Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009078.1 Hibiscus syriacus cultivar Beakdansim tig00112517_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: 829977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:484505 original size:30 final size:30
Alignment explanation
Indices: 484433--484513 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
484423 TTTCATTAAA
*
484433 CGACGCACGTCAGCACAACCCTTTGAAGGT
1 CGACGCACGTTAGCACAACCCTTTGAAGGT
*
484463 CGATGCACGTTAGCACAACCCTTTGAAGGT
1 CGACGCACGTTAGCACAACCCTTTGAAGGT
* *
484493 C-AGCGCATGTTAGCAAAACCC
1 CGA-CGCACGTTAGCACAACCC
484514 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 44 0.98
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (30 bp):
CGACGCACGTTAGCACAACCCTTTGAAGGT
Found at i:488344 original size:61 final size:62
Alignment explanation
Indices: 488244--488386 Score: 261
Period size: 61 Copynumber: 2.3 Consensus size: 62
488234 TTGTAGTCGC
*
488244 TAGTTGCCTCCCCTGGGTACATAAGTTTCGTTCATTTTTTTTATTTCGTG-TTTTTATATTG
1 TAGTAGCCTCCCCTGGGTACATAAGTTTCGTTCATTTTTTTTATTTCGTGTTTTTTATATTG
*
488305 TAGTAGCCTCCCCTGGTTACATAAGTTTCGTTCATTTTTTTTATTTCGTGTTTTTTATATTG
1 TAGTAGCCTCCCCTGGGTACATAAGTTTCGTTCATTTTTTTTATTTCGTGTTTTTTATATTG
488367 TAGTAGCCTCCCCTGGGTAC
1 TAGTAGCCTCCCCTGGGTAC
488387 CAAAAACACC
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
61 48 0.62
62 30 0.38
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (62 bp):
TAGTAGCCTCCCCTGGGTACATAAGTTTCGTTCATTTTTTTTATTTCGTGTTTTTTATATTG
Found at i:489330 original size:19 final size:19
Alignment explanation
Indices: 489306--489345 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
489296 TGATTGTTTG
489306 ATCTAACTATGTTTCGACA
1 ATCTAACTATGTTTCGACA
489325 ATCTAACTATGTTTCGACA
1 ATCTAACTATGTTTCGACA
489344 AT
1 AT
489346 AGGGATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCTAACTATGTTTCGACA
Found at i:509611 original size:30 final size:30
Alignment explanation
Indices: 509541--509611 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
509531 CAATATTATA
* **
509541 ATAATAAAATAAGGTTAAAATAAAATTAAT
1 ATAATAAAATAAGGTTAAAACAAAACGAAT
**
509571 GCAATAAAATAAGGTTAAAACAAAACGAAT
1 ATAATAAAATAAGGTTAAAACAAAACGAAT
*
509601 ATAATTAAATA
1 ATAATAAAATA
509612 GTAAAATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (30 bp):
ATAATAAAATAAGGTTAAAACAAAACGAAT
Found at i:512753 original size:20 final size:20
Alignment explanation
Indices: 512730--512792 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
512720 TAACGCAAAC
* *
512730 TCCAATTTCGCAACTTAGTT
1 TCCAAATTCGCAACTTAATT
512750 TCCAAATTCGCAACACTTAATT
1 TCCAAATTCGC-A-ACTTAATT
*
512772 T-CAAATTCGCAACTTGATT
1 TCCAAATTCGCAACTTAATT
512791 TC
1 TC
512793 TGAATTCACA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.22
20 11 0.30
21 10 0.27
22 8 0.22
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (20 bp):
TCCAAATTCGCAACTTAATT
Found at i:512799 original size:41 final size:40
Alignment explanation
Indices: 512736--512864 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 40
512726 AAACTCCAAT
** * *
512736 TTCGCAACTT-AGTTTCCAAATTCGCAACACTTAATTTCAAA
1 TTCGCAACTTGA-TTTCTGAATTCACAACAC-GAATTTCAAA
* ****
512777 TTCGCAACTTGATTTCTGAATTCACAACGCGAATTTTGTT
1 TTCGCAACTTGATTTCTGAATTCACAACACGAATTTCAAA
* * * *
512817 TTCGCAACTCGATTTCTGAATTCACTACACGAATTTTAAT
1 TTCGCAACTTGATTTCTGAATTCACAACACGAATTTCAAA
512857 TTCGCAAC
1 TTCGCAAC
512865 ATATTTTAGT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 48 0.66
41 24 0.33
42 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (40 bp):
TTCGCAACTTGATTTCTGAATTCACAACACGAATTTCAAA
Found at i:512804 original size:20 final size:20
Alignment explanation
Indices: 512775--512841 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
512765 CTTAATTTCA
* *
512775 AATTCGCAACTTGATTTCTG
1 AATTCACAACTCGATTTCTG
*
512795 AATTCACAACGCGAATTT-TG
1 AATTCACAACTCG-ATTTCTG
** *
512815 TTTTCGCAACTCGATTTCTG
1 AATTCACAACTCGATTTCTG
512835 AATTCAC
1 AATTCAC
512842 TACACGAATT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (20 bp):
AATTCACAACTCGATTTCTG
Found at i:512823 original size:40 final size:40
Alignment explanation
Indices: 512754--512864 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 40
512744 TTAGTTTCCA
* * * * *
512754 AATTCGCAACACTTAATTTCAAATTCGCAACTTGATTTCTG
1 AATTCACAACAC-GAATTTTAATTTCGCAACTCGATTTCTG
* **
512795 AATTCACAACGCGAATTTTGTTTTCGCAACTCGATTTCTG
1 AATTCACAACACGAATTTTAATTTCGCAACTCGATTTCTG
*
512835 AATTCACTACACGAATTTTAATTTCGCAAC
1 AATTCACAACACGAATTTTAATTTCGCAAC
512865 ATATTTTAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 48 0.83
41 10 0.17
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (40 bp):
AATTCACAACACGAATTTTAATTTCGCAACTCGATTTCTG
Found at i:512872 original size:18 final size:18
Alignment explanation
Indices: 512849--512883 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
512839 CACTACACGA
512849 ATTTTAATTTCGCAACAT
1 ATTTTAATTTCGCAACAT
*
512867 ATTTTAGTTTCGCAACA
1 ATTTTAATTTCGCAACA
512884 CAAATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (18 bp):
ATTTTAATTTCGCAACAT
Found at i:513040 original size:14 final size:15
Alignment explanation
Indices: 513021--513058 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
513011 TCCTCATCCC
513021 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
513035 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
513051 TAATTTTT
1 TAATTTTT
513059 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:513675 original size:12 final size:12
Alignment explanation
Indices: 513654--513687 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
513644 ACCACATTTC
*
513654 CAATACCAAACA
1 CAATATCAAACA
513666 CAATATCAAACA
1 CAATATCAAACA
*
513678 CAATCTCAAA
1 CAATATCAAA
513688 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:513840 original size:24 final size:24
Alignment explanation
Indices: 513813--513866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
513803 GTATTCGAAA
513813 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
513837 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
513861 TTTGAT
1 TTTGAT
513867 GATGTTTCAG
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:516421 original size:18 final size:18
Alignment explanation
Indices: 516398--516433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
516388 AAGCAAAAGG
* *
516398 AAATCAGAATCGCAATCA
1 AAATCAAAATCCCAATCA
516416 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
516434 TAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:516903 original size:64 final size:64
Alignment explanation
Indices: 516821--516988 Score: 282
Period size: 64 Copynumber: 2.6 Consensus size: 64
516811 AATTTAAAAC
516821 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
* *** * *
516885 AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
516949 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
516989 GTGTACCCTA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 97 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:518635 original size:21 final size:21
Alignment explanation
Indices: 518611--518662 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
518601 TGCAACAATC
* * *
518611 TCACTTAGAGTGGCTACCTCA
1 TCACTTAAAGTAGATACCTCA
*
518632 TCACGTAAAGTAGATACCTCA
1 TCACTTAAAGTAGATACCTCA
*
518653 CCACTTAAAG
1 TCACTTAAAG
518663 AACCATTGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
TCACTTAAAGTAGATACCTCA
Found at i:520112 original size:21 final size:21
Alignment explanation
Indices: 520088--520127 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
520078 AGAATGGGGA
*
520088 GAATCGGTACCCCTTCATAGG
1 GAATCGATACCCCTTCATAGG
*
520109 GAATCGATACCCTTTCATA
1 GAATCGATACCCCTTCATA
520128 ATATTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGG
Found at i:520257 original size:19 final size:19
Alignment explanation
Indices: 520233--520287 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
520223 AGCCTCGGAG
*
520233 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
* *
520252 TACTGTTTAAATAGTAATT
1 TACTGTTCAAACAGTAATT
*
520271 TACTGTTCAAATAGTAA
1 TACTGTTCAAACAGTAA
520288 ATTATTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:520298 original size:19 final size:19
