCCCACTTAAATGGGTTCAGAACTTAGGTTTAGAGCTTTGGAAA
GCCTTTAAAAAATCTAAAAACACTAAAAGAAAACATTATTACAACTATTTATCTGGGAAAAAATA
TTCAAATGTAAATAAAGTTGATCGAAAATAAATTAAAATTTAAACTTATAATTTTCGCTGAAGAA
GACAACCGGTTAATCGATTTTGTCATGACTCTCAATGTCCCCAATGGAATCACCAAGCTATCGCA
ACGGCCCCTTCAGGTGGCCCGGGTTTGCATTCCGACTTTGAATCCTGATGGAGTCACCACCGATC
ATTTTGTATGAGATAGATCGGACACCTTGATTT
Found at i:662487 original size:5 final size:5
Alignment explanation
Indices: 662477--662508 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
662467 GAAATCGGAT
*
662477 AATCG AATCG AATCG AATTG AATCG AATCG AA
1 AATCG AATCG AATCG AATCG AATCG AATCG AA
662509 ATTTTACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (5 bp):
AATCG
Found at i:664121 original size:15 final size:16
Alignment explanation
Indices: 664101--664133 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
664091 TCGATCTAAG
*
664101 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
664116 TATCGAATTTTATATT
1 TATCGAATTTTATATT
664132 TA
1 TA
664134 AGTTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:665229 original size:34 final size:35
Alignment explanation
Indices: 665156--665262 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 35
665146 GATAAATTCT
* * *
665156 AAATGTTTACAGTTATTAGATGATTTTCAATTATC
1 AAATATTTACAGATATTAGATGATTTACAATTATC
*
665191 AAATATTTACAGATATTAGATGA-TTACAGTTATC
1 AAATATTTACAGATATTAGATGATTTACAATTATC
* ** *
665225 AAATATTTACAAATATCGGATGTTTTACAATTATC
1 AAATATTTACAGATATTAGATGATTTACAATTATC
665260 AAA
1 AAA
665263 CACATATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 28 0.45
35 34 0.55
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40
Consensus pattern (35 bp):
AAATATTTACAGATATTAGATGATTTACAATTATC
Found at i:665234 original size:17 final size:17
Alignment explanation
Indices: 665156--665235 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
665146 GATAAATTCT
* *
665156 AAATGTTTACAGTTATT
1 AAATATTTACAGTTATC
* * *
665173 AGATGATTTTCAATTATC
1 AAAT-ATTTACAGTTATC
* *
665191 AAATATTTACAGATATT
1 AAATATTTACAGTTATC
*
665208 AGATGA-TTACAGTTATC
1 AAAT-ATTTACAGTTATC
665225 AAATATTTACA
1 AAATATTTACA
665236 AATATCGGAT
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
16 1 0.02
17 32 0.70
18 13 0.28
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (17 bp):
AAATATTTACAGTTATC
Found at i:665241 original size:17 final size:17
Alignment explanation
Indices: 665187--665241 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
665177 GATTTTCAAT
665187 TATCAAATATTTACAGA
1 TATCAAATATTTACAGA
* * *
665204 TATTAGATGA-TTACAGT
1 TATCAAAT-ATTTACAGA
*
665221 TATCAAATATTTACAAA
1 TATCAAATATTTACAGA
665238 TATC
1 TATC
665242 GGATGTTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (17 bp):
TATCAAATATTTACAGA
Found at i:666903 original size:2 final size:2
Alignment explanation
Indices: 666896--666943 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
666886 AGTTATTTTC
666896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
666938 AT AT AT
1 AT AT AT
666944 TATTATGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:667012 original size:20 final size:17
Alignment explanation
Indices: 666988--667031 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
666978 ATAAGTTATT
666988 ATTATATACTATAGTACAC
1 ATTATATACT-TA-TACAC
667007 ATT-TATATCTTATACAC
1 ATTATATA-CTTATACAC
667024 ATTATATA
1 ATTATATA
667032 AGTTAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTATATACTTATACAC
Found at i:670461 original size:15 final size:16
Alignment explanation
Indices: 670441--670473 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
670431 TCAATTTAAG
*
670441 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
670456 TATCGAATTTTATATT
1 TATCGAATTTTATATT
670472 TA
1 TA
670474 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:671559 original size:17 final size:17
Alignment explanation
Indices: 671539--671604 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
671529 CATCAAATAT
671539 TTACAGATATCAGATGA
1 TTACAGATATCAGATGA
* *
671556 TTACAGCTATCAAAT-A
1 TTACAGATATCAGATGA
*
671572 TTTACAGATATCAGATGTT
1 -TTACAGATATCAGATG-A
*
671591 TTACAGTTATCAGA
1 TTACAGATATCAGA
671605 CATAAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 26 0.65
18 13 0.32
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (17 bp):
TTACAGATATCAGATGA
Found at i:671573 original size:34 final size:35
Alignment explanation
Indices: 671530--671602 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
671520 AATTTCAGTC
671530 ATCAAATATTTACAGATATCAGATG-ATTACAGCT
1 ATCAAATATTTACAGATATCAGATGTATTACAGCT
* *
671564 ATCAAATATTTACAGATATCAGATGTTTTACAGTT
1 ATCAAATATTTACAGATATCAGATGTATTACAGCT
671599 ATCA
1 ATCA
671603 GACATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 25 0.69
35 11 0.31
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (35 bp):
ATCAAATATTTACAGATATCAGATGTATTACAGCT
Found at i:673073 original size:22 final size:22
Alignment explanation
Indices: 673047--673097 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
673037 TTTGTAATGA
673047 TCCCTTAAATTCGATCATACAC
1 TCCCTTAAATTCGATCATACAC
673069 TCCCTTAAATTCGATCATACAC
1 TCCCTTAAATTCGATCATACAC
673091 TCCCTTA
1 TCCCTTA
673098 GCGTATCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (22 bp):
TCCCTTAAATTCGATCATACAC
Found at i:680286 original size:15 final size:16
Alignment explanation
Indices: 680266--680298 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
680256 TCGATTTAAG
*
680266 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
680281 TATCGAATTTTATATT
1 TATCGAATTTTATATT
680297 TA
1 TA
680299 AGTTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:681343 original size:18 final size:18
Alignment explanation
Indices: 681316--681370 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
681306 ATTCTAAATG
681316 TTTACAGTTATTAGATGA
1 TTTACAGTTATTAGATGA
* * *
681334 TTTTCAGTTATCAAAT-A
1 TTTACAGTTATTAGATGA
*
681351 TTTACAGATATTAGATGA
1 TTTACAGTTATTAGATGA
681369 TT
1 TT
681371 ATAGTTATCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (18 bp):
TTTACAGTTATTAGATGA
Found at i:681382 original size:34 final size:35
Alignment explanation
Indices: 681311--681395 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 35
681301 GATAAATTCT
* * *
681311 AAATGTTTACAGTTATTAGATGATTTTCAGTTATC
1 AAATATTTACAGATATTAGATGATTATCAGTTATC
681346 AAATATTTACAGATATTAGATGATTAT-AGTTATC
1 AAATATTTACAGATATTAGATGATTATCAGTTATC
*
681380 AAATATTTACAAATAT
1 AAATATTTACAGATAT
681396 CGGATGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 22 0.48
35 24 0.52
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (35 bp):
AAATATTTACAGATATTAGATGATTATCAGTTATC
Found at i:684395 original size:24 final size:23
Alignment explanation
Indices: 684351--684398 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
684341 ATAAAGATGC
*
684351 TTATTTTATATGTTATAATATAG
1 TTATTTTATATATTATAATATAG
684374 TTATTTTCATATATATATATATATA
1 TTATTTT-ATATAT-TATA-ATATA
