Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:941133 original size:58 final size:58
Alignment explanation
Indices: 940988--941155 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 58
940978 AATAATCTAT
* * * * * *
940988 TAATTATTGGGCACTGTTGTTGAGTTTTTCAACTCTTAAAAGTTACAAAATTGTCATC
1 TAATTATAGGGCATTCTTGTTGAGCTTTTCAACTATTAAAAGTTACAAAATTGTCACC
* * * * *
941046 TAATTATAGTGCGTTGTTGTTGAGTTTTTCAACTGTTAAAAGTTACAAAATCT-TCACC
1 TAATTATAGGGCATTCTTGTTGAGCTTTTCAACTATTAAAAGTTACAAAAT-TGTCACC
* *
941104 TAATTATAGGGCATTACTTGTTTA-CTTTTCTAACAATTAAAAGTTACAAAAT
1 TAATTATAGGGCATT-CTTGTTGAGCTTTTC-AACTATTAAAAGTTACAAAAT
941156 GATTATTTGG
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
58 68 0.72
59 26 0.28
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (58 bp):
TAATTATAGGGCATTCTTGTTGAGCTTTTCAACTATTAAAAGTTACAAAATTGTCACC
Found at i:942459 original size:19 final size:19
Alignment explanation
Indices: 942418--942459 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
942408 ATGACCAACA
* *
942418 AATTCGCAACGCCATCTCG
1 AATTCGCAACGCCAACTCC
*
942437 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCCAACTCC
942456 AATT
1 AATT
942460 TCGTAACACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.21
Consensus pattern (19 bp):
AATTCGCAACGCCAACTCC
Found at i:942523 original size:20 final size:19
Alignment explanation
Indices: 942498--942585 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 19
942488 CTGAATTTCA
942498 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
942518 AATTCGCAA-TGCGAATTTTG
1 AATTCGCAACT-CG-ATTTTG
**
942538 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
*
942558 AATTCGCAACACGAATTTT-
1 AATTCGCAACTCG-ATTTTG
942577 AATTTCGCA
1 AA-TTCGCA
942586 CCAGGTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 8 0.14
20 39 0.68
21 10 0.18
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:942544 original size:40 final size:40
Alignment explanation
Indices: 942477--942585 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
942467 ACAGTTTCCA
* *
942477 AATTCGCAACACTGAATTTCAAATTCGCAACTCGA-TTTCTG
1 AATTCGCAACAC-GAATTTTAATTTCGCAACTCGATTTTC-G
** **
942518 AATTCGCAATGCGAATTTTGTTTTCGCAACTCGATTTTCG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTTCG
942558 AATTCGCAACACGAATTTTAATTTCGCA
1 AATTCGCAACACGAATTTTAATTTCGCA
942586 CCAGGTTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
40 43 0.75
41 14 0.25
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTTCG
Found at i:947637 original size:21 final size:21
Alignment explanation
Indices: 947611--947728 Score: 146
Period size: 21 Copynumber: 5.6 Consensus size: 21
947601 GTAAATCGGG
* *
947611 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGATGGGAGGGGC
**
947632 CTCTTGAATGATGACAGGGGC
1 CTCTTGAATGATGGGAGGGGC
**
947653 CTCTTGAATTTTGGGAGGGGC
1 CTCTTGAATGATGGGAGGGGC
*
947674 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAATGATGGGAGGGGC
* *
947695 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAATGATGGGAGGGGC
*
947716 CTCTTGAACGATG
1 CTCTTGAATGATG
947729 ACAAATGAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGATGGGAGGGGC
Found at i:947670 original size:42 final size:42
Alignment explanation
Indices: 947611--947731 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
947601 GTAAATCGGG
* *
947611 CTCTTGAATGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAATGATGGGAGGGGCCTCTTGAATGATGACAGGGGC
** *
947653 CTCTTGAATTTTGGGAGGGGCCTCTTGAATGATGAGAGGGGC
1 CTCTTGAATGATGGGAGGGGCCTCTTGAATGATGACAGGGGC
* * *
947695 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACA
1 CTCTTGAATGATGGGAGGGGCCTCTTGAATGATGACA
947732 AATGAATCAG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGATGGGAGGGGCCTCTTGAATGATGACAGGGGC
Found at i:947890 original size:12 final size:12
Alignment explanation
Indices: 947871--947912 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
947861 GGGCCGCTAA
*
947871 AAATAAATTAAT
1 AAATAAATCAAT
*
947883 ACATAAATCAAT
1 AAATAAATCAAT
947895 AAATAAA-CAAAT
1 AAATAAATC-AAT
947907 AAATAA
1 AAATAA
947913 TGTCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:948068 original size:42 final size:42
Alignment explanation
Indices: 948039--948139 Score: 193
Period size: 42 Copynumber: 2.4 Consensus size: 42
948029 ATAAAGTAGA
948039 TACCTCACCACGTAAAGCACCATTGTCATCGCATAAAACATC
1 TACCTCACCACGTAAAGCACCATTGTCATCGCATAAAACATC
*
948081 TATCTCACCACGTAAAGCACCATTGTCATCGCATAAAACATC
1 TACCTCACCACGTAAAGCACCATTGTCATCGCATAAAACATC
948123 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
948140 ACCGTACCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.22
Consensus pattern (42 bp):
TACCTCACCACGTAAAGCACCATTGTCATCGCATAAAACATC
Found at i:948075 original size:21 final size:21
Alignment explanation
Indices: 948051--948117 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
948041 CCTCACCACG
948051 TAAAGCACCATTGTCATCGCA
1 TAAAGCACCATTGTCATCGCA
* * * * * *
948072 TAAAACATC-TATCTCACCACG
1 TAAAGCACCAT-TGTCATCGCA
948093 TAAAGCACCATTGTCATCGCA
1 TAAAGCACCATTGTCATCGCA
948114 TAAA
1 TAAA
948118 ACATCTACCT
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.24
Consensus pattern (21 bp):
TAAAGCACCATTGTCATCGCA
Found at i:948417 original size:42 final size:42
Alignment explanation
Indices: 948336--948434 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
948326 GTGATGGAAT
* * * *
948336 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCAGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
*
948378 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATC-GACTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAG-CTCGATC
948420 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
948435 AAGTGAGGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
Found at i:949840 original size:20 final size:20
Alignment explanation
Indices: 949815--949853 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
949805 TCGCATTGCG
949815 ATTTTCGTGTTGCGAATTTT
1 ATTTTCGTGTTGCGAATTTT
949835 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
949854 AAGTTTAAAA
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:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTT
Found at i:950219 original size:21 final size:22
Alignment explanation
Indices: 950192--950248 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
950182 GATGGAGATA
950192 GACGGATTTCGCCGAAGAT-GG
1 GACGGATTTCGCCGAAGATGGG
* * *
950213 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
950235 GACGGATGTCGCCG
1 GACGGATTTCGCCG
950249 TAGAGAGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:950375 original size:19 final size:20
Alignment explanation
Indices: 950353--950390 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
950343 AATATTGTGT
950353 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
950372 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
950391 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:950439 original size:20 final size:20
Alignment explanation
Indices: 950416--950462 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
950406 TGACTTTTGT
*
950416 GTTGCGAATT-CGAGATTCGC
1 GTTGCGAATTAC-AAATTCGC
*
950436 GTTGCGATTTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
950456 GTTGCGA
1 GTTGCGA
950463 TTTTGTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:950559 original size:2 final size:2
Alignment explanation
Indices: 950552--950592 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
950542 TTTTCTCTTT
950552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
950593 TATTTATGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:956932 original size:21 final size:21
Alignment explanation
Indices: 956894--956934 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
956884 ATCTGTTAAG
**
956894 ATTTAGAGATTTGGGGTTTAT
1 ATTTAGAGATTTAAGGTTTAT
*
956915 ATTTAGGGATTTAAGGTTTA
1 ATTTAGAGATTTAAGGTTTA
956935 GGGTTTATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
ATTTAGAGATTTAAGGTTTAT
Found at i:958399 original size:62 final size:62
Alignment explanation
Indices: 958328--958513 Score: 331
Period size: 62 Copynumber: 3.0 Consensus size: 62
958318 GATGATTATA
*
958328 ATGTAGTATATGTTTAGAATTTTCTTACTTCATTGTTAGCGCACACTGCACACACACTATGT
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACACTATGT
* *
958390 ATGTAGTATATGTTTAGAATTTTTTTACTTTATTGTTAGCGCACACTG--CACACACTATGC
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACACTATGT
958450 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACACTATGT
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACACTATGT
958512 AT
1 AT
958514 ACATGGTTGC
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
60 58 0.50
62 59 0.50
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (62 bp):
ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACACTATGT
Found at i:958471 original size:60 final size:60
Alignment explanation
Indices: 958328--958504 Score: 309
Period size: 60 Copynumber: 2.9 Consensus size: 60
958318 GATGATTATA
* *
958328 ATGTAGTATATGTTTAGAATTTTCTTACTTCATTGTTAGCGCACACTGCACACACACTATGT
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTG--CACACACTATGC
*
958390 ATGTAGTATATGTTTAGAATTTTTTTACTTTATTGTTAGCGCACACTGCACACACTATGC
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACTATGC
958450 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACAC
1 ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACAC
958505 ACTATGTATA
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 65 0.59
62 46 0.41