Alignment explanation
Indices: 520260--520298 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
520250 TTTACTGTTT
* *
520260 AAATAGTAATTTACTGTTC
1 AAATAGTAAATTACTATTC
*
520279 AAATAGTAAATTATTATTC
1 AAATAGTAAATTACTATTC
520298 A
1 A
520299 TAAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATAGTAAATTACTATTC
Found at i:520397 original size:29 final size:31
Alignment explanation
Indices: 520363--520422 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
520353 AAATTTTGAA
*
520363 TAAATTCAACT-AAGTCCAAATA-CATTTTG
1 TAAATTCAACTCAAGTCCAAAAACCATTTTG
*
520392 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAACTCAAGTCCAAAAACCATTTTG
520423 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAACTCAAGTCCAAAAACCATTTTG
Found at i:521451 original size:20 final size:20
Alignment explanation
Indices: 521428--521484 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
521418 TCTGAAACTT
*
521428 AAAATCGCAACGGGAAAATG
1 AAAATCGCAACGCGAAAATG
*
521448 AAAATCGCAACGCAAAAATG
1 AAAATCGCAACGCGAAAATG
521468 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
521485 CTACAATTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:521552 original size:20 final size:20
Alignment explanation
Indices: 521493--521541 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
521483 AACTACAATT
521493 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
521513 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
*
521533 GTGTTGCGA
1 GCGTTGCGA
521542 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.47
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTC
Found at i:521910 original size:22 final size:22
Alignment explanation
Indices: 521880--521942 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
521870 AGATGGAGAT
*
521880 AGACAGATTTCGTCGGAGATCG
1 AGACGGATTTCGTCGGAGATCG
*
521902 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGTCGGAGATCG
* * *
521924 GGACGTATGTCGTCGGAGA
1 AGACGGATTTCGTCGGAGA
521943 GAGTGAGAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (22 bp):
AGACGGATTTCGTCGGAGATCG
Found at i:522129 original size:20 final size:20
Alignment explanation
Indices: 522105--522194 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
522095 TGACTTCTGT
*
522105 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAGATTCGC
* *
522125 ATTGC-AATTTACAGATTCGT
1 GTTGCGAA-TTACAGATTCGC
*
522145 G-TGTCGATTTACAGATTCGC
1 GTTG-CGAATTACAGATTCGC
* *
522165 GTTGCGATTTACAGATTCAC
1 GTTGCGAATTACAGATTCGC
522185 GTTGCGAATT
1 GTTGCGAATT
522195 TAGAAACTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.07
20 51 0.88
21 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:531380 original size:35 final size:36
Alignment explanation
Indices: 531323--531424 Score: 179
Period size: 35 Copynumber: 2.9 Consensus size: 36
531313 ACGGTGATGG
*
531323 ACATTGATACACAAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
531359 ACATTGATAC-CGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
531394 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
531425 ATACTCAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 33 0.52
36 30 0.48
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:546359 original size:22 final size:22
Alignment explanation
Indices: 546327--546398 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
546317 AGTCACTCGA
546327 GACATATCCAGTGGTCCTTCAG
1 GACATATCCAGTGGTCCTTCAG
* * **
546349 GACGTATCCAGTGGTCATTTGG
1 GACATATCCAGTGGTCCTTCAG
*
546371 GACATATCTAGTGGTCCTT-AGG
1 GACATATCCAGTGGTCCTTCA-G
546393 GACATA
1 GACATA
546399 GTGGTCCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (22 bp):
GACATATCCAGTGGTCCTTCAG
Found at i:546402 original size:18 final size:18
Alignment explanation
Indices: 546379--546414 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
546369 GGGACATATC
546379 TAGTGGTCCTTAGGGACA
1 TAGTGGTCCTTAGGGACA
*
546397 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTAGGGACA
546415 AATACTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (18 bp):
TAGTGGTCCTTAGGGACA
Found at i:547280 original size:17 final size:18
Alignment explanation
Indices: 547247--547280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
547237 TGACATTTTG
*
547247 GTATCGGTACTCTAGGGA
1 GTATCGATACTCTAGGGA
547265 GTATCGATAC-CTAGGG
1 GTATCGATACTCTAGGG
547281 TCTCAGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (18 bp):
GTATCGATACTCTAGGGA
Found at i:547388 original size:20 final size:20
Alignment explanation
Indices: 547365--547409 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
547355 CTTGGGTAGG
*
547365 GTATCAACACTATAAGTCCA
1 GTATCAACAATATAAGTCCA
* * *
547385 GTATCGATAATGTAAGTCCA
1 GTATCAACAATATAAGTCCA
547405 GTATC
1 GTATC
547410 GATACAAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCAACAATATAAGTCCA
Found at i:556961 original size:20 final size:20
Alignment explanation
Indices: 556945--556987 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
556935 TATTATTTTC
556945 TATTAATTAATAATATTATA
1 TATTAATTAATAATATTATA
* *
556965 TATTATTTAAT-TTATTAT-
1 TATTAATTAATAATATTATA
556983 TATTA
1 TATTA
556988 TTACCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTAATTAATAATATTATA
Found at i:556985 original size:15 final size:17
Alignment explanation
Indices: 556955--556986 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
556945 TATTAATTAA
556955 TAATATTATATATTATT
1 TAATATTATATATTATT
556972 TAAT-TTAT-TATTATT
1 TAATATTATATATTATT
556987 ATTACCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATATTATATATTATT
Found at i:557214 original size:60 final size:60
Alignment explanation
Indices: 557086--557214 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 60
557076 CACGTGGTCT
* * *
557086 CTCGACTATAGGGTAATACTTTGTTGAGTCCCTTAACTATCAAAAGTTACAAAATGGTCC
1 CTCGACTATAGGATAATACTTTGTTGAGTCCCTTAACTATCAAAAGTTACAAAATGATCA
* * * * *
557146 CCCAACTATAGGATATTGCTTTGTTGAGTTTCCC-T-ACTATTAAAAGTTACAAAATGATCA
1 CTCGACTATAGGATAATACTTTGTTGAG--TCCCTTAACTATCAAAAGTTACAAAATGATCA
557206 CTCGACTAT
1 CTCGACTAT
557215 TCATTATATT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
60 52 0.91
61 1 0.02
62 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (60 bp):
CTCGACTATAGGATAATACTTTGTTGAGTCCCTTAACTATCAAAAGTTACAAAATGATCA
Found at i:563033 original size:36 final size:36
Alignment explanation
Indices: 562950--563036 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
562940 TCATTGACCG
* *
562950 CCTCATTCACATTAGGTGATGCAGAACCATCAACCA
1 CCTCATTCACAGTAGGTGATGCAGAACCAGCAACCA
* * ** *
562986 CCTTATTCACAGTAGGTGATGTAGAATTAGCAACTA
1 CCTCATTCACAGTAGGTGATGCAGAACCAGCAACCA
*
563022 CCTCATGCACAGTAG
1 CCTCATTCACAGTAG
563037 TTGTATTTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (36 bp):
CCTCATTCACAGTAGGTGATGCAGAACCAGCAACCA
Found at i:572127 original size:23 final size:21
Alignment explanation
Indices: 572100--572141 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
572090 ATATAATAAA
572100 TAATATTATTTATTATAAAAACT
1 TAATATTA-TTATT-TAAAAACT
572123 TAATATTATTATTTAAAAA
1 TAATATTATTATTTAAAAA
572142 ATATTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATTATTATTTAAAAACT
Found at i:572310 original size:21 final size:21
Alignment explanation
Indices: 572285--572369 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
572275 TCTATACAAA
572285 TAAAAATATTATATTATATTT
1 TAAAAATATTATATTATATTT
* *
572306 TAAAATTATTAATAAATATATTT
1 TAAAAATATT-AT-ATTATATTT
* *
572329 TAAGAA-ATTATATAATATTAT
1 TAAAAATATTATATTATATT-T
* *
572350 T-AGACTATTATATTAATATT
1 TAAAAATATTATATT-ATATT
572370 AAATACATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.18
21 20 0.39
22 10 0.20
23 12 0.24
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAAAATATTATATTATATTT
Found at i:572329 original size:23 final size:26
Alignment explanation
Indices: 572299--572345 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
572289 AATATTATAT
572299 TATATTTT-A-AAATTAT-TAATAAA
1 TATATTTTAAGAAATTATATAATAAA
572322 TATATTTTAAGAAATTATATAATA
1 TATATTTTAAGAAATTATATAATA
572346 TTATTAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 7 0.33
26 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TATATTTTAAGAAATTATATAATAAA
Found at i:572345 original size:22 final size:21
Alignment explanation
