Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 27
Found at i:568059 original size:18 final size:18
Alignment explanation
Indices: 568033--568067 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
568023 TCGAAAGGAC
*
568033 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
568051 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
568068 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:571817 original size:25 final size:23
Alignment explanation
Indices: 571768--571817 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
571758 TTTAAGGATA
** *
571768 AATTTTTAATTTAACTTTAGTAG
1 AATTTTTAATTTAACTACAGAAG
571791 AATTTTTATTATTTAACTACAGAAG
1 AATTTTTA--ATTTAACTACAGAAG
571816 AA
1 AA
571818 GGATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
25 14 0.64
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (23 bp):
AATTTTTAATTTAACTACAGAAG
Found at i:573499 original size:32 final size:32
Alignment explanation
Indices: 573435--573611 Score: 144
Period size: 32 Copynumber: 5.5 Consensus size: 32
573425 CTCCTCTCCG
* * * * *
573435 TCCTCGCAATGTTGCTTCCCTTCAACTGGGTTC
1 TCCTCGCAATGTTTC-TGCATTCAAGTAGGTTC
573468 TCCTCGCAATGTTTCTGCATTCAAGTAGGTTC
1 TCCTCGCAATGTTTCTGCATTCAAGTAGGTTC
* *
573500 TCCTCGCATTGTTTCTGCCAATCAAGTAGG-T-
1 TCCTCGCAATGTTTCTG-CATTCAAGTAGGTTC
* * * * *
573531 TCCTCGCATTGTTACTTCCATTCGAGGA-GTTC
1 TCCTCGCAATGTTTC-TGCATTCAAGTAGGTTC
** * *
573563 TCCTTTCAATGTTTCTGCCATTCGAGGAGGTTC
1 TCCTCGCAATGTTTCTG-CATTCAAGTAGGTTC
*
573596 TCCTTGCAATGTTTCT
1 TCCTCGCAATGTTTCT
573612 TCCATTTGAG
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.01
31 23 0.19
32 52 0.43
33 44 0.37
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (32 bp):
TCCTCGCAATGTTTCTGCATTCAAGTAGGTTC
Found at i:573563 original size:63 final size:66
Alignment explanation
Indices: 573463--573632 Score: 186
Period size: 63 Copynumber: 2.6 Consensus size: 66
573453 CCTTCAACTG
* * * * * *
573463 GGTTCTCCTCGCAATGTTTC-TGCATTCAAGTAGGTTCTCCTCGCATTGTTTCTGCCAATCAAGT
1 GGTTCTCCTCGCAATGTTACTTCCATTCGAGGAGGTTCTCCTCGCAATGTTTCTGCCAATCAAGG
573527 A
66 A
* ** * *
573528 GG-T-TCCTCGCATTGTTACTTCCATTCGAGGA-GTTCTCCTTTCAATGTTTCTGCCATTCGAGG
1 GGTTCTCCTCGCAATGTTACTTCCATTCGAGGAGGTTCTCCTCGCAATGTTTCTGCCAATCAAGG
573590 A
66 A
* * *
573591 GGTTCTCCTTGCAATGTTTCTTCCATTTGAGGAGGTTCTCCT
1 GGTTCTCCTCGCAATGTTACTTCCATTCGAGGAGGTTCTCCT
573633 TTTTCTCCTC
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
63 41 0.48
64 11 0.13
65 26 0.30
66 8 0.09
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (66 bp):
GGTTCTCCTCGCAATGTTACTTCCATTCGAGGAGGTTCTCCTCGCAATGTTTCTGCCAATCAAGG
A
Found at i:573633 original size:33 final size:33
Alignment explanation
Indices: 573435--573632 Score: 181
Period size: 33 Copynumber: 6.1 Consensus size: 33
573425 CTCCTCTCCG
* * * *
573435 TCCTCGCAATGTTGCTTCCCTTCAACTG-GGTTC
1 TCCTCGCAATGTTTCTTCCATTCGA-GGAGGTTC
* * *
573468 TCCTCGCAATGTTTC-TGCATTCAAGTAGGTTC
1 TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
* * * * *
573500 TCCTCGCATTGTTTCTGCCAATCAAGTAGG-T-
1 TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
* *
573531 TCCTCGCATTGTTACTTCCATTCGAGGA-GTTC
1 TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
** *
573563 TCCTTTCAATGTTTCTGCCATTCGAGGAGGTTC
1 TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
* *
573596 TCCTTGCAATGTTTCTTCCATTTGAGGAGGTTC
1 TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
573629 TCCT
1 TCCT
573633 TTTTCTCCTC
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
30 1 0.01
31 24 0.17
32 50 0.36
33 63 0.46
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (33 bp):
TCCTCGCAATGTTTCTTCCATTCGAGGAGGTTC
Found at i:573980 original size:10 final size:10
Alignment explanation
Indices: 573965--574007 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
573955 TTTAATAAAT
573965 AAACGAACAC
1 AAACGAACAC
573975 AAACGAACGAAC
1 AAACGAAC--AC
573987 ATAAACGAACAC
1 --AAACGAACAC
573999 AAACGAACA
1 AAACGAACA