684399 TATATAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 5 0.24
25 4 0.19
26 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATTTTATATATTATAATATAG
Found at i:685692 original size:22 final size:21
Alignment explanation
Indices: 685653--685694 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
685643 CCATCTCTAT
* *
685653 TTCATCATCAACACCATCAAC
1 TTCATCATCAAAAACATCAAC
685674 TTCATCCATCAAAAACATCAA
1 TTCAT-CATCAAAAACATCAA
685695 TTCCGCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
TTCATCATCAAAAACATCAAC
Found at i:687962 original size:15 final size:16
Alignment explanation
Indices: 687942--687974 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
687932 TCAATTTAAG
*
687942 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
687957 TATCGAATTTTATATT
1 TATCGAATTTTATATT
687973 TA
1 TA
687975 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:689051 original size:17 final size:18
Alignment explanation
Indices: 689012--689085 Score: 75
Period size: 17 Copynumber: 4.3 Consensus size: 18
689002 TGTTTATAGT
*
689012 TATCAAATAATTTTCAG-
1 TATCAAATAATTTACAGA
689029 TCATCAAAT-ATTTACAGA
1 T-ATCAAATAATTTACAGA
* * *
689047 TATCATATGA-TTACAGC
1 TATCAAATAATTTACAGA
689064 TATCAAAT-ATTTACAGA
1 TATCAAATAATTTACAGA
689081 TATCA
1 TATCA
689086 GATGTTTTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.02
17 38 0.79
18 9 0.19
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (18 bp):
TATCAAATAATTTACAGA
Found at i:689069 original size:34 final size:35
Alignment explanation
Indices: 689031--689103 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 35
689021 ATTTTCAGTC
*
689031 ATCAAATATTTACAGATATCATATG-ATTACAGCT
1 ATCAAATATTTACAGATATCAGATGTATTACAGCT
* *
689065 ATCAAATATTTACAGATATCAGATGTTTTACAGTT
1 ATCAAATATTTACAGATATCAGATGTATTACAGCT
689100 ATCA
1 ATCA
689104 GACATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 24 0.69
35 11 0.31
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (35 bp):
ATCAAATATTTACAGATATCAGATGTATTACAGCT
Found at i:689096 original size:18 final size:17
Alignment explanation
Indices: 689039--689105 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
689029 TCATCAAATA
*
689039 TTTACAGATATCATATG
1 TTTACAGATATCAGATG
* * * *
689056 ATTACAGCTATCAAATA
1 TTTACAGATATCAGATG
689073 TTTACAGATATCAGATG
1 TTTACAGATATCAGATG
*
689090 TTTTACAGTTATCAGA
1 -TTTACAGATATCAGA
689106 CATAAATTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (17 bp):
TTTACAGATATCAGATG
Found at i:695818 original size:14 final size:14
Alignment explanation
Indices: 695795--695824 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
695785 AGACCTCGAT
*
695795 AAAAAGTAAAATAA
1 AAAAAATAAAATAA
695809 AAAAAATAAAATAA
1 AAAAAATAAAATAA
695823 AA
1 AA
695825 TACTAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAAATAAAATAA
Found at i:695843 original size:3 final size:3
Alignment explanation
Indices: 695813--695869 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
695803 AAATAAAAAA
* * *
695813 AAT AA- AAT AA- AAT ACT AAT ACT ACT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
695859 AAT ATAT AAT A
1 AAT A-AT AAT A
695870 TATACTTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 40 0.85
4 3 0.06
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:695934 original size:15 final size:16
Alignment explanation
Indices: 695908--695948 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
695898 TAAAATACAT
*
695908 AATATCTATATTTCAAA
1 AATATATAT-TTTCAAA
*
695925 ACTATATATTTTCAAA
1 AATATATATTTTCAAA
695941 AATATATA
1 AATATATA
695949 ATTATGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATATTTTCAAA
Found at i:696039 original size:2 final size:2
Alignment explanation
Indices: 695993--696020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
695983 CCATTTTCAA
695993 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
696021 TTAAAAACTA
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:696348 original size:22 final size:22
Alignment explanation
Indices: 696303--696367 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
696293 GAACGAGCAA
* * *
696303 AATAACAGCTAGAAATTGAAAC
1 AATAACAGTTAGAAATAGTAAC
*
696325 AATAACAGTTAGAAATAGTTAC
1 AATAACAGTTAGAAATAGTAAC
*
696347 AATAACAATTAGAAATAGTAA
1 AATAACAGTTAGAAATAGTAA
696368 TAACTAGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23
Consensus pattern (22 bp):
AATAACAGTTAGAAATAGTAAC
Found at i:696801 original size:31 final size:32
Alignment explanation
Indices: 696760--696836 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
696750 TCAGTATTGC
*
696760 ATTCAGATAATGCATAGAAGAGTTAGTATT-A
1 ATTCAGATAATGCATAGAAGAGTTAATATTAA
* * ** *
696791 ATTCAAATAATGTATATCAGAGTTAATGTTAA
1 ATTCAGATAATGCATAGAAGAGTTAATATTAA
696823 ATTCAGATAATGCA
1 ATTCAGATAATGCA
696837 CAAGAATGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (32 bp):
ATTCAGATAATGCATAGAAGAGTTAATATTAA
Found at i:704835 original size:22 final size:22
Alignment explanation
Indices: 704801--704847 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
704791 AAATAGTAAT
* * *
704801 AGTAACTATTAGAAACATTAAC
1 AGTAACAACTAGAAACAATAAC
704823 AGTAACAACTAGAAACAATAAC
1 AGTAACAACTAGAAACAATAAC
704845 AGT
1 AGT
704848 TAGGATGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (22 bp):
AGTAACAACTAGAAACAATAAC
Found at i:705270 original size:32 final size:32
Alignment explanation
Indices: 705222--705336 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 32
705212 TAGTAGTATC
* * *
705222 AGTATTGTATTTAGATAATTCATATCAGAGTT
1 AGTATTGCATTTAGATAATGCATATCAGAGTA
* * *
705254 AGTATTGCATTCAGATAATGCATAGCAGAGAA
1 AGTATTGCATTTAGATAATGCATATCAGAGTA
* * * *
705286 AGTATTGCATTTAGATAATGCACATGAGCGTC
1 AGTATTGCATTTAGATAATGCATATCAGAGTA
*
705318 AGTATAGCATTTAGATAAT
1 AGTATTGCATTTAGATAAT
705337 ACACAACAGA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (32 bp):
AGTATTGCATTTAGATAATGCATATCAGAGTA
Found at i:707098 original size:43 final size:43
Alignment explanation
Indices: 707037--707119 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
707027 CCCTCTAGTG
*
707037 AAAGTTCTTTGGTGGAATCACAAAGTTGAGAAAGCTAACTGTC
1 AAAGTTCTTTGGCGGAATCACAAAGTTGAGAAAGCTAACTGTC
707080 AAAGTTCTTTGGCGGAATCACAAAGTTGAGAAAGCTAACT
1 AAAGTTCTTTGGCGGAATCACAAAGTTGAGAAAGCTAACT
707120 AGGAAAGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (43 bp):
AAAGTTCTTTGGCGGAATCACAAAGTTGAGAAAGCTAACTGTC
Found at i:708384 original size:20 final size:20
Alignment explanation
Indices: 708340--708378 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
708330 CACAAATCTG
*
708340 GAATTTAATGTTAGAATGTT
1 GAATTTAATGTTAAAATGTT
*
708360 GAATTTGATGTTAAAATGT
1 GAATTTAATGTTAAAATGT
708379 GAAATTGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (20 bp):
GAATTTAATGTTAAAATGTT
Found at i:708493 original size:14 final size:14
Alignment explanation
Indices: 708474--708501 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
708464 TGACTATTGG