Indices: 572285--572346 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
572275 TCTATACAAA
* *
572285 TAAAAATATTATATTATATTT
1 TAAAATTATTATAATATATTT
572306 TAAAATTATTAATAAATATATTT
1 TAAAATTATT-AT-AATATATTT
572329 TAAGAAATTA-TATAATAT
1 T-A-AAATTATTATAATAT
572347 TATTAGACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 9 0.26
22 7 0.20
23 11 0.31
24 2 0.06
25 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAATTATTATAATATATTT
Found at i:572550 original size:25 final size:25
Alignment explanation
Indices: 572498--572565 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
572488 AGTATCATAA
*
572498 TTTATTATAAT-ATAAT-TGATTAT
1 TTTATTATAATAATAATATTATTAT
* *
572521 ATTATTGTAATAATAATATTATTAT
1 TTTATTATAATAATAATATTATTAT
* * *
572546 TTTATTTTATTAAAAATATT
1 TTTATTATAATAATAATATT
572566 GATATATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 9 0.25
24 5 0.14
25 22 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTATTATAATAATAATATTATTAT
Found at i:574166 original size:31 final size:27
Alignment explanation
Indices: 574103--574168 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
574093 TTTCTTTTAG
*
574103 ATTTATTTATTTATTTCAAAATTACTT
1 ATTTATTTATTTATTTCAAAATTACTC
* *
574130 GTTTATTTATTTATTTTAAATTTATGTACTC
1 ATTTATTTATTTATTTCAAA---AT-TACTC
574161 ATTTATTT
1 ATTTATTT
574169 TGGTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 18 0.58
30 2 0.06
31 11 0.35
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (27 bp):
ATTTATTTATTTATTTCAAAATTACTC
Found at i:574197 original size:22 final size:22
Alignment explanation
Indices: 574131--574222 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
574121 AAATTACTTG
*
574131 TTTATTTATTTATTTTAAATTTA
1 TTTATTTAGTTA-TTTAAATTTA
* * * * ***
574154 TGTACTCATTTATTTTGGTTTA
1 TTTATTTAGTTATTTAAATTTA
574176 TTTATTTAGTTATTTAAATTTA
1 TTTATTTAGTTATTTAAATTTA
* *
574198 TTT-GTTAGTTATTTCGAATTTA
1 TTTATTTAGTTATTT-AAATTTA
574220 TTT
1 TTT
574223 GTTTGTTTGT
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
21 10 0.19
22 34 0.64
23 9 0.17
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (22 bp):
TTTATTTAGTTATTTAAATTTA
Found at i:574200 original size:4 final size:4
Alignment explanation
Indices: 574065--574191 Score: 51
Period size: 4 Copynumber: 31.0 Consensus size: 4
574055 GATGGTAATT
* * * * **
574065 TTTA TTTA TTTA TTTA TTTG TTTG TTTG TTTC TTT- TAGA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * ** * * *
574112 TTTA TTTCAAA ATTA CTTG TTTA TTTA TTTA TTT- TAAA TTTA TGTA CTCA
1 TTTA TTT---A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
574162 TTTA TTTTGG TTTA TTTA TTTA GTTA TTTA
1 TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA
574192 AATTTATTTG
Statistics
Matches: 91, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
3 2 0.02
4 80 0.88
5 6 0.07
7 3 0.03
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:574223 original size:22 final size:21
Alignment explanation
Indices: 574172--574225 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
574162 TTTATTTTGG
*
574172 TTTATTTATTTAGTTATTTAAA
1 TTTATTT-GTTAGTTATTTAAA
*
574194 TTTATTTGTTAGTTATTTCGAA
1 TTTATTTGTTAGTTATTT-AAA
574216 TTTATTTGTT
1 TTTATTTGTT
574226 TGTTTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.65
Consensus pattern (21 bp):
TTTATTTGTTAGTTATTTAAA
Found at i:574645 original size:14 final size:14
Alignment explanation
Indices: 574626--574710 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 14
574616 TAAATATATG
574626 TTTATTTATTGTAA
1 TTTATTTATTGTAA
*
574640 TTTATTTATTTATAATA
1 TTTATTTA-TTGT-A-A
* *
574657 TTTAATTT-TTTTAG
1 TTT-ATTTATTGTAA
*
574671 TTTTTGTTATTGTAA
1 TTTAT-TTATTGTAA
*
574686 TTT-TTTATGGTAA
1 TTTATTTATTGTAA
*
574699 TTT-TTTAATGTA
1 TTTATTTATTGTA
574711 TTCGTACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
13 19 0.34
14 14 0.25
15 11 0.20
16 4 0.07
17 4 0.07
18 4 0.07
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (14 bp):
TTTATTTATTGTAA
Found at i:574689 original size:23 final size:22
Alignment explanation
Indices: 574626--574693 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
574616 TAAATATATG
574626 TTTAT-TTATTGTAATTTATTTA
1 TTTATATTATTGTAATTT-TTTA
*
574648 TTTATAATATT-TAATTTTTTTA
1 TTTATATTATTGTAA-TTTTTTA
* *
574670 GTTTTTGTTATTGTAATTTTTTA
1 -TTTATATTATTGTAATTTTTTA
574693 T
1 T
574694 GGTAATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 13 0.34
23 22 0.58
24 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTATATTATTGTAATTTTTTA
Found at i:576100 original size:17 final size:17
Alignment explanation
Indices: 576050--576100 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
576040 TTTCTTTTAA
576050 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
***
576067 AATCAACTTTAAATTATT
1 AAT-TTGTTTAAATTATT
*
576085 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
576101 CCTTGAACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTGTTTAAATTATT
Found at i:576782 original size:18 final size:18
Alignment explanation
Indices: 576725--576792 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
576715 AATGTTGCTT
576725 CCACGTCAGAAATCTCTG
1 CCACGTCAGAAATCTCTG
* *
576743 CCATGTCA-AGAATATCTG
1 CCACGTCAGA-AATCTCTG
* *
576761 CCACGCCAGAAATCTCTA
1 CCACGTCAGAAATCTCTG
*
576779 CCACGTCAGGAATC
1 CCACGTCAGAAATC
576793 CCTCAGTAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 1 0.03
18 38 0.95
19 1 0.03
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.21
Consensus pattern (18 bp):
CCACGTCAGAAATCTCTG
Found at i:577586 original size:14 final size:15
Alignment explanation
Indices: 577562--577590 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
577552 AAGGGGGAAG
577562 TTATCTTCTTCTTCT
1 TTATCTTCTTCTTCT
577577 TTAT-TTCTTCTTCT
1 TTATCTTCTTCTTCT
577591 CCATCGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATCTTCTTCTTCT
Found at i:579422 original size:24 final size:24
Alignment explanation
Indices: 579344--579432 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
579334 AAATCTTATA
*
579344 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
579367 TGGCACTTCGGTGTAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* **
579390 CGGTTCTTCGG-GACAATTTCTACG
1 TGGCACTTCGGTG-CAATTTCTACG
579414 TGGCACTTCGGTGCAATTT
1 TGGCACTTCGGTGCAATTT
579433 ATTTGAGCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.02
23 29 0.55
24 22 0.42
25 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.34
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:580169 original size:21 final size:22
Alignment explanation
Indices: 580140--580181 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
580130 TAATAGTACC
*
580140 GTAGCA-GGGTATCGGTTCCCT
1 GTAGCAGGGGAATCGGTTCCCT
*
580161 GTAGTAGGGGAATCGGTTCCC
1 GTAGCAGGGGAATCGGTTCCC
580182 CTCTTTGAAT
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:0.17, C:0.21, G:0.36, T:0.26
Consensus pattern (22 bp):
GTAGCAGGGGAATCGGTTCCCT
Found at i:582101 original size:32 final size:32
Alignment explanation
Indices: 582052--582114 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
582042 CCAGGTGAAC
*
582052 AATGAGCATCGAACTTAACGAATAACAAGTCT
1 AATGAGCAACGAACTTAACGAATAACAAGTCT
* * *
582084 AATGAGCAACGAGCTTAACGAGTAACGAGTC
1 AATGAGCAACGAACTTAACGAATAACAAGTC
582115 GAGCAACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (32 bp):
AATGAGCAACGAACTTAACGAATAACAAGTCT
Found at i:588085 original size:21 final size:21
Alignment explanation
Indices: 588060--588100 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
588050 TAATGAATAG
*
588060 TGCTACAGTGCATCGATGCAT
1 TGCTACAGCGCATCGATGCAT
*
588081 TGCTACAGCGTATCGATGCA
1 TGCTACAGCGCATCGATGCA
588101 CCAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTACAGCGCATCGATGCAT
Found at i:588146 original size:21 final size:21
Alignment explanation
Indices: 588122--588165 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
588112 AAGCAGAATT
*
588122 GTGCATCGATGCATTGCTACA
1 GTGCATCGATGCACTGCTACA
*
588143 GTGCATCGATGCACTGGTACA
1 GTGCATCGATGCACTGCTACA
588164 GT
1 GT
588166 AACTTTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:592728 original size:21 final size:21
Alignment explanation
Indices: 592702--592745 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