574008 AACACAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 17 0.59
12 4 0.14
14 8 0.28
ACGTcount: A:0.60, C:0.26, G:0.12, T:0.02
Consensus pattern (10 bp):
AAACGAACAC
Found at i:573985 original size:14 final size:14
Alignment explanation
Indices: 573966--574016 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
573956 TTAATAAATA
573966 AACGAACACAAACG
1 AACGAACACAAACG
*
573980 AACG-A-ACATA--
1 AACGAACACAAACG
573990 AACGAACACAAACG
1 AACGAACACAAACG
*
574004 AACAAACACAAAC
1 AACGAACACAAAC
574017 AAACAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.13
11 1 0.03
12 8 0.27
13 1 0.03
14 16 0.53
ACGTcount: A:0.61, C:0.27, G:0.10, T:0.02
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:573995 original size:24 final size:23
Alignment explanation
Indices: 573963--574040 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 23
573953 CATTTAATAA
573963 ATAAACGAACACAAACGAACGAAC
1 ATAAACGAACACAAACGAAC-AAC
573987 ATAAACGAACACAAACGAACAAAC
1 ATAAACGAACACAAACGAAC-AAC
* * *
574011 ACAAACAAACAATAAACGAACAAC
1 ATAAACGAAC-ACAAACGAACAAC
574035 ATAAAC
1 ATAAAC
574041 ACAAAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 39 0.81
25 9 0.19
ACGTcount: A:0.63, C:0.24, G:0.08, T:0.05
Consensus pattern (23 bp):
ATAAACGAACACAAACGAACAAC
Found at i:574017 original size:20 final size:20
Alignment explanation
Indices: 573980--574017 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
573970 AACACAAACG
*
573980 AACGAACATAAACGAACACA
1 AACGAACATAAACAAACACA
574000 AACGAACA-AACACAAACA
1 AACGAACATAA-ACAAACA
574018 AACAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.63, C:0.26, G:0.08, T:0.03
Consensus pattern (20 bp):
AACGAACATAAACAAACACA
Found at i:574021 original size:14 final size:14
Alignment explanation
Indices: 573989--574045 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
573979 GAACGAACAT
*
573989 AAACGAACACAAAC
1 AAACAAACACAAAC
*
574003 GAACAAACACAAAC
1 AAACAAACACAAAC
* *
574017 AAACAATAAACGAAC
1 AAACAA-ACACAAAC
*
574032 AACATAAACACAAA
1 AA-ACAAACACAAA
574046 AAAAACTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
14 17 0.52
15 13 0.39
16 3 0.09
ACGTcount: A:0.67, C:0.25, G:0.05, T:0.04
Consensus pattern (14 bp):
AAACAAACACAAAC
Found at i:574051 original size:24 final size:24
Alignment explanation
Indices: 573975--574051 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
573965 AAACGAACAC
* * * *
573975 AAACGAACGAACATAAACGAACAC
1 AAACGAACAAACATAAACAAAAAA
* *
573999 AAACGAACAAACACAAACAAACAAT
1 AAACGAACAAACATAAACAAA-AAA
574024 AAACGAAC-AACATAAACACAAAAA
1 AAACGAACAAACATAAACA-AAAAA
574048 AAAC
1 AAAC
574052 TTATTCGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 33 0.75
25 11 0.25
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.04
Consensus pattern (24 bp):
AAACGAACAAACATAAACAAAAAA
Found at i:578204 original size:17 final size:18
Alignment explanation
Indices: 578182--578215 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
578172 TCAGCCGGTC
578182 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
578199 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
578216 CTAGTAGCGG
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:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:583642 original size:26 final size:26
Alignment explanation
Indices: 583597--583704 Score: 87
Period size: 26 Copynumber: 4.0 Consensus size: 26
583587 ATATTTATAA
*
583597 ATATTTATTAATATTATAATAATATATT
1 ATATTT-TTAATAATATAATAA-ATATT
* *
583625 ATATTTTT-ATATTATAATAAATAATC
1 ATATTTTTAATAATATAATAAAT-ATT
* *
583651 A-ATTATTATAATAATATAAGATTATATT
1 ATATT-TT-TAATAATATAATA-AATATT
*
583679 TTA-TTTTAATAATATAATAAATATT
1 ATATTTTTAATAATATAATAAATATT
583704 A
1 A
583705 AAAATGTATA
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
25 10 0.15
26 29 0.45
27 5 0.08
28 18 0.28
29 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
ATATTTTTAATAATATAATAAATATT
Found at i:583664 original size:23 final size:21
Alignment explanation
