Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:551042 original size:18 final size:18
Alignment explanation
Indices: 551005--551045 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
550995 AGAACAGCAC
*
551005 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACGACCA
551023 GAGGAACAAGCAC-ATCCA
1 GAGGAACAAGCACGA-CCA
551041 GAGGA
1 GAGGA
551046 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.44, C:0.22, G:0.32, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACGACCA
Found at i:553077 original size:21 final size:21
Alignment explanation
Indices: 553004--553083 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
552994 AAATCCTACG
* *
553004 GTGGTGGCATCTGAAATAACT
1 GTGGTGGCATCTAAAATAGCT
* *
553025 GTGGTGGCATCAAAAATGGCT
1 GTGGTGGCATCTAAAATAGCT
** ** *
553046 ACGGTACCATCTAAAATAGTT
1 GTGGTGGCATCTAAAATAGCT
553067 GTGGTGGCATCTAAAAT
1 GTGGTGGCATCTAAAAT
553084 GGCTACAGAA
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (21 bp):
GTGGTGGCATCTAAAATAGCT
Found at i:555140 original size:60 final size:59
Alignment explanation
Indices: 555059--555189 Score: 163
Period size: 60 Copynumber: 2.2 Consensus size: 59
555049 ACGTTTTATG
* * * * *
555059 ATCCACGCCTTCCAACGTGGCGCCAGCTCGGATAGAACCCCGCGAAGATGCGCCTCATA
1 ATCCGCGCTTTCCAACGTGGCGCCAGCTCGAACAGAACCCCGCGAAGACGCGCCTCATA
* * * * *
555118 ATCCGCGTCTTTCCACCGTGGCGCTAGCTCGAACAGAACCCCGCGAAGGCGCGCTTCATG
1 ATCCGCG-CTTTCCAACGTGGCGCCAGCTCGAACAGAACCCCGCGAAGACGCGCCTCATA
555178 ATCCGCGCTTTC
1 ATCCGCGCTTTC
555190 TCAGAAAGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 11 0.18
60 50 0.82
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.18
Consensus pattern (59 bp):
ATCCGCGCTTTCCAACGTGGCGCCAGCTCGAACAGAACCCCGCGAAGACGCGCCTCATA
Found at i:555726 original size:49 final size:49
Alignment explanation
Indices: 555672--555765 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
555662 AAATGGCCCC
*
555672 GTACCTCATATAAGGACAAAATAA-TCTAATTGCATAAACTCAAAAAAAT
1 GTACCTCATATAAGGACAAAATAACT-TAATTACATAAACTCAAAAAAAT
* * *
555721 GTACCTCATGTAAGGACAATATAACTTAATTACATGAACTCAAAA
1 GTACCTCATATAAGGACAAAATAACTTAATTACATAAACTCAAAA
555766 CAATCAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 39 0.98
50 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (49 bp):
GTACCTCATATAAGGACAAAATAACTTAATTACATAAACTCAAAAAAAT
Found at i:557248 original size:29 final size:29
Alignment explanation
Indices: 557167--557286 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 29
557157 TCTCATGCAA
* * *
557167 AATCATGACATAGATCAAATCCCATGCAA-
1 AATCAGGACAGAGATAAAATCCCATG-AAG
* ** * *
557196 AATCAGGA-TGCTATCAAATTCCATGAAG
1 AATCAGGACAGAGATAAAATCCCATGAAG
*
557224 AATCAGGACAGAGATAAAATCCCATGTAG
1 AATCAGGACAGAGATAAAATCCCATGAAG
* * *
557253 AATCAGGACGGGGATAAAATCCCATGCAG
1 AATCAGGACAGAGATAAAATCCCATGAAG
557282 AATCA
1 AATCA
557287 AGAATGCATC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.03
28 20 0.27
29 52 0.70
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (29 bp):
AATCAGGACAGAGATAAAATCCCATGAAG
Found at i:557836 original size:18 final size:17
Alignment explanation
Indices: 557815--557874 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
557805 ATTGGTTCAA
557815 TCAGACCGATTCATAGAG
1 TCAGACCGATTCA-AGAG
*
557833 TCAGACTGATTCAAGAGG
1 TCAGACCGATTCAAGA-G
* * *
557851 TCAAATCGATTCAGAGGG
1 TCAGACCGATTCA-AGAG
557869 TCAGAC
1 TCAGAC
557875 TGGATCAATC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (17 bp):
TCAGACCGATTCAAGAG
Found at i:558941 original size:16 final size:16
Alignment explanation
Indices: 558919--558957 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
558909 CACAAAGATG
*
558919 AACAATCTCAAAAGTA
1 AACAATCCCAAAAGTA
*
558935 AATAATCCCAAAAGTA
1 AACAATCCCAAAAGTA
558951 AACAATC
1 AACAATC
558958 GAGCTAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAATCCCAAAAGTA
Found at i:561399 original size:55 final size:55
Alignment explanation
Indices: 561331--561457 Score: 220
Period size: 55 Copynumber: 2.3 Consensus size: 55
561321 CAGTACCTCC
*
561331 TGGGGGTTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAA-CTTTACA
1 TGGGGG-TATCGGTACCCTCCGAGCAATCTGTTATTTCTCGAAGCCAAATC-TTACA
561387 TGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGAAGCCAAATCTTACA
1 TGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGAAGCCAAATCTTACA
561442 TGGGGGTATCGGTACC
1 TGGGGGTATCGGTACC
561458 TCCTTGGGGG
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
55 62 0.90
56 7 0.10
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (55 bp):
TGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGAAGCCAAATCTTACA
Found at i:563692 original size:13 final size:14
Alignment explanation
Indices: 563676--563713 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
563666 ATGGGTAATT
*
563676 TTTGAAAATCGAG-
1 TTTGAAAATCAAGA
563689 TTTGAAAA-CAAGA
1 TTTGAAAATCAAGA
563702 TTTGAAAATCAA
1 TTTGAAAATCAA
563714 TATATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (14 bp):
TTTGAAAATCAAGA
Found at i:563763 original size:20 final size:20
Alignment explanation
Indices: 563738--563775 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
563728 ATTTTTCATG
563738 AAAACAACATAATTAAATAA
1 AAAACAACATAATTAAATAA
563758 AAAACAACATAATTAAAT
1 AAAACAACATAATTAAAT
563776 TTCGAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAACAACATAATTAAATAA
Found at i:564211 original size:23 final size:23
Alignment explanation
Indices: 564168--564233 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
564158 TATCAGTACC
*
564168 CTCAAGAGGGGTTTCGATACCCA
1 CTCAAGAGGGGTATCGATACCCA
*
564191 CTCAA-AGGGCGTATCGGTACCCA
1 CTCAAGAGGG-GTATCGATACCCA
564214 -TACAAG-GGGGTATCGATACC
1 CT-CAAGAGGGGTATCGATACC
564234 TAGCGCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 15 0.41
23 22 0.59
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CTCAAGAGGGGTATCGATACCCA
Found at i:570126 original size:76 final size:76
Alignment explanation
Indices: 570002--570202 Score: 284
Period size: 76 Copynumber: 2.7 Consensus size: 76
569992 CGTTATAAGT
* * * *
570002 TGGGGGTATCAGTATCTCC-T-GGGGGTATTGGTACCCTCCGAGCAATCTGTTATTTCTCGTAGC
1 TGGGGGTATCGGTACCTCCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGC
*
570065 CGAA-CTTTACA
66 CAAATC-TTACA
*
570076 TGGGGGTATCGGTACC-CTCTTGGGGGGTATCGGTACCTTCCGAGCAATCTGTTATTTCTCGGAG
1 TGGGGGTATCGGTACCTC-CTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAG
570140 CCAAATCTTACA
65 CCAAATCTTACA
* *
570152 TGGGGGTATCGGTACCTCCTTGGGGGGTATCGGTACCCTCTGGGCAATCTG
1 TGGGGGTATCGGTACCTCCTTGGGGGGTATCGGTACCCTCCGAGCAATCTG
570203 GTTTTTCAGT
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
73 1 0.01
74 15 0.13
75 1 0.01
76 94 0.83
77 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.30
Consensus pattern (76 bp):
TGGGGGTATCGGTACCTCCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGC
CAAATCTTACA
Found at i:573795 original size:51 final size:50
Alignment explanation
Indices: 573678--573807 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
573668 ACTAGTGTAC
* * *
573678 GTATGTGTTAACTACTACACTTTTTTATTTTATTCACCTACACATTCTAA
1 GTATGTGTTAAATGCTACACTTTTTTATTTTATTCACCTACACATGCTAA
* * ** * * *
573728 GCATGTGTTAAGTGCTACACTTTTTTATTTTATTTGCTTTCATCGGTGC-AA
1 GTATGTGTTAAATGCTACACTTTTTTATTTTATTCACCTACA-C-ATGCTAA
573779 GTATGTGTTAAATGCTACACTTTTTTATT
1 GTATGTGTTAAATGCTACACTTTTTTATT
573808 CACTTGCAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
50 35 0.52
51 30 0.45
52 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (50 bp):
GTATGTGTTAAATGCTACACTTTTTTATTTTATTCACCTACACATGCTAA
Found at i:575571 original size:2 final size:2
Alignment explanation
Indices: 575559--575589 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
575549 AAGCTTCATA
575559 AT AT A- 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
575590 CGCATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:576124 original size:16 final size:16
Alignment explanation
Indices: 576105--576138 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
576095 CAATATACGA
576105 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
576121 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
576137 AT
1 AT
576139 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:576212 original size:16 final size:18
Alignment explanation
Indices: 576180--576213 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
576170 TATTAATGTA
576180 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
576198 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
576214 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:576883 original size:129 final size:130
Alignment explanation
Indices: 576680--576926 Score: 415
Period size: 129 Copynumber: 1.9 Consensus size: 130
576670 AATTTTCTTC
* * *
576680 TAATTAGGTGGTGACATGTGTCACCAATAATATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