592692 AAGCAGAATT
*
592702 GTGCATCGATGCATTGCTACA
1 GTGCATCGATGCACTGCTACA
*
592723 GTGCATCGATGTACTGCTACA
1 GTGCATCGATGCACTGCTACA
592744 GT
1 GT
592746 AACTTTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:601884 original size:20 final size:20
Alignment explanation
Indices: 601859--601897 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
601849 TTCCCATTGA
*
601859 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
601879 AGTGCATCGATGCATTCTT
1 AGTGCATCGATGCATTCTT
601898 TAACAGGTGT
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:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:602421 original size:10 final size:10
Alignment explanation
Indices: 602406--602460 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
602396 TTTGGTGTTT
602406 TAAGCTTATA
1 TAAGCTTATA
* *
602416 TAAGCTTTCTT
1 TAAGC-TTATA
602427 TAAGCTTATA
1 TAAGCTTATA
* *
602437 TAAGCTTTCTT
1 TAAGC-TTATA
602448 TAAGCTTATA
1 TAAGCTTATA
602458 TAA
1 TAA
602461 TACTCAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:602430 original size:21 final size:21
Alignment explanation
Indices: 602404--602460 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
602394 CTTTTGGTGT
602404 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
602425 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
602446 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
602461 TACTCAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:602432 original size:11 final size:11
Alignment explanation
Indices: 602416--602454 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
602406 TAAGCTTATA
602416 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
602427 TAAGC-TTATA
1 TAAGCTTTCTT
602437 TAAGCTTTCTT
1 TAAGCTTTCTT
602448 TAAGCTT
1 TAAGCTT
602455 ATATAATACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:603020 original size:21 final size:21
Alignment explanation
Indices: 602996--603046 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
602986 ATTATTTTTG
602996 TATGATGTTATTTGTTTTTCT
1 TATGATGTTATTTGTTTTTCT
603017 TATGATGTTATTTGTTTTTCT
1 TATGATGTTATTTGTTTTTCT
603038 TATGATGTT
1 TATGATGTT
603047 TAATAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.65
Consensus pattern (21 bp):
TATGATGTTATTTGTTTTTCT
Found at i:606058 original size:20 final size:20
Alignment explanation
Indices: 606033--606075 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
606023 TTTGATCATG
*
606033 ATATTTCAATATG-CATGTAT
1 ATATTTC-ATATGACATATAT
606053 ATATTTCATATGACATATAT
1 ATATTTCATATGACATATAT
606073 ATA
1 ATA
606076 ACCAAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCATATGACATATAT
Found at i:606917 original size:19 final size:20
Alignment explanation
Indices: 606880--606918 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
606870 TTTTTCATTT
606880 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
606900 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
606919 TGAACATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:612856 original size:20 final size:20
Alignment explanation
Indices: 612816--612856 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
612806 TTTGATCATG
*
612816 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
612836 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
612856 A
1 A
612857 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:613740 original size:21 final size:21
Alignment explanation
Indices: 613716--613755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
613706 TTTTCATTTA
613716 AGGGGGAATAGATACCCCCCC
1 AGGGGGAATAGATACCCCCCC
* *
613737 AGGGGGAATCGCTACCCCC
1 AGGGGGAATAGATACCCCC
613756 TGAACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.30, T:0.10
Consensus pattern (21 bp):
AGGGGGAATAGATACCCCCCC
Found at i:616099 original size:9 final size:9
Alignment explanation
Indices: 616085--616131 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
616075 CAAGTTCATG
616085 AAAATGAAA
1 AAAATGAAA
616094 AAAATGAAA
1 AAAATGAAA
*
616103 AATGATGAAA
1 AA-AATGAAA
*
616113 AATGATGAAA
1 AA-AATGAAA
616123 AAAATGAAA
1 AAAATGAAA
616132 TTACGAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 17 0.49
10 18 0.51
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (9 bp):
AAAATGAAA
Found at i:616120 original size:20 final size:19
Alignment explanation
Indices: 616085--616131 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
616075 CAAGTTCATG
*
616085 AAAATGAAAAA-AATGAAA
1 AAAATGAAAAATGATGAAA
*
616103 AATGATGAAAAATGATGAAA
1 AA-AATGAAAAATGATGAAA
616123 AAAATGAAA
1 AAAATGAAA
616132 TTACGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATGAAAAATGATGAAA
Found at i:619696 original size:21 final size:20
Alignment explanation
Indices: 619658--619696 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
619648 AATGGAATGA
*
619658 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
619678 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
619697 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:621736 original size:2 final size:2
Alignment explanation
Indices: 621729--621767 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
621719 TCAATCACAA
621729 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
621768 TACATTGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:622685 original size:2 final size:2
Alignment explanation
Indices: 622678--622709 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
622668 TGTGATTTGG
622678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
622710 AAACATCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:623085 original size:15 final size:15
Alignment explanation
Indices: 623065--623100 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
623055 AAATTAATCG
623065 ATTAATAAATTAAAT
1 ATTAATAAATTAAAT
623080 ATTAAT-AATTAAAT
1 ATTAATAAATTAAAT
623094 -TTAATAA
1 ATTAATAA
623101 CATTGCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAATAAATTAAAT
Found at i:629192 original size:21 final size:21
Alignment explanation
Indices: 629137--629194 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
629127 AGACTCTATC
* * *
629137 AATCCTACCACCACTACTGAA
1 AATCCTACAACCATTGCTGAA
*
629158 AATCCTACATCCATTGCTGAA
1 AATCCTACAACCATTGCTGAA
*
629179 AGTCCTACAACCATTG
1 AATCCTACAACCATTG
629195 TTATTCTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.33, G:0.09, T:0.24
Consensus pattern (21 bp):
AATCCTACAACCATTGCTGAA
Found at i:630622 original size:25 final size:25
Alignment explanation
Indices: 630592--630651 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
630582 AGCTCGATTG
630592 GAGCTCGATTTTGAGCTCAAGACTC
1 GAGCTCGATTTTGAGCTCAAGACTC
*
630617 GAGCTCGATTTTGAGCTCGAGACTC
1 GAGCTCGATTTTGAGCTCAAGACTC
*
630642 AAGCTCGATT
1 GAGCTCGATT
630652 GAAGCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (25 bp):
GAGCTCGATTTTGAGCTCAAGACTC
Found at i:630669 original size:23 final size:23
Alignment explanation
Indices: 630643--630702 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
630633 TCGAGACTCA
* *
630643 AGCTCGATTGAAGCTTGATTTTG
1 AGCTCGATTGAAACTCGATTTTG
630666 AGCTCGATTGAAACTCGATTTTG
1 AGCTCGATTGAAACTCGATTTTG
* *
630689 AGCTCAATTCAAAC
1 AGCTCGATTGAAAC
630703 GAAAACATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (23 bp):
AGCTCGATTGAAACTCGATTTTG
Found at i:632239 original size:21 final size:21
Alignment explanation
Indices: 632214--632328 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
632204 ATATAATTGG
*
632214 ATTTAGGGCTTAGGGTTTAGA
1 ATTTAGGGTTTAGGGTTTAGA
* *
632235 ATTTAAGGTTTAAGGTTTA-A
1 ATTTAGGGTTTAGGGTTTAGA
* * * *
632255 GGTTTTGAGTTTAGGGTTTATA
1 -ATTTAGGGTTTAGGGTTTAGA
* * *
632277 ATTTACGGTCTAGGGTTTAGG
1 ATTTAGGGTTTAGGGTTTAGA
* * *
632298 ATTTAGGATTTAGGATTTAGG
1 ATTTAGGGTTTAGGGTTTAGA
*
632319 ATTTAAGGTT
1 ATTTAGGGTT
632329 AATTACAAAT
Statistics
Matches: 71, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.01
21 69 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.29, T:0.43
Consensus pattern (21 bp):
ATTTAGGGTTTAGGGTTTAGA
Found at i:632273 original size:7 final size:7
Alignment explanation
Indices: 632215--632328 Score: 66
Period size: 7 Copynumber: 16.3 Consensus size: 7
632205 TATAATTGGA
632215 TTTAGGG
1 TTTAGGG