Indices: 583608--583666 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
583598 TATTTATTAA
* *
583608 TATTATAATAATATATTATAT
1 TATTATAATAATAAATAATAT
*
583629 TTTTATATTATAATAAATAATCAAT
1 TATTATA--ATAATAAATAAT--AT
583654 TATTATAATAATA
1 TATTATAATAATA
583667 TAAGATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 6 0.20
23 16 0.53
25 8 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTATAATAATAAATAATAT
Found at i:583689 original size:46 final size:46
Alignment explanation
Indices: 583606--583704 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
583596 AATATTTATT
583606 AATATTATAATAATATATTATATTTTTATATTATAATAA-ATAATCA
1 AATATTATAATAATATATTATATTTTTATATTATAATAATATAAT-A
*
583652 ATTATTATAATAATATAAGATTATA-TTTTAT-TT-TAATAATATAATA
1 AATATTATAATAATAT---ATTATATTTTTATATTATAATAATATAATA
583698 AATATTA
1 AATATTA
583705 AAAATGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
46 28 0.60
47 7 0.15
48 6 0.13
49 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (46 bp):
AATATTATAATAATATATTATATTTTTATATTATAATAATATAATA
Found at i:583836 original size:19 final size:18
Alignment explanation
Indices: 583814--583876 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
583804 ATATATTAAA
583814 TAAACTAATTAATATTTTT
1 TAAA-TAATTAATATTTTT
* * **
583833 TAAATATTTATTAGTTTAC
1 TAAATAATTAATA-TTTTT
*
583852 TAAATAATTAATATATTT
1 TAAATAATTAATATTTTT
583870 TATAATA
1 TA-AATA
583877 TTTTTATTTC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (18 bp):
TAAATAATTAATATTTTT
Found at i:583895 original size:38 final size:38
Alignment explanation
Indices: 583812--583895 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 38
583802 AAATATATTA
* *
583812 AATAAACTAATTAATATTTTTTAAATATTTATTAGTTT
1 AATAAAATAATTAATATATTTTAAATATTTATTAGTTT
*
583850 ACT-AAATAATTAATATATTTTATAATATTT-TTA-TTT
1 AATAAAATAATTAATATATTTTA-AATATTTATTAGTTT
583886 CAATAAAATA
1 -AATAAAATA
583896 TACCAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 3 0.08
37 22 0.56
38 14 0.36
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (38 bp):
AATAAAATAATTAATATATTTTAAATATTTATTAGTTT
Found at i:584146 original size:18 final size:15
Alignment explanation
Indices: 584109--584154 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 15
584099 AACATTTTCC
584109 AGAAAATATTTTTTT
1 AGAAAATATTTTTTT
584124 AGAAAATAATTTATTTT
1 AGAAAAT-ATTT-TTTT
584141 ACGAAAAATATTTT
1 A-G-AAAATATTTT
584155 CGGAAAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 6 0.22
18 5 0.19
19 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (15 bp):
AGAAAATATTTTTTT
Found at i:584496 original size:19 final size:20
Alignment explanation
Indices: 584468--584508 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
584458 TTAAAACCTC
584468 AAATAATAATA-AATATTTT
1 AAATAATAATACAATATTTT
*
584487 AAATATTAATACAATATTTT
1 AAATAATAATACAATATTTT
584507 AA
1 AA
584509 GAATACAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATAATACAATATTTT
Found at i:585452 original size:19 final size:18
Alignment explanation
Indices: 585407--585453 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
585397 ATAGATAAAA
* *
585407 ATTTATTTAAATTATTAT
1 ATTTTTTTAAAATATTAT
585425 -TTTTATTTAAAATATTAAT
1 ATTTT-TTTAAAATATT-AT
585444 ATTTTTTTAA
1 ATTTTTTTAA
585454 TAATTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 7 0.29
20 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTTTAAAATATTAT
Found at i:585881 original size:16 final size:18
Alignment explanation
Indices: 585850--585890 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
585840 ATTAAATCTC
585850 TATTTTTATGAATAAAAA
1 TATTTTTATGAATAAAAA
*
585868 TATTTTT-T-AATAAACA
1 TATTTTTATGAATAAAAA
585884 TATTTTT
1 TATTTTT
585891 CGAATTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
17 1 0.05
18 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTTTTATGAATAAAAA
Found at i:588236 original size:37 final size:36
Alignment explanation