**
576745 CCTGGTTAAATGATTAATTTATTAAATT-TATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
576809 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
576874 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
576927 TATATAAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 85 0.78
130 24 0.22
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:577372 original size:35 final size:35
Alignment explanation
Indices: 577322--577397 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
577312 AATTGAATTT
* *
577322 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
577357 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
577392 AATTGA
1 AATTGA
577398 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:580528 original size:17 final size:16
Alignment explanation
Indices: 580497--580529 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
580487 TACTATTCAC
580497 GTGAATAGTAAATTTT
1 GTGAATAGTAAATTTT
*
580513 GTGAATAGTAAAATTT
1 GTGAATAGTAAATTTT
580529 G
1 G
580530 GTCGGCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (16 bp):
GTGAATAGTAAATTTT
Found at i:581342 original size:18 final size:18
Alignment explanation
Indices: 581319--581354 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
581309 AAGAAAGATT
581319 TTACCTGTTATAATTGTG
1 TTACCTGTTATAATTGTG
581337 TTACCTGTTATAATTGTG
1 TTACCTGTTATAATTGTG
581355 GCAAGAAGGG
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:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
TTACCTGTTATAATTGTG
Found at i:595440 original size:20 final size:20
Alignment explanation
Indices: 595415--595453 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
595405 TATGGGTTCA
*
595415 AGTATCGATACTAGATGAAC
1 AGTATCAATACTAGATGAAC
595435 AGTATCAATACTAGATGAA
1 AGTATCAATACTAGATGAA
595454 TTGGGATGAA
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:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AGTATCAATACTAGATGAAC
Found at i:596681 original size:32 final size:32
Alignment explanation
Indices: 596637--596755 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
596627 ACTAACAGTA
* *
596637 TGTTGCATTCAGATAATGCATAGTAGCGTTAG
1 TGTTGCATTCAGATAATGCATAGCAGTGTTAG
* * * *
596669 TGTTTCATTCAGACAATGCACAACAGTGTTAG
1 TGTTGCATTCAGATAATGCATAGCAGTGTTAG
** * * * *
596701 TGTCACATTTAGATAAAGCATAGCAATGTCAG
1 TGTTGCATTCAGATAATGCATAGCAGTGTTAG
* *
596733 TGTTGCATTCAAATAATGTATAG
1 TGTTGCATTCAGATAATGCATAG
596756 TAGTTACAAT
Statistics
Matches: 66, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTTGCATTCAGATAATGCATAGCAGTGTTAG
Found at i:601578 original size:20 final size:21
Alignment explanation
Indices: 601553--601604 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
601543 TTTTCCCAAT
*
601553 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
601573 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
601594 TCGCAATGCGA
1 TCGCAATGCGA
601605 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:601618 original size:20 final size:20
Alignment explanation
Indices: 601593--601686 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
601583 AATTGGAAAA
*
601593 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
601613 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
601634 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
601654 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
601674 TTCGCAACGCGAT
1 ATCGCAACGCGAT
601687 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:602293 original size:19 final size:19
Alignment explanation
Indices: 602246--602287 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
602236 ACGAGAGAAT
*
602246 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
602265 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
602284 CGCA
1 CGCA
602288 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:602305 original size:19 final size:19
Alignment explanation
Indices: 602283--602433 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
602273 GAAACAAAAA
*
602283 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
602302 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
602321 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
602340 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* ** **
602354 TCTCGTCACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
602373 TCGTGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
602392 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
602412 ATCTCGTTGCTATTTTCATT
1 -TCGCGTTGCGATTTTCATT
602432 TC
1 TC
602434 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
14 8 0.07
16 2 0.02
17 3 0.03
19 64 0.59
20 30 0.28
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:604493 original size:21 final size:21
Alignment explanation
Indices: 604469--604535 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
604459 TCATTCCTCG
604469 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
604490 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
604511 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
604532 AGAG
1 AGAG
604536 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:604493 original size:42 final size:42
Alignment explanation
Indices: 604417--604535 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
604407 GACTCGCCTG
* * * *
604417 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
604459 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
604501 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
604536 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:605912 original size:14 final size:14
Alignment explanation
Indices: 605893--605928 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
605883 ATTGTTTAAT
605893 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
605907 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
605921 TGATTTGT
1 TGATTTGT
605929 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:606072 original size:14 final size:14
Alignment explanation
Indices: 606053--606109 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
606043 GCGAAATGAA
606053 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
606067 AATCGCAACGCAAAATAAA
1 AATCGCAACG----A-GAG
606086 AATCGCAACGAGAG
1 AATCGCAACGAGAG
606100 AATCGCAACG
1 AATCGCAACG
606110 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
15 1 0.03
18 1 0.03
19 11 0.32
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:606088 original size:33 final size:33
Alignment explanation
Indices: 606035--606124 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
606025 AAAAAGTACT
* *
606035 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
*
606068 ATCGCAACGCAAAATAAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
* *
606101 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATAAAAATCGC
606125 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
Found at i:606166 original size:33 final size:32
Alignment explanation
Indices: 606124--606250 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
606114 ATTAAATTCG
*
606124 CGTTGCGATTTTTATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
606157 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
606190 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
606223 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
606251 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:606183 original size:19 final size:19
Alignment explanation
Indices: 606120--606250 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
606110 CGAAATTAAA
* *
606120 TTCGCGTTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
*
606139 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
606155 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
606172 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
606186 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
606205 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
606221 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
606238 TTCGCATTGCGAT
1 TTCGCATTGCGAT
606251 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 23 0.28
16 13 0.16
17 12 0.14
19 35 0.42
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:606207 original size:66 final size:66
Alignment explanation
Indices: 606117--606249 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
606107 ACGCGAAATT
* *
606117 AAATTCGCGTTGCGATTTTTATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
606182 G
66 G
*
606183 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
606248 G
66 G
606249 A
1 A
606250 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:607800 original size:14 final size:14
Alignment explanation
Indices: 607781--607808 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
607771 ATATATTGAT
607781 ATGAGTCAACAGAA
1 ATGAGTCAACAGAA
607795 ATGAGTCAACAGAA
1 ATGAGTCAACAGAA
607809 TTATATTGAT