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (60 bp):
ATGTAGTATATGTTTAGAATTTTCTTACTTTATTGTTAGCGCACACTGCACACACTATGC
Found at i:961424 original size:2 final size:2
Alignment explanation
Indices: 961417--961450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
961407 GGTCCCCACT
961417 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
961451 GACTTGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:963417 original size:32 final size:32
Alignment explanation
Indices: 963380--963446 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
963370 CGTAACGAAG
963380 TATTATGTCTTTTGAATTATATCAATTGACTT
1 TATTATGTCTTTTGAATTATATCAATTGACTT
963412 TATTATGTCTTTTGAATTATATCAATTGACTT
1 TATTATGTCTTTTGAATTATATCAATTGACTT
963444 TAT
1 TAT
963447 AATATTCGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (32 bp):
TATTATGTCTTTTGAATTATATCAATTGACTT
Found at i:963549 original size:53 final size:53
Alignment explanation
Indices: 963491--963613 Score: 237
Period size: 53 Copynumber: 2.3 Consensus size: 53
963481 CATCGAAGCA
963491 ACAAATGAACAAATCAATTATCATAATATATCACGTAAAATAATTTTGAGGAC
1 ACAAATGAACAAATCAATTATCATAATATATCACGTAAAATAATTTTGAGGAC
*
963544 ACAAATGAACAAATCAATTATCATAATATATCACTTAAAATAATTTTGAGGAC
1 ACAAATGAACAAATCAATTATCATAATATATCACGTAAAATAATTTTGAGGAC
963597 ACAAATGAACAAATCAA
1 ACAAATGAACAAATCAA
963614 ATTTATAAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 69 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (53 bp):
ACAAATGAACAAATCAATTATCATAATATATCACGTAAAATAATTTTGAGGAC
Found at i:972463 original size:19 final size:19
Alignment explanation
Indices: 972439--972477 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
972429 AAGATTTAAC
972439 TTACAAATTTACAATATGA
1 TTACAAATTTACAATATGA
972458 TTACAAATTTACAATATGA
1 TTACAAATTTACAATATGA
972477 T
1 T
972478 CCGATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
TTACAAATTTACAATATGA
Found at i:976060 original size:38 final size:38
Alignment explanation
Indices: 976009--976081 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
975999 CAGAATCACT
976009 ATAATGATTGCAGACTGTTGATGTCGTCCGCGTGGACA
1 ATAATGATTGCAGACTGTTGATGTCGTCCGCGTGGACA
976047 ATAATGATTGCAGACTGTTGATGTCGTCCGCGTGG
1 ATAATGATTGCAGACTGTTGATGTCGTCCGCGTGG
976082 GAAGATCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (38 bp):
ATAATGATTGCAGACTGTTGATGTCGTCCGCGTGGACA
Found at i:979490 original size:85 final size:82
Alignment explanation
Indices: 979350--979520 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 82
979340 AAACTCAAGT
979350 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGT
1 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG-TGT
979415 T-AGTATTTCAATTAGGA
65 TAAGTATTTCAATTAGGA
* * *
979432 TTTAGGATATTATTTTAAATAGTATTTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGT
1 TTTAGGATAATATTTT-AA-A-CATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGT
* * *
979497 TTTAAGTGTTTTAATTAGGA
63 GTTAAGTATTTCAATTAGGA
979517 TTTA
1 TTTA
979521 AGATGTTGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
82 15 0.19
83 2 0.03
84 4 0.05
85 58 0.73
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (82 bp):
TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTGTT
AAGTATTTCAATTAGGA
Found at i:979533 original size:85 final size:85
Alignment explanation
Indices: 979374--979533 Score: 250
Period size: 85 Copynumber: 1.9 Consensus size: 85
979364 TTAAACATTA
*
979374 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAAGA
979439 TATTATTTTAAATAGTATTT
66 TATTATTTTAAATAGTATTT
* * *
979459 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG-TTTTAAGTGTTTTAATTAGGATTTAAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGGATTTAAG
* *
979523 ATGTTGTTTTA
65 ATATTATTTTA
979534 GGAATTATCT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 3 0.04
85 65 0.96
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (85 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAAGA
TATTATTTTAAATAGTATTT
Found at i:979849 original size:18 final size:18
Alignment explanation
Indices: 979826--979860 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
979816 TTCTGGGGCA
* *
979826 TATTTTCCAAATCAAAAT
1 TATTTTCAAAACCAAAAT
979844 TATTTTCAAAACCAAAA
1 TATTTTCAAAACCAAAA
979861 GTCAACGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (18 bp):
TATTTTCAAAACCAAAAT
Found at i:980161 original size:27 final size:26
Alignment explanation
Indices: 980130--980181 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
980120 TTGCAATAAT
*
980130 TTTTTTATCCATATCTCTTTTATTTCA
1 TTTTTAATCCATATCT-TTTTATTTCA
**
980157 TTTTTAATCTTTATCTTTTTATTTC
1 TTTTTAATCCATATCTTTTTATTTC
980182 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTTAATCCATATCTTTTTATTTCA
Found at i:981747 original size:21 final size:21
Alignment explanation
Indices: 981723--981774 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
981713 GCAATTTCAT
981723 AAGAAAAGCTGGTTACATCCC
1 AAGAAAAGCTGGTTACATCCC
** *
981744 AAGAAAAATTGGTTACGTCCC
1 AAGAAAAGCTGGTTACATCCC
*
981765 AGGAAAAGCT
1 AAGAAAAGCT
981775 AATTGCATCC
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:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
AAGAAAAGCTGGTTACATCCC
Found at i:985926 original size:11 final size:11
Alignment explanation
Indices: 985898--985948 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
985888 TATTCTATTT
985898 TTTTA-TTTCA
1 TTTTATTTTCA
985908 TTTTATTTTCA
1 TTTTATTTTCA
* *
985919 -TTTAATTTCG
1 TTTTATTTTCA
*
985929 TGTTATTTTCA
1 TTTTATTTTCA
985940 TTTTATTTT
1 TTTTATTTT
985949 TAGCAAACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 13 0.39
11 20 0.61
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:985994 original size:15 final size:15
Alignment explanation
Indices: 985974--986002 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
985964 CATTCTATTT
985974 ATTTTATTTTAATTA
1 ATTTTATTTTAATTA
985989 ATTTTATTTTAATT
1 ATTTTATTTTAATT
986003 TTTCTGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTATTTTAATTA
Found at i:989865 original size:79 final size:80
Alignment explanation
Indices: 989725--989878 Score: 222
Period size: 79 Copynumber: 1.9 Consensus size: 80
989715 AAACATTATA
* *
989725 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAGTTAGAATTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGAATTTAAGA
989790 TATTATTTTAAATAG
66 TATTATTTTAAATAG
* * * *
989805 TATTTTATCTTTGTTTTAGG-ATTTTAGTTTAAATAG-TTTTAAGTGTTTTAATTAGGATTTAAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGAATTTAAG
*
989868 ATGTTATTTTA
65 ATATTATTTTA
989879 GGAATTATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 3 0.05
79 43 0.65
80 20 0.30
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (80 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGAATTTAAGA
TATTATTTTAAATAG
Found at i:989901 original size:79 final size:78
Alignment explanation
Indices: 989722--989909 Score: 193
Period size: 79 Copynumber: 2.4 Consensus size: 78
989712 TTTAAACATT
* * *
989722 ATATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATGTTAGTATTTCAGTTAGAATTTA
1 ATATATTTTAGCTTTCTTTTAGG-ATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGAATTTA
*
989787 GGATATTATTTTAA
65 AGATATTATTTTAA
* * * * * *
989801 ATAGTATTTTATCTTTGTTTTAGGATTTTAGTTTAAATAG-TTTTAAGTGTTTTAATTAGGATTT
1 ATA-TATTTTAGCTTTCTTTTAGGATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGAATTT
*
989865 AAGATGTTATTTTAGGA
64 AAGATATTATTTTA--A
*
989882 AT-TATCTTTAGC-TTCTTTTAGGAATTTA
1 ATATAT-TTTAGCTTTCTTTTAGGATTTTA
989910 AAGGCTATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 63 0.67
80 25 0.27
81 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (78 bp):
ATATATTTTAGCTTTCTTTTAGGATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGAATTTAA
GATATTATTTTAA
Found at i:996083 original size:6 final size:6
Alignment explanation
Indices: 996072--996110 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
996062 AAATCAAGGA
996072 AAAAAT AAAAAT -AAAA- AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
996111 GAACGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 8 0.26
6 23 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:996092 original size:16 final size:16
Alignment explanation
Indices: 996071--996109 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
996061 AAAATCAAGG
996071 AAAAAATAAAAATAAA
1 AAAAAATAAAAATAAA
996087 AAAAAATAAAAATAAA
1 AAAAAATAAAAATAAA
996103 AATAAAA
1 AA-AAAA
996110 AGAACGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAATAAAAATAAA
Found at i:996119 original size:22 final size:22
Alignment explanation
Indices: 996072--996119 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
996062 AAATCAAGGA
*
996072 AAAAATAAAAATAAAAAAAAAT
1 AAAAATAAAAATAAAAAAAAAG
* *
996094 AAAAATAAAAATAAAAAGAACG
1 AAAAATAAAAATAAAAAAAAAG
996116 AAAA
1 AAAA
996120 TAGAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAAATAAAAATAAAAAAAAAG
Found at i:1001523 original size:9 final size:9
Alignment explanation
Indices: 1001495--1001527 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1001485 ATATTATTCT
1001495 TTAATTAAA
1 TTAATTAAA
*
1001504 TT-ATAAAA
1 TTAATTAAA
1001512 TTAATTAAA
1 TTAATTAAA
1001521 TTAATTA
1 TTAATTA
1001528 GTATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:1002092 original size:27 final size:29
Alignment explanation
Indices: 1002033--1002093 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1002023 CTTTATGTCT
* *
1002033 TTATTATTATTTTAATTATCCATTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
*