Indices: 588186--588258 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 36
588176 GACTAGCCAG
588186 TCTAGCCCAAGAATACCTCTAAAATGGCATGAAATT
1 TCTAGCCCAAGAATACCTCTAAAATGGCATGAAATT
588222 TCTAGCCACAAGAATACCTCTAAAATGGCATGAAATT
1 TCTAGCC-CAAGAATACCTCTAAAATGGCATGAAATT
588259 CTTCTTTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 7 0.19
37 29 0.81
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (36 bp):
TCTAGCCCAAGAATACCTCTAAAATGGCATGAAATT
Found at i:592466 original size:5 final size:5
Alignment explanation
Indices: 592456--592487 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
592446 GGGAAATCAA
592456 AAATT AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AA
592488 TTTCTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:594302 original size:16 final size:16
Alignment explanation
Indices: 594283--594339 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
594273 TTGTCATTTA
594283 ATCTCATCGTGTCTTC
1 ATCTCATCGTGTCTTC
* * *
594299 ATCTCCATGGTCATCATTTA
1 ATCT-CATCGT-GTC--TTC
594319 ATCTCATCGTGTCTTC
1 ATCTCATCGTGTCTTC
594335 ATCTC
1 ATCTC
594340 CATGGTCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 11 0.35
17 5 0.16
18 4 0.13
19 5 0.16
20 6 0.19
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.42
Consensus pattern (16 bp):
ATCTCATCGTGTCTTC
Found at i:594319 original size:36 final size:36
Alignment explanation
Indices: 594276--594383 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
594266 AACAGCTTTG
594276 TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
1 TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
594312 TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
1 TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
*
594348 TCATTTAATCTTATCGTGTCTTCATCTCCATGGTCA
1 TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
594384 AACTCAATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (36 bp):
TCATTTAATCTCATCGTGTCTTCATCTCCATGGTCA
Found at i:599921 original size:15 final size:16
Alignment explanation
Indices: 599898--599930 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
599888 CCGATTTAAG
599898 TATCAAA-TTTATATT
1 TATCAAATTTTATATT
*
599913 TATCGAATTTTATATT
1 TATCAAATTTTATATT
599929 TA
1 TA
599931 AGCTTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATCAAATTTTATATT
Found at i:618922 original size:21 final size:21
Alignment explanation
Indices: 618898--618939 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
618888 AAGGGTTTTT
618898 TATT-TTTATATTATTAAAATA
1 TATTCTTTA-ATTATTAAAATA
618919 TATTCTTTAATTATTAAAATA
1 TATTCTTTAATTATTAAAATA
618940 ATAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTCTTTAATTATTAAAATA
Found at i:623216 original size:21 final size:20
Alignment explanation
Indices: 623155--623218 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
623145 CGGAAACAAT
623155 AATAAATTTAATATTTTAAA
1 AATAAATTTAATATTTTAAA
* * * *
623175 ATTAAATTTGAAAAGTATAAA
1 AATAAATTT-AATATTTTAAA
*
623196 AATAAATTTAATATTTTTAA
1 AATAAATTTAATATTTTAAA
623216 AAT
1 AAT
623219 GATTTTAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AATAAATTTAATATTTTAAA
Found at i:626613 original size:22 final size:22
Alignment explanation
Indices: 626568--626615 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
626558 AATATGTGTA
*
626568 TACCCTAAAATTAATTTGTTCT
1 TACCCTAAAATTAATTTGTCCT
626590 TACCCT-AAATTAATTTGTGCCT
1 TACCCTAAAATTAATTTGT-CCT
626612 TACC
1 TACC
626616 TCGAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (22 bp):
TACCCTAAAATTAATTTGTCCT
Found at i:631189 original size:46 final size:45
Alignment explanation
Indices: 631030--631193 Score: 179
Period size: 45 Copynumber: 3.6 Consensus size: 45
631020 AATCGAAGGC
* * *
631030 TTTTGATTATTGGGTTG-TCAAAAGTAAAATCAAATAATTAGTTCC
1 TTTTGATTATTGGATTGCT-AAAAGTAAAATCAAATGATTAGTTCA
*
631075 TTTTTATTATTGTG-TTGCTAAAAGTAAAATCAAATGATTAGTTCA
1 TTTTGATTATTG-GATTGCTAAAAGTAAAATCAAATGATTAGTTCA
* * * * * *
631120 TTTCGATTATTGAATTTCCAAAATTAAAAATCAAATGATTAGTACA