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:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
ATGAGTCAACAGAA
Found at i:608733 original size:24 final size:24
Alignment explanation
Indices: 608699--608752 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
608689 CTGAAACATC
* *
608699 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
608723 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
608747 ATCAAA
1 ATCAAA
608753 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:609834 original size:20 final size:20
Alignment explanation
Indices: 609809--609866 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
609799 ATTCATTTGA
609809 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
609829 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
609849 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
609867 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:609909 original size:14 final size:16
Alignment explanation
Indices: 609889--609962 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
609879 TGAAAATCGC
609889 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
609904 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
609921 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
609940 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
609956 -TTGCGAT
1 ATTGCGAT
609963 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:609926 original size:19 final size:19
Alignment explanation
Indices: 609885--609952 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
609875 GAAATGAAAA
609885 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
609901 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
609918 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
609937 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
609953 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:609928 original size:52 final size:52
Alignment explanation
Indices: 609866--609980 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
609856 AACGAGAAAA
* ***
609866 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
609918 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
609970 TCGCGTTGCGA
1 TCGCATTGCGA
609981 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:610088 original size:14 final size:14
Alignment explanation
Indices: 610069--610105 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
610059 CATCAATTAA
610069 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
610083 ACAAATCATCTTTT
1 ACAAATCAACATTT
610097 ACAAATCAA
1 ACAAATCAA
610106 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:612035 original size:14 final size:14
Alignment explanation
Indices: 612016--612073 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
612006 TTTCATTTCG
612016 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
612030 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
612046 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
612062 CGTTGCGATTTT
1 CGTTGCGATTTT
612074 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:612080 original size:33 final size:33
Alignment explanation
Indices: 611999--612089 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
611989 ACTATCGCAA
*
611999 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
612032 TTGCGA-TTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
612064 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
612090 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:612108 original size:20 final size:19
Alignment explanation
Indices: 612074--612128 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
612064 TTGCGATTTT
*
612074 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
612093 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
612113 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
612129 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:612654 original size:18 final size:18
Alignment explanation
Indices: 612610--612654 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
612600 GTCGATCAGA
*
612610 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
612628 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
*
612646 TTATGGCTC
1 TGATGGCTC
612655 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.16, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:614308 original size:22 final size:22
Alignment explanation
Indices: 614281--614324 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
614271 GATGGAGATA
614281 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
614303 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
614325 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:614626 original size:20 final size:20
Alignment explanation
Indices: 614512--614625 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
614502 GATTATGTAT
614512 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
614532 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
614552 TATCGCGTTGCAAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
614572 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
614593 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
614613 TATCGCATTGCGA
1 TATCGCGTTGCGA
614626 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:614629 original size:41 final size:41
Alignment explanation
Indices: 614492--614627 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
614482 CGCTTTGAAA
* *
614492 ATCGCATTACGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * * *
614533 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCAAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
614573 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
614614 ATCGCATTGCGATT
1 ATCGCATTGCGATT
614628 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.40
41 40 0.53
42 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:617921 original size:63 final size:63
Alignment explanation
Indices: 617822--617947 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
617812 AGCTGTTCGA
*
617822 AGGGGATAAGCATCATCAAAAGGGTATTCAGTTACCATTAATGGTCCCAGTTGCCGACTTGCG
1 AGGGGATAAACATCATCAAAAGGGTATTCAGTTACCATTAATGGTCCCAGTTGCCGACTTGCG
617885 AGGGGATAAACATCATCAAAAGGGTATTCAGTTACCATTAATGGTCCCAGTTGCCGACTTGCG
1 AGGGGATAAACATCATCAAAAGGGTATTCAGTTACCATTAATGGTCCCAGTTGCCGACTTGCG
617948 GCCAGTTATC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (63 bp):
AGGGGATAAACATCATCAAAAGGGTATTCAGTTACCATTAATGGTCCCAGTTGCCGACTTGCG
Found at i:622677 original size:18 final size:17
Alignment explanation
Indices: 622645--622678 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
622635 CTTGAAAATT
622645 TTAAAATTTTATATATC
1 TTAAAATTTTATATATC
*
622662 TTAAATATTTTTTATAT
1 TTAAA-ATTTTATATAT
622679 TTTTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAAATTTTATATATC
Found at i:629959 original size:28 final size:28
Alignment explanation
Indices: 629861--629960 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 28
629851 TTTTTTTAAA
* *
629861 ATTCGGGTTGGGTTTTTTTAAGTTTGAT
1 ATTCGGGTCGGGTTTTTTTAAGTGTGAT
* *
629889 ATTGGGGTTGGGTCGGGTTTTTTTAAGTGTGGT
1 A-T----TCGGGTCGGGTTTTTTTAAGTGTGAT
*
629922 ATTCGAGTCGGGTTTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTTTTTTTAAGTGTGAT
629950 ATTCGGGTCGG
1 ATTCGGGTCGG
629961 ATTCTAGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 34 0.58
29 1 0.02
32 1 0.02
33 23 0.39
ACGTcount: A:0.13, C:0.06, G:0.35, T:0.46
Consensus pattern (28 bp):
ATTCGGGTCGGGTTTTTTTAAGTGTGAT
Found at i:630557 original size:16 final size:16
Alignment explanation
Indices: 630536--630584 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
630526 AGGTTTCAGT
630536 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
*
630552 TTCAGATTCAAATTCC
1 TTCAGATTCTAATTCC
630568 TTCACAGATTCTAATTC
1 TT--CAGATTCTAATTC
630585 TCTCATAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 17 0.59
18 12 0.41
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (16 bp):
TTCAGATTCTAATTCC
Found at i:631794 original size:64 final size:64
Alignment explanation
Indices: 631667--631786 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
631657 AATGTTATAT
631667 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
*
631731 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAAT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAAT
631787 GTAATAGGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (64 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
Found at i:632443 original size:200 final size:197
Alignment explanation
Indices: 631829--632531 Score: 740
Period size: 200 Copynumber: 3.5 Consensus size: 197
631819 AAAGTAAATC
* * * *
631829 GGTATATTTATACCGGTAACATTGTAAATTTACCTATTACAATATTATTATCGGTTACGATGTTT
1 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
** * * * * *
631894 TTTAGATCGATACAATTT-TAAATGTATCGACACTTTATGCTTGCATCTGGTTGGGTATTCATAT