1002062 -TATT-TTATTTTAAATA-CTAGTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
1002088 TTATTA
1 TTATTA
1002094 GGATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATTATTATTTTAAATATCCAGTATATA
Found at i:1003428 original size:3 final size:3
Alignment explanation
Indices: 1003420--1003483 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
1003410 ATAATATTTG
1003420 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
1003466 TAA T-A TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
1003484 TGTAATATAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1003491 original size:20 final size:20
Alignment explanation
Indices: 1003420--1003483 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
1003410 ATAATATTTG
1003420 TAATAATAATAATA--ATAA
1 TAATAATAATAATATGATAA
1003438 TAATAATAAATAATA--ATAA
1 TAATAAT-AATAATATGATAA
1003457 TAATAATAATAATATGATAA
1 TAATAATAATAATATGATAA
1003477 TAATAAT
1 TAATAAT
1003484 TGTAATATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.33
19 18 0.42
20 11 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TAATAATAATAATATGATAA
Found at i:1003500 original size:2 final size:2
Alignment explanation
Indices: 1003488--1003518 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1003478 AATAATTGTA
1003488 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
1003519 TATTAGACGA
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:1003803 original size:20 final size:20
Alignment explanation
Indices: 1003775--1003828 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1003765 AAAACATCCT
* * *
1003775 ACCCTGAGGTTTTATAGATG
1 ACCCGGAGGTTTTACAAATG
* *
1003795 ACCCGGAGGATTTACAAATT
1 ACCCGGAGGTTTTACAAATG
1003815 ACCCGGAGGTTTTA
1 ACCCGGAGGTTTTA
1003829 ATTTTCTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:1003856 original size:119 final size:119
Alignment explanation
Indices: 1003646--1003927 Score: 449
Period size: 119 Copynumber: 2.4 Consensus size: 119
1003636 AAATTAAAGT
* *
1003646 AAAAACATCATACCCAGAGGTTTTACAGATGACCCGGAGG-TTTATAAATCAACCGGAGGATTTA
1 AAAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTA
* *
1003710 ATTTTCTAGAACATTAAATGAGAAACTTTCGTAATCGTTTTCTCATTTTCATGC
66 ATTTTCTAGAACATTAAATGAGAAACTTTCGTAATCGCTTTCTCATTTTCATAC
* * * * *
1003764 AAAAACATCCTACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTA
1 AAAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTA
*
1003829 ATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATAC
66 ATTTTCTAGAACATTAAATGAGAAACTTTCGTAATCGCTTTCTCATTTTCATAC
* *
1003883 GAAAACATCTTACCCTGAGGTTTTACAGATGACCCGGAGGATTTA
1 AAAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGATTTA
1003928 ATTTTCTTGA
Statistics
Matches: 150, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
118 37 0.25
119 113 0.75
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (119 bp):
AAAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTA
ATTTTCTAGAACATTAAATGAGAAACTTTCGTAATCGCTTTCTCATTTTCATAC
Found at i:1003976 original size:99 final size:99
Alignment explanation
Indices: 1003795--1004244 Score: 542
Period size: 99 Copynumber: 4.3 Consensus size: 99
1003785 TTTATAGATG
* * * * * *
1003795 ACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
* * *
1003860 TAATCGCTTTCTCATTTTCATACGAAAACATCTT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
1003894 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
*
1003959 TAATCACTTTCTCATTTTCATGTGAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
* * * **
1003993 ACCCTGAGGTTTTACAGATGACCCCGAGGTTTTACAAATTACCTGGAGGT-TTTAATTTTCTAGA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTT---AATT---T-----TCTTGAA-CAT-T--A
*
1004057 ACTTTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGCGAAAACATCCT
51 A------ATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCT
*
1004112 ACCCTGAGGTTTTACAGATGACACGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
*
1004177 TAATCACTTTCTCATTTTCATGCAAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
1004211 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTA
1004245 CAAATTTGTG
Statistics
Matches: 303, Mismatches: 26, Indels: 44
0.81 0.07 0.12
Matches are distributed among these distances:
99 199 0.66
102 4 0.01
105 3 0.01
107 1 0.00
108 2 0.01
109 8 0.03
110 2 0.01
111 1 0.00
113 3 0.01
116 4 0.01
119 76 0.25
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (99 bp):
ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
TAATCACTTTCTCATTTTCATGCGAAAACATCCT
Found at i:1004041 original size:20 final size:20
Alignment explanation
Indices: 1003993--1004046 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1003983 AAAACATCCT
* *
1003993 ACCCTGAGGTTTTACAGATG
1 ACCCCGAGGTTTTACAAATG
*
1004013 ACCCCGAGGTTTTACAAATT
1 ACCCCGAGGTTTTACAAATG
**
1004033 ACCTGGAGGTTTTA
1 ACCCCGAGGTTTTA
1004047 ATTTTCTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
ACCCCGAGGTTTTACAAATG
Found at i:1004076 original size:218 final size:218
Alignment explanation
Indices: 1003698--1004250 Score: 980
Period size: 218 Copynumber: 2.5 Consensus size: 218
1003688 TATAAATCAA
* * **
1003698 CCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTCGTAATCGTTTTCTCATTTTCATG
1 CCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
*
1003763 CAAAAACATCCTACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTT
66 CAAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTT
*
1003828 AATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACGAAAACATCT
131 AATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACGAAAACATCC
1003893 TACCCTGAGGTTTTACAGATGAC
196 TACCCTGAGGTTTTACAGATGAC
1003916 CCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
1 CCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
** * * *
1003981 TGAAAACATCCTACCCTGAGGTTTTACAGATGACCCCGAGGTTTTACAAATTACCTGGAGGTTTT
66 CAAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTT
* *
1004046 AATTTTCTAGAACTTTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGCGAAAACATCC
131 AATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACGAAAACATCC
1004111 TACCCTGAGGTTTTACAGATGAC
196 TACCCTGAGGTTTTACAGATGAC
*
1004134 ACGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
1 CCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
1004199 CAAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATT
66 CAAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATT
1004251 TGTGGAAAAT
Statistics
Matches: 317, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 317 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (218 bp):
CCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATG
CAAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTT
AATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATACGAAAACATCC
TACCCTGAGGTTTTACAGATGAC
Found at i:1004110 original size:119 final size:119
Alignment explanation
Indices: 1003894--1004133 Score: 399
Period size: 119 Copynumber: 2.0 Consensus size: 119
1003884 AAAACATCTT
* * *
1003894 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
1 ACCCCGAGGTTTTACAAATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
*
1003959 TAATCACTTTCTCATTTTCATGTGAAAACATCCTACCCTGAGGTTTTACAGATG
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* * * *
1004013 ACCCCGAGGTTTTACAAATTACCTGGAGGTTTTAATTTTCTAGAACTTTAAATGAGAAACTTTGG
1 ACCCCGAGGTTTTACAAATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
*
1004078 TAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
1004132 AC
1 AC
1004134 ACGGAGGATT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 112 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (119 bp):
ACCCCGAGGTTTTACAAATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
TAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
Found at i:1006986 original size:14 final size:14
Alignment explanation
Indices: 1006967--1006994 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1006957 TTGATTCAAT
1006967 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
1006981 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
1006995 CTCTGATGTA
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:1013306 original size:9 final size:9
Alignment explanation
Indices: 1013278--1013310 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1013268 ATATTATTCT
1013278 TTAATTAAA
1 TTAATTAAA
*
1013287 TT-ATAAAA
1 TTAATTAAA
1013295 TTAATTAAA
1 TTAATTAAA
1013304 TTAATTA
1 TTAATTA
1013311 GTATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:1013868 original size:27 final size:29
Alignment explanation
Indices: 1013809--1013869 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1013799 CTTTATGTCT
* *
1013809 TTATTATTATTTTAATTATCCATTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
*
1013838 -TATT-TTATTTTAAATA-CTAGTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
1013864 TTATTA
1 TTATTA
1013870 GGATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATTATTATTTTAAATATCCAGTATATA
Found at i:1015218 original size:3 final size:3
Alignment explanation
Indices: 1015210--1015272 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
1015200 GTAATATTTG
* **
1015210 TAA TAA TAA TAA TAA TAA TAA TAA T-A TGA TAA TAA TAA TTG TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1015256 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1015273 TATTATTGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
2 4 0.08
3 49 0.92
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1023918 original size:2 final size:2
Alignment explanation