*
632222 CTTAGGG
1 TTTAGGG
**
632229 TTTAGAA
1 TTTAGGG
*
632236 TTTAAGG
1 TTTAGGG
*
632243 TTTAAGG
1 TTTAGGG
*
632250 TTTAAGG
1 TTTAGGG
* *
632257 TTTTGAG
1 TTTAGGG
632264 TTTAGGG
1 TTTAGGG
***
632271 TTTATAA
1 TTTAGGG
*
632278 TTTACGG
1 TTTAGGG
*
632285 TCTAGGG
1 TTTAGGG
*
632292 TTTAGGA
1 TTTAGGG
*
632299 TTTAGGA
1 TTTAGGG
*
632306 TTTAGGA
1 TTTAGGG
*
632313 TTTAGGA
1 TTTAGGG
*
632320 TTTAAGG
1 TTTAGGG
632327 TT
1 TT
632329 AATTACAAAT
Statistics
Matches: 83, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 83 1.00
ACGTcount: A:0.25, C:0.03, G:0.29, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:632555 original size:21 final size:21
Alignment explanation
Indices: 632510--632556 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
632500 ACCATTTTCA
632510 ATTTTTCTATTGTTTTATTGT
1 ATTTTTCTATTGTTTTATTGT
*
632531 -TTTTTCTTATT-TTTTATTTT
1 ATTTTTC-TATTGTTTTATTGT
632551 ATTTTT
1 ATTTTT
632557 ATACGTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (21 bp):
ATTTTTCTATTGTTTTATTGT
Found at i:639022 original size:29 final size:30
Alignment explanation
Indices: 638978--639060 Score: 143
Period size: 29 Copynumber: 2.8 Consensus size: 30
638968 TCTCACCTAA
638978 CTAAGTTGATGTAAGCAATGACATCTTTAT
1 CTAAGTTGATGTAAGCAATGACATCTTTAT
639008 C-AAGTTGATGTAAGCAATGACATCTTTAT
1 CTAAGTTGATGTAAGCAATGACATCTTTAT
*
639037 CTAA-TTGATGTAAGCGATGACATC
1 CTAAGTTGATGTAAGCAATGACATC
639061 AATTTAGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
29 48 0.94
30 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (30 bp):
CTAAGTTGATGTAAGCAATGACATCTTTAT
Found at i:642027 original size:13 final size:13
Alignment explanation
Indices: 642006--642077 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
641996 ATTGAAATTA
*
642006 ATAACAAATAAAT
1 ATAATAAATAAAT
642019 ATAATAAATAAAT
1 ATAATAAATAAAT
642032 ATAAT-AAT--AT
1 ATAATAAATAAAT
*
642042 -TAATTAAT-AAT
1 ATAATAAATAAAT
* *
642053 ATCAATTATTAAAT
1 AT-AATAAATAAAT
642067 ATAATAAATAA
1 ATAATAAATAA
642078 TTTAAATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
11 2 0.04
12 4 0.08
13 30 0.60
14 5 0.10
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:642108 original size:27 final size:27
Alignment explanation
Indices: 642069--642126 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
642059 TATTAAATAT
*
642069 AATAAATAATTTA-AATATAGTAATTAA
1 AATAAATAATTTATAA-ATAATAATTAA
*
642096 AATAAA-AATTTTATAAATAATAATTAT
1 AATAAATAA-TTTATAAATAATAATTAA
642123 AATA
1 AATA
642127 TATTTTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 23 0.85
28 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AATAAATAATTTATAAATAATAATTAA
Found at i:642119 original size:48 final size:49
Alignment explanation
Indices: 642013--642119 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 49
642003 TTAATAACAA
* **
642013 ATAAATATAATAAATAAATATAATAATATTAATTAATAATATCAATTAT
1 ATAAATATAATAAATAAATATAATAATAGTAATTAATAATAAAAATTAT
* *
642062 -TAAATATAATAAAT-AATTTAA-ATATAGTAATTAA-AATAAAAATTTT
1 ATAAATATAATAAATAAATATAATA-ATAGTAATTAATAATAAAAATTAT
642108 ATAAATAATAAT
1 ATAAAT-ATAAT
642120 TATAATATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 10 0.20
47 21 0.42
48 19 0.38
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (49 bp):
ATAAATATAATAAATAAATATAATAATAGTAATTAATAATAAAAATTAT
Found at i:642188 original size:21 final size:21
Alignment explanation
Indices: 642164--642204 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
642154 AATTATATGT
642164 ATAATA-TATTAAATATAATAA
1 ATAATATTA-TAAATATAATAA
*
642185 ATAATATTATAATTATAATA
1 ATAATATTATAAATATAATA
642205 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATTATAAATATAATAA
Found at i:644569 original size:14 final size:14
Alignment explanation
Indices: 644552--644601 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
644542 ATTTCAAAAT
644552 ATATTATAATTATA
1 ATATTATAATTATA
644566 ATATTATTAATTAT-
1 ATATTA-TAATTATA
* *
644580 TTATTATAGTTA-A
1 ATATTATAATTATA
644593 CATATTATA
1 -ATATTATA
644602 CATATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.17
14 18 0.60
15 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
ATATTATAATTATA
Found at i:646618 original size:83 final size:83
Alignment explanation
Indices: 646490--646677 Score: 277
Period size: 83 Copynumber: 2.2 Consensus size: 83
646480 CTGAATGAAA
* * * *
646490 TCGAACTCGTCAGGTCTTTAGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCG-AAGGT-TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
*
646555 TGCCTTGGAGCTGAGCGTGG
64 TGCCTTGGAGCTGAGCGTAG
* * *
646575 TCGAACTCGAAGGTTTTTGTTGGCAGATATCCCTTCTAGCCTTGAGTTATGCTATGAATGATGTG
1 TCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
646640 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
*
646658 TCGAACTCGAAGGTCTTTGT
1 TCGAACTCGAAGGTTTTTGT
646678 GTTTCAAGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
83 81 0.86
84 4 0.04
85 9 0.10
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.34
Consensus pattern (83 bp):
TCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:646725 original size:28 final size:28
Alignment explanation
Indices: 646679--646769 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
646669 GGTCTTTGTG
*
646679 TTTCAAGAGAAA-TATTTTCAAAGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
646707 TTTCAAGAGAAACGATTTCAAAGGTTTTTTGT
1 TTTCAAGAGAAACGATTTCAAAGG---TTT-T
* *
646739 GTTTCAAGAGAAACGACTTCAAAGGATTT
1 -TTTCAAGAGAAACGATTTCAAAGGTTTT
646768 TT
1 TT
646770 GTGTTTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 23 0.43
29 2 0.04
30 2 0.04
31 3 0.06
32 1 0.02
33 23 0.43
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:646748 original size:33 final size:32
Alignment explanation
Indices: 646667--646785 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
646657 GTCGAACTCG
* *
646667 AAGGTCTTTGTGTTTCAAGAGAAA-TATTTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGA-TTTCA
646699 AAGG--TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
*
646727 AAGGTTTTTTGTGTTTCAAGAGAAACGACTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACGATTTCA
646760 AAGGATTTTTGTGTTTCAAGAGAAAC
1 AAGG-TTTTTGTGTTTCAAGAGAAAC
646786 TGTCTCCAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.27
29 2 0.03
30 3 0.04
31 3 0.04
32 5 0.06
33 44 0.56
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
Found at i:646898 original size:37 final size:36
Alignment explanation
Indices: 646839--646943 Score: 138
Period size: 37 Copynumber: 2.9 Consensus size: 36
646829 AAAGATTGGT
*
646839 GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTC
* *
646876 GTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
* * *
646912 GGTTCAAAAAGAAACTGTCTCAAGGGAGACAA
1 GTTTC-AAGAGAAACTGTCTCAAGAGAGACAA
646944 TGGTGAGCAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 6 0.10
37 54 0.90
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
Found at i:647275 original size:105 final size:106
Alignment explanation
Indices: 646959--648237 Score: 2095
Period size: 105 Copynumber: 12.2 Consensus size: 106
646949 AGCACGATTC
** * * * *
646959 CCTTCGTCATGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
647023 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
647065 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * **
647130 TTCGTCGTGAAGTTAAACATGCGTTGTCAAGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
647171 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
647235 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
647276 CTTTCGCTCTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
647340 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
647381 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * *
647446 TTCATCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
647487 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
*
647549 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
647590 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
*
647652 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
647693 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
647757 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
647798 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---G-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