708474 GATGGAAATTTAAT
1 GATGGAAATTTAAT
708488 GATGGAAATTTAAT
1 GATGGAAATTTAAT
708502 TAAATTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
GATGGAAATTTAAT
Found at i:716473 original size:28 final size:28
Alignment explanation
Indices: 716433--716486 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
716423 TAGAAACTAA
*
716433 AATAATAATAGTTAAAAATAGTAACAGT
1 AATAATAACAGTTAAAAATAGTAACAGT
*
716461 AATAGTAACAGTTAAAAATAGTAACA
1 AATAATAACAGTTAAAAATAGTAACA
716487 ATAACAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (28 bp):
AATAATAACAGTTAAAAATAGTAACAGT
Found at i:716482 original size:16 final size:16
Alignment explanation
Indices: 716431--716486 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
716421 GCTAGAAACT
* *
716431 AAAATAATAATAGTTA
1 AAAATAGTAACAGTTA
716447 AAAATAGTAACAG-T-
1 AAAATAGTAACAGTTA
716461 --AATAGTAACAGTTA
1 AAAATAGTAACAGTTA
716475 AAAATAGTAACA
1 AAAATAGTAACA
716487 ATAACAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 11 0.32
13 1 0.03
15 1 0.03
16 21 0.62
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (16 bp):
AAAATAGTAACAGTTA
Found at i:716935 original size:32 final size:32
Alignment explanation
Indices: 716886--716967 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
716876 AGTAGTAACT
* *
716886 GTATTGCATTCATATAATACATACAAGAGTTA
1 GTATTGCATTCAGATAATACATACAAGAGTAA
* ** *
716918 GTATTGCAATCAGATAATGTATAGAAGAGTAA
1 GTATTGCATTCAGATAATACATACAAGAGTAA
* *
716950 GTGTTGCATTTAGATAAT
1 GTATTGCATTCAGATAAT
716968 GCACATGAGC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (32 bp):
GTATTGCATTCAGATAATACATACAAGAGTAA
Found at i:720061 original size:20 final size:20
Alignment explanation
Indices: 720020--720061 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
720010 ATGAAATAGA
*
720020 TAATGTAGAAAGTTGGAGTT
1 TAATGTAGAAAGTTGGAATT
*
720040 TAATGTTAGAAGGTT-GAATT
1 TAATG-TAGAAAGTTGGAATT
720060 TA
1 TA
720062 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (20 bp):
TAATGTAGAAAGTTGGAATT
Found at i:727048 original size:16 final size:16
Alignment explanation
Indices: 727009--727048 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
726999 TTCCAATAAC
727009 ATTTAATAACTTGTAA
1 ATTTAATAACTTGTAA
* *
727025 GTTCAATAACTTGTAA
1 ATTTAATAACTTGTAA
727041 ATTTAATA
1 ATTTAATA
727049 TCAATTTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (16 bp):
ATTTAATAACTTGTAA
Found at i:730846 original size:156 final size:157
Alignment explanation
Indices: 730583--730953 Score: 458
Period size: 156 Copynumber: 2.4 Consensus size: 157
730573 TTCCTCCTTC
* ** *
730583 ATTTTAAGTCCATTTTTTACCAAATTTGAAACACACACTCCTAAAACATAGTAGAATACATGTGT
1 ATTTTAAGTCCATTTTTTACCAAATTTGAACCACATGCTCCTAAAACATAGTAGAATAAATGTGT
*
730648 ACTTCCAATTCATCTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAAGTTTTCA-AA
66 ACTTCCAATTCATATTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAAGTTTTCATAA
* * * * *
730712 TTTTGGTATTTCTTCGATTCGTCATTT
131 TCTTCGTATTCCTTCAATTCGTCAGTT
* * * * * * *
730739 ATTTTAAGTCCAATTTTTACCAAATTTGAGCCACATGCTCCTAAACCATATTGGAATAAATTTTT
1 ATTTTAAGTCCATTTTTTACCAAATTTGAACCACATGCTCCTAAAACATAGTAGAATAAATGTGT
* * * *
730804 ACTTTCAATTCCTATTTTTTATAAC-AATTTTATATTTTTCAATTTAGTCCTTCAATTTTTCATA
66 ACTTCCAATTCATATTTTTGATAACAAATTTT-TATTTTTCAATTTAGTCCTTCAAGTTTTCATA
* * *
730868 ATCTTCTTATTCCTTCAATTTGTGAGTT
130 ATCTTCGTATTCCTTCAATTCGTCAGTT
* * * * *
730896 ATTTTAAGTCCCTTTTTTACCAAATTTGAACCACATGCTCATATAACACAATAGAATA
1 ATTTTAAGTCCATTTTTTACCAAATTTGAACCACATGCTCCTAAAACATAGTAGAATA
730954 CCTATGTGAC
Statistics
Matches: 180, Mismatches: 33, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
155 6 0.03
156 104 0.58
157 70 0.39
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (157 bp):
ATTTTAAGTCCATTTTTTACCAAATTTGAACCACATGCTCCTAAAACATAGTAGAATAAATGTGT
ACTTCCAATTCATATTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAAGTTTTCATAA
TCTTCGTATTCCTTCAATTCGTCAGTT
Found at i:732678 original size:11 final size:11
Alignment explanation
Indices: 732662--732686 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
732652 AATATTGATT
732662 TGGGTTTTAAA
1 TGGGTTTTAAA
732673 TGGGTTTTAAA
1 TGGGTTTTAAA
732684 TGG
1 TGG
732687 AATGGGTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:733494 original size:31 final size:30
Alignment explanation
Indices: 733456--733525 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
733446 CTTTTAAAAC
*
733456 TTGCAATA-CAGTCCCCAAACATTTAGTCTGT
1 TTGCAATATCAGCCCCCAAA-ATTTAGT-TGT
**
733487 TTGCAATATGGGCCCCCAAAATTTAGTTGT
1 TTGCAATATCAGCCCCCAAAATTTAGTTGT
733517 TTGCAATAT
1 TTGCAATAT
733526 GGTCTCTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 12 0.34
31 15 0.43
32 8 0.23
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (30 bp):
TTGCAATATCAGCCCCCAAAATTTAGTTGT
Found at i:733520 original size:30 final size:32
Alignment explanation
Indices: 733468--733527 Score: 106
Period size: 30 Copynumber: 1.9 Consensus size: 32
733458 GCAATACAGT
733468 CCCCAAACATTTAGTCTGTTTGCAATATGGGC
1 CCCCAAACATTTAGTCTGTTTGCAATATGGGC
733500 CCCCAAA-ATTTAGT-TGTTTGCAATATGG
1 CCCCAAACATTTAGTCTGTTTGCAATATGG
733528 TCTCTGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 14 0.50
31 7 0.25
32 7 0.25
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (32 bp):
CCCCAAACATTTAGTCTGTTTGCAATATGGGC
Found at i:735267 original size:71 final size:71
Alignment explanation
Indices: 735167--735308 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
735157 GCCAACGAGT
735167 GTTGCCATAAGTAGTTGAGATTCAGGATTTTAAGTTTGTAAGATCAAGTTTGAATTTCATCACCG
1 GTTGCCATAAGTAGTTGAGATTCAGGATTTTAAGTTTGTAAGATCAAGTTTGAATTTCATCACCG
735232 TCACTC
66 TCACTC
* * *
735238 GTTGGCATAAGTAGTTGAGATTCATGATTTTAAGTTTGTAAGATCAAGTTTGAATTTCATCACTG
1 GTTGCCATAAGTAGTTGAGATTCAGGATTTTAAGTTTGTAAGATCAAGTTTGAATTTCATCACCG
735303 TCACTC
66 TCACTC
735309 TTAGTGGACA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (71 bp):
GTTGCCATAAGTAGTTGAGATTCAGGATTTTAAGTTTGTAAGATCAAGTTTGAATTTCATCACCG
TCACTC
Found at i:736255 original size:20 final size:20
Alignment explanation
Indices: 736230--736281 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
736220 AGTGCCCAAT
*
736230 AATAACAAAACTGGTAGAAA
1 AATAACAAAACCGGTAGAAA
736250 AATAACAAAACCGGTAGAAA
1 AATAACAAAACCGGTAGAAA
*
736270 AATAATAAAACC
1 AATAACAAAACC
736282 AATAGCACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.62, C:0.13, G:0.12, T:0.13
Consensus pattern (20 bp):
AATAACAAAACCGGTAGAAA
Found at i:739152 original size:26 final size:26
Alignment explanation
Indices: 739103--739156 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
739093 GAAGGTTCCG
739103 GGAGAGAAAAGAAGGGTGGCTGTGGA
1 GGAGAGAAAAGAAGGGTGGCTGTGGA
* *
739129 GGAGATGAAGAGAAGGGT-GTTGTGGA
1 GGAGA-GAAAAGAAGGGTGGCTGTGGA
739155 GG
1 GG
739157 GAAAGGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.52, T:0.15
Consensus pattern (26 bp):
GGAGAGAAAAGAAGGGTGGCTGTGGA
Found at i:739165 original size:27 final size:27
Alignment explanation