66 TTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTT---TATGC--A-
* * * *
631958 TTTATTCTGGAAAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGACCTATTA
124 TTTATTCTGGACAAAAGTATCGACAAAAATTAACAA-GTGTCGATACATTATGTT-GACCTATTT
*
632022 TCTCATAAAAT
187 TCTCATAAACT
*
632033 CGGTATATTTATACCGGTTACATTG-AACATTTACCTATTACATTATACTTAT-GGTTTCGATGT
1 -GGTATATTTATACCGGTTACATTGTAA-ATTTACCTATTACATTATAATTATCGGTTTCGATGT
** * * * *
632096 TTCCGGGATTGATATTTTTTATAAATGTATCGACACTTTATG-GTTGCACC-C-TTTTTGGTATT
64 TTTTGGGATCGATA-CTTTTATAAATGTATCGACACTTTATGCG-TGCACCTCGTTTAT-GCATT
* * *
632158 TATTCTGGACTAAAAGTATCGACACAAATTTAGCAAGTGTCGATAC-TTGATGCTGACCTATTTT
126 TATTCTGGAC-AAAAGTATCGACA-AAAATTAACAAGTGTCGATACATT-ATGTTGACCTATTTT
* *
632222 ATCATAAAACC
188 CTCAT-AAACT
* *
632233 GGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTTTCGATGTTT
1 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
632298 TTGGGATCGATACTTTTAATAAATGTATCGACAATTTATGCGTGCACCTCGTTTGTGCATTCATC
66 TTGGGATCGATACTTTT-ATAAATGTATCGACACTTTATGCGTGCACCTCGTTTATGCATTTATT
* * *
632363 CTGGACAATAAGTATCGACAAAAATTACACAAGTGTCGATACATTATGTTGACATGTTTTCTAAT
130 CTGGACAA-AAGTATCGACAAAAATTA-ACAAGTGTCGATACATTATGTTGACCTATTTTCTCAT
*
632428 TAACT
193 AAACT
* * * *
632433 GGTATATTTATACCGGTTACATTGTTAATTTATCTATTACATTATAATTATTGGTTTTGATGTTT
1 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TT
* *
632498 TTTGGG-TCGATACTTGTATAAAATATATCGACAC
65 TTTGGGATCGATACTTTTAT-AAATGTATCGACAC
632532 ATATTTAGGT
Statistics
Matches: 419, Mismatches: 58, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
198 13 0.03
199 90 0.21
200 153 0.37
201 61 0.15
202 6 0.01
203 2 0.00
204 24 0.06
205 70 0.17
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (197 bp):
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTATGCATTTATTC
TGGACAAAAGTATCGACAAAAATTAACAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAA
CT
Found at i:636096 original size:251 final size:251
Alignment explanation
Indices: 635640--636131 Score: 686
Period size: 251 Copynumber: 2.0 Consensus size: 251
635630 TTTCGATATT
* * * *
635640 TTTTGGGATCGACACTTTTTGAAAATGTATTGATACTTTATGCGTTCACCCTTTTTAGCATCCAT
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTAGCATCCAT
* * * *
635705 TATGGACAAAAATTATCGACACAATATTAATAAGTGTCGATAAATATTATAGACTTATTCTCACA
66 TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAAAATTATAGACATATTCTCACA
* * *
635770 TAAAACTGGTATATGTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTC
131 TAAAACCGGTATATGTATACCGGGTATATTACAAAATTACCCATTACATTATAATTATGGGTTTC
* *
635835 GATGTTTTTGGGATTGACACTTTTAATAAATGTATCGACACTTTATGCGTGCAACCC
196 GATGTTTTTGGG-TCGACACTTTTAATAAATGGATCGACACTTTATGCGTGCAACCC
* * *
635892 TTTT-GGATCGACACTCTATGAAAATGTATCGACGCTTTGTAG-GTTCACCCTTTTTGGCATCCA
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTAGCATCCA
* * **
635955 TTCTGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAAAATTGTAGACATATT-TTTC
65 TTATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAAAATTATAGACATATTCTCAC
*
636019 ATAAAACCGGTATATTTATACCGGGTATATTGA-AAAATTACCCATTACATTATAATTATGGGTT
130 ATAAAACCGGTATATGTATACCGGGTATATT-ACAAAATTACCCATTACATTATAATTATGGGTT
* ** * *
636083 TCGATATTTTTTGGGTCGTTACTTTTTATATATGGATCGACACTTTATG
194 TCGAT-GTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATG
636132 GAAAACTTTA
Statistics
Matches: 211, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
250 93 0.44
251 113 0.54
252 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (251 bp):
TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTAGCATCCAT
TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAAAATTATAGACATATTCTCACA
TAAAACCGGTATATGTATACCGGGTATATTACAAAATTACCCATTACATTATAATTATGGGTTTC
GATGTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATGCGTGCAACCC
Found at i:637411 original size:6 final size:6
Alignment explanation
Indices: 637401--637446 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
637391 CTTGTTTGGA
* * * *
637401 TCATCA TCATCG TCGTCG TCATCT TCATCG TCATCT TCATCG TCAT
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCAT
637447 TGACCGCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (6 bp):
TCATCG
Found at i:637431 original size:12 final size:12
Alignment explanation
Indices: 637401--637446 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
637391 CTTGTTTGGA
* *
637401 TCATCATCATCG
1 TCATCGTCATCT
*
637413 TCGTCGTCATCT
1 TCATCGTCATCT
637425 TCATCGTCATCT
1 TCATCGTCATCT
637437 TCATCGTCAT
1 TCATCGTCAT
637447 TGACCGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:638507 original size:38 final size:38
Alignment explanation
Indices: 638456--638532 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
638446 TCAAACAATA
638456 AACCCAGGTCAATGACACGTTCGGGACGAATCTTCCTT
1 AACCCAGGTCAATGACACGTTCGGGACGAATCTTCCTT
*
638494 AACCCAGGTCAATGACATGTTCGGGACGAATCTTCCTT
1 AACCCAGGTCAATGACACGTTCGGGACGAATCTTCCTT
638532 A
1 A
638533 CTTTAAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (38 bp):
AACCCAGGTCAATGACACGTTCGGGACGAATCTTCCTT
Found at i:639385 original size:201 final size:201
Alignment explanation
Indices: 638943--640238 Score: 1856
Period size: 201 Copynumber: 6.7 Consensus size: 201
638933 TTTAAATTAA
* * *
638943 TATCGACACAAAATTAAAAACGTATCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
* *
639008 ATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT-TTGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* *
639072 ATCGACACTTTTTGAAAATGTATCGACAATTTAAGCGTTCACCCTTTTTGGCATCCATTCTGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
639137 CAAAAG
196 CAAAAG
* *
639143 CATCGACACAAAATTAAAAATGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
639208 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
*
639273 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAT
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
639338 CAAAAG
196 CAAAAG
* *
639344 TATCGACATAAAATTAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
* *
639409 TTTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
*
639474 ATCGATACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
639539 CAAAAG
196 CAAAAG
* * *
639545 TATCTACACAAAATTAAAAAAGTGTCGATACATATTGTAGACATATTCTCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
* *
639610 ATTTATACCGGTTACATTGTAAATTTATCTGTTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * *
639675 ATCTACATTTTTTGAAAATCTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTTTGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
639740 CAAAAG
196 CAAAAG
* *
639746 TATCGACACAAAATTAAAAACGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
* * * *
639811 ATTTATACCGGTTACATTGTAAATTTACTTATTACATTATAATTACGGGTTTCGATCTTTCTGAG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* *
639876 ATCGACAC--TTT----ATG---CG------T-T-C--AC-CCTTTT-TGGCATCCATTCTGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
639920 CAAAAG
196 CAAAAG
*
639926 TATCGACACAAAATTAAAAAAGTATCGATACATGTTGTAGACCTA-T-TCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
*
639989 ATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* *
640054 ATCGACA-----T-----T-T-T----A-----TGCGTTCACCTTTTTTGGCATCCATTATGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
640098 CAAAAG
196 CAAAAG
* * *
640104 TATCGACACAAAATTAAAAAACTGTCGATACATGTTGTAGACATGTTCTCTCATAAAATCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
* * * * * *
640169 ATTTATACCAGTTACATTGAAAATTTACCTATTACATTATACTTAT-GGATGCATATGTTTCTGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTC-GATGTTTCTGG
640233 GATCGA
130 GATCGA
640239 TAAATTTTAC
Statistics
Matches: 1019, Mismatches: 65, Indels: 44
0.90 0.06 0.04
Matches are distributed among these distances:
173 1 0.00
174 2 0.00
175 1 0.00
176 1 0.00
177 6 0.01
178 147 0.14
179 6 0.01
180 139 0.14
181 5 0.00
182 1 0.00
184 1 0.00
185 1 0.00
186 1 0.00
192 2 0.00
195 2 0.00
199 3 0.00
200 120 0.12
201 580 0.57
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (201 bp):
TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTAT
ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
CAAAAG
Found at i:640083 original size:178 final size:179
Alignment explanation
Indices: 639696--640238 Score: 849
Period size: 180 Copynumber: 3.0 Consensus size: 179
639686 TTGAAAATCT
*
639696 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTTTGGACCAAAAGTATCGACACAAAATT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACCAAAAGTATCGACACAAAATT
* *
639761 AAAAACGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTAC
66 AAAAAAGTGTCGATACATGTTGTAGACCTA-TCTCTCATAAAATCGGTATATTTATACCGGTTAC
* * * * *
639826 ATTGTAAATTTACTTATTACATTATAATTACGGGTTTCGATCTTTCTGAG
130 ATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
*
639876 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACCAAAAGTATCGACACAAAATT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACCAAAAGTATCGACACAAAATT
*
639941 AAAAAAGTATCGATACATGTTGTAGACCTAT-TCTCATAAAATCGGTATATTTATACCGGTTACA
66 AAAAAAGTGTCGATACATGTTGTAGACCTATCTCTCATAAAATCGGTATATTTATACCGGTTACA
640005 TTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
131 TTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* *
640054 ATCGACATTTTATGCGTTCACCTTTTTTGGCATCCATTATGGACCAAAAGTATCGACACAAAATT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACCAAAAGTATCGACACAAAATT
* * * *
640119 AAAAAACTGTCGATACATGTTGTAGACATGTTCTCTCATAAAATCGGTATATTTATACCAGTTAC
66 AAAAAAGTGTCGATACATGTTGTAGACCT-ATCTCTCATAAAATCGGTATATTTATACCGGTTAC
* * * *
640184 ATTGA-AAATTTACCTATTACATTATACTTAT-GGATGCATATGTTTCTGGG
130 ATT-ATAAATTTACCTATTACATTATAATTATGGGTTTC-GATGTTTCTGGG
640234 ATCGA
1 ATCGA
640239 TAAATTTTAC
Statistics
Matches: 338, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
178 165 0.49
179 6 0.02
180 166 0.49
181 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (179 bp):
ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACCAAAAGTATCGACACAAAATT
AAAAAAGTGTCGATACATGTTGTAGACCTATCTCTCATAAAATCGGTATATTTATACCGGTTACA
TTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
Found at i:642362 original size:32 final size:32
Alignment explanation
Indices: 642317--642377 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
642307 CATCTTAAGA
* *
642317 TCACTCCTTAACACCTCAACTTCTTTCACACT
1 TCACCCCTCAACACCTCAACTTCTTTCACACT
*
642349 TCACCCCTCAACACCTCTACTTCTTTCAC
1 TCACCCCTCAACACCTCAACTTCTTTCAC
642378 CACTCCATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (32 bp):
TCACCCCTCAACACCTCAACTTCTTTCACACT
Found at i:642434 original size:21 final size:21
Alignment explanation
Indices: 642408--642459 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
642398 CCACTTCCCC
642408 CTTCGACTCTCTCAAGTTTCT
1 CTTCGACTCTCTCAAGTTTCT
642429 CTTCGACTCTCTCAAGTTTCT
1 CTTCGACTCTCTCAAGTTTCT
642450 CTTCGACTCT
1 CTTCGACTCT
642460 TGATTGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.13, C:0.35, G:0.10, T:0.42
Consensus pattern (21 bp):
CTTCGACTCTCTCAAGTTTCT
Found at i:644750 original size:20 final size:19
Alignment explanation
Indices: 644705--644750 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
644695 TCGATAGCGC
*
644705 TTTACCGATTTTATCATTT
1 TTTACCAATTTTATCATTT
*
644724 TAATACCAATTTTATCATATT
1 T-TTACCAATTTTATCAT-TT
644745 TTTACC
1 TTTACC
644751 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTACCAATTTTATCATTT
Found at i:645220 original size:24 final size:24
Alignment explanation
Indices: 645193--645241 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
645183 AATAGAAAAC
*
645193 AATAGGGAAAACAATAAAAGGCTT
1 AATAGGGAAAACAACAAAAGGCTT
645217 AATAGGGAAAACAACAAAAGGCTT
1 AATAGGGAAAACAACAAAAGGCTT
645241 A
1 A
645242 CTCTCAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.14
Consensus pattern (24 bp):
AATAGGGAAAACAACAAAAGGCTT
Found at i:648704 original size:42 final size:42
Alignment explanation
Indices: 648612--648877 Score: 225
Period size: 42 Copynumber: 6.4 Consensus size: 42
648602 AACGTTGAAA
* *
648612 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTTTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TTC
* ***
648656 TG--AATCGCGTTGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
648696 AGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTC
648736 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-C
* * *
648779 A-AGAATCGCAACCCGA--TT-CAGAAAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-C
* ***
648819 A-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TT-C
*
648861 A-AGAATCGCAACGCGAT
1 AGAAAATCGCAACGCGAT
648878 TCAGAAAATG
Statistics
Matches: 192, Mismatches: 18, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
39 4 0.02
40 88 0.46
41 2 0.01
42 93 0.48
43 4 0.02
44 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:648705 original size:20 final size:20
Alignment explanation
Indices: 648680--648886 Score: 260
Period size: 20 Copynumber: 10.2 Consensus size: 20
648670 ATCTTCCAAG
648680 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
648700 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
648720 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
648740 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAA
*
648762 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
648782 AATCGCAACCCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
648802 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
648822 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
*
648842 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAA
648864 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
648884 AAT
1 AAT
648887 GAGTAAATTC
Statistics
Matches: 167, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.03
20 125 0.75
21 2 0.01
22 32 0.19
23 3 0.02
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGATTCAGAA
Found at i:648744 original size:82 final size:82
Alignment explanation
Indices: 648667--648886 Score: 322
Period size: 82 Copynumber: 2.7 Consensus size: 82
648657 GAATCGCGTT
*
648667 GCGATCTTCCAAGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGC
1 GCGATCTTCCAAGAATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCAGAAAATCGCAACGC
648731 GATT-CAGAAAATCGCAAC
65 GATTCCA-AAAATCGCAAC
*
648749 GCGATCTTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCG
1 GCGATCTTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCG
*
648814 ATTCCAAGAATCGCAAC
66 ATTCCAAAAATCGCAAC
***
648831 GCGAT-TAAGAA-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
1 GCGATCTTCCAAGAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAAAAT
648887 GAGTAAATTC
Statistics
Matches: 127, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
80 13 0.10
81 3 0.02
82 107 0.84
83 4 0.03
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.16
Consensus pattern (82 bp):
GCGATCTTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCG
ATTCCAAAAATCGCAAC
Found at i:648800 original size:102 final size:102
Alignment explanation
Indices: 648673--648879 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
648663 CGTTGCGATC
* *
648673 TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCA
1 TTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCGATTCCA-AAAATCGCAACGCGATTAA
648737 GAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA
65 GAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA
*
648775 TTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 TTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCGATTCCAAAAATCGCAACGCGATTAAG
648840 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA
66 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA
648877 TTC
1 TTC
648880 AGAAAATGAG
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 99 0.98
103 2 0.02
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (102 bp):
TTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCGATTCCAAAAATCGCAACGCGATTAAG
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA
Found at i:648993 original size:6 final size:6
Alignment explanation
Indices: 648982--649145 Score: 321
Period size: 6 Copynumber: 27.5 Consensus size: 6
648972 GACACGTATT
648982 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
649030 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
649078 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
649126 ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
649146 CGAGACGAGA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.03
6 153 0.97
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:649678 original size:6 final size:6
Alignment explanation
Indices: 649642--649723 Score: 129
Period size: 6 Copynumber: 14.5 Consensus size: 6
649632 TCTCGTCTCG
649642 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
649685 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
649724 AATGCGTGTC
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.33
6 51 0.67
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:649844 original size:20 final size:20
Alignment explanation
Indices: 649819--650128 Score: 277
Period size: 20 Copynumber: 15.2 Consensus size: 20
649809 GAATTTACTC
649819 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
649839 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
649859 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
649881 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
649901 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
649921 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
649943 ATTTTCTGAATGGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
649963 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
649983 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
650003 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* * *