647859 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
647900 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
647964 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
648005 CCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* *
648070 TTTGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
648111 CCTTCGCTCTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
648175 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
648216 CCTTCGTTGAGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAAATT
648238 TACTCTCGAG
Statistics
Matches: 1108, Mismatches: 57, Indels: 17
0.94 0.05 0.01
Matches are distributed among these distances:
102 100 0.09
103 204 0.18
104 1 0.00
105 473 0.43
106 329 0.30
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:647434 original size:211 final size:211
Alignment explanation
Indices: 646959--648237 Score: 2079
Period size: 211 Copynumber: 6.1 Consensus size: 211
646949 AGCACGATTC
** * * *
646959 CCTTCGTCATGAAGTTGAAATTGACTCT-AGAATTG-GAAAATTGTTTATTGACAACCAGCGGTC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGAG-AAGTTGTTTGTTGACAACCAGCGGTC
* *
647022 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
64 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
647087 GGCTCTGAAATT-GAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACATG
129 GGCTCTGAAATTGGA-AAG-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
**
647151 CGTTGTCAAGAGTCCAATAT
192 CGTTGTCTGGAGTCCAATAT
*
647171 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * *
647235 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTCTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
647300 CTCTGAAATTGGAAAGT-TGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATTGGAAAGTGT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
647364 TGTCTGGAGTCCAATAT
195 TGTCTGGAGTCCAATAT
* *
647381 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
* *
647446 TTCATCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
* *
647511 CTCTGAAATTGGGAA--GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTT
131 CTCTGAAATTGGAAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
647574 GTCTGGAGTCCAATAT
196 GTCTGGAGTCCAATAT
* *
647590 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---GTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
647652 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
*
647717 CTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATT-GGAAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
647781 TGTCTGGAGTCCAATAT
195 TGTCTGGAGTCCAATAT
*
647798 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA---G-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
* *
647859 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
*
647924 CTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATT-GGAAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
647988 TGTCTGGAGTCCAATAT
195 TGTCTGGAGTCCAATAT
*
648005 CCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
* *
648070 TTTGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
648135 CTCTGAAATTGGAAAGT-TGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATTGGAAAGTGT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
648199 TGTCTGGAGTCCAATAT
195 TGTCTGGAGTCCAATAT
*
648216 CCTTCGTTGAGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAAATT
648238 TACTCTCGAG
Statistics
Matches: 1010, Mismatches: 43, Indels: 29
0.93 0.04 0.03
Matches are distributed among these distances:
206 95 0.09
207 206 0.20
208 101 0.10
209 98 0.10
210 108 0.11
211 363 0.36
212 37 0.04
213 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (211 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
CTCTGAAATTGGAAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTCTGGAGTCCAATAT
Found at i:651907 original size:3 final size:3
Alignment explanation
Indices: 651892--651937 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
651882 AAAAGAAAAA
*
651892 AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
651936 AA
1 AA
651938 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:651970 original size:22 final size:25
Alignment explanation
Indices: 651921--651977 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
651911 TAATAATAAT
*
651921 AATAATAAAATAGATAACAAAGAAA
1 AATAATAAAATAGATAAAAAAGAAA
*
651946 AATAA-AAGATAG-TAAAAAAG-AA
1 AATAATAAAATAGATAAAAAAGAAA
651968 AATAATAAAA
1 AATAATAAAA
651978 AAAAATAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.25
23 10 0.36
24 6 0.21
25 5 0.18
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (25 bp):
AATAATAAAATAGATAAAAAAGAAA
Found at i:651981 original size:12 final size:12
Alignment explanation
Indices: 651863--652007 Score: 61
Period size: 12 Copynumber: 12.0 Consensus size: 12
651853 TATATTATAA
651863 AATAAAAACAAAT
1 AATAAAAA-AAAT
*
651876 -ATAAAAAAAAG
1 AATAAAAAAAAT
* *
651887 AA-AAAAATATT
1 AATAAAAAAAAT
* *
651898 AAT-ATAATAAT
1 AATAAAAAAAAT
* *
651909 AATAATAATAAT
1 AATAAAAAAAAT
*
651921 AAT-AATAAAAT
1 AATAAAAAAAAT
651932 AGATAACAAAGAAA-
1 A-ATAA-AAA-AAAT
* *
651946 AATAAAAGATAGT
1 AATAAAA-AAAAT
651959 AA-AAAAGAAAAT
1 AATAAAA-AAAAT
651971 AATAAAAAAAAAT
1 AAT-AAAAAAAAT
*
651984 AGATAAAAAATA-
1 A-ATAAAAAAAAT
*
651996 AATAAAGAAAAT
1 AATAAAAAAAAT
652008 GACCAAAATG
Statistics
Matches: 102, Mismatches: 17, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
11 34 0.33
12 35 0.34
13 21 0.21
14 9 0.09
15 3 0.03
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (12 bp):
AATAAAAAAAAT
Found at i:651989 original size:14 final size:13
Alignment explanation
Indices: 651863--652000 Score: 61
Period size: 15 Copynumber: 10.2 Consensus size: 13
651853 TATATTATAA
*
651863 AATAAAAACAAAT
1 AATAAAAAAAAAT
651876 -ATAAAAAAAAGA-
1 AATAAAAAAAA-AT
*
651888 AA-AAAATATTAATAT
1 AATAAAA-A--AAAAT
*
651903 AATAATAATAATAAT
1 AATAA-AA-AAAAAT
*
651918 AATAATAATAAAAT
1 AATAA-AAAAAAAT
*
651932 AGATAACAAAGAAA-
1 A-ATAA-AAAAAAAT
* * *
651946 AATAAAAGATAGT
1 AATAAAAAAAAAT
*
651959 AA-AAAAGAAAAT
1 AATAAAAAAAAAT
651971 AATAAAAAAAAAT
1 AATAAAAAAAAAT
651984 AGATAAAAAATAAAT
1 A-ATAAAAAA-AAAT
651999 AA
1 AA
652001 AGAAAATGAC
Statistics
Matches: 96, Mismatches: 16, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
12 26 0.27
13 19 0.20
14 16 0.17
15 29 0.30
16 2 0.02
17 4 0.04
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (13 bp):
AATAAAAAAAAAT
Found at i:651998 original size:15 final size:14
Alignment explanation
Indices: 651960--651999 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
651950 AAAGATAGTA
651960 AAAAAGAAAATA-AT
1 AAAAA-AAAATAGAT
651974 AAAAAAAAATAGAT
1 AAAAAAAAATAGAT
651988 AAAAAATAAATA
1 AAAAAA-AAATA
652000 AAGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.25
14 13 0.54
15 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAAAAAATAGAT
Found at i:651998 original size:28 final size:28
Alignment explanation
Indices: 651915--652000 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
651905 TAATAATAAT
* * *
651915 AATAATAATAATAAAATAGATAACAAAGA
1 AATAATAA-AAAAAAATAGATAAAAAAAA
*
651944 AA-AAT---AAAAGATAG-TAAAAAAGAA
1 AATAATAAAAAAAAATAGATAAAAAA-AA
*
651968 AATAATAAAAAAAAATAGATAAAAAATA
1 AATAATAAAAAAAAATAGATAAAAAAAA
651996 AATAA
1 AATAA
652001 AGAAAATGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
23 6 0.13
24 10 0.22
25 3 0.07
28 17 0.38
29 9 0.20
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.17
Consensus pattern (28 bp):
AATAATAAAAAAAAATAGATAAAAAAAA
Found at i:652006 original size:29 final size:29
Alignment explanation
Indices: 651939--652007 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
651929 AATAGATAAC
651939 AAAGAAAAATAAAAGATAGTAAAAAAGAAA
1 AAAG-AAAATAAAAGATAGTAAAAAAGAAA
* *
651969 ATAATAAAA-AAAA-ATAGATAAAAAATAAA
1 A-AAGAAAATAAAAGATAG-TAAAAAAGAAA
651998 TAAAGAAAAT
1 -AAAGAAAAT
652008 GACCAAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
28 4 0.12
29 20 0.62
30 6 0.19
31 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAGAAAATAAAAGATAGTAAAAAAGAAA
Found at i:654770 original size:16 final size:16
Alignment explanation
Indices: 654713--654797 Score: 72
Period size: 16 Copynumber: 5.4 Consensus size: 16