Indices: 1023911--1023935 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1023901 CTCATAGTTC
1023911 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1023936 CAAGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1029160 original size:33 final size:33
Alignment explanation
Indices: 1029123--1029258 Score: 107
Period size: 33 Copynumber: 4.1 Consensus size: 33
1029113 ATCCTTATAA
**
1029123 CCAACCGC-CACAACTAGGTGCTAATCCATATGG
1 CCAACC-CTCACAACTAAATGCTAATCCATATGG
*
1029156 CCAACCCTCACAGCTAAATGCTAATCCATATGG
1 CCAACCCTCACAACTAAATGCTAATCCATATGG
* ** * *
1029189 TCAA-CCTGTGCAGCCAAATGCTAATCCATATGG
1 CCAACCCT-CACAACTAAATGCTAATCCATATGG
* * * * *
1029222 TCAA-CTTGCACAGCCAAATGCTAATCCATATGC
1 CCAACCCT-CACAACTAAATGCTAATCCATATGG
1029255 CCAA
1 CCAA
1029259 ACCATACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 4 0.04
33 85 0.96
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (33 bp):
CCAACCCTCACAACTAAATGCTAATCCATATGG
Found at i:1029272 original size:33 final size:33
Alignment explanation
Indices: 1029141--1029273 Score: 137
Period size: 33 Copynumber: 4.0 Consensus size: 33
1029131 CACAACTAGG
* *
1029141 TGCTAATCCATATGGCCAACCCTCACAGCTAAA
1 TGCTAATCCATATGGCCAACCATCACAGCCAAA
* **
1029174 TGCTAATCCATATGGTCAACC-TGTGCAGCCAAA
1 TGCTAATCCATATGGCCAACCAT-CACAGCCAAA
* *
1029207 TGCTAATCCATATGGTCAA-CTTGCACAGCCAAA
1 TGCTAATCCATATGGCCAACCAT-CACAGCCAAA
* *
1029240 TGCTAATCCATATGCCCAAACCAT-ACAACCAAA
1 TGCTAATCCATATGGCC-AACCATCACAGCCAAA
1029273 T
1 T
1029274 TTGAATAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
32 2 0.02
33 80 0.93
34 2 0.02
35 2 0.02
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (33 bp):
TGCTAATCCATATGGCCAACCATCACAGCCAAA
Found at i:1029272 original size:66 final size:66
Alignment explanation
Indices: 1029141--1029273 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
1029131 CACAACTAGG
* ** * * *
1029141 TGCTAATCCATATGGCCAACCCTCACAGCTAAATGCTAATCCATATGGTCAACCTGTGCAGCCAA
1 TGCTAATCCATATGGCCAACCCTCACAGCCAAATGCTAATCCATATGCCCAACCTATACAACCAA
1029206 A
66 A
* *
1029207 TGCTAATCCATATGGTCAA-CTTGCACAGCCAAATGCTAATCCATATGCCCAAACC-ATACAACC
1 TGCTAATCCATATGGCCAACCCT-CACAGCCAAATGCTAATCCATATGCCC-AACCTATACAACC
1029270 AAA
64 AAA
1029273 T
1 T
1029274 TTGAATAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.89
67 4 0.07
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (66 bp):
TGCTAATCCATATGGCCAACCCTCACAGCCAAATGCTAATCCATATGCCCAACCTATACAACCAA
A
Found at i:1031070 original size:31 final size:31
Alignment explanation
Indices: 1031003--1031062 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1030993 CAATTTAAGG
*
1031003 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1031034 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1031063 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1031191 original size:19 final size:19
Alignment explanation
Indices: 1031140--1031192 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1031130 ATAGTAATTT
* *
1031140 ACTATTTGAACAGCAAATT
1 ACTATTTGAACAGTAAATC
1031159 ACTATTTGAACAGTAAATC
1 ACTATTTGAACAGTAAATC
* *
1031178 ATTGTTTGAACAGTA
1 ACTATTTGAACAGTA
1031193 CCCGAGGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (19 bp):
ACTATTTGAACAGTAAATC
Found at i:1031401 original size:21 final size:21
Alignment explanation
Indices: 1031368--1031407 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1031358 TTTTTGTAGA
*
1031368 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1031390 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1031408 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1034639 original size:19 final size:19
Alignment explanation
Indices: 1034607--1034677 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
1034597 ACAAAAATGT
* *
1034607 TTTTATGAATAGTAATTTAC
1 TTTT-TGAACAGTAAATTAC
1034627 TTTTTGAACAGTAAATTAC
1 TTTTTGAACAGTAAATTAC
* *
1034646 TATTTGAACAGTAAATCA-
1 TTTTTGAACAGTAAATTAC
1034664 TTGTTTGAACAGTA
1 TT-TTTGAACAGTA
1034678 CCCGAGGCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.02
19 40 0.89
20 4 0.09
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (19 bp):
TTTTTGAACAGTAAATTAC
Found at i:1034809 original size:21 final size:21
Alignment explanation
Indices: 1034783--1034824 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1034773 ATTTGAATAT
*
1034783 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1034804 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1034825 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1034885 original size:21 final size:21
Alignment explanation
Indices: 1034852--1034891 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1034842 TTTTTGCAGA
*
1034852 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1034874 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1034892 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1038440 original size:22 final size:22
Alignment explanation
Indices: 1038414--1038465 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1038404 TTTGTTTTCA
1038414 ATCATTTCTGCATGGTTTTGCT
1 ATCATTTCTGCATGGTTTTGCT
1038436 ATCATTTCTGCATGGTTTTGCT
1 ATCATTTCTGCATGGTTTTGCT
1038458 ATCATTTC
1 ATCATTTC
1038466 AAAATCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (22 bp):
ATCATTTCTGCATGGTTTTGCT
Found at i:1040334 original size:59 final size:60
Alignment explanation
Indices: 1040266--1040395 Score: 199
Period size: 60 Copynumber: 2.2 Consensus size: 60
1040256 TACCACTATA
* *
1040266 GCCACTCAACTAAACCCTATCAAAC-ATGTGGCCATCTAAGAATTTTTACTATCAATTTG
1 GCCACTCAACTAAACCCTATCAAACAATGCGGCCATCTAAGAATTTATACTATCAATTTG
* * *
1040325 GCCACTCAACTATACCCTATCAAACAATGCGGCCATTTAAGAATTTATGCTATCAATTTG
1 GCCACTCAACTAAACCCTATCAAACAATGCGGCCATCTAAGAATTTATACTATCAATTTG
*
1040385 GCCTCTCAACT
1 GCCACTCAACT
1040396 TTCTTGCCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 24 0.38
60 40 0.62
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (60 bp):
GCCACTCAACTAAACCCTATCAAACAATGCGGCCATCTAAGAATTTATACTATCAATTTG
Found at i:1048542 original size:12 final size:12
Alignment explanation
Indices: 1048523--1048600 Score: 75
Period size: 12 Copynumber: 6.5 Consensus size: 12
1048513 AATAAATGTC
1048523 GCTGAGGGTGCT
1 GCTGAGGGTGCT
*
1048535 GGTGAGGGTGCT
1 GCTGAGGGTGCT
**
1048547 GCTGATTGTGCT
1 GCTGAGGGTGCT
*
1048559 GCTGAGGGTGTT
1 GCTGAGGGTGCT
* *
1048571 GGTGAGGGTGTT
1 GCTGAGGGTGCT
* **
1048583 GTTGATTGTGCT
1 GCTGAGGGTGCT
1048595 GCTGAG
1 GCTGAG
1048601 AGGCTTGCTG
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.09, C:0.10, G:0.47, T:0.33
Consensus pattern (12 bp):
GCTGAGGGTGCT
Found at i:1048574 original size:36 final size:36
Alignment explanation
Indices: 1048523--1048600 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
1048513 AATAAATGTC
1048523 GCTGAGGGTGCTGGTGAGGGTGCTGCTGATTGTGCT
1 GCTGAGGGTGCTGGTGAGGGTGCTGCTGATTGTGCT
* * *
1048559 GCTGAGGGTGTTGGTGAGGGTGTTGTTGATTGTGCT
1 GCTGAGGGTGCTGGTGAGGGTGCTGCTGATTGTGCT
1048595 GCTGAG
1 GCTGAG
1048601 AGGCTTGCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.09, C:0.10, G:0.47, T:0.33
Consensus pattern (36 bp):
GCTGAGGGTGCTGGTGAGGGTGCTGCTGATTGTGCT
Found at i:1048640 original size:63 final size:65
Alignment explanation
Indices: 1048573--1048702 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 65
1048563 AGGGTGTTGG
* * *
1048573 TGAGGGTGTTGTTGATTGTGCTGCTGAGAGGCTTGCTGAAAATGTAGTTG-T-TGCTGGTCTTGA
1 TGAGGGTGCTGGTGATTATGCTGCTGAGAGGCTTGCTGAAAATGTAGTTGATCTGCTGGTCTTGA
*
1048636 TGAGGGTGCTGGTGATTATGCTGCTGAGAGGGTTGCTGAAAATGTAGTTGATGCTGCTGGTCTTG
1 TGAGGGTGCTGGTGATTATGCTGCTGAGAGGCTTGCTGAAAATGTAGTTGAT-CTGCTGGTCTTG
1048701 A
65 A
1048702 T
1 T
1048703 AATATTGGAG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 46 0.77
64 1 0.02
66 13 0.22
ACGTcount: A:0.17, C:0.10, G:0.37, T:0.36
Consensus pattern (65 bp):
TGAGGGTGCTGGTGATTATGCTGCTGAGAGGCTTGCTGAAAATGTAGTTGATCTGCTGGTCTTGA
Found at i:1051328 original size:24 final size:20
Alignment explanation
Indices: 1051271--1051328 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1051261 TTCCCCTTGA
*
1051271 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1051291 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1051314 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1051329 CTACCCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1051344 original size:19 final size:19
Alignment explanation
Indices: 1051320--1051356 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1051310 TAACATGTGC
1051320 ATCGATGCACTACCCATGT
1 ATCGATGCACTACCCATGT
1051339 ATCGATGCACTACCCATG
1 ATCGATGCACTACCCATG
1051357 CATTGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (19 bp):
ATCGATGCACTACCCATGT
Found at i:1055160 original size:19 final size:19
Alignment explanation
Indices: 1055136--1055201 Score: 123
Period size: 19 Copynumber: 3.5 Consensus size: 19
1055126 CTTTAACATG
1055136 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
1055155 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
*
1055174 TGCATCGATGCACTACTCA
1 TGCATCGATGCACTACCCA
1055193 TGCATCGAT
1 TGCATCGAT
1055202 ACACAAATCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACTACCCA
Found at i:1059939 original size:13 final size:13
Alignment explanation
Indices: 1059923--1059959 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1059913 CATCAATTAA
1059923 AAAATCATTTTCG
1 AAAATCATTTTCG
1059936 AAAATCATTTTCG
1 AAAATCATTTTCG
1059949 AAAATCATTTT
1 AAAATCATTTT
1059960 ATTTCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (13 bp):
AAAATCATTTTCG