Indices: 739112--739165 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
739102 GGGAGAGAAA
* *
739112 AGAAGGGTGGCTGTGGAGGAGATGAAG
1 AGAAGGGTGGCTGTGGAGGAAAGGAAG
*
739139 AGAAGGGT-GTTGTGGAGGGAAAGGAAG
1 AGAAGGGTGGCTGTGGA-GGAAAGGAAG
739166 GTGTGTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.31, C:0.02, G:0.52, T:0.15
Consensus pattern (27 bp):
AGAAGGGTGGCTGTGGAGGAAAGGAAG
Found at i:739617 original size:33 final size:33
Alignment explanation
Indices: 739578--739645 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
739568 TCATTCATAT
*
739578 CTAATATATAAATCGATTAATTTAAATTATGTA
1 CTAATATATAAATCGATTAATTCAAATTATGTA
* * *
739611 CTAATATATTAATTGATTAATTCAAATTGTGTA
1 CTAATATATAAATCGATTAATTCAAATTATGTA
739644 CT
1 CT
739646 GAGACAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (33 bp):
CTAATATATAAATCGATTAATTCAAATTATGTA
Found at i:740183 original size:3 final size:3
Alignment explanation
Indices: 740175--740218 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
740165 TCATACTCTT
740175 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
740219 TTGTCGTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:741413 original size:41 final size:41
Alignment explanation
Indices: 741368--741466 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
741358 TAGCGGTATT
* *
741368 TTTAGCGGCGTTTTTTGA-ACAAATGCCGCAAAAAACCTAAC
1 TTTAGAGGCGTTTTGT-ATACAAATGCCGCAAAAAACCTAAC
* * *
741409 TTTAGAGGCG-TTTGTATACAAATGCCGCAAAAGATCTTAC
1 TTTAGAGGCGTTTTGTATACAAATGCCGCAAAAAACCTAAC
*
741449 TTTAGTGGCG-TTTGTATA
1 TTTAGAGGCGTTTTGTATA
741467 AAAACGCTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.02
40 41 0.80
41 9 0.18
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTAGAGGCGTTTTGTATACAAATGCCGCAAAAAACCTAAC
Found at i:741437 original size:40 final size:40
Alignment explanation
Indices: 741386--741466 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
741376 CGTTTTTTGA
741386 ACAAATGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
1 ACAAATGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
* * * *
741426 ACAAATGCCGCAAAAGATCTTACTTTAGTGGCGTTTGTAT
1 ACAAATGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
741466 A
1 A
741467 AAAACGCTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (40 bp):
ACAAATGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
Found at i:741709 original size:43 final size:41
Alignment explanation
Indices: 741407--741875 Score: 433
Period size: 41 Copynumber: 11.4 Consensus size: 41
741397 AAAAAACCTA
* * * * * * *
741407 ACTTTAGAGGCGTTTGTATACAAATGCCGCAAAAGA-TCTT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* * * * *
741447 ACTTTAGTGGCGTTTGTATAAAAACGCTGCTAAAGATTAGT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* * * *
741488 A-TTGTAGTGGCGTTTTTACACAAACGCCGGTATAGAATCGT
1 ACTT-TAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* * * * *
741529 TCTTTAGGGGCATTTTTATACAAACGCCGCTAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* * *
741570 ACTTTAGTGGCGTTTTTATAAAAGCGCTGCTATA-ACTCAT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* * *
741610 ACTTTACTGGCGTTTTTATAAAAACGCTGCTATA-ACTCAT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
* *
741650 ACTTTAGTGGCGTTTTTGTTTAAAAACGTCGCTATAGACTCGT
1 ACTTTAGTGGCG-TTTT-TATAAAAACGCCGCTATAGACTCGT
* * * * *
741693 ACTTTAGTGGCATTTTTGTTTACAAACGTCGCTATAGACTTGT
1 ACTTTAGTGGC-GTTTT-TATAAAAACGCCGCTATAGACTCGT
* * * *
741736 ACTTTAGTGGCGTTTTTGTTTACAAACGTCGCTATAGACTTGT
1 ACTTTAGTGGCG-TTTT-TATAAAAACGCCGCTATAGACTCGT
* *
741779 ACTTTAGTGGCGTTTTTATAAAAACGCCGCAAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
** * * * *
741820 ACGCTAGTGGCGTTTTTATACAAACACCGCAAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
741861 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
741876 GTACCGCAAA
Statistics
Matches: 368, Mismatches: 53, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
40 87 0.24
41 163 0.44
42 21 0.06
43 97 0.26
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGT
Found at i:741746 original size:86 final size:84
Alignment explanation
Indices: 741509--741871 Score: 341
Period size: 86 Copynumber: 4.4 Consensus size: 84
741499 GTTTTTACAC
* * * * * *
741509 AAACGCCGGTATAGAATCGTTCTTTAGGGGCA-TTTTTATACAAACGCCGCTAAAGACTCGTACT
1 AAACGTCGCTATAGACTCGTACTTTAGTGGCATTTTTTATACAAACG-CGCTATAGACTCGTACT
*
741573 TTAGTGGCG-TTTT-TATAA
65 TTAGTGGCGTTTTTGTTTAA
* * * * * *
741591 AAGCG-CTGCTATA-ACTCATACTTTACTGGC-GTTTTTATAAAAACGCTGCTATA-ACTCATAC
1 AAACGTC-GCTATAGACTCGTACTTTAGTGGCATTTTTTATACAAACGC-GCTATAGACTCGTAC
741652 TTTAGTGGCGTTTTTGTTTAA
64 TTTAGTGGCGTTTTTGTTTAA
* *
741673 AAACGTCGCTATAGACTCGTACTTTAGTGGCATTTTTGTTTACAAACGTCGCTATAGACTTGTAC
1 AAACGTCGCTATAGACTCGTACTTTAGTGGCATTTTT-TATACAAACG-CGCTATAGACTCGTAC
*
741738 TTTAGTGGCGTTTTTGTTTAC
64 TTTAGTGGCGTTTTTGTTTAA
* * * * * *
741759 AAACGTCGCTATAGACTTGTACTTTAGTGGC-GTTTTTATAAAAACGCCGCAAAAGACTCGTACG
1 AAACGTCGCTATAGACTCGTACTTTAGTGGCATTTTTTATACAAACG-CGCTATAGACTCGTACT
* * *
741823 CTAGTGGCG-TTTT-TATAC
65 TTAGTGGCGTTTTTGTTTAA
** * *
741841 AAACACCGCAAAAGACTCGTACTTTAGTGGC
1 AAACGTCGCTATAGACTCGTACTTTAGTGGC
741872 GTTTGTACCG
Statistics
Matches: 234, Mismatches: 36, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
80 18 0.08
81 35 0.15
82 53 0.23
83 20 0.09
84 33 0.14
85 18 0.08
86 57 0.24
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (84 bp):
AAACGTCGCTATAGACTCGTACTTTAGTGGCATTTTTTATACAAACGCGCTATAGACTCGTACTT
TAGTGGCGTTTTTGTTTAA
Found at i:744540 original size:43 final size:42
Alignment explanation
Indices: 744472--744792 Score: 322
Period size: 43 Copynumber: 7.5 Consensus size: 42
744462 ATGGTAATTA
* * *
744472 GCGGCGTTTGTATCCAAAAATGCCGCTATATATCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACATTTT
* *
744515 GTGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACATTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACATTTT
* * *
744558 GCGGCATTTGTGTCCAAAAACGCCACTATAGGTCTGACATTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACATTTT
* * * * * *
744601 ACGGTGTTTGTTCTACAAACGCCAG-TATAGGTCTTATC-TTTT
1 GCGGCGTTTGTTCCAAAAACGCC-GCTATAGATCTGA-CATTTT
744643 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACATTTT
* * * ** * *
744686 GCGGCGTTTTTTCTAGAAACGCCGCTATTTATCATAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACATTTT
* * * *
744729 GCGGCGTTTATTCCAAAAACGCCACTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACATTTT
*
744772 GCGGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTTCCAAAAACG
744793 TTGTAATAGA
Statistics
Matches: 231, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
42 54 0.23
43 177 0.77
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACATTTT
Found at i:744653 original size:85 final size:85
Alignment explanation
Indices: 744472--744792 Score: 351
Period size: 85 Copynumber: 3.8 Consensus size: 85
744462 ATGGTAATTA
* * * * * *