1 TTTTGATTATTGGATTGCTAAAAGT-AAAATCAAATGATTAGTTCA
* *
631166 TTTTGATTATTGGATTGGTAAAATTAAA
1 TTTTGATTATTGGATTGCTAAAAGTAAA
631194 GGATTAATTC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
45 59 0.59
46 41 0.41
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (45 bp):
TTTTGATTATTGGATTGCTAAAAGTAAAATCAAATGATTAGTTCA
Found at i:633031 original size:110 final size:110
Alignment explanation
Indices: 632837--633035 Score: 260
Period size: 110 Copynumber: 1.8 Consensus size: 110
632827 GGCAACAACA
* *
632837 ATCAAGTACTGAATATCCCATAGCCAGGCAACAGAGACATGTAAATCCCTTAGGCAAGGAAGCAG
1 ATCAAGTACTGAAGATCCCATAGCCAGGCAACAAAGACATGTAAATCCCTTAGGCAAGGAAGCAG
*
632902 AAAAGTAGAGGCAGACCCAGAAGATATCAAATGGGACCCACAATG
66 AAAAGTAAAGGCAGACCCAGAAGATATCAAATGGGACCCACAATG
* * * * * **
632947 ATCAAGTATTGAAGATCTCATATCCGGGCAACAAAGA-A-GTAAATCCTTTAGGTGTA-GAAGCA
1 ATCAAGTACTGAAGATCCCATAGCCAGGCAACAAAGACATGTAAATCCCTTAGG-CAAGGAAGCA
633009 GAAAAGTAACAAGGCAGACCCAGAAGA
65 GAAAAGT-A-AAGGCAGACCCAGAAGA
633036 CACCTCAACA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
108 26 0.34
109 3 0.04
110 47 0.62
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (110 bp):
ATCAAGTACTGAAGATCCCATAGCCAGGCAACAAAGACATGTAAATCCCTTAGGCAAGGAAGCAG
AAAAGTAAAGGCAGACCCAGAAGATATCAAATGGGACCCACAATG
Found at i:635458 original size:4 final size:4
Alignment explanation
Indices: 635449--635487 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
635439 CCTAAACACT
* * *
635449 TATA TATA TATA TATA TATA TATT TATA TGTA TGTA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
635488 GTGTGTTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (4 bp):
TATA
Found at i:635489 original size:6 final size:6
Alignment explanation
Indices: 635449--635487 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
635439 CCTAAACACT
* * *
635449 TATATA TATATA TATATA TATATT TATATG TATGTA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TAT
635488 GTGTGTTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (6 bp):
TATATA
Found at i:635489 original size:10 final size:10
Alignment explanation
Indices: 635449--635487 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
635439 CCTAAACACT
635449 TATATATATA
1 TATATATATA
635459 TATATATATA
1 TATATATATA
* *
635469 TATTTATATG
1 TATATATATA
*
635479 TATGTATAT
1 TATATATAT
635488 GTGTGTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (10 bp):
TATATATATA
Found at i:639104 original size:24 final size:24
Alignment explanation
Indices: 639077--639189 Score: 131
Period size: 24 Copynumber: 4.7 Consensus size: 24
639067 TTCGATTTGA
* *
639077 ATTCTGATCTGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
639101 ATTCTGATATGATA-TCTGACATGA
1 ATTCTGATATGATACT-TGACATGG
*
639125 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
639149 ATTCTGATCTGATACTTGATC-TGG
1 ATTCTGATATGATACTTGA-CATGG
* *
639173 ATTTTGATATAATACTT
1 ATTCTGATATGATACTT
639190 AACCTGATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
23 1 0.01
24 75 0.96
25 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:639344 original size:31 final size:33
Alignment explanation
Indices: 639277--639344 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 33
639267 TATACCTGGA
*
639277 GGCTCATCGGCTGTGTGCTCAGGGCCTTACTTATT
1 GGCTCATCGGCTGTGTGCTCAAGG-C-TACTTATT
*
639312 GGCTCCTCGGCTGTGTGCTCAAGG-T-CTTATT
1 GGCTCATCGGCTGTGTGCTCAAGGCTACTTATT
639343 GG
1 GG
639345 ACTTGACGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.26
32 1 0.03
35 22 0.71
ACGTcount: A:0.10, C:0.25, G:0.31, T:0.34
Consensus pattern (33 bp):
GGCTCATCGGCTGTGTGCTCAAGGCTACTTATT
Found at i:645340 original size:156 final size:156
Alignment explanation
Indices: 645064--645372 Score: 528
Period size: 156 Copynumber: 2.0 Consensus size: 156
645054 CAGAAAGCTG
* * *
645064 ATCCCTCTCAAGCATAACTGATTGAAGGTCTGCCTCAAGACTAGATACTCTCTTTTCTGATTCTT
1 ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTATTTTCTGACTCTT
* *