654703 TAAGAAATAT
654713 TTTAATTATTTATTATA
1 TTTAATTA-TTATTATA
* *
654730 TTTAATAATTAATAGTA
1 TTTAATTATTATTA-TA
654747 -TTAATTATTATTATA
1 TTTAATTATTATTATA
654762 TTT-A-T-TTATTATA
1 TTTAATTATTATTATA
* *
654775 TTTATTTGTTATTA-A
1 TTTAATTATTATTATA
654790 TTTCAATT
1 TTT-AATT
654798 TGAAAGATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
15 8 0.14
16 27 0.48
17 9 0.16
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAATTATTATTATA
Found at i:654779 original size:13 final size:13
Alignment explanation
Indices: 654754--654786 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
654744 GTATTAATTA
654754 TTATTATATTTAT
1 TTATTATATTTAT
654767 TTATTATATTTAT
1 TTATTATATTTAT
*
654780 TTGTTAT
1 TTATTAT
654787 TAATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:655295 original size:15 final size:14
Alignment explanation
Indices: 655277--655359 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
655267 TTTTATCATA
655277 TAAATTTTATAAATT
1 TAAA-TTTATAAATT
***
655292 TAAATTTATCTCTTT
1 TAAATTTAT-AAATT
*
655307 TAAATTTAAAAATT
1 TAAATTTATAAATT
***
655321 TAAATTTATCTCTTT
1 TAAATTTAT-AAATT
*
655336 TAAATTTTAAAAATT
1 TAAA-TTTATAAATT
655351 TAAATTTAT
1 TAAATTTAT
655360 CTATTACATA
Statistics
Matches: 49, Mismatches: 16, Indels: 7
0.68 0.22 0.10
Matches are distributed among these distances:
14 19 0.39
15 26 0.53
16 4 0.08
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATTTATAAATT
Found at i:655319 original size:29 final size:30
Alignment explanation
Indices: 655277--655361 Score: 154
Period size: 29 Copynumber: 2.9 Consensus size: 30
655267 TTTTATCATA
*
655277 TAAATTTTATAAATTTAAATTTATCTCTTT
1 TAAATTTTAAAAATTTAAATTTATCTCTTT
655307 TAAA-TTTAAAAATTTAAATTTATCTCTTT
1 TAAATTTTAAAAATTTAAATTTATCTCTTT
655336 TAAATTTTAAAAATTTAAATTTATCT
1 TAAATTTTAAAAATTTAAATTTATCT
655362 ATTACATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 28 0.53
30 25 0.47
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAATTTTAAAAATTTAAATTTATCTCTTT
Found at i:662947 original size:20 final size:20
Alignment explanation
Indices: 662922--662966 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
662912 CTCTTCTCTT
662922 GTGTTTAATTGCTTGGATAG
1 GTGTTTAATTGCTTGGATAG
*
662942 GTGTTTGATTGCTTGGATAG
1 GTGTTTAATTGCTTGGATAG
662962 GTGTT
1 GTGTT
662967 CTTACCCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.47
Consensus pattern (20 bp):
GTGTTTAATTGCTTGGATAG
Found at i:675490 original size:15 final size:15
Alignment explanation
Indices: 675470--675511 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
675460 GTGGAGGGTC
675470 AGGTGTCACAGGCTT
1 AGGTGTCACAGGCTT
675485 AGGTGTCACAGGCTT
1 AGGTGTCACAGGCTT
*
675500 GGGTGTCACAGG
1 AGGTGTCACAGG
675512 ATCTACTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (15 bp):
AGGTGTCACAGGCTT
Found at i:679463 original size:20 final size:21
Alignment explanation
Indices: 679435--679489 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
679425 CCTGAAAGAA
* *
679435 AATATAAAATATA-TATATTT
1 AATAAAAAATAAATTATATTT
679455 AATAAAAAATAAAATTATATTT
1 AATAAAAAAT-AAATTATATTT
*
679477 AATAAACAATAAA
1 AATAAAAAATAAA
679490 AAAATTATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.30
21 5 0.17
22 16 0.53
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAAATAAATTATATTT
Found at i:679476 original size:22 final size:22
Alignment explanation
Indices: 679448--679490 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
679438 ATAAAATATA
679448 TATATTTAATAAAAAATAAAAT
1 TATATTTAATAAAAAATAAAAT
*
679470 TATATTTAATAAACAATAAAA
1 TATATTTAATAAAAAATAAAA
679491 AAATTATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TATATTTAATAAAAAATAAAAT
Found at i:679493 original size:25 final size:22
Alignment explanation
Indices: 679448--679498 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 22
679438 ATAAAATATA
*
679448 TATATTTAATAAAAAATAAAAT
1 TATATTTAATAAAAAAAAAAAT
679470 TATATTTAATAAACAATAAAAAAAT
1 TATATTTAAT-AA-AA-AAAAAAAT
679495 TATA
1 TATA
679499 CATTTTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 2 0.08
24 2 0.08
25 11 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TATATTTAATAAAAAAAAAAAT
Found at i:680966 original size:37 final size:37
Alignment explanation
Indices: 680916--680994 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
680906 TATGATATTG
680916 CAACTTGGAAGCTATAGTATATCAATCACCATCACGA
1 CAACTTGGAAGCTATAGTATATCAATCACCATCACGA
680953 CAACTTGGAAGCTATAGTATATCAATCACCATCACGA
1 CAACTTGGAAGCTATAGTATATCAATCACCATCACGA
680990 CAACT
1 CAACT
680995 CTTCCCATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (37 bp):
CAACTTGGAAGCTATAGTATATCAATCACCATCACGA
Found at i:682486 original size:19 final size:20
Alignment explanation
Indices: 682434--682488 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
682424 TAGATTCTAC
* *
682434 AATATAATTTGTATAAATAT
1 AATATAATTTATATAAATAA
**
682454 AAT-TTTTTTATATAAATAA
1 AATATAATTTATATAAATAA
682473 AATATAATTTTATATA
1 AATATAA-TTTATATA
682489 TTATCAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 15 0.56
20 4 0.15
21 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATAATTTATATAAATAA
Found at i:698344 original size:13 final size:13
Alignment explanation
Indices: 698334--698403 Score: 95
Period size: 13 Copynumber: 5.4 Consensus size: 13
698324 TCTATGACGT
698334 GCATTTATGACAC
1 GCATTTATGACAC
*
698347 GCATTTATGACAT
1 GCATTTATGACAC
698360 GCATTTATGACAC
1 GCATTTATGACAC
* *
698373 ACATTTATGACGC
1 GCATTTATGACAC
* *
698386 TCATTTATGACGC
1 GCATTTATGACAC
698399 GCATT
1 GCATT
698404 GAGCGTCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (13 bp):
GCATTTATGACAC
Found at i:698362 original size:26 final size:26
Alignment explanation
Indices: 698326--698403 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
698316 GTCATAAATC
*
698326 TATGACGTGCATTTATGACACGCATT
1 TATGACATGCATTTATGACACGCATT
*
698352 TATGACATGCATTTATGACACACATT
1 TATGACATGCATTTATGACACGCATT
* *
698378 TATGACGCT-CATTTATGACGCGCATT
1 TATGAC-ATGCATTTATGACACGCATT
698404 GAGCGTCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 45 0.98
27 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (26 bp):
TATGACATGCATTTATGACACGCATT
Found at i:698497 original size:85 final size:84
Alignment explanation
Indices: 698379--698536 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 84
698369 ACACACATTT
* * *
698379 ATGACGCTCATTTATGACGCGCATTGAGCGTCATTGAAGCCCCTATCATAAATAAAGATGACACG
1 ATGACACTCATGTATGACGCGCATTGAGCGTCATTGAAGCCCC-ATCATAAATAAAGATGACACA
698444 CATTTGTGTATCATAAATTA
65 CATTTGTGTATCATAAATTA
** * * * *
698464 ATGACACTCATGTATGACTTGCATTGCGTGTCATTGAAGCCCCGTCATAAATGAAGATGACACAC
1 ATGACACTCATGTATGACGCGCATTGAGCGTCATTGAAGCCCCATCATAAATAAAGATGACACAC
698529 ATTTGTGT
66 ATTTGTGT
698537 GTCGTGATTG
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 27 0.42
85 37 0.58
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (84 bp):
ATGACACTCATGTATGACGCGCATTGAGCGTCATTGAAGCCCCATCATAAATAAAGATGACACAC
ATTTGTGTATCATAAATTA
Found at i:700491 original size:285 final size:282
Alignment explanation
Indices: 699972--700538 Score: 1107
Period size: 285 Copynumber: 2.0 Consensus size: 282
699962 CAAGTAATAC
699972 TATGCTTTCAGTCTCGACAGGGTATTCAAGCAGTATGTATTTTTTGCTGACAGAAGTAACTCATT
1 TATGCTTTCAGTCTCGACAGGGTATTCAAGCAGTATGTATTTTTTGCTGACAGAAGTAACTCATT
700037 ACACAACACAAACCACACCATAATAAGGAAAACACTATAGCACACACCAAACAATTCCAATCATA
66 ACACAACACAAACCACACCATAATAAGGAAAACACTATAGCACACACCAAACAATTCCAATCATA
700102 CCACAGTTAAATACTTACCAAATACTTGATGCAAAGAAGGCACTTATAAGTATTACACATGTTGC
131 CCACAGTTAAATACTTACCAAATACTTGATGCAAAGAAGGCACTTATAAGTATTACACATGTTGC
700167 ATATCTACAACACCGAGAACATTTGTTTAGGAAAAAGAACATCGATATTGTAGCTAAGCATTAAC
196 ATATCTACAACACCGAGAACATTTGTTTAGGAAAAAGAACATCGATATTGTAGCTAAGCATTAAC
700232 TGAGAATAATAACGGCTATTTT
261 TGAGAATAATAACGGCTATTTT
700254 TATGCTTTCAGTCTCGACAGGGTATTCAAGCAGTATGTATTTTTTGCTGACAGAAGTAACTCATT
1 TATGCTTTCAGTCTCGACAGGGTATTCAAGCAGTATGTATTTTTTGCTGACAGAAGTAACTCATT
700319 ACACAACACAAACCACACCATAATAAGGAAAACACTATAGCACACACCAAACACAAATTCCAATC
66 ACACAACACAAACCACACCATAATAAGGAAAACACTATAGCACACACC-AA-AC-AATTCCAATC
700384 ATACCACAGTTAAATACTTACCAAATACTTGATGCAAAGAAGGCACTTATAAGTATTACACATGT
128 ATACCACAGTTAAATACTTACCAAATACTTGATGCAAAGAAGGCACTTATAAGTATTACACATGT