650023 ATTTTATGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
*** *
650043 ATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
650065 ATCTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
650085 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* **
650105 GTTTTGAT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
650124 ATTTT
1 ATTTT
650129 GTTGGTCATT
Statistics
Matches: 240, Mismatches: 38, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
19 19 0.08
20 162 0.68
21 17 0.07
22 42 0.17
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:649924 original size:62 final size:62
Alignment explanation
Indices: 649819--650128 Score: 384
Period size: 62 Copynumber: 5.1 Consensus size: 62
649809 GAATTTACTC
* *
649819 ATTTTCTTAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
* *
649881 ATTCTT-GGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
* *
649943 ATTTTCTGAATGGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
* * *
650003 ATTTTCTGAATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
* ** * * * * *
650065 ATCTTCT-TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTT-TT-G-ATATCGCGTTGCG
1 ATTTTCTGAATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
650124 ATTTT
1 ATTTT
650129 GTTGGTCATT
Statistics
Matches: 218, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
59 15 0.07
60 53 0.24
61 12 0.06
62 136 0.62
63 2 0.01
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (62 bp):
ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
Found at i:653553 original size:21 final size:21
Alignment explanation
Indices: 653505--653572 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
653495 TATCACATTA
* *
653505 CGATTTCCCAAATTCGCGTTG
1 CGATTTTCCTAATTCGCGTTG
653526 CGATTTTCCTAATTCGCGTTG
1 CGATTTTCCTAATTCGCGTTG
* **
653547 CGATTTTCTTAATTCGCAATG
1 CGATTTTCCTAATTCGCGTTG
653568 CGATT
1 CGATT
653573 ACGTAAATCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
CGATTTTCCTAATTCGCGTTG
Found at i:653585 original size:20 final size:20
Alignment explanation
Indices: 653560--653705 Score: 188
Period size: 20 Copynumber: 7.3 Consensus size: 20
653550 TTTTCTTAAT
653560 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
653580 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* * *
653600 TCGCAATACGGTTATGTAAA
1 TCGCAATGCGATTACGTAAA
* *
653620 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
653641 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
653661 TCGCATTGCGATTACGT-AT
1 TCGCAATGCGATTACGTAAA
*
653680 TCGCATTGCGATTTA-GTAAA
1 TCGCAATGCGA-TTACGTAAA
653700 TCGCAA
1 TCGCAA
653706 CGAGATTCTG
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 14 0.13
20 79 0.72
21 17 0.15
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:654593 original size:24 final size:24
Alignment explanation
Indices: 654566--654619 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
654556 GTATTCGAAA
654566 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
654590 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
654614 TTTGAT
1 TTTGAT
654620 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:657156 original size:20 final size:19
Alignment explanation
Indices: 657128--657182 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
657118 CAATCATCTT
*
657128 AATGTCTATCGCAACGCGTA
1 AATGACTATCGCAACGCG-A
*
657148 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
657167 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
657183 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:657192 original size:14 final size:14
Alignment explanation
Indices: 657173--657260 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
657163 GCGAAATGAA
657173 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
657187 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
657206 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
657220 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
657239 AATCGCAACGAGGG
1 AATCGCAACGAGAG
657253 AATCGCAA
1 AATCGCAA
657261 ACAACAACAA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:657197 original size:33 final size:33
Alignment explanation
Indices: 657155--657260 Score: 203
Period size: 33 Copynumber: 3.2 Consensus size: 33
657145 GTAAATGACT
657155 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
657188 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
657221 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
657254 ATCGCAA
1 ATCGCAA
657261 ACAACAACAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:657244 original size:19 final size:19
Alignment explanation
Indices: 657135--657246 Score: 100
Period size: 19 Copynumber: 6.4 Consensus size: 19
657125 CTTAATGTCT
* **
657135 ATCGCAACGCGTAAATGACT
1 ATCGCAATGCG-AAATGAAA
657155 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
657174 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
657188 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
657207 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
657221 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
657240 ATCGCAA
1 ATCGCAA
657247 CGAGGGAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 33 0.44
20 10 0.13
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:657513 original size:14 final size:14
Alignment explanation
Indices: 657494--657532 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
657484 TAATGGGGAG
657494 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
657508 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
657522 GAATCTCTGCA
1 TAATCCCTGCA
657533 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:658345 original size:14 final size:14
Alignment explanation
Indices: 658326--658362 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
658316 CATCAATTAA
658326 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
658340 ACAAATCATCTTTT
1 ACAAATCAACTTTT
658354 ACAAATCAA
1 ACAAATCAA
658363 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:659437 original size:14 final size:14
Alignment explanation
Indices: 659418--659454 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
659408 AGCCATTTCG
659418 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
659432 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
659446 CGTTGCGAT
1 CGTTGCGAT
659455 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:660046 original size:20 final size:20
Alignment explanation
Indices: 660023--660136 Score: 183
Period size: 20 Copynumber: 5.7 Consensus size: 20
660013 CGATAGTCAG
660023 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
660043 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
660063 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
660083 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
660104 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
660124 ATTCGCATTGCGA
1 ATTCGCATTGCGA
660137 ATTTGAGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
20 67 0.79
21 18 0.21
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:660099 original size:41 final size:40
Alignment explanation
Indices: 660023--660136 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
660013 CGATAGTCAG
660023 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* *
660063 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGT
* *
660104 AATCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
660137 ATTTGAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 31 0.46
41 36 0.54
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:660149 original size:41 final size:40
Alignment explanation
Indices: 660025--660158 Score: 180
Period size: 41 Copynumber: 3.3 Consensus size: 40
660015 ATAGTCAGAT
*
660025 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* *
660065 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGTAA
* *
660106 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTTGA-GAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTT-ACGTAA
*
660147 TCGCAATGCGAT
1 TCGCATTGCGAT
660159 AGTCAGAATC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
40 28 0.34
41 53 0.65
42 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
Found at i:660151 original size:61 final size:61
Alignment explanation
Indices: 660025--660158 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
660015 ATAGTCAGAT
* * ** *
660025 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
* *
660086 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTTGAGAAA
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
*
660147 TCGCAATGCGAT
1 TCGCATTGCGAT
660159 AGTCAGAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
Found at i:660169 original size:61 final size:61
Alignment explanation
Indices: 660025--660177 Score: 175
Period size: 61 Copynumber: 2.5 Consensus size: 61
660015 ATAGTCAGAT