Found at i:1060432 original size:21 final size:23
Alignment explanation
Indices: 1060380--1060456 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
1060370 AGCAGAGTGA
* *
1060380 ATCGATACACATTCAAGGAATGC
1 ATCGATGCACATTCAAGGGATGC
* * * *
1060403 ATCGGTGCACCTTC-ATGG-TGT
1 ATCGATGCACATTCAAGGGATGC
1060424 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTCAAGGGATGC
1060447 ATCGATGCAC
1 ATCGATGCAC
1060457 TGTCTAGTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 14 0.33
22 5 0.12
23 23 0.55
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
ATCGATGCACATTCAAGGGATGC
Found at i:1062938 original size:20 final size:21
Alignment explanation
Indices: 1062900--1062938 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1062890 AAGTTTTAAG
* *
1062900 ATCATCAATTTTCTTTTGATA
1 ATCATCAATTTACTCTTGATA
1062921 ATCAT-AATTTACTCTTGA
1 ATCATCAATTTACTCTTGA
1062939 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
ATCATCAATTTACTCTTGATA
Found at i:1066289 original size:23 final size:23
Alignment explanation
Indices: 1066263--1066351 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
1066253 TCCTTATGGA
* * *
1066263 CAATTTTATATGGCACTACGATG
1 CAATTCTACATGGCACTTCGATG
* *
1066286 CAATTCTACGTGGCACTTCGGTG
1 CAATTCTACATGGCACTTCGATG
*
1066309 CAATTCTACGTGGCACTTC-AGTG
1 CAATTCTACATGGCACTTCGA-TG
1066332 CAATTCTACATGGCACTTCG
1 CAATTCTACATGGCACTTCG
1066352 GTATAATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (23 bp):
CAATTCTACATGGCACTTCGATG
Found at i:1066359 original size:23 final size:23
Alignment explanation
Indices: 1066273--1066353 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
1066263 CAATTTTATA
* *
1066273 TGGCACTACGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1066296 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1066319 TGGCACTTCAGTGCAATTCTACA
1 TGGCACTTCGGTGCAATTCTACG
1066342 TGGCACTTCGGT
1 TGGCACTTCGGT
1066354 ATAATTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1067004 original size:19 final size:20
Alignment explanation
Indices: 1066959--1067009 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1066949 ACTGTTCACA
* * *
1066959 ATACTATTTACACAGTATCG
1 ATACTATTCATACAGTATAG
1066979 ATACTATTCATACAGTATAG
1 ATACTATTCATACAGTATAG
1066999 -TACTATTCATA
1 ATACTATTCATA
1067010 AAAACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
ATACTATTCATACAGTATAG
Found at i:1068574 original size:2 final size:2
Alignment explanation
Indices: 1068567--1068599 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1068557 AACAATTTTA
1068567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1068600 GTTTGATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1068590 original size:204 final size:201
Alignment explanation
Indices: 1068183--1068584 Score: 677
Period size: 198 Copynumber: 2.0 Consensus size: 201
1068173 TAAGTATGAG
*
1068183 CCAATTTCATATATAAATATAATTTTAAGGACTAAATTGAATAAATATAAAATTTAAAATTTAAA
1 CCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAATAAATATAAAATTTAAAATTT-AA
* **
1068248 TTTAAATATATTAAAGGATGTAGAGGGATCAAATCGAAATAATTATAAATGTGAGGAAAATTGTA
65 --TAAATATATTAAAGAATACAGAGGGATCAAATCGAAATAATTATAAATGTGAGGAAAATTGTA
*
1068313 AAATGGACTGAATTGCATTCATTTCAAAAGTTGAGGAGAAATTTGAAACAATTATAATATATATA
128 AAATGGACTAAATTGCATTCATTTCAAAAGTTGAGGAGAAATTTGAAACAATTATAATATATATA
1068378 TATATATAT
193 TATATATAT
*
1068387 CCAATTTCATATGCAAATATAATTTTAAGGACTAAATTGAATAAATATACAAA-TTAAAA-TT-A
1 CCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAATAAATATA-AAATTTAAAATTTAA
1068449 -AAATATATTAAAGAATACAGAGGGATCAAATCGAAATAATTATAAATGTGAGGAAAATTGTAAA
65 TAAATATATTAAAGAATACAGAGGGATCAAATCGAAATAATTATAAATGTGAGGAAAATTGTAAA
*
1068513 ATGGACTAAATTGCATTCATTTCAAAAGTTGAGGAGAAATTTGAAACAATTTTAATATATATATA
130 ATGGACTAAATTGCATTCATTTCAAAAGTTGAGGAGAAATTTGAAACAATTATAATATATATATA
1068578 TATATAT
195 TATATAT
1068585 ATATATATAT
Statistics
Matches: 190, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
198 131 0.69
201 1 0.01
203 2 0.01
204 53 0.28
205 3 0.02
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (201 bp):
CCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAATAAATATAAAATTTAAAATTTAAT
AAATATATTAAAGAATACAGAGGGATCAAATCGAAATAATTATAAATGTGAGGAAAATTGTAAAA
TGGACTAAATTGCATTCATTTCAAAAGTTGAGGAGAAATTTGAAACAATTATAATATATATATAT
ATATAT
Found at i:1068682 original size:13 final size:13
Alignment explanation
Indices: 1068634--1068682 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1068624 AATGCATGTA
*
1068634 TATATATTATAA-
1 TATACATTATAAG
*
1068646 TGTACATTATAAG
1 TATACATTATAAG
* *
1068659 TATATAATATAAG
1 TATACATTATAAG
1068672 TATACATTATA
1 TATACATTATA
1068683 CTTATAATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (13 bp):
TATACATTATAAG
Found at i:1068688 original size:26 final size:25
Alignment explanation
Indices: 1068634--1068682 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1068624 AATGCATGTA
* *
1068634 TATATATTATAATGTACATTATAAG
1 TATATAATATAATATACATTATAAG
1068659 TATATAATATAAGTATACATTATA
1 TATATAATATAA-TATACATTATA
1068683 CTTATAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
TATATAATATAATATACATTATAAG
Found at i:1069335 original size:23 final size:22
Alignment explanation
Indices: 1069302--1069349 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
1069292 TATATATATA
1069302 TATATTAAAATT-TTAAGTTAAAT
1 TATATTAAAATTATTAA-TT-AAT
*
1069325 TATATTTAAATTATTAATTAAT
1 TATATTAAAATTATTAATTAAT
1069347 TAT
1 TAT
1069350 TACATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTAAAATTATTAATTAAT
Found at i:1069707 original size:75 final size:75
Alignment explanation
Indices: 1069567--1069719 Score: 220
Period size: 75 Copynumber: 2.0 Consensus size: 75
1069557 ATTAATTATC
**
1069567 ATAGTTTATTATAAATTCAAAATCTCACAAATTCATCAAAGTCTTGCAACTATATCAATTGAACT
1 ATAGTTTATTATAAATTCAAAATCTCACAAATTCATCAAAGTCTCACAACTATATCAATTGAACT
1069632 TATAAGTAAT
66 TATAAGTAAT
* * *
1069642 ATAGTTTATTATAAATTCAAAATCTTACAACTTCATC-AATTCTCACAACT-TCATCAATTGTAA
1 ATAGTTTATTATAAATTCAAAATCTCACAAATTCATCAAAGTCTCACAACTAT-ATCAATTG-AA
*
1069705 CTTATAAGTCAT
64 CTTATAAGTAAT
1069717 ATA
1 ATA
1069720 AATACCAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
73 1 0.01
74 18 0.26
75 51 0.73
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.37
Consensus pattern (75 bp):
ATAGTTTATTATAAATTCAAAATCTCACAAATTCATCAAAGTCTCACAACTATATCAATTGAACT
TATAAGTAAT
Found at i:1070912 original size:6 final size:5
Alignment explanation
Indices: 1070888--1070922 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1070878 GTTCGAATTT
*
1070888 TTTTA TTTTA TTTTA TTTTA TTTT- TATTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1070923 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 24 0.89
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1070919 original size:14 final size:15
Alignment explanation
Indices: 1070888--1070922 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1070878 GTTCGAATTT
*
1070888 TTTTATTTTATTTTA
1 TTTTATTTTATATTA
1070903 TTTTATTTT-TATTA
1 TTTTATTTTATATTA
1070917 TTTTAT
1 TTTTAT
1070923 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATATTA
Found at i:1071116 original size:37 final size:36
Alignment explanation
Indices: 1070990--1071420 Score: 452
Period size: 37 Copynumber: 11.8 Consensus size: 36
1070980 TTTGAAAATG
* * * *
1070990 TATATATTATATAGTTTTGAAAACATTTTGAATA--
1 TATATAATATATAGTTTTGAAAATATTTTAAAAACT
* *
1071024 TATATAATATATATTTTTTGAAAACATTTTGAAATATA-T
1 TATATAATATATA-GTTTTGAAAATATTTT-AAA-A-ACT
1071063 ATATATAATATATAGTTTTTGAAAATATTTTAAAAACT
1 -TATATAATATATAG-TTTTGAAAATATTTTAAAAACT
* *
1071101 TGTATAATATATAGTTTTGAAAACATTTTAAAAACT
1 TATATAATATATAGTTTTGAAAATATTTTAAAAACT
*
1071137 TATATCATATATAGTTTTG-AAATCATTTTGAAAAACT
1 TATATAATATATAGTTTTGAAAAT-ATTTT-AAAAACT
1071174 TATATAATATATAGTTTTG-AAATCATTTTGAAAAACT
1 TATATAATATATAGTTTTGAAAAT-ATTTT-AAAAACT
*
1071211 TATATAATATATAGTTTTG-AAATCATTTTGAAAACT
1 TATATAATATATAGTTTTGAAAAT-ATTTTAAAAACT
*
1071247 TATATAATATATAATTTTGAAAATATTTTTAAAAACT
1 TATATAATATATAGTTTTGAAAATA-TTTTAAAAACT
* * * * *
1071284 TATATAATATATAATTTTAAAAACATTTTTTTGAAAACA
1 TATATAATATATAGTTTT-GAAA-A-TATTTTAAAAACT
* *
1071323 TATATAATATATAGTTTT-AAAACATTATTGAAAAC-
1 TATATAATATATAGTTTTGAAAATATT-TTAAAAACT
**
1071358 TATATAATATATAGTTTTGAAAACCTTTT-AAAA-T
1 TATATAATATATAGTTTTGAAAATATTTTAAAAACT
1071392 ATATATAATATATAGTTTT-AAAATATTTT
1 -TATATAATATATAGTTTTGAAAATATTTT
1071421 TTTGAAAATA
Statistics
Matches: 353, Mismatches: 25, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
34 24 0.07
35 58 0.16
36 86 0.24
37 121 0.34
38 6 0.02
39 30 0.08
40 28 0.08
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAATATTTTAAAAACT
Found at i:1071148 original size:147 final size:142
Alignment explanation
Indices: 1070990--1071420 Score: 532
Period size: 147 Copynumber: 3.0 Consensus size: 142
1070980 TTTGAAAATG
* * *
1070990 TATATATTATATAGTTTTGAAAACATTTTG-AATATATATAATATATATTTTTTGAAAACATTTT
1 TATATAATATATAGTTTTGAAAACATTTTGAAAAATATATAATATATA-GTTTTGAAAACATTTT
*
1071054 GAAATATATATATATAATATATAGTTTTTGAAAATATTTTAAAAACTTGTATAATATATAGTTTT
65 GAAA-A-AT-TATATAATATATAG-TTTTGAAAATATTTT-AAAACTTATATAATATATAGTTTT
*
1071119 GAAAACATTTTAAAAACT
125 GAAAATATTTTAAAAACT
* * *
1071137 TATATCATATATAGTTTTGAAATCATTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTT
1 TATATAATATATAGTTTTGAAAACATTTTGAAAAA--TATATAATATATAGTTTTGAAAACATTT
*
1071202 TGAAAAACTTATATAATATATAGTTTTG-AAATCATTTTGAAAACTTATATAATATATAATTTTG
64 TGAAAAA-TTATATAATATATAGTTTTGAAAAT-ATTTT-AAAACTTATATAATATATAGTTTTG