645129 CCAAATCAGTAGCTAGTGACCCACTATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
66 CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
645194 CTTTCATGATTAGCATCTGAAAGAGC
131 CTTTCATGATTAGCATCTGAAAGAGC
*
645220 ATCCCTCTCCAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTATTTTCTGACTCTT
1 ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTATTTTCTGACTCTT
* *
645285 TCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTT
66 CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
* *
645350 TTTTCATGATTAGCTTCTGAAAG
131 CTTTCATGATTAGCATCTGAAAG
645373 TGCCACTCCT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
156 143 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (156 bp):
ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTATTTTCTGACTCTT
CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
CTTTCATGATTAGCATCTGAAAGAGC
Found at i:655016 original size:2 final size:2
Alignment explanation
Indices: 655009--655033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
654999 TGTTTATCCA
655009 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
655034 AACTAGCTAG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:657977 original size:28 final size:26
Alignment explanation
Indices: 657928--657984 Score: 60
Period size: 28 Copynumber: 2.1 Consensus size: 26
657918 ACGAGCAATG
* **
657928 AGCATGAGTTGAACAAGTTTTTTAAACA
1 AGCACGAGTTGAACAA-AATTTTAAA-A
*
657956 AGCACGAGTTGAGCAAAATTTTAAAA
1 AGCACGAGTTGAACAAAATTTTAAAA
657982 AGC
1 AGC
657985 TTAACAAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.16
27 7 0.28
28 14 0.56
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (26 bp):
AGCACGAGTTGAACAAAATTTTAAAA
Found at i:660392 original size:18 final size:19
Alignment explanation
Indices: 660369--660408 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
660359 CCTGGAAGTT
660369 CAAAAAAAAAAT-CAGAAA
1 CAAAAAAAAAATCCAGAAA
*
660387 C-AAAAAAAATTCCAGAAA
1 CAAAAAAAAAATCCAGAAA
660405 CAAA
1 CAAA
660409 TACGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 9 0.47
18 8 0.42
19 2 0.11
ACGTcount: A:0.72, C:0.15, G:0.05, T:0.07
Consensus pattern (19 bp):
CAAAAAAAAAATCCAGAAA
Found at i:660393 original size:17 final size:18
Alignment explanation
Indices: 660371--660408 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
660361 TGGAAGTTCA
660371 AAAAAAAAAT-CAGAAAC
1 AAAAAAAAATCCAGAAAC
*
660388 AAAAAAAATTCCAGAAAC
1 AAAAAAAAATCCAGAAAC
660406 AAA
1 AAA
660409 TACGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.74, C:0.13, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAAAAAATCCAGAAAC
Found at i:660547 original size:65 final size:65
Alignment explanation
Indices: 660460--660593 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 65
660450 TGAGATGTAC
* *
660460 AAAAACAAGGTGGTAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACCATACAAACTTAAG
1 AAAAACAAGCTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACCATACAAACTTAAG
* * *
660525 AAAAACAAGCTGATAAGGCAATAAATTCTATCCAAACAAACAAAATACAACTATACAAGCTTAAG
1 AAAAACAAGCTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACCATACAAACTTAAG
660590 AAAA
1 AAAA
660594 TGCATATATG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.16
Consensus pattern (65 bp):
AAAAACAAGCTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACCATACAAACTTAAG
Found at i:662891 original size:111 final size:111
Alignment explanation
Indices: 662697--662920 Score: 430
Period size: 111 Copynumber: 2.0 Consensus size: 111
662687 TGTCAAAGTG
*
662697 AATAAGAAGAGTACAGGACTTCTCCATTTCTAGAAATTTCCTGGCAACACAAAGAAAAAATAAAA
1 AATAAGAAGAGTACAGGACTTCTCCATTTCTAAAAATTTCCTGGCAACACAAAGAAAAAATAAAA
*
662762 TATTCAAATATTCAACCAAAAATATGGTAGAAAATTAGGATTCTCA
66 TATTAAAATATTCAACCAAAAATATGGTAGAAAATTAGGATTCTCA
662808 AATAAGAAGAGTACAGGACTTCTCCATTTCTAAAAATTTCCTGGCAACACAAAGAAAAAATAAAA
1 AATAAGAAGAGTACAGGACTTCTCCATTTCTAAAAATTTCCTGGCAACACAAAGAAAAAATAAAA
662873 TATTAAAATATTCAACCAAAAATATGGTAGAAAATTAGGATTCTCA
66 TATTAAAATATTCAACCAAAAATATGGTAGAAAATTAGGATTCTCA