* * * * * ** *
660025 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGATTCACGTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
* * *
660086 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTTGAGAAA
1 TCGCAATGCGATTCACGTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
660147 TCGCAATGCGATAGTCA-G-AATCGCGTTGCGA
1 TCGCAATGCGAT--TCACGTAATCGCGTTGCGA
660178 ATCTGGAAAC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
61 78 0.96
62 1 0.01
63 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (61 bp):
TCGCAATGCGATTCACGTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTTCAGAAA
Found at i:669300 original size:2 final size:2
Alignment explanation
Indices: 669293--669327 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
669283 GTTCGCAAGT
669293 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
669328 TCTATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:669335 original size:2 final size:2
Alignment explanation
Indices: 669330--669401 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
669320 CTCTCTCTTC
669330 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
669372 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
669402 AAATTAAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:669720 original size:2 final size:2
Alignment explanation
Indices: 669713--669745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
669703 GTTCGCAAGT
669713 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
669746 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:669750 original size:2 final size:2
Alignment explanation
Indices: 669745--669782 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
669735 TCTCTCTCTC
669745 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
669783 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:670570 original size:32 final size:32
Alignment explanation
Indices: 670534--670624 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
670524 TATTTAATTA
670534 TTTTATTGATCTACTCATACTATTATGTTGAT
1 TTTTATTGATCTACTCATACTATTATGTTGAT
* *
670566 TTTTATTTAT-TA---ATA-GATTA---T--T
1 TTTTATTGATCTACTCATACTATTATGTTGAT
670588 T--TATTGATCTACTCATACTATTATGTTGAT
1 TTTTATTGATCTACTCATACTATTATGTTGAT
670618 TTTTATT
1 TTTTATT
670625 TATTAATAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 24
0.61 0.06 0.34
Matches are distributed among these distances:
20 6 0.14
21 2 0.05
22 2 0.05
24 4 0.09
25 4 0.09
27 4 0.09
28 4 0.09
30 2 0.05
31 2 0.05
32 13 0.30
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (32 bp):
TTTTATTGATCTACTCATACTATTATGTTGAT
Found at i:670586 original size:52 final size:52
Alignment explanation
Indices: 670519--670635 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
670509 TCTCTAATAA
670519 TTATTTATT--TA-ATTATTTTATTGATCTACTCATACTATTATGTTGATTT
1 TTATTTATTAATAGATTATTTTATTGATCTACTCATACTATTATGTTGATTT
670568 TTATTTATTAATAGATTATTTTATTGATCTACTCATACTATTATGTTGATTT
1 TTATTTATTAATAGATTATTTTATTGATCTACTCATACTATTATGTTGATTT
670620 TTATTTATTAATAGAT
1 TTATTTATTAATAGAT
670636 ACTTGCAATC
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
49 9 0.14
51 2 0.03
52 54 0.83
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (52 bp):
TTATTTATTAATAGATTATTTTATTGATCTACTCATACTATTATGTTGATTT
Found at i:673313 original size:27 final size:27
Alignment explanation
Indices: 673283--673358 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
673273 ACTTAATTAT
*
673283 ATATTTATATTTTATTTTAATAATTTA
1 ATATTAATATTTTATTTTAATAATTTA
* ***
673310 ATATTAACATTCTTA-AAAAATAATTTA
1 ATATTAATATT-TTATTTTAATAATTTA
*
673337 TTACTTAATATTTTATTTTAAT
1 ATA-TTAATATTTTATTTTAAT
673359 TACTTGAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTAATATTTTATTTTAATAATTTA
Found at i:673914 original size:6 final size:6
Alignment explanation
Indices: 673903--673935 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
673893 TAATCATAGT
673903 ACTGGA ACTGGA ACTGGA ACTGGA ACTGGA ACT
1 ACTGGA ACTGGA ACTGGA ACTGGA ACTGGA ACT
673936 CACCTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.18
Consensus pattern (6 bp):
ACTGGA
Found at i:676698 original size:16 final size:16
Alignment explanation
Indices: 676679--676714 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
676669 TATTTGAGAT
676679 TTAGTAACTTAAGGAA
1 TTAGTAACTTAAGGAA
*
676695 TTAGTAACTTGAGGAA
1 TTAGTAACTTAAGGAA
676711 TTAG
1 TTAG
676715 GGAAGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (16 bp):
TTAGTAACTTAAGGAA
Found at i:677837 original size:30 final size:30
Alignment explanation
Indices: 677743--677845 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
677733 AACAAGGTTA
**
677743 TGTTCATGTTCGTTTGCTTATTTTTGAAGG
1 TGTTCATGTTCGTTTATTTATTTTTGAAGG
* * * *
677773 TTTTCGTGTTCGTTTA---AATTTTCAA--
1 TGTTCATGTTCGTTTATTTATTTTTGAAGG
* *
677798 T-ATCGTGTTCGTTTATTTATTTTTGAAGG
1 TGTTCATGTTCGTTTATTTATTTTTGAAGG
677827 TGTTCATGTTCGTTTATTT
1 TGTTCATGTTCGTTTATTT
677846 CTTGTTCACG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
24 13 0.23
25 1 0.02
27 14 0.25
29 1 0.02
30 28 0.49
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (30 bp):
TGTTCATGTTCGTTTATTTATTTTTGAAGG
Found at i:677898 original size:35 final size:35
Alignment explanation
Indices: 677870--677952 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
677860 TGTTCATTTA
677870 ATGTTC-GTGAACTTGTTCGTTTATATGTTCATGAAC
1 ATGTTCAGTGAAC--GTTCGTTTATATGTTCATGAAC
* *
677906 ATGTTCATTTAACGTTCGTTTATATGTTCATGAAC
1 ATGTTCAGTGAACGTTCGTTTATATGTTCATGAAC
*
677941 ACGTTCA-TGAAC
1 ATGTTCAGTGAAC
677953 ATGTTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 4 0.10
35 28 0.67
36 6 0.14
37 4 0.10
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (35 bp):
ATGTTCAGTGAACGTTCGTTTATATGTTCATGAAC
Found at i:677904 original size:24 final size:23
Alignment explanation
Indices: 677848--677922 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
677838 GTTTATTTCT
*
677848 TGTTCACGAACATGTTCATTTAA
1 TGTTCATGAACATGTTCATTTAA
* * *
677871 TGTTCGTGAACTTGTTCGTTTATA
1 TGTTCATGAACATGTTCATTTA-A
677895 TGTTCATGAACATGTTCATTTAA
1 TGTTCATGAACATGTTCATTTAA
*
677918 CGTTC
1 TGTTC
677923 GTTTATATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 23 0.53
24 20 0.47
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTTCATGAACATGTTCATTTAA
Found at i:677934 original size:47 final size:46
Alignment explanation
Indices: 677848--677985 Score: 132
Period size: 47 Copynumber: 3.0 Consensus size: 46
677838 GTTTATTTCT
* * ** *
677848 TGTTCACGAACATGTTCATTTAATGTTCGTGAACTTGTTCGTTTATA
1 TGTTCATGAACATGTTCATTTAACGTTCGTTTA-TTGTTCGTTTACA
* **
677895 TGTTCATGAACATGTTCATTTAACGTTCGTTTATATGTTCATGAACA
1 TGTTCATGAACATGTTCATTTAACGTTCGTTTAT-TGTTCGTTTACA
* ** * * *
677942 CGTTCATGAACATGTTTGTTTAGCGTTCATTTAGTGTTCGTTTA
1 TGTTCATGAACATGTTCATTTAACGTTCGTTTATTGTTCGTTTA
677986 GCGTTGTTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
46 8 0.11
47 65 0.89
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (46 bp):
TGTTCATGAACATGTTCATTTAACGTTCGTTTATTGTTCGTTTACA
Found at i:677984 original size:22 final size:22
Alignment explanation
Indices: 677954--678018 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
677944 TTCATGAACA
677954 TGTTTGTTTAGCGTTCATTTAG
1 TGTTTGTTTAGCGTTCATTTAG
* **
677976 TGTTCGTTTAGCGTTGTTTTAG
1 TGTTTGTTTAGCGTTCATTTAG
* *
677998 TGTTTGTTTATCGTTCGTTTA
1 TGTTTGTTTAGCGTTCATTTA
678019 TATATTCATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.11, C:0.09, G:0.23, T:0.57
Consensus pattern (22 bp):
TGTTTGTTTAGCGTTCATTTAG
Found at i:678267 original size:12 final size:12
Alignment explanation
Indices: 678234--678259 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
678224 AAACGAACTC
678234 ATAAATGAGCTT
1 ATAAATGAGCTT
678246 ATAAATGAGCTT
1 ATAAATGAGCTT
678258 AT
1 AT
678260 TCATGAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAAATGAGCTT
Found at i:682147 original size:83 final size:83
Alignment explanation
Indices: 682008--682174 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
681998 CATCTCAAGC
682008 TCAAGTGAGGTAATTGTAAAAAGAATTAAGGTGGCAGTGAAAGCAAAATTGTATAGCCTTAGTTT
1 TCAAGTGAGGTAATTGTAAAAAGAATTAAGGTGGCAGTGAAAGCAAAATTGTATAGCCTTAGTTT
682073 ACATAGAGTAGATGATGG
66 ACATAGAGTAGATGATGG
682091 TCAAGTGAGGTAATTGTAAAAAGAATTAAGGTGGCAGTGAAAGCAAAATTGTATAGCCTTAGTTT
1 TCAAGTGAGGTAATTGTAAAAAGAATTAAGGTGGCAGTGAAAGCAAAATTGTATAGCCTTAGTTT
682156 ACATAGAGTAGATGATGG
66 ACATAGAGTAGATGATGG
682174 T
1 T
682175 AATAGATTCT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.28
Consensus pattern (83 bp):
TCAAGTGAGGTAATTGTAAAAAGAATTAAGGTGGCAGTGAAAGCAAAATTGTATAGCCTTAGTTT
ACATAGAGTAGATGATGG
Found at i:682806 original size:51 final size:50
Alignment explanation
Indices: 682745--682851 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 50
682735 TTTCATTGAT
* *
682745 AAAAAAAGTTATATATCAAATTATGAGTAAATATTATTTTATAATTATTCA