744472 GCGGCGTTTGTATCCAAAAATGCCGCTATATATCTGACTTTTTGTGGCGTTTGTGTCCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTGCGGCGTTTGT-TCTAAAAACG
*
744537 CCGCTATAGGTCTGACATTTT
65 CCGCTATAGGTCTTACATTTT
* * * * * *
744558 GCGGCATTTGTGTCCAAAAACGCCACTATAGGTCTGACATTTTACGGTGTTTGTTCTACAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTGCGGCGTTTGTTCTAAAAACGC
744623 CAG-TATAGGTCTTATC-TTTT
66 C-GCTATAGGTCTTA-CATTTT
* * *
744643 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTTTCTAGAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTGCGGCGTTTGTTCTAAAAACGC
*** * *
744708 CGCTATTTATCATAACTTTTT
66 CGCTATAGGTC-TTACATTTT
* * * *
744729 GCGGCGTTTAT-TCCAAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCACTATAGATCT-GACATTTTGCGGCGTTTGTTCTAAAAACG
744793 TTGTAATAGA
Statistics
Matches: 197, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
84 1 0.01
85 109 0.55
86 87 0.44
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTGCGGCGTTTGTTCTAAAAACGC
CGCTATAGGTCTTACATTTT
Found at i:744749 original size:128 final size:128
Alignment explanation
Indices: 744473--744792 Score: 324
Period size: 128 Copynumber: 2.5 Consensus size: 128
744463 TGGTAATTAG
* * * * *
744473 CGGCGTTTGTATCCAAAAATGCCGCTAT--ATATCTGACTTTTTGTGGCGTTTGTGTCCAAAAAC
1 CGGCGTTTAT-TCCAAAAACGCCACTATAGATATC-GACCTTTTGCGGCGTTTGT-TCCAAAAAC
* * *
744536 GCCGCTATAGGTCTGACATTTTGCGGCATTTGTGTCCAAAAACGCCACTATAGGTCTGACATTTT
63 GCCGCTATAGATCTGACATTTTGCGGCATTTGTGTCCAAAAACGCCACTATAGATCTAACATTTT
744601 A
128 A
* * * * * * * * *
744602 CGGTGTTTGTTCTACAAACGCCAGTATAGGTCT-TATCTTTTGCGGCGTTTGTATCCAAAAACGC
1 CGGCGTTTATTCCAAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGT-TCCAAAAACGC
* * * * * ** * *
744666 CGCTATAGATCTGACATTTTGCGGCGTTT-TTTCTAGAAACGCCGCTATTTATCATAACTTTTTG
65 CGCTATAGATCTGACATTTTGCGGCATTTGTGTCCAAAAACGCCACTATAGATC-TAACATTTTA
*
744730 CGGCGTTTATTCCAAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACG
1 CGGCGTTTATTCCAAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAACG
744793 TTGTAATAGA
Statistics
Matches: 152, Mismatches: 35, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
127 17 0.11
128 107 0.70
129 26 0.17
130 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (128 bp):
CGGCGTTTATTCCAAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
GCTATAGATCTGACATTTTGCGGCATTTGTGTCCAAAAACGCCACTATAGATCTAACATTTTA
Found at i:745534 original size:29 final size:30
Alignment explanation
Indices: 745451--745534 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 30
745441 TTAAAATGCT
* **
745451 AGAAATTTAAA-GGAAGAAAT-TAAAATATT
1 AGAAATTTAAAGGGTAGAAATATAAAA-AAC
* *
745480 A-AAA-TTAAAGGGTATAAATGTAAAAAAC
1 AGAAATTTAAAGGGTAGAAATATAAAAAAC
*
745508 AGAAATTTAAAGGGTGGAAATATAAAA
1 AGAAATTTAAAGGGTAGAAATATAAAA
745535 GCATAAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.11
28 12 0.27
29 9 0.20
30 18 0.41
ACGTcount: A:0.58, C:0.01, G:0.17, T:0.24
Consensus pattern (30 bp):
AGAAATTTAAAGGGTAGAAATATAAAAAAC
Found at i:745826 original size:16 final size:16
Alignment explanation
Indices: 745805--745847 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
745795 CATTTAATAA
745805 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
745821 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
745837 ATAAACAAACA
1 ATAAACGAACA
745848 TAAACGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.60, C:0.23, G:0.09, T:0.07
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:746597 original size:28 final size:28
Alignment explanation
Indices: 746553--746606 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
746543 GATTGGCTTA
*
746553 AACATAAATGAATGAACATAAACGAAAG
1 AACATAAATGAACGAACATAAACGAAAG
*
746581 AACATAACTGAACGAACATAAACGAA
1 AACATAAATGAACGAACATAAACGAA
746607 CGTTCACGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.13
Consensus pattern (28 bp):
AACATAAATGAACGAACATAAACGAAAG
Found at i:746607 original size:14 final size:14
Alignment explanation
Indices: 746553--746608 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
746543 GATTGGCTTA
* *
746553 AACATAAATGAATG
1 AACATAAACGAACG
*
746567 AACATAAACGAAAG
1 AACATAAACGAACG
746581 AACAT-AACTGAACG
1 AACATAAAC-GAACG
746595 AACATAAACGAACG
1 AACATAAACGAACG
746609 TTCACGAGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 3 0.08
14 31 0.84
15 3 0.08
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:748437 original size:19 final size:19
Alignment explanation
Indices: 748415--748451 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
748405 ATTCGAGATC
*
748415 AAAAAGAAATTTAGGATTT
1 AAAAAGAAATTGAGGATTT
*
748434 AAAATGAAATTGAGGATT
1 AAAAAGAAATTGAGGATT
748452 GTGTTGCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (19 bp):
AAAAAGAAATTGAGGATTT
Found at i:755698 original size:59 final size:59
Alignment explanation
Indices: 755601--755728 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
755591 CGTGTGCTAA
* * * * *
755601 CCCGAGTATGACACATAAGGTAATGCCCACCATCTGCACTAGTTATACTTTAGTGTAGT
1 CCCGAATATGACACATAAGGTAATGCCCACCATATGCACTAGTTATACATTAGTGCAAT
**
755660 CCCGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACATTAGTGCAAT
1 CCCGAATATGACACATAAGGTAATGCCCACCATATGCACTAGTTATACATTAGTGCAAT
*
755719 CCTGAATATG
1 CCCGAATATG
755729 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTAATGCCCACCATATGCACTAGTTATACATTAGTGCAAT
Found at i:760967 original size:12 final size:12
Alignment explanation
Indices: 760950--760974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
760940 ATCTATGTAG
760950 TTAAAGGGACTT
1 TTAAAGGGACTT
760962 TTAAAGGGACTT
1 TTAAAGGGACTT
760974 T
1 T
760975 GAACGTTCAA
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTAAAGGGACTT
Found at i:768277 original size:23 final size:23
Alignment explanation
Indices: 768246--768296 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
768236 TGCCTAGTGA
768246 GTATCGATACTTCCCTTACCTTG
1 GTATCGATACTTCCCTTACCTTG
*
768269 GTATTGATACTTCCCTTACCTTG
1 GTATCGATACTTCCCTTACCTTG
768292 GTATC
1 GTATC
768297 AGTACCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (23 bp):
GTATCGATACTTCCCTTACCTTG
Found at i:776303 original size:20 final size:20
Alignment explanation
Indices: 776259--776297 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
776249 CACAAATCTG
776259 GAATTTAATGTTAGAATGTT
1 GAATTTAATGTTAGAATGTT
*
776279 GAATTTGATGTTAGAATGT
1 GAATTTAATGTTAGAATGT
776298 GAAATTGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (20 bp):
GAATTTAATGTTAGAATGTT
Found at i:784449 original size:22 final size:23
Alignment explanation
Indices: 784424--784498 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 23
784414 ACTAAAATAA
*
784424 TAATAGTTAA-AAATAGTAACAG
1 TAATAGTTAACAAATAGAAACAG
* * *
784446 TAATA-ATAACAGATAGAAACAT
1 TAATAGTTAACAAATAGAAACAG
* *
784468 TAACAG-TAACAACTAGAAACAG
1 TAATAGTTAACAAATAGAAACAG
784490 TAATAGTTA
1 TAATAGTTA
784499 GGATGCCATA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.07
22 36 0.88
23 2 0.05
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (23 bp):