1071266 AAAATATTTTTAAAAACT
126 AAAATA-TTTTAAAAACT
* *
1071284 TATATAATATATAATTTTAAAAACATTTTTTTGAAAACATATATAATATATAGTTTT-AAAACAT
1 TATATAATATATAGTTTTGAAAACA---TTTTGAAAA-ATATATAATATATAGTTTTGAAAACAT
* **
1071348 TATTG-AAAACTATATAATATATAGTTTTGAAAACCTTTTAAAA-TATATATAATATATAGTTTT
62 T-TTGAAAAATTATATAATATATAGTTTTGAAAATATTTTAAAACT-TATATAATATATAGTTTT
1071411 -AAAATATTTT
125 GAAAATATTTT
1071421 TTTGAAAATA
Statistics
Matches: 252, Mismatches: 19, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
144 4 0.02
145 11 0.04
146 59 0.23
147 97 0.38
148 19 0.08
149 39 0.15
150 22 0.09
151 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (142 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAAATATATAATATATAGTTTTGAAAACATTTTG
AAAAATTATATAATATATAGTTTTGAAAATATTTTAAAACTTATATAATATATAGTTTTGAAAAT
ATTTTAAAAACT
Found at i:1071217 original size:110 final size:108
Alignment explanation
Indices: 1070990--1071420 Score: 527
Period size: 110 Copynumber: 3.9 Consensus size: 108
1070980 TTTGAAAATG
* * *
1070990 TATATATTATATAGTTTTGAAAACATTTTGAATA-TATATAATATATATTTTTTGAAAACATTTT
1 TATATAATATATAGTTTTGAAAACATTTTGAAAACTATATAATATATA-GTTTTGAAAACATTTT
1071054 GAAATATATATATATAATATATAGTTTTTGAAAATATTTT-AAAAACT
65 GAAA-A-ATATATATAATATATAG-TTTT-AAAATATTTTGAAAAACT
* * * *
1071101 TGTATAATATATAGTTTTGAAAACATTTTAAAAACTTATATCATATATAGTTTTGAAATCATTTT
1 TATATAATATATAGTTTTGAAAACATTTTGAAAAC-TATATAATATATAGTTTTGAAAACATTTT
*
1071166 GAAAAACT-TATATAATATATAGTTTTGAAATCATTTTGAAAAACT
65 GAAAAA-TATATATAATATATAGTTTTAAAAT-ATTTTGAAAAACT
* * *
1071211 TATATAATATATAGTTTTGAAATCATTTTGAAAACTTATATAATATATAATTTTGAAAATATTTT
1 TATATAATATATAGTTTTGAAAACATTTTGAAAAC-TATATAATATATAGTTTTGAAAACATTTT
* * * *
1071276 TAAAAACT-TATATAATATATAATTTTAAAAACATTTTTTTG-AAAACA
65 GAAAAA-TATATATAATATATAGTTTT--AAA-A-TATTTTGAAAAACT
*
1071323 TATATAATATATAGTTTT-AAAACATTATTGAAAACTATATAATATATAGTTTTGAAAACCTTTT
1 TATATAATATATAGTTTTGAAAACATT-TTGAAAACTATATAATATATAGTTTTGAAAACATTTT
1071387 --AAAATATATATAATATATAGTTTTAAAATATTTT
65 GAAAAATATATATAATATATAGTTTTAAAATATTTT
1071421 TTTGAAAATA
Statistics
Matches: 283, Mismatches: 26, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
105 5 0.02
106 1 0.00
107 3 0.01
108 5 0.02
109 30 0.11
110 104 0.37
111 65 0.23
112 51 0.18
113 18 0.06
114 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (108 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAACTATATAATATATAGTTTTGAAAACATTTTG
AAAAATATATATAATATATAGTTTTAAAATATTTTGAAAAACT
Found at i:1071547 original size:19 final size:21
Alignment explanation
Indices: 1071520--1071559 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1071510 GGTCCAGAAA
1071520 GGGTGTGGG-TTG-CCCAACC
1 GGGTGTGGGCTTGACCCAACC
*
1071539 GGGTTTGGGCTTGACCCAACC
1 GGGTGTGGGCTTGACCCAACC
1071560 TAATCTCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGTGTGGGCTTGACCCAACC
Found at i:1072520 original size:22 final size:23
Alignment explanation
Indices: 1072492--1072544 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1072482 TGGTAATTTA
*
1072492 AATTTTAGTTATTTATT-TTTTT
1 AATTTTAGTAATTTATTCTTTTT
*
1072514 AATTTTAG-AATTTTTTCTTTTT
1 AATTTTAGTAATTTATTCTTTTT
*
1072536 AGTTTTAGT
1 AATTTTAGT
1072545 GGTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.68
Consensus pattern (23 bp):
AATTTTAGTAATTTATTCTTTTT
Found at i:1072561 original size:9 final size:9
Alignment explanation
Indices: 1072549--1072587 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1072539 TTTAGTGGTT
1072549 TTTATTTTA
1 TTTATTTTA
*
1072558 TTTATTTAA
1 TTTATTTTA
1072567 TTTATTTTA
1 TTTATTTTA
*
1072576 -TTACTTTA
1 TTTATTTTA
1072584 TTTA
1 TTTA
1072588 ACATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1072679 original size:7 final size:7
Alignment explanation
Indices: 1072667--1072776 Score: 70
Period size: 7 Copynumber: 15.9 Consensus size: 7
1072657 TGATTTACTT
1072667 TTTTTTA
1 TTTTTTA
1072674 TTTTTTA
1 TTTTTTA
1072681 TTTTTTA
1 TTTTTTA
1072688 -TTTTTA
1 TTTTTTA
*
1072694 TTTTCTA
1 TTTTTTA
1072701 --TTTTA
1 TTTTTTA
1072706 TTTATTTAA
1 TTT-TTT-A
* *
1072715 TATTTAA
1 TTTTTTA
1072722 TATTTTTA
1 T-TTTTTA
1072730 -TTTTTA
1 TTTTTTA
1072736 TCTTTTTGA
1 T-TTTTT-A
*
1072745 -TTTAT-
1 TTTTTTA
*
1072750 TTTTTTC
1 TTTTTTA
* *
1072757 CTTTTTC
1 TTTTTTA
1072764 TTTTTTA
1 TTTTTTA
1072771 TTTTTT
1 TTTTTT
1072777 CCCTTTGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.05
6 16 0.20
7 43 0.53
8 14 0.17
9 4 0.05
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:1072691 original size:13 final size:13
Alignment explanation
Indices: 1072667--1072775 Score: 87
Period size: 13 Copynumber: 7.9 Consensus size: 13
1072657 TGATTTACTT
1072667 TTTTTTATTTTTTA
1 TTTTTTA-TTTTTA
1072681 TTTTTTATTTTTA
1 TTTTTTATTTTTA
*
1072694 TTTTCTA-TTTTA
1 TTTTTTATTTTTA
*
1072706 TTTATTTAATATTTAA
1 TTT-TTT-AT-TTTTA
1072722 TATTTTTATTTTTA
1 T-TTTTTATTTTTA
1072736 TCTTTTTGATTTATT-
1 T-TTTTT-ATTT-TTA
** *
1072751 TTTTTCCTTTTTC
1 TTTTTTATTTTTA
1072764 TTTTTTATTTTT
1 TTTTTTATTTTT
1072776 TCCCTTTGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
12 10 0.13
13 27 0.35
14 22 0.28
15 7 0.09
16 10 0.13
17 2 0.03
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1075352 original size:21 final size:21
Alignment explanation
Indices: 1075322--1075369 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1075312 TAATTTTCAA
*
1075322 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1075343 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1075364 ACATTG
1 ACATTG
1075370 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1091809 original size:27 final size:27
Alignment explanation
Indices: 1091771--1091824 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1091761 TGGGAAGTGG
1091771 GGCTCTAAAGTGGGTTTTAGGCCTTGA
1 GGCTCTAAAGTGGGTTTTAGGCCTTGA
1091798 GGCTCTAAAGTGGGTTTTAGGCCTTGA
1 GGCTCTAAAGTGGGTTTTAGGCCTTGA
1091825 TTGTAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (27 bp):
GGCTCTAAAGTGGGTTTTAGGCCTTGA
Found at i:1100273 original size:51 final size:51
Alignment explanation
Indices: 1100134--1100273 Score: 199
Period size: 51 Copynumber: 2.7 Consensus size: 51
1100124 TTTAGTGTTG
* * *
1100134 GAATTAAGTGATGATTTCACTGGTGTAAGTCTATGTTATATATCACTACTA
1 GAATTAAGTGATGATTTAACCGATGTAAGTCTATGTTATATATCACTACTA
* * *
1100185 GAATTAAGTGATCATTTAATCGTTGTAAGTCTATGTTATATATCACTACTA
1 GAATTAAGTGATGATTTAACCGATGTAAGTCTATGTTATATATCACTACTA
* * *
1100236 GAATTAAGTGATGATTTAACCAATGTATGTCTGTGTTA
1 GAATTAAGTGATGATTTAACCGATGTAAGTCTATGTTA
1100274 AGTTTCACCA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (51 bp):
GAATTAAGTGATGATTTAACCGATGTAAGTCTATGTTATATATCACTACTA
Found at i:1100407 original size:77 final size:77
Alignment explanation
Indices: 1100210--1100511 Score: 444
Period size: 77 Copynumber: 3.9 Consensus size: 77
1100200 TTAATCGTTG
* * *
1100210 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAATGTATGTCTGTGTTAA
1 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
*
1100275 GTTTCACCAGTA
66 GTTTCACCGGTA
* * *
1100287 T-AGTCTATGTTATATATCACTGCTAGAATTAAGTGATGATTTAACTAGTGTAAGTCAATGTTAA
1 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
1100351 GTTTCACCGGTA
66 GTTTCACCGGTA
* *
1100363 TAAGTCTATGCTATATATCACTACTGGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
1 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
* *
1100428 GTTTTACCGGTG
66 GTTTCACCGGTA
** * ** *
1100440 TAAGTCTATGTTATATATCACTGTTGGAATTAAGTGATGATTTAACTGGTGTAAGTTTATGTTAA
1 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
1100505 GTTTCAC
66 GTTTCAC
1100512 AAGTGTAAGT
Statistics
Matches: 203, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
76 69 0.34
77 134 0.66
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (77 bp):
TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
GTTTCACCGGTA
Found at i:1100428 original size:153 final size:154
Alignment explanation
Indices: 1100210--1100511 Score: 480
Period size: 153 Copynumber: 2.0 Consensus size: 154
1100200 TTAATCGTTG
* * *
1100210 TAAGTCTATGTTATATATCACTACTAGAATTAAGTGATGATTTAACCAATGTATGTCTGTGTTAA
1 TAAGTCTATGCTATATATCACTACTAGAATTAAGTGATGATTTAACCAATGTAAGTCTATGTTAA
1100275 GTTTCACCAGTAT-AGTCTATGTTATATATCACTGCTAGAATTAAGTGATGATTTAACTAGTGTA
66 GTTTCACCAGTATAAGTCTATGTTATATATCACTGCTAGAATTAAGTGATGATTTAACTAGTGTA
1100339 AGTCAATGTTAAGTTTCACCGGTA
131 AGTCAATGTTAAGTTTCACCGGTA
* *
1100363 TAAGTCTATGCTATATATCACTACTGGAATTAAGTGATGATTTAACCAGTGTAAGTCTATGTTAA
1 TAAGTCTATGCTATATATCACTACTAGAATTAAGTGATGATTTAACCAATGTAAGTCTATGTTAA
* * * * * *
1100428 GTTTTACCGGTGTAAGTCTATGTTATATATCACTGTTGGAATTAAGTGATGATTTAACTGGTGTA
66 GTTTCACCAGTATAAGTCTATGTTATATATCACTGCTAGAATTAAGTGATGATTTAACTAGTGTA
**
1100493 AGTTTATGTTAAGTTTCAC
131 AGTCAATGTTAAGTTTCAC
1100512 AAGTGTAAGT
Statistics
Matches: 135, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
153 70 0.52
154 65 0.48
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (154 bp):
TAAGTCTATGCTATATATCACTACTAGAATTAAGTGATGATTTAACCAATGTAAGTCTATGTTAA
GTTTCACCAGTATAAGTCTATGTTATATATCACTGCTAGAATTAAGTGATGATTTAACTAGTGTA
AGTCAATGTTAAGTTTCACCGGTA
Found at i:1100749 original size:68 final size:68
Alignment explanation
Indices: 1100670--1100817 Score: 181
Period size: 68 Copynumber: 2.2 Consensus size: 68
1100660 GCCCCGAAGG
* * * * *
1100670 ATTAAAGTGACTCACACGGGAGTACATAGTCATATTATTCAGGGTGACTCGCATAGGAGCCTC-A
1 ATTAGAGTGACTCACACGAGAGAACATAATCATATTATTCAGGGTGACTCGCAAAGGAGCC-CAA
1100734 AAGA
65 AAGA
* * * *
1100738 ATTAGAGTGACTCACGCGAGAGAACCTAATCATATTATTCCGGGTGACTTGCAAAGGAGCCCAAA
1 ATTAGAGTGACTCACACGAGAGAACATAATCATATTATTCAGGGTGACTCGCAAAGGAGCCCAAA