662919 AA
1 AA
662921 GCTAGGAGTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (111 bp):
AATAAGAAGAGTACAGGACTTCTCCATTTCTAAAAATTTCCTGGCAACACAAAGAAAAAATAAAA
TATTAAAATATTCAACCAAAAATATGGTAGAAAATTAGGATTCTCA
Found at i:665515 original size:3 final size:3
Alignment explanation
Indices: 665507--665573 Score: 118
Period size: 3 Copynumber: 22.3 Consensus size: 3
665497 TTCATAGAGG
665507 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA
665553 A-A AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA A
665574 AGGTTAATGG
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:668029 original size:31 final size:31
Alignment explanation
Indices: 667986--668048 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
667976 TAAGGGTACA
667986 TGATCCCGAACGTTACCGATAC-GTTCGATTT
1 TGATCCCGAACGTTACCGAT-CTGTTCGATTT
* *
668017 TGATCCCTAACGTTATCGATCTGTTCGATTT
1 TGATCCCGAACGTTACCGATCTGTTCGATTT
668048 T
1 T
668049 AGTCATCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (31 bp):
TGATCCCGAACGTTACCGATCTGTTCGATTT
Found at i:674584 original size:24 final size:24
Alignment explanation
Indices: 674557--674602 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
674547 CTCAGACTCT
*
674557 ACCTTGACCTCTGTCTTCGCCTCC
1 ACCTTGACCTCTGCCTTCGCCTCC
* *
674581 ACCTTTACCTCTGCCTTTGCCT
1 ACCTTGACCTCTGCCTTCGCCT
674603 TTGCCTCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.11, T:0.37
Consensus pattern (24 bp):
ACCTTGACCTCTGCCTTCGCCTCC
Found at i:674653 original size:42 final size:42
Alignment explanation
Indices: 674556--674653 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
674546 TCTCAGACTC
**
674556 TACCT-TGACCTCTGTCTTCGCCTCCACCTTTACCTCTGCCTT
1 TACCTCTG-CCTCTGTCTTCGCCTCCACCTTTACCTCCACCTT
* * * *
674598 TGCCTTTGCCTCTGTC-TCAGCCTCTATCTTTACCTCCACCTT
1 TACCTCTGCCTCTGTCTTC-GCCTCCACCTTTACCTCCACCTT
*
674640 TACCTCTGTCTCTG
1 TACCTCTGCCTCTG
674654 ACGCTGCCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.04
42 42 0.91
43 2 0.04
ACGTcount: A:0.09, C:0.41, G:0.10, T:0.40
Consensus pattern (42 bp):
TACCTCTGCCTCTGTCTTCGCCTCCACCTTTACCTCCACCTT
Found at i:674759 original size:6 final size:6
Alignment explanation
Indices: 674750--674775 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
674740 TCTGCTTTTG
674750 CTCTGC CTCTGC CTCTGC CTCTGC CT
1 CTCTGC CTCTGC CTCTGC CTCTGC CT
674776 TTTTCTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
CTCTGC
Found at i:674789 original size:30 final size:29
Alignment explanation
Indices: 674740--674797 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
674730 TGCCTCAGGT
* *
674740 TCTGCTTTTGCTCTGCCTCTGCCTCTGCC
1 TCTGCTTTTGCTCTACCTCTACCTCTGCC
*
674769 TCTGCCTTTTTCTCTACCTCTACCTCTGC
1 TCTG-CTTTTGCTCTACCTCTACCTCTGC
674798 GTCGATTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.03, C:0.41, G:0.12, T:0.43
Consensus pattern (29 bp):
TCTGCTTTTGCTCTACCTCTACCTCTGCC
Found at i:675371 original size:39 final size:39
Alignment explanation
Indices: 675314--675395 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
675304 CATTCTTCAG
* *
675314 CTTTTGGTGTTTTAGTATCATCCACTTCACCCTGATCAC
1 CTTTTGGTGTTTCAGTATCACCCACTTCACCCTGATCAC
* * * *
675353 CTTTTGGTGTTTCGGTATCACCCCCTTCACCCTGGTCAT
1 CTTTTGGTGTTTCAGTATCACCCACTTCACCCTGATCAC
675392 CTTT
1 CTTT
675396 CACACCTCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.13, C:0.30, G:0.15, T:0.41
Consensus pattern (39 bp):
CTTTTGGTGTTTCAGTATCACCCACTTCACCCTGATCAC
Found at i:685867 original size:12 final size:12
Alignment explanation
Indices: 685852--685882 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
685842 CCGTAGAAGC
685852 CTCACGCAAAAG
1 CTCACGCAAAAG
685864 CTCACGCAAAAG
1 CTCACGCAAAAG
685876 CTCACGC
1 CTCACGC
685883 TTCTCCTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.39, G:0.16, T:0.10
Consensus pattern (12 bp):
CTCACGCAAAAG
Found at i:691958 original size:7 final size:7
Alignment explanation
Indices: 691946--691982 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