TAATAGTTAACAAATAGAAACAG
Found at i:785837 original size:22 final size:22
Alignment explanation
Indices: 785781--785854 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
785771 TACATTCTTT
** * *
785781 AAAGATGATAGACACACTCTTC
1 AAAGATGATAGATTCTCTTTTC
785803 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
*
785825 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTC
785847 AAAGATGA
1 AAAGATGA
785855 AAGCCTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTC
Found at i:786594 original size:45 final size:45
Alignment explanation
Indices: 786530--787194 Score: 1035
Period size: 45 Copynumber: 14.8 Consensus size: 45
786520 CTATTTCCCA
* * *
786530 CATCTGTTATCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
786575 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
786621 C-TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
786665 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
786710 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
786755 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
786800 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCTGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
786845 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
786890 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
786935 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
786980 CACCTATAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
787025 CACCTGCAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
787070 CATCTGTAAGCCTTTAAGTGCATGATGTTTTCAAAATCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
787115 CATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* ** * * * *
787160 TATCCATAAGACATACAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
787195 TGAGATATTA
Statistics
Matches: 569, Mismatches: 49, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
44 14 0.02
45 542 0.95
46 13 0.02
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:787459 original size:3 final size:3
Alignment explanation
Indices: 787447--787484 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
787437 TTTTTTATCA
*
787447 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
787485 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:788930 original size:3 final size:3
Alignment explanation
Indices: 788917--788976 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
788907 TTATTTGCAA
*
788917 TAT TA- TAT TAT TAT TAT TAT TAT TATT TATT TAT GTTT TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT -TAT T-AT TAT TAT
*
788965 T-T TGT TAT TAT T
1 TAT TAT TAT TAT T
788977 TTCATCTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.08
3 34 0.69
4 11 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:788933 original size:11 final size:11
Alignment explanation
Indices: 788917--788976 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
788907 TTATTTGCAA
788917 TATTATATTAT
1 TATTATATTAT
788928 TATTATTATTAT
1 TATTA-TATTAT
788940 TATT-TATTTAT
1 TATTATA-TTAT
*
788951 GTTTTA-ATTAT
1 -TATTATATTAT
* *
788962 TATTTTGTTAT
1 TATTATATTAT
788973 TATT
1 TATT
788977 TTCATCTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.12
11 21 0.52
12 14 0.35
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTATATTAT
Found at i:789504 original size:20 final size:20
Alignment explanation
Indices: 789481--789532 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
789471 CGAATGTAAA
789481 TTAAATTCATATTCGAATTC
1 TTAAATTCATATTCGAATTC
789501 TTAAATTCATATTCGAATTC
1 TTAAATTCATATTCGAATTC
789521 TTAAATTC-TATT
1 TTAAATTCATATT
789533 ATTAGAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (20 bp):
TTAAATTCATATTCGAATTC
Found at i:798695 original size:14 final size:14
Alignment explanation
Indices: 798676--798717 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
798666 AATGGGAATT
798676 AATCCATGCATATA
1 AATCCATGCATATA
* *
798690 AATCCATGCGTAAA
1 AATCCATGCATATA
798704 AATCTC-TGCATATA
1 AATC-CATGCATATA
798718 GACAGAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (14 bp):
AATCCATGCATATA
Found at i:812099 original size:3 final size:3
Alignment explanation
Indices: 812091--812129 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
812081 TCTCTCTCTC
812091 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
812130 CCTTTCTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:820754 original size:22 final size:22
Alignment explanation
Indices: 820729--820778 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
820719 AATGTACCGA
*
820729 ATCGTGATTTTGAAACGATCCG
1 ATCGTGATTTTGAAACAATCCG
*
820751 ATCGCGATTTTGAAACAATCCG
1 ATCGTGATTTTGAAACAATCCG
*
820773 AACGTG
1 ATCGTG
820779 TTCGTACCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (22 bp):
ATCGTGATTTTGAAACAATCCG
Found at i:823065 original size:22 final size:22
Alignment explanation
Indices: 823038--823079 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
823028 AACGTTTCAT
823038 TTTATACTCATTACTATTTTGA
1 TTTATACTCATTACTATTTTGA
*
823060 TTTATACTCATTACTCTTTT
1 TTTATACTCATTACTATTTT
823080 TTAAACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATACTCATTACTATTTTGA
Found at i:824546 original size:17 final size:17
Alignment explanation
Indices: 824520--824552 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
824510 AATAAAGTAT
824520 AAAAATAATA-ATAATG
1 AAAAATAATACATAATG
824536 AAAATATAATACATAAT
1 AAAA-ATAATACATAAT
824553 AATAGTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAATACATAATG
Found at i:826257 original size:105 final size:105
Alignment explanation
Indices: 826134--826898 Score: 1318
Period size: 105 Copynumber: 7.4 Consensus size: 105
826124 GTATTGTTCC
* * *
826134 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
826199 CAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
826239 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAAGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
826304 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
826344 GAGTCCAATATCCTTCGTTGCGAATGTTGAAATTGGCTCTGAATTT-----A------TTGACAA
1 GAGTCCAATATCCTTCGTTGTGAA-GTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAA
* *
826398 CCAGTGGTCCCTTCGTCGTGAAGTCGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
826439 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
826504 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
826544 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
826609 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
826649 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
826714 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
826754 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
826819 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
826859 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
826899 GGTAAAACCT
Statistics
Matches: 631, Mismatches: 17, Indels: 24
0.94 0.03 0.04
Matches are distributed among these distances:
94 21 0.03
95 68 0.11
99 1 0.00
101 1 0.00
105 520 0.82
106 20 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:827736 original size:58 final size:58
Alignment explanation
Indices: 827649--827761 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 58
827639 TCTTTTCTCT
* * *
827649 TTTTTTTTTTTTTTTTTTTTTTAATTTAGGGCGCCCT-TCCGGGTTTTCACCCTAAACG
1 TTTTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCCTCT-CGGGTTTTCACCCTAAACG
* *
827707 TTTTTTTTTTTTTTTTTTTTTCAACTTAGGACGTCCTCTCGGGTTTTCATCCTAA
1 TTTTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
827762 GCGAAGTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 48 0.98
59 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.57
Consensus pattern (58 bp):
TTTTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:838543 original size:17 final size:18
Alignment explanation
Indices: 838521--838554 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
838511 ATAAAGTATA
838521 AAAATATAATA-ATAATG
1 AAAATATAATACATAATG
838538 AAAATATAATACATAAT
1 AAAATATAATACATAAT
838555 AATAGTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAATACATAATG
Found at i:840928 original size:2 final size:2
Alignment explanation
Indices: 840921--840947 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
840911 AAAAGGTTAA
840921 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
840948 GAAATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:841665 original size:2 final size:2
Alignment explanation
Indices: 841658--841691 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
841648 TAAATTTTTA
841658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
841692 TTAAATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:842125 original size:3 final size:3
Alignment explanation
Indices: 842111--842145 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
842101 GAAGAGACGA
842111 GGC GGAC GGC GGC GGC GGC GGC GGC GGC GGC GGC G
1 GGC GG-C GGC GGC GGC GGC GGC GGC GGC GGC GGC G
842146 CGCGAGAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.31, G:0.66, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:842894 original size:21 final size:20
Alignment explanation
Indices: 842870--842940 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
842860 ACTTCGACTG
842870 TCGCAACGAATTCAGAATAAA
1 TCGCAACGAATTC-GAATAAA
*
842891 TCGCAACGCGAACTTCGACT--A
1 TCGCAA--CGAA-TTCGAATAAA
*
842912 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAA-TTCGAATAAA
842933 TCGCAACG
1 TCGCAACG
842941 CAAACTTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 9 0.22
21 22 0.54
23 7 0.17
24 3 0.07
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAACGAATTCGAATAAA
Found at i:842956 original size:21 final size:20
Alignment explanation
Indices: 842890--842961 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
842880 TTCAGAATAA
*
842890 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGC-AACTTGGACT
* *
842911 ATCGCAACG-AATTTGGAAT
1 ATCGCAACGCAACTTGGACT
842930 AAATCGCAACGCAAACTTGGACT
1 --ATCGCAACGC-AACTTGGACT
842953 ATCGCAACG
1 ATCGCAACG
842962 AATTTGGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 7 0.17
21 27 0.64
23 8 0.19
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCAACTTGGACT
Found at i:842966 original size:42 final size:42
Alignment explanation
Indices: 842859--842977 Score: 179
Period size: 42 Copynumber: 2.9 Consensus size: 42
842849 AGTCGTTGCG
* ** *
842859 AACTTCGACTGTCGCAACGAATTCAGAATAAATCGCAACGCG
1 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCA
842901 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCA
1 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCA
*
842943 AACTTGGACTATCGCAACGAATTTGG-A-AAATCGCA
1 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCA
842978 TTGCGATAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 8 0.11
41 1 0.01
42 63 0.88
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCA
Found at i:842975 original size:19 final size:19
Alignment explanation
Indices: 842911--842977 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
842901 AACTTCGACT
842911 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* **
842932 ATCGCAACGCAAACTTGGACT
1 ATCGCAACG--AATTTGGAAA
842953 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
842972 ATCGCA
1 ATCGCA
842978 TTGCGATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 13 0.34
21 18 0.47
22 1 0.03
23 6 0.16
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:843002 original size:21 final size:21
Alignment explanation
Indices: 842973--843025 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
842963 ATTTGGAAAA
*
842973 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
842994 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
843015 TCGCGTTGCGA
1 TCGCGTTGCGA
843026 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:843639 original size:79 final size:79
Alignment explanation
Indices: 843481--843637 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 79
843471 AAAATAACAT
* * * * *
843481 TTTAGGTTGCGCCCAATATTAACATTTCCGGTAGAAAATATAATGTTTTAGGTAGCGCTTTACTG
1 TTTAGGTAGCGCCCAATATTAACATTTCCGGCAGAAAAAATAATGTTTTAGGTAGCACTTTACCG
843546 GAAATGTTAAAAAA
66 GAAATGTTAAAAAA
843560 TTTAGGTAGCGCCCAATATTAACATTTCTC-GCA-AAAAAATAATGTTTTAGGTAGCACTTTACC
1 TTTAGGTAGCGCCCAATATTAACATTTC-CGGCAGAAAAAATAATGTTTTAGGTAGCACTTTACC
*
843623 GTAAATGTTAAAAAA
65 GGAAATGTTAAAAAA
843638 ATATTAACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
78 41 0.58
79 29 0.41
80 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (79 bp):
TTTAGGTAGCGCCCAATATTAACATTTCCGGCAGAAAAAATAATGTTTTAGGTAGCACTTTACCG
GAAATGTTAAAAAA
Found at i:845701 original size:20 final size:20
Alignment explanation
Indices: 845663--845701 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
845653 GTTCGATTCG
**
845663 AGTTGACTCAGACTGGTTCA
1 AGTTGACTCAGACCAGTTCA
845683 AGTTGACTCAGACCAGTTC
1 AGTTGACTCAGACCAGTTC
845702 TAGGAGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTTGACTCAGACCAGTTCA
Found at i:847722 original size:30 final size:28
Alignment explanation
Indices: 847669--847735 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
847659 TTTTGTTTTT
**
847669 TATATTATTTAATTATTAAAATATAATA
1 TATATTATTTAACCATTAAAATATAATA
847697 TATATTAATTTAACCATTGAAAATATAATA
1 TATATT-ATTTAACCATT-AAAATATAATA
*
847727 AATAATTAT
1 TAT-ATTAT
847736 AAATATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.18
29 9 0.27
30 15 0.45
31 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (28 bp):
TATATTATTTAACCATTAAAATATAATA
Found at i:855613 original size:24 final size:26
Alignment explanation
Indices: 855568--855646 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 26
855558 AATTATTTAT
* * * *
855568 ATATATATATATATATATATAATATTA
1 ATATATATTTA-ATTTAAATAATATAA
855595 ATA-A-ATTTAATTTAAATAA-A-AA
1 ATATATATTTAATTTAAATAATATAA
*
855617 ATATATATTTAATTTAAAT-ATATAT
1 ATATATATTTAATTTAAATAATATAA
855642 ATATA