*
1100803 AGG
66 AGA
*
1100806 ATTAGCGTGACT
1 ATTAGAGTGACT
1100818 TGCATAGGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 67 0.99
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (68 bp):
ATTAGAGTGACTCACACGAGAGAACATAATCATATTATTCAGGGTGACTCGCAAAGGAGCCCAAA
AGA
Found at i:1100819 original size:31 final size:31
Alignment explanation
Indices: 1100781--1100848 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1100771 ATTATTCCGG
*
1100781 GTGACTTGCAAAGGAGCCCAAAAGGATTAGC
1 GTGACTTGCAAAGGAGCCCAAAAGGATTAGA
*
1100812 GTGACTTGCATAGGAGCCCAAAAGGATTAGA
1 GTGACTTGCAAAGGAGCCCAAAAGGATTAGA
1100843 GTGACT
1 GTGACT
1100849 CACACAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (31 bp):
GTGACTTGCAAAGGAGCCCAAAAGGATTAGA
Found at i:1100858 original size:31 final size:31
Alignment explanation
Indices: 1100792--1100859 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1100782 TGACTTGCAA
* ** *
1100792 AGGAGCCCAAAAGGATTAGCGTGACTTGCAT
1 AGGAGCCCAAAAGGATTAGAGTGACTCACAC
1100823 AGGAGCCCAAAAGGATTAGAGTGACTCACAC
1 AGGAGCCCAAAAGGATTAGAGTGACTCACAC
1100854 AGGAGC
1 AGGAGC
1100860 ACATAATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (31 bp):
AGGAGCCCAAAAGGATTAGAGTGACTCACAC
Found at i:1102608 original size:39 final size:38
Alignment explanation
Indices: 1102507--1102619 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
1102497 GGCTCCTTGG
** **
1102507 CTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATTT
1 CTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCATAA
* * *
1102545 GTTTTTGCTCAGGGTAAGTCCTTACTACAGGCTCCTCAA
1 CTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCAT-AA
* * *
1102584 CTTTGTGCTTAGGGTAAGTCCTTACTGCAGACTCAT
1 CTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCAT
1102620 CTGCTTTGTG
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
38 31 0.51
39 30 0.49
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (38 bp):
CTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCATAA
Found at i:1102627 original size:39 final size:39
Alignment explanation
Indices: 1102506--1102688 Score: 199
Period size: 39 Copynumber: 4.7 Consensus size: 39
1102496 AGGCTCCTTG
* *
1102506 GCTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATTT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * * *
1102545 G-TTTTTGCTCAGGGTAAGTCCTTACTACAGGCTCCTCA
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * *
1102583 ACTTTGTGCTTAGGGTAAGTCCTTACTGCAGACTCATCT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * * *
1102622 GCTTTGTG-TACTGGATAAGACCTTACTGCAGGCTCCTCT
1 GCTTTGTGCT-CAGGGTAAGTCCTTACTGCAGGCTCATCT
* * *
1102661 GCTTTGTGCACATGGTAAGTCTTTACTG
1 GCTTTGTGCTCAGGGTAAGTCCTTACTG
1102689 GGTATACAGG
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 32 0.28
39 83 0.72
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
Found at i:1102669 original size:78 final size:77
Alignment explanation
Indices: 1102495--1102688 Score: 221
Period size: 78 Copynumber: 2.5 Consensus size: 77
1102485 CCGCTTTCCT
* * * * *
1102495 CAGGCTCCT-TGGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATTTGTTTTTGCTCAGGG
1 CAGGCTCCTCT-GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGACTCATCTGTTTGTGCTCAGGA
*
1102559 TAAGTCCTTACTA
65 TAAGACCTTACTA
** * *
1102572 CAGGCTCCTCAACTTTGTGCTTAGGGTAAGTCCTTACTGCAGACTCATCTGCTTTGTG-TACTGG
1 CAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGACTCATCTG-TTTGTGCT-CAGG
*
1102636 ATAAGACCTTACTG
64 ATAAGACCTTACTA
* * *
1102650 CAGGCTCCTCTGCTTTGTGCACATGGTAAGTCTTTACTG
1 CAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTG
1102689 GGTATACAGG
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
77 45 0.46
78 52 0.54
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.36
Consensus pattern (77 bp):
CAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGACTCATCTGTTTGTGCTCAGGAT
AAGACCTTACTA
Found at i:1105759 original size:265 final size:267
Alignment explanation
Indices: 1105284--1105804 Score: 798
Period size: 265 Copynumber: 2.0 Consensus size: 267
1105274 CTACGAAGAA
* * *
1105284 AAGTGTTATATCTATACCGATCATAAGAGTCTGAAGTATCTACTTACTCAGAAAGAGTTGAATTT
1 AAGTGTTATATCTATACCAATCATAAGAGCCTAAAGTATCTACTTACTCAGAAAGAGTTGAATTT
* *
1105349 GAGACAGCGTCGCTGGTTGGAGCTTCTAAAGAACTATGATTGTAAGATAGAATATCATCCAGGGA
66 GAGACAGCGTCGCTGGTTGGAGCTTCTAAAGAACTATGATTGTAAAATAGAATATCATCCAAGGA
* * *
1105414 ATATTAATGTGGTGGTCGACGCCTTGAGTCGTAAGGCAATATCTTATCTGAGAGTCTTGCTCGCC
131 AGACTAATGTGGTGGTCGACGCCTTGAGTCGTAAGGCAATATCTTATATGAGAGTCTTGCTCGCC
*
1105479 AGCTTGAGTTTATTTGATGATTG-CAGTCTGTTAGCAGAGTTACAAGTTAAACCCACTTTGGTTG
196 AGCTTGAGTTTATTTGATGA-CGCCAGTCTGTTAGCAGAGTTACAAGTTAAACCCACTTTGGTTG
1105543 ATCCAGAT
260 ATCCAGAT
* *
1105551 AAGTGTTATATCTATACTAATCATAAGAGCCTAAAGTATCTGCTTACTCAG-AA-AGTTGAATTT
1 AAGTGTTATATCTATACCAATCATAAGAGCCTAAAGTATCTACTTACTCAGAAAGAGTTGAATTT
* * *
1105614 GTGACAGCGTCGCTGGTTGGAGCTTCTAAAGGACTATGATTGTAAAATAGAGTATCATCCAAGGA
66 GAGACAGCGTCGCTGGTTGGAGCTTCTAAAGAACTATGATTGTAAAATAGAATATCATCCAAGGA
* ** * *
1105679 AGGCTAATGTGGTGGTCGACGCCTTGAGTCGTAAGGTGATAT-TTGATATGAGGGTCTTGTTCGC
131 AGACTAATGTGGTGGTCGACGCCTTGAGTCGTAAGGCAATATCTT-ATATGAGAGTCTTGCTCGC
* **
1105743 CAGCTTGAGTTTATTTGATGACGCCAGTCTGTTAGTAGAGTTGTAAGTTAAACCCACTTTGG
195 CAGCTTGAGTTTATTTGATGACGCCAGTCTGTTAGCAGAGTTACAAGTTAAACCCACTTTGG
1105805 CTGAGGAGAT
Statistics
Matches: 230, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
264 3 0.01
265 179 0.78
266 2 0.01
267 46 0.20
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (267 bp):
AAGTGTTATATCTATACCAATCATAAGAGCCTAAAGTATCTACTTACTCAGAAAGAGTTGAATTT
GAGACAGCGTCGCTGGTTGGAGCTTCTAAAGAACTATGATTGTAAAATAGAATATCATCCAAGGA
AGACTAATGTGGTGGTCGACGCCTTGAGTCGTAAGGCAATATCTTATATGAGAGTCTTGCTCGCC
AGCTTGAGTTTATTTGATGACGCCAGTCTGTTAGCAGAGTTACAAGTTAAACCCACTTTGGTTGA
TCCAGAT
Found at i:1108752 original size:39 final size:39
Alignment explanation
Indices: 1108698--1108889 Score: 276
Period size: 39 Copynumber: 4.9 Consensus size: 39
1108688 GATTTCCGCA
* * * *
1108698 GCTCCTCGGTTTTGTGCTCAGGTTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
*
1108737 GCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* * *
1108776 GCTCCTCAGCTTTATGCACAAGGTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
** *
1108815 GCTCCTCTGCTTTGTGCACAGTATAAGACCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
*
1108854 GCTCATCTGCTTTGTGCACAGGGTAAGTCCTTACTG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTG
1108890 GGTGTACAGG
Statistics
Matches: 136, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 136 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.32
Consensus pattern (39 bp):
GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
Found at i:1113594 original size:40 final size:40
Alignment explanation
Indices: 1113539--1113618 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1113529 TAAGGATATG
1113539 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1113579 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1113619 GTGGATCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (40 bp):
TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
Found at i:1123303 original size:36 final size:35
Alignment explanation
Indices: 1123253--1123483 Score: 224
Period size: 35 Copynumber: 6.5 Consensus size: 35
1123243 GTCTGGAGTT
* *
1123253 TATAGTTTTAAAAATTTTTTTCTTGAAATATATATA
1 TATAGTTTTGAAAATATTTTT-TTGAAATATATATA
1123289 TATAGTTTTGAAAATA-TTTTTTGAAATATATATAA
1 TATAGTTTTGAAAATATTTTTTTGAAATATATAT-A
*
1123324 TATAGTTTTTGAAAATACTTTTTTGAAATATATATA
1 TATAG-TTTTGAAAATATTTTTTTGAAATATATATA
*
1123360 TATAGTTTTGAAAA-ATATTTTTCGAAACATATATAATA
1 TATAGTTTTGAAAATAT-TTTTTTG-AA-ATATAT-ATA
** *
1123398 TATAG-TTT-AAAA-ACATTTTTGAAACATATAATA
1 TATAGTTTTGAAAATATTTTTTTGAAATATAT-ATA
* * *
1123431 TATAGTTTTTAAAA-AATTTTTTGAAA-ACATATAA
1 TATAGTTTTGAAAATATTTTTTTGAAATATATAT-A
* *
1123465 TATAATTTTGAAAACATTT
1 TATAGTTTTGAAAATATTT
1123484 GTGAAAACGT
Statistics
Matches: 170, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
33 16 0.09
34 35 0.21
35 47 0.28
36 38 0.22
37 26 0.15
38 8 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
TATAGTTTTGAAAATATTTTTTTGAAATATATATA
Found at i:1123355 original size:35 final size:36
Alignment explanation
Indices: 1123253--1123509 Score: 204
Period size: 35 Copynumber: 7.3 Consensus size: 36
1123243 GTCTGGAGTT
* **
1123253 TATAG-TTTTAAAAATTTTTTTCTTG-AAATATATATA
1 TATAGTTTTTGAAAATACTTTT-TTGAAAATATATA-A
1123289 TATAG-TTTTGAAAATA-TTTTTTGAAATATATATAA
1 TATAGTTTTTGAAAATACTTTTTTGAAA-ATATATAA
1123324 TATAGTTTTTGAAAATACTTTTTTG-AAATATATATA
1 TATAGTTTTTGAAAATACTTTTTTGAAAATATATA-A
*
1123360 TATAG-TTTTGAAAAATA-TTTTTCGAAACATATATAA
1 TATAGTTTTTG-AAAATACTTTTTTGAAA-ATATATAA
* *
1123396 TATA-TAGTTT-AAAA-ACATTTTTGAAACATATA-ATA
1 TATAGT-TTTTGAAAATACTTTTTTGAAA-ATATATA-A
* *
1123431 TATAGTTTTT-AAAA-AATTTTTTGAAAACATATAA
1 TATAGTTTTTGAAAATACTTTTTTGAAAATATATAA
* * *
1123465 TATA-ATTTTG-AAA-ACATTTGTGAAAACGTATATAA
1 TATAGTTTTTGAAAATACTTTTTTGAAAA--TATATAA
1123500 TATAGTTTTT
1 TATAGTTTTT
1123510 AAACATATAG
Statistics
Matches: 187, Mismatches: 16, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
33 17 0.09
34 14 0.07
35 81 0.43
36 58 0.31
37 17 0.09
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
TATAGTTTTTGAAAATACTTTTTTGAAAATATATAA
Found at i:1123369 original size:71 final size:69
Alignment explanation
Indices: 1123270--1123478 Score: 269
Period size: 71 Copynumber: 3.0 Consensus size: 69
1123260 TTAAAAATTT