700449 TGCATATCTACAACACCGAGAACATTTGTTTAGGAAAAAGAACATCGATATTGTAGCTAAGCATT
193 TGCATATCTACAACACCGAGAACATTTGTTTAGGAAAAAGAACATCGATATTGTAGCTAAGCATT
700514 AACTGAGAATAATAACGGCTATTTT
258 AACTGAGAATAATAACGGCTATTTT
700539 AGATAAAGAA
Statistics
Matches: 282, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
282 113 0.40
283 2 0.01
284 2 0.01
285 165 0.59
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (282 bp):
TATGCTTTCAGTCTCGACAGGGTATTCAAGCAGTATGTATTTTTTGCTGACAGAAGTAACTCATT
ACACAACACAAACCACACCATAATAAGGAAAACACTATAGCACACACCAAACAATTCCAATCATA
CCACAGTTAAATACTTACCAAATACTTGATGCAAAGAAGGCACTTATAAGTATTACACATGTTGC
ATATCTACAACACCGAGAACATTTGTTTAGGAAAAAGAACATCGATATTGTAGCTAAGCATTAAC
TGAGAATAATAACGGCTATTTT
Found at i:701467 original size:3 final size:3
Alignment explanation
Indices: 701461--701523 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
701451 TTCATTTAAA
* *
701461 TAT TAT T-T ATAT TAT CAT TAT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
701506 TAT TAT TAT TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
701524 GAGAGATCCA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:702222 original size:14 final size:14
Alignment explanation
Indices: 702203--702237 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
702193 GTAAACGCCC
702203 TTCGGGCCAGCCGT
1 TTCGGGCCAGCCGT
702217 TTCGGGCCAGCCGT
1 TTCGGGCCAGCCGT
702231 TTCGGGC
1 TTCGGGC
702238 TTAAATAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.34, G:0.37, T:0.23
Consensus pattern (14 bp):
TTCGGGCCAGCCGT
Found at i:702745 original size:13 final size:14
Alignment explanation
Indices: 702727--702757 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
702717 TTATTTACAA
702727 TATTATTATTTT-T
1 TATTATTATTTTAT
702740 TATTATTATTTTAT
1 TATTATTATTTTAT
702754 TATT
1 TATT
702758 TATATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:702973 original size:113 final size:110
Alignment explanation
Indices: 702847--703076 Score: 259
Period size: 113 Copynumber: 2.1 Consensus size: 110
702837 TCATATTTTA
* * * * *
702847 ATTTATTTATTTTTTAATAT-TAAGAAAGGA-CAGTCTTAAAATAACTGGATGTCCATTTTCTGA
1 ATTTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TTTTCTGA
* * *
702910 TATTTTTAAATAAATAAATATCCTATTTTTTAAA-ATTATATATTAATT
65 TATTTCTAAATAAATAAATATCCTA-TTTATAAATA-TATAAATTAA-T
* ** * *
702958 ATTTATTTATTTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTTCTTTTCTGA
1 ATTTATTTA-TTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGA
**
703023 TATTTCTAAATAAATAAATATTGTATTTATAAATATATAAATTAAT
65 TATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
703069 ATTTATTT
1 ATTTATTT
703077 CATAATTATA
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
111 18 0.18
112 27 0.27
113 39 0.39
114 16 0.16
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (110 bp):
ATTTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGAT
ATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:703070 original size:27 final size:27
Alignment explanation
Indices: 703032--703086 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
703022 ATATTTCTAA
703032 ATAAATAAATATTGTATTT-ATAAATAT
1 ATAAATAAATATT-TATTTCATAAATAT
* *
703059 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
703086 A
1 A
703087 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:703590 original size:14 final size:15
Alignment explanation
Indices: 703564--703592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
703554 GTTTTCAAAT
703564 TTTTTATACTTATTA
1 TTTTTATACTTATTA
703579 TTTTTATA-TTATTA
1 TTTTTATACTTATTA
703593 AGTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATACTTATTA
Found at i:713866 original size:13 final size:13
Alignment explanation
Indices: 713848--713904 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
713838 ATTATGCTTG
**
713848 AAGAAAAAATGAA
1 AAGAAAAAAAAAA
713861 AAGAAAAAAAAAA
1 AAGAAAAAAAAAA
713874 AAGAAAAAAAAGAA
1 AAGAAAAAAAA-AA
713888 AA-AAAAGAAAAAA
1 AAGAAAA-AAAAAA
713901 AAGA
1 AAGA
713905 TGAACACCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 30 0.77
14 9 0.23
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Found at i:713868 original size:1 final size:1
Alignment explanation
Indices: 713859--713902 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
713849 AGAAAAAATG
* * * *
713859 AAAAGAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
713903 GATGAACACC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:713880 original size:9 final size:9
Alignment explanation
Indices: 713851--713904 Score: 83
Period size: 9 Copynumber: 6.0 Consensus size: 9
713841 ATGCTTGAAG
*
713851 AAAAAATGA
1 AAAAAAAGA
713860 AAAGAAAA-A
1 AAA-AAAAGA
713869 AAAAAAAGA
1 AAAAAAAGA
713878 AAAAAAAGA
1 AAAAAAAGA
713887 AAAAAAAGA
1 AAAAAAAGA
713896 AAAAAAAGA
1 AAAAAAAGA
713905 TGAACACCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
8 4 0.10
9 35 0.83
10 3 0.07
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:714607 original size:23 final size:23
Alignment explanation
Indices: 714581--714625 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
714571 CACCACAGCT
*
714581 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
714604 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
714626 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:716242 original size:21 final size:21
Alignment explanation
Indices: 716218--716262 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
716208 TTTTGTTCGT
* *
716218 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
716239 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
716260 TTG
1 TTG
716263 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:717865 original size:114 final size:114
Alignment explanation
Indices: 717664--717887 Score: 369
Period size: 114 Copynumber: 2.0 Consensus size: 114
717654 GTGCCACGTT
*
717664 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * *
717729 ATTTGGTATGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTCGGTAGGAACCCTAAAACCAATCATTGGAATTAAAAGATGAATTTG
717778 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
717843 GTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 ATTCGGTAGGAACC-CTAAAACCAATCATTGGAATTAAAAGATGAA
717888 CTGCATGATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 101 0.99
115 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTCGGTAGGAACCCTAAAACCAATCATTGGAATTAAAAGATGAATTTG
Found at i:718799 original size:116 final size:112
Alignment explanation
Indices: 718601--719263 Score: 843
Period size: 116 Copynumber: 5.9 Consensus size: 112
718591 AGTTCAAGTC
** * *
718601 CATCATTCAATGGATCAACATT-CCAGAGAAAGTTTATAATGAGAATAA--C-TCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
718662 GGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
66 -GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
*
718710 CATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCGTCATCTG-A-A
*
718774 TGGAAGAAGAAGTTCTTAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
63 --GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
*
718826 CATCATTTGATGGATCAACATTGCCTAGTAG--AGTTCATAATGAGAAGAACTCATCATCTGAAG
1 CATCATTTGATGGATCAACATTGCC-AG-AGAAAGTTCATAATGAGAAGAACTCGTCATCT---G
718889 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
61 AA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
*
718942 CATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAAT--G-AGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
* * **
719003 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
* * * *
719051 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * * ** *
719116 GAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
* * * *
719163 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* *
719225 TAAGAAGTTCACAATGAGAAG-ATCTTGTTCAACCTTTTG
66 GAAGAAGTTCATAATGAGAAGAAT-TTGTTCAACCTTTTG
719264 CATAATTCTA
Statistics
Matches: 509, Mismatches: 22, Indels: 46
0.88 0.04 0.08
Matches are distributed among these distances:
108 2 0.00
109 147 0.29
110 26 0.05
111 1 0.00
112 115 0.23
113 22 0.04
114 2 0.00
115 2 0.00
116 183 0.36
117 5 0.01
118 1 0.00
119 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (112 bp):
CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
Done.