1 ATATA
855647 CCCGGCCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 22 0.51
25 10 0.23
26 1 0.02
27 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATATTTAATTTAAATAATATAA
Found at i:855628 original size:19 final size:19
Alignment explanation
Indices: 855604--855643 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
855594 AATAAATTTA
855604 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
855623 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
855642 AT
1 AT
855644 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:855688 original size:12 final size:12
Alignment explanation
Indices: 855663--855709 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
855653 CCGATTCGCA
855663 ACCCAATA-CCG
1 ACCCAATACCCG
855674 ACCCAATACCCG
1 ACCCAATACCCG
*
855686 ACCCAATACCTG
1 ACCCAATACCCG
*
855698 GCCCAATACCCG
1 ACCCAATACCCG
855710 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.32, C:0.47, G:0.11, T:0.11
Consensus pattern (12 bp):
ACCCAATACCCG
Found at i:855690 original size:23 final size:24
Alignment explanation
Indices: 855663--855709 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
855653 CCGATTCGCA
855663 ACCCAATACC-GACCCAATACCCG
1 ACCCAATACCTGACCCAATACCCG
*
855686 ACCCAATACCTGGCCCAATACCCG
1 ACCCAATACCTGACCCAATACCCG
855710 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.32, C:0.47, G:0.11, T:0.11
Consensus pattern (24 bp):
ACCCAATACCTGACCCAATACCCG
Found at i:856061 original size:17 final size:17
Alignment explanation
Indices: 856041--856075 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
856031 ATTCTTTTAT
856041 TTGTTT-ATGAATTTAAA
1 TTGTTTAAT-AATTTAAA
856058 TTGTTTAATAATTTAAA
1 TTGTTTAATAATTTAAA
856075 T
1 T
856076 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
TTGTTTAATAATTTAAA
Found at i:856093 original size:45 final size:45
Alignment explanation
Indices: 856035--856129 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 45
856025 TGTATAATTC
*
856035 TTTTATTTGTTTATGAATTTAA-ATTGTTTAATAATTTAAATAT-T
1 TTTTATTTCTTTATGAATTTAATATT-TTTAATAATTTAAATATGT
*** * *
856079 TTTTATATTCTTTATTCTTTTAATATTTTTACTATTTTAAATATGT
1 TTTTAT-TTCTTTATGAATTTAATATTTTTAATAATTTAAATATGT
856125 TTTTA
1 TTTTA
856130 GGTTAAAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
44 6 0.14
45 27 0.64
46 9 0.21
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.63
Consensus pattern (45 bp):
TTTTATTTCTTTATGAATTTAATATTTTTAATAATTTAAATATGT
Found at i:856109 original size:9 final size:9
Alignment explanation
Indices: 856052--856127 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
856042 TGTTTATGAA
856052 TTTAA-ATT
1 TTTAATATT
*
856060 GTTTAATAAT
1 -TTTAATATT
*
856070 TTAAATATT
1 TTTAATATT
*
856079 TTTTATATT
1 TTTAATATT
856088 CTTT-AT-TCT
1 -TTTAATAT-T
856097 TTTAATATT
1 TTTAATATT
*
856106 TTTACTATT
1 TTTAATATT
*
856115 TTAAATATGT
1 TTTAATAT-T
856125 TTT
1 TTT
856128 TAGGTTAAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
8 4 0.08
9 39 0.75
10 9 0.17
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTAATATT
Found at i:856495 original size:2 final size:2
Alignment explanation
Indices: 856488--856535 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
856478 ATCAAAGTGA
856488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
856530 AT AT AT
1 AT AT AT
856536 TTGTCTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:857428 original size:103 final size:105
Alignment explanation
Indices: 857281--857571 Score: 394
Period size: 103 Copynumber: 2.8 Consensus size: 105
857271 GAAGTATCAG
* * * * * *
857281 TACTACATTATTTTGGGCTTCAGTATCGATATTATATATGGTATC-GATACCATTGTAGGATTAT
1 TACTTCATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCAG-TACCATTTTAGCATTCT
* *
857345 GTTTTGACAGTATCAGTACTATACCT-ACAA-TATTGGTAC
65 GTTTTGACAGTATCGGTACTATACCTAACAAGTATCGGTAC
* * *
857384 TACTTTATTATTTTGGGTTTCAATATCTATATCATATATGGTATCAGTACCATTTTAGCATTCTG
1 TACTTCATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCAGTACCATTTTAGCATTCTG
* * * *
857449 TTTTGAAAATATCGGTAC--TGCCTAAGAAGTATCGGTAC
66 TTTTGACAGTATCGGTACTATACCTAACAAGTATCGGTAC
*
857487 TACTTCATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCAGTACCATTTTAGCATTCTA
1 TACTTCATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCAGTACCATTTTAGCATTCTG
857552 TTTTGACAGTATCGGTACTA
66 TTTTGACAGTATCGGTACTA
857572 CTTCTATATT
Statistics
Matches: 162, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
101 4 0.02
102 3 0.02
103 154 0.95
104 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (105 bp):
TACTTCATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCAGTACCATTTTAGCATTCTG
TTTTGACAGTATCGGTACTATACCTAACAAGTATCGGTAC
Found at i:860113 original size:16 final size:17
Alignment explanation
Indices: 860092--860125 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
860082 ATTACTTAAA
*
860092 AATTAATTTTTGA-TAC
1 AATTAATTATTGACTAC
860108 AATTAATTATTGACTAC
1 AATTAATTATTGACTAC
860125 A
1 A
860126 TCTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (17 bp):
AATTAATTATTGACTAC
Found at i:865246 original size:22 final size:22
Alignment explanation
Indices: 865221--865268 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
865211 GCAGAAATTG
865221 TTAAAGTGAAAAGGTAG-AATAT
1 TTAAAGTGAAAAGG-AGCAATAT
*
865243 TT-AAGTGAAAAGGGGCAATAT
1 TTAAAGTGAAAAGGAGCAATAT
865264 TTAAA
1 TTAAA
865269 TGGTCAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (22 bp):
TTAAAGTGAAAAGGAGCAATAT
Found at i:866197 original size:22 final size:22
Alignment explanation
Indices: 866169--866219 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
866159 ACATTACATC
866169 ATTCGATAATGTATATAACTTT
1 ATTCGATAATGTATATAACTTT
866191 ATTCGATAATGTATATAACTTT
1 ATTCGATAATGTATATAACTTT
*
866213 AATCGAT
1 ATTCGAT
866220 CTCATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (22 bp):
ATTCGATAATGTATATAACTTT
Found at i:870142 original size:16 final size:17
Alignment explanation
Indices: 870117--870150 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
870107 CCAAGGTGTC
870117 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
870133 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
870150 A
1 A
870151 TAATGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:870922 original size:18 final size:18
Alignment explanation
Indices: 870899--870934 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
870889 AATTCCAAGA
870899 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
870917 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
870935 TTTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:871035 original size:19 final size:19
Alignment explanation
Indices: 871011--871050 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
871001 CATCTTTCTT
871011 AATATTAAAAAAATAAATA
1 AATATTAAAAAAATAAATA
*
871030 AATATTAAAAAAATAATTA
1 AATATTAAAAAAATAAATA
871049 AA
1 AA
871051 AAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATTAAAAAAATAAATA
Done.