1123270 TTTTCTTGAAATATATATATATAGTTTTGAAAATATTTTTTGAAATATATATAATATAGTTTTTG
1 TTTT-TTGAAATATATATATATAGTTTTGAAAATATTTTTTGAAA-ATATATAATATA-TTTTTG
1123335 AAAATAC
63 AAAATAC
* *
1123342 TTTTTTGAAATATATATATATAGTTTTGAAAAATATTTTTCGAAACATATATAATATATAGTTT-
1 TTTTTTGAAATATATATATATAGTTTTG-AAAATATTTTTTGAAA-ATATATAATATAT-TTTTG
1123406 AAAA-AC
63 AAAATAC
* * * * * *
1123412 ATTTTTGAAACATATAATATATAGTTTTTAAAAAATTTTTTGAAAACATATAATATAATTTTGAA
1 TTTTTTGAAATATAT-ATATATAGTTTTGAAAATATTTTTTGAAAATATATAATATATTTTTGAA
1123477 AA
65 AA
1123479 CATTTGTGAA
Statistics
Matches: 122, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
68 3 0.02
69 15 0.12
70 29 0.24
71 41 0.34
72 34 0.28
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (69 bp):
TTTTTTGAAATATATATATATAGTTTTGAAAATATTTTTTGAAAATATATAATATATTTTTGAAA
ATAC
Found at i:1126038 original size:7 final size:7
Alignment explanation
Indices: 1126030--1126061 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1126020 TGGTATATAA
*
1126030 TTCATAA
1 TTCATAT
1126037 TTCATAT
1 TTCATAT
1126044 TTCATAT
1 TTCATAT
1126051 TTCATAT
1 TTCATAT
1126058 TTCA
1 TTCA
1126062 GTCACATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (7 bp):
TTCATAT
Found at i:1131887 original size:52 final size:50
Alignment explanation
Indices: 1131824--1131925 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 50
1131814 CATCCTCTCG
*
1131824 GCCGCACTTTGCCAGGGAATCATAGTTAAAGCTTAACTCAAACGTTTCGAA
1 GCCGCACTTTGCCAGGGAATCATAGTTAAAGCTTAACTC-AACGGTTCGAA
1131875 GCCGCAGCTTTGCCAGGGAATCATAGTTAAAGCTTAACTCAACGGTTCGAA
1 GCCGCA-CTTTGCCAGGGAATCATAGTTAAAGCTTAACTCAACGGTTCGAA
1131926 ACCCTCTTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 16 0.33
52 33 0.67
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (50 bp):
GCCGCACTTTGCCAGGGAATCATAGTTAAAGCTTAACTCAACGGTTCGAA
Found at i:1132568 original size:15 final size:15
Alignment explanation
Indices: 1132548--1132581 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1132538 AGATTAATGC
* *
1132548 AGAGTGATGGGGAAG
1 AGAGTGAAGGAGAAG
1132563 AGAGTGAAGGAGAAG
1 AGAGTGAAGGAGAAG
1132578 AGAG
1 AGAG
1132582 GGAAAGGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (15 bp):
AGAGTGAAGGAGAAG
Found at i:1132664 original size:22 final size:22
Alignment explanation
Indices: 1132617--1132664 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
1132607 TTAACTTTTT
* *
1132617 ATTTTTTTCAATTTTCATTATTA
1 ATTTTTTT-AATTTTAATTATAA
1132640 ATTTTTTT-ATTTTAATTACTAA
1 ATTTTTTTAATTTTAATTA-TAA
1132662 ATT
1 ATT
1132665 CATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 5 0.23
23 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTTAATTTTAATTATAA
Found at i:1133506 original size:42 final size:42
Alignment explanation
Indices: 1133444--1133552 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
1133434 CCATTAGCGA
* * *
1133444 CGTTTTTAATGCAAACGCCGCTAAAAAT-TGGTATA-TAGTGG
1 CGTTTTTGATACAAACGCCGCTAAAAATATGGTATATTA-CGG
* **
1133485 CGTTTTATGATACAAATGCCGCTAAATGTATGGTATATTACGG
1 CGTTTT-TGATACAAACGCCGCTAAAAATATGGTATATTACGG
*
1133528 CGTTTTTGTTACAAACGCCGCTAAA
1 CGTTTTTGATACAAACGCCGCTAAA
1133553 TAACACAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
41 6 0.11
42 34 0.60
43 15 0.26
44 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (42 bp):
CGTTTTTGATACAAACGCCGCTAAAAATATGGTATATTACGG
Found at i:1133908 original size:18 final size:18
Alignment explanation
Indices: 1133887--1133923 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1133877 TGTGCTGCCA
* *
1133887 CTGCTTCTCTCTCTGCTT
1 CTGCTGCTCTCTCGGCTT
1133905 CTGCTGCTCTCTCGGCTT
1 CTGCTGCTCTCTCGGCTT
1133923 C
1 C
1133924 CCTTGCTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.43
Consensus pattern (18 bp):
CTGCTGCTCTCTCGGCTT
Found at i:1137791 original size:40 final size:41
Alignment explanation
Indices: 1137690--1137846 Score: 187
Period size: 40 Copynumber: 3.9 Consensus size: 41
1137680 TTTATACAAA
* * * *
1137690 AAAACGCCACTTTTGATT-ACATTATTGTGGCGTTTGCTAAT
1 AAAACGCCACTATTGATTAACACTATTGCGGCGTTTGCT-AC
* * *
1137731 AAAACACCACTATTGTTTAACACTATTGCGACGTTTGTCTA-
1 AAAACGCCACTATTGATTAACACTATTGCGGCGTTTG-CTAC
*
1137772 AAAACGCCACTA-TGATTAACACTATTACGGCGTTTG-TAC
1 AAAACGCCACTATTGATTAACACTATTGCGGCGTTTGCTAC
*
1137811 AAAATGCCACTATTGATTAACACTATTGCGGCGTTT
1 AAAACGCCACTATTGATTAACACTATTGCGGCGTTT
1137847 TAGGAACAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 11 0.11
40 43 0.43
41 26 0.26
42 16 0.16
43 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (41 bp):
AAAACGCCACTATTGATTAACACTATTGCGGCGTTTGCTAC
Found at i:1137929 original size:42 final size:41
Alignment explanation
Indices: 1137878--1137988 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
1137868 GTGTAATATA
1137878 TGCGGCGTTTGTGGTAAAAACGCCGCTAATTTACCACTCTAT
1 TGCGGCGTTTGTGGTAAAAACGCCGCTAATTTA-CACTCTAT
* * * * *
1137920 TGTGGCGTTT-TGGCT-AAATCGTCGCAAAAATTTATACTCTAT
1 TGCGGCGTTTGTGG-TAAAAACGCCGC--TAATTTACACTCTAT
1137962 TGCGGCGTTTGTGG-AAAAAC-CCGCTAA
1 TGCGGCGTTTGTGGTAAAAACGCCGCTAA
1137989 AGTATCAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
39 2 0.04
41 14 0.25
42 30 0.55
43 9 0.16
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
TGCGGCGTTTGTGGTAAAAACGCCGCTAATTTACACTCTAT
Found at i:1138487 original size:15 final size:15
Alignment explanation
Indices: 1138467--1138509 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1138457 AGTAGTATGA
*
1138467 TTTTTATTTTTTTTT
1 TTTTTATTTTTTTTG
1138482 TTTTTATTTTCTTTTG
1 TTTTTATTTT-TTTTG
*
1138498 TTTTTCTTTTTT
1 TTTTTATTTTTT
1138510 GTTAATTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.05, C:0.05, G:0.02, T:0.88
Consensus pattern (15 bp):
TTTTTATTTTTTTTG
Found at i:1141188 original size:260 final size:253
Alignment explanation
Indices: 1140707--1141217 Score: 959
Period size: 260 Copynumber: 2.0 Consensus size: 253
1140697 TGACTCATAA
1140707 ATACCGGTAAAGGAAAGTCTCGTAGAGGGGGTTACGTATGTAGGTTGGGGGTGCGGGGGTGGACC
1 ATACCGGTAAAGGAAAGTCTCGTAGAGGGGGTTACGTATGTAGGTTGGGGGTGCGGGGGTGGACC
1140772 CAGCGTACTGTACAAGGTTATTTTTGTAAATATGTACCAGGGTTTATTTATTATAAAAGAAATGT
66 CAGCGTACTGTACAAGGTTATTTTTGTAAATATGTACCAGGGTTTATTTATTATAAAAGAAATGT
1140837 AACCTTAACCTATGAGACATTGAATTGAATAAAAAAAAATCTAGCGCCGCCTAAGGCACCGAGAA
131 AACCTTAACCTATGAGACATTGAATTGAATAAAAAAAAATCTAGCGCCGCCTAAGGCACCGAGAA
1140902 CGTAAGCACATTGCTGAACCTCGTTAAAATTCTTGTGTTTTTCCTGTTTTCTTTACAT
196 CGTAAGCACATTGCTGAACCTCGTTAAAATTCTTGTGTTTTTCCTGTTTTCTTTACAT
1140960 ATACCGGTAAAGGAAAGTCTCGTAGAGGGGGTTACGATTATGTAGGTTGGGGGTGCGGGGGGTGC
1 ATACCGGTAAAGGAAAGTCTCGTAGAGGGGGTTACG--TATGTAGGTTGGGGGTGC-GGGGGTG-
1141025 GACCCAGCAGTACTGTACAAGGTTATTTTTGTAAATATGTACCAGGGTTTATTTATTATAAAATG
62 GACCCAGC-GTACTGTACAAGGTTATTTTTGTAAATATGTACCAGGGTTTATTTATTATAAAA-G
1141090 AAATGTAACCTTAACCTATGAGACATTGAATTGAATAAAAAAAAAATCTAGCGCCGCCTAAGGCA
125 AAATGTAACCTTAACCTATGAGACATTGAATTGAAT-AAAAAAAAATCTAGCGCCGCCTAAGGCA
1141155 CCGAGAACGTAAGCACATTGCTGAACCTCGTTAAAATTCTTGTGTTTTTCCTGTTTTCTTTAC
189 CCGAGAACGTAAGCACATTGCTGAACCTCGTTAAAATTCTTGTGTTTTTCCTGTTTTCTTTAC
1141218 CCGATTCTTC
Statistics
Matches: 251, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
253 36 0.14
255 18 0.07
256 7 0.03
257 8 0.03
258 54 0.22
259 37 0.15
260 91 0.36
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (253 bp):
ATACCGGTAAAGGAAAGTCTCGTAGAGGGGGTTACGTATGTAGGTTGGGGGTGCGGGGGTGGACC
CAGCGTACTGTACAAGGTTATTTTTGTAAATATGTACCAGGGTTTATTTATTATAAAAGAAATGT
AACCTTAACCTATGAGACATTGAATTGAATAAAAAAAAATCTAGCGCCGCCTAAGGCACCGAGAA
CGTAAGCACATTGCTGAACCTCGTTAAAATTCTTGTGTTTTTCCTGTTTTCTTTACAT
Found at i:1147334 original size:64 final size:63
Alignment explanation
Indices: 1147262--1147382 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 63
1147252 ATGGTTCAAG
* *
1147262 GTGTATCGATGCACATA-AAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACA-AGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* * * *
1147326 GTGTATCGATGCACAAGTAGTGCATTGATGGACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
1147383 AGATTTATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 18 0.36
64 32 0.64
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:1152339 original size:60 final size:61
Alignment explanation
Indices: 1152254--1152375 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
1152244 AATTCTTATA
* * *
1152254 ATATTTTAAAATTGAGATAAAAATAAAATATATTTTTAC-AGTTAATA-TAAGAATAAAATAT
1 ATATTTTAAAATTAAAATAAAAATAAAATATA-TTTAACAAGTTAA-AGTAAGAATAAAATAT
* * *
1152315 ATATTTT-AAATTAAAATAATAATAAATTATATTTAACAATTTAAAGTAAGAATAAAATAT
1 ATATTTTAAAATTAAAATAAAAATAAAATATATTTAACAAGTTAAAGTAAGAATAAAATAT
1152375 A
1 A
1152376 ATAAGAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 6 0.11
60 40 0.75
61 7 0.13
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (61 bp):
ATATTTTAAAATTAAAATAAAAATAAAATATATTTAACAAGTTAAAGTAAGAATAAAATAT
Found at i:1152349 original size:27 final size:30
Alignment explanation
Indices: 1152254--1152375 Score: 115
Period size: 30 Copynumber: 4.0 Consensus size: 30
1152244 AATTCTTATA
* * *
1152254 ATATTTTAAAATTGAGATAAAAATAAAATAT
1 ATATTTT-AAATTAAAATAAGAATAAAATAT
* *
1152285 AT-TTTTACAGTTAATATAAGAATAAAATAT
1 ATATTTTA-AATTAAAATAAGAATAAAATAT
*
1152315 ATATTTTAAATTAAAATAATAAT-AAAT-T
1 ATATTTTAAATTAAAATAAGAATAAAATAT
* *
1152343 ATATTTAACAATTTAAAGTAAGAATAAAATAT
1 ATATTTTA-AA-TTAAAATAAGAATAAAATAT
1152375 A
1 A
1152376 ATAAGAAAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
28 8 0.11
29 7 0.09
30 47 0.63
31 11 0.15
32 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
ATATTTTAAATTAAAATAAGAATAAAATAT
Done.