1 AAAAAAAGTTATAAATCAAATTATGAGTAAATATTATTTTATAA-TATGCA
* *
682796 AAAAAAAGTTATAAATTAAATTATGAGTAAATATTATTTTATTATATGCA
1 AAAAAAAGTTATAAATCAAATTATGAGTAAATATTATTTTATAATATGCA
682846 AAAAAA
1 AAAAAA
682852 TCAAATTATG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 11 0.21
51 41 0.79
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (50 bp):
AAAAAAAGTTATAAATCAAATTATGAGTAAATATTATTTTATAATATGCA
Found at i:683597 original size:26 final size:26
Alignment explanation
Indices: 683568--683619 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
683558 AAATTGATAT
683568 ATTTCATATATAATA-ATTTCTTTTAA
1 ATTT-ATATATAATATATTTCTTTTAA
* *
683594 ATTTATTTATAATATATTTTTTTTAA
1 ATTTATATATAATATATTTCTTTTAA
683620 TTTTTGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATATATAATATATTTCTTTTAA
Found at i:683936 original size:27 final size:26
Alignment explanation
Indices: 683884--683938 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
683874 TACCTTTTTA
* *
683884 TATTTTTATTATAGTTTAAGTTAATG
1 TATTTTTATCATAGTTTAAGTAAATG
683910 TATTTTATATCATAGTATTAA-TAAATG
1 TATTTT-TATCATAGT-TTAAGTAAATG
683937 TA
1 TA
683939 AGTATTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 15 0.60
28 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (26 bp):
TATTTTTATCATAGTTTAAGTAAATG
Found at i:684294 original size:13 final size:13
Alignment explanation
Indices: 684276--684302 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
684266 AGCTTTGCCC
684276 ATTTTAATTTAAA
1 ATTTTAATTTAAA
684289 ATTTTAATTTAAA
1 ATTTTAATTTAAA
684302 A
1 A
684303 ATAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTAATTTAAA
Found at i:684338 original size:18 final size:18
Alignment explanation
Indices: 684311--684348 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
684301 AAATAAAAAT
*
684311 AAAAACCATAAAATTAAA
1 AAAAACCATAAAAATAAA
*
684329 AAAAATCATAAAAATAAA
1 AAAAACCATAAAAATAAA
684347 AA
1 AA
684349 GAAGTCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAACCATAAAAATAAA
Found at i:684667 original size:30 final size:31
Alignment explanation
Indices: 684621--684687 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
684611 TTAGAGAATA
*
684621 AAATT-ATATTTGATCTAAAA-TTTAATATT
1 AAATTAATATTTGATCTAAAATTTTAATAAT
*
684650 AAATTAATATTTTATCTAAAATTTTAATAAT
1 AAATTAATATTTGATCTAAAATTTTAATAAT
684681 AAATTAA
1 AAATTAA
684688 AAATTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 5 0.15
30 14 0.41
31 15 0.44
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (31 bp):
AAATTAATATTTGATCTAAAATTTTAATAAT
Found at i:685261 original size:37 final size:36
Alignment explanation
Indices: 685219--685295 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
685209 AACATAACGT
685219 TAAA-TTTTGAACAACAGTATTAAAATGAAACAAAAAC
1 TAAATTTTTGAAC-A-AGTATTAAAATGAAACAAAAAC
* * *
685256 TAAATTTTTTAACAAGTATTAAAATGAAATAAAAAT
1 TAAATTTTTGAACAAGTATTAAAATGAAACAAAAAC
685292 TAAA
1 TAAA
685296 CTTCATGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 24 0.67
37 5 0.14
38 7 0.19
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (36 bp):
TAAATTTTTGAACAAGTATTAAAATGAAACAAAAAC
Found at i:690447 original size:18 final size:19
Alignment explanation
Indices: 690412--690448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
690402 CACGGAATGT
690412 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
690432 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
690449 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:695953 original size:18 final size:18
Alignment explanation
Indices: 695914--695954 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
695904 AGTAACTATG
*
695914 ACAAAAAAATTTGTCACG
1 ACAAAAAAATTTGTCACA
*
695932 ACAAAAAAATTTGTTACA
1 ACAAAAAAATTTGTCACA
695950 ACAAA
1 ACAAA
695955 TAATGAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (18 bp):
ACAAAAAAATTTGTCACA
Found at i:698702 original size:43 final size:44
Alignment explanation
Indices: 698610--698724 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 44
698600 CGATTGTTCA
* * * * * *
698610 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATT
1 ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTAGCATG
* *
698654 A-AAACGCCGCAATAGGTGTTGATATTTAACGGTATTTGGCA-G
1 ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTAGCATG
*
698696 ACAAACGCCGCAATA-GTCGTTGATGTTTA
1 ACAAACGCCGCAATAGGT-GTTGATATTTA
698725 GTGGCGTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 3 0.05
43 56 0.93
44 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTAGCATG
Found at i:699183 original size:21 final size:20
Alignment explanation
Indices: 699158--699204 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
699148 GATATATACT
*
699158 TCTCTGTTCTGCCACTACCTC
1 TCTCTGTGCTGCCACT-CCTC
* *
699179 TCTCTGTGCTGCCGCTGCTC
1 TCTCTGTGCTGCCACTCCTC
699199 TCTCTG
1 TCTCTG
699205 CTTCCACTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.04, C:0.40, G:0.17, T:0.38
Consensus pattern (20 bp):
TCTCTGTGCTGCCACTCCTC
Found at i:699201 original size:18 final size:18
Alignment explanation
Indices: 699178--699240 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
699168 GCCACTACCT
*
699178 CTCTCTGTGCTGCCGCTG
1 CTCTCTGTGCTTCCGCTG
* *
699196 CTCTCTCTGCTTCCACTG
1 CTCTCTGTGCTTCCGCTG
*
699214 CGCTCTAGCTGCTTCCGCTG
1 CTCTCT-G-TGCTTCCGCTG
699234 CTGCTCT
1 CT-CTCT
699241 AACTGCTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 20 0.57
20 11 0.31
21 4 0.11
ACGTcount: A:0.03, C:0.41, G:0.21, T:0.35
Consensus pattern (18 bp):
CTCTCTGTGCTTCCGCTG
Found at i:699218 original size:20 final size:21
Alignment explanation
Indices: 699192--699250 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
699182 CTGTGCTGCC
**
699192 GCTGCTCTCTCTGCTTCCACT
1 GCTGCTCTAACTGCTTCCACT
* *
699213 GC-GCTCTAGCTGCTTCCGCT
1 GCTGCTCTAACTGCTTCCACT
699233 GCTGCTCTAACTGCTTCC
1 GCTGCTCTAACTGCTTCC
699251 GCTATTGCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.07, C:0.41, G:0.19, T:0.34
Consensus pattern (21 bp):
GCTGCTCTAACTGCTTCCACT
Found at i:699241 original size:21 final size:20
Alignment explanation
Indices: 699185--699253 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
699175 CCTCTCTCTG
*
699185 TGCTGCCGCTGCT-CTCT-C
1 TGCTTCCGCTGCTGCTCTAC
*
699203 TGCTTCCACTGC-GCTCTAGC
1 TGCTTCCGCTGCTGCTCTA-C
699223 TGCTTCCGCTGCTGCTCTAAC
1 TGCTTCCGCTGCTGCTCT-AC
699244 TGCTTCCGCT
1 TGCTTCCGCT
699254 ATTGCTCTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 14 0.33
20 12 0.28
21 16 0.37
22 1 0.02
ACGTcount: A:0.06, C:0.41, G:0.20, T:0.33
Consensus pattern (20 bp):
TGCTTCCGCTGCTGCTCTAC
Found at i:699259 original size:21 final size:21
Alignment explanation
Indices: 699193--699261 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
699183 TGTGCTGCCG
** * *
699193 CTGCTCTCTCTGCTTCCACTG
1 CTGCTCTAACTGCTTCCGCTA
* *
699214 C-GCTCTAGCTGCTTCCGCTG
1 CTGCTCTAACTGCTTCCGCTA
699234 CTGCTCTAACTGCTTCCGCTA
1 CTGCTCTAACTGCTTCCGCTA
*
699255 TTGCTCT
1 CTGCTCT
699262 CCCTTGCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.07, C:0.39, G:0.17, T:0.36
Consensus pattern (21 bp):
CTGCTCTAACTGCTTCCGCTA
Found at i:699615 original size:19 final size:19
Alignment explanation
Indices: 699572--699621 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
699562 AATAATTAAT
699572 TAAA-ATAAAAAGTCATGG
1 TAAATATAAAAAGTCATGG
699590 TACAAATATAAATAAGTCA-GG
1 T--AAATATAAA-AAGTCATGG
*
699611 TAAATTTAAAA
1 TAAATATAAAA
699622 CATCTACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 3 0.11
21 8 0.30
22 6 0.22
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (19 bp):
TAAATATAAAAAGTCATGG
Found at i:703099 original size:151 final size:150
Alignment explanation
Indices: 702824--703126 Score: 556
Period size: 151 Copynumber: 2.0 Consensus size: 150
702814 TTCTCTCTCA
702824 TCATTTCATGCTATTACTAATTTTTCTCATCTCATTTGAATTTCTAGTAAAGATGTAAAACCACT
1 TCATTTCATGCTATTACTAA-TTTTCTCATCTCATTTGAATTTCTAGTAAAGATGTAAAACCACT
702889 TGCTCAATTTAATTGGGAGAATTGTACTCGTTTAAGGCATGGCTGCATCGAGAAAACAACAATTA
65 TGCTCAATTTAATTGGGAGAATTGTACTCGTTTAAGGCATGGCTGCATCGAGAAAACAACAATTA
702954 AAACCCTAAACCAAGAAACAAC
130 AAACCCTAAACCAA-AAACAAC
702976 TCATTTCATGCTAATTACTAA-TTTCTCATCTCATTTGAATTTCTAGTAAAGATGTAAAACCACT
1 TCATTTCATGCT-ATTACTAATTTTCTCATCTCATTTGAATTTCTAGTAAAGATGTAAAACCAC-
703040 TTGCTCAATTTAA-TGGGAGAATTGTACTCGTTTAAGGCATGGCTGCATCGAGAAAACAACAATT
64 TTGCTCAATTTAATTGGGAGAATTGTACTCGTTTAAGGCATGGCTGCATCGAGAAAACAACAATT
703104 AAAACCCTAAACCAAAAACAAC
129 AAAACCCTAAACCAAAAACAAC
703126 T
1 T
703127 AAATGATAGT
Statistics
Matches: 149, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
150 8 0.05
151 108 0.72
152 25 0.17
153 8 0.05
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (150 bp):
TCATTTCATGCTATTACTAATTTTCTCATCTCATTTGAATTTCTAGTAAAGATGTAAAACCACTT
GCTCAATTTAATTGGGAGAATTGTACTCGTTTAAGGCATGGCTGCATCGAGAAAACAACAATTAA
AACCCTAAACCAAAAACAAC
Done.