691936 TCTTTATTGC
691946 AGGTTGA
1 AGGTTGA
691953 AGGTTGA
1 AGGTTGA
691960 AGGTTGA
1 AGGTTGA
691967 AGGTTGA
1 AGGTTGA
691974 AGGTTGA
1 AGGTTGA
691981 AG
1 AG
691983 TCTATTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (7 bp):
AGGTTGA
Found at i:696260 original size:19 final size:19
Alignment explanation
Indices: 696236--696272 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
696226 GAGATACACA
696236 ACATCTGAATTCTAATACC
1 ACATCTGAATTCTAATACC
696255 ACATCTGAATTCTAATAC
1 ACATCTGAATTCTAATAC
696273 TATAGTATTT
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:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (19 bp):
ACATCTGAATTCTAATACC
Found at i:699880 original size:31 final size:30
Alignment explanation
Indices: 699844--699924 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
699834 ATTTTGATCA
*
699844 AAAAAGATGATACATTTTAAATACTTAGATG
1 AAAAAGATGATA-ATTTTAAATACTTAAATG
* * *
699875 AAAAAGTTAAATAA-TTTAAATATTTAAATG
1 AAAAAGAT-GATAATTTTAAATACTTAAATG
*
699905 AAAAATATGATATATTTTAA
1 AAAAAGATGATA-ATTTTAA
699925 TAACTTATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
29 3 0.08
30 21 0.52
31 13 0.32
32 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (30 bp):
AAAAAGATGATAATTTTAAATACTTAAATG
Found at i:702702 original size:21 final size:21
Alignment explanation
Indices: 702651--702694 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
702641 ATGAAACCCT
*
702651 CGAGGGAGAGGTGATCTTTGG
1 CGAGGGAGAGGGGATCTTTGG
702672 CGAGGGAGAGGGGATCTTTGG
1 CGAGGGAGAGGGGATCTTTGG
702693 CG
1 CG
702695 TTGGAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.50, T:0.20
Consensus pattern (21 bp):
CGAGGGAGAGGGGATCTTTGG
Found at i:716614 original size:20 final size:20
Alignment explanation
Indices: 716589--716630 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
716579 GAAGAAGAAA
*
716589 AAACAACGGCAAAAAACCGT
1 AAACAACGACAAAAAACCGT
* *
716609 AAACAATGACAAAAAATCGT
1 AAACAACGACAAAAAACCGT
716629 AA
1 AA
716631 GCTACCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.10
Consensus pattern (20 bp):
AAACAACGACAAAAAACCGT
Found at i:722503 original size:2 final size:2
Alignment explanation
Indices: 722496--722529 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
722486 AGTTCCTTTA
722496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
722530 TTCTAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:729419 original size:23 final size:23
Alignment explanation
Indices: 729392--729436 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
729382 TAAAACCCTA
*
729392 AAAATACTAAAGATAATCCTAAG
1 AAAATACAAAAGATAATCCTAAG
*
729415 AAAATACAAAAGATAATTCTAA
1 AAAATACAAAAGATAATCCTAA
729437 AAATAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAATACAAAAGATAATCCTAAG
Found at i:732003 original size:2 final size:2
Alignment explanation
Indices: 731996--732028 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
731986 TATTATAGCA
731996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
732029 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:732033 original size:2 final size:2
Alignment explanation
Indices: 732028--732062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
732018 ATATATATAT
732028 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 A
732063 TGTAAATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:732231 original size:17 final size:17
Alignment explanation
Indices: 732183--732236 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 17
732173 TAACTGTATC
732183 AATTATCAAATATTCTT
1 AATTATCAAATATTCTT
* *
732200 ATTTGTCAAA-A---TT
1 AATTATCAAATATTCTT
732213 AATTATCAAATATTCTT
1 AATTATCAAATATTCTT
732230 AAATTAT
1 -AATTAT
732237 AATCTAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
16 1 0.04
17 10 0.36
18 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (17 bp):
AATTATCAAATATTCTT
Found at i:733140 original size:21 final size:21
Alignment explanation
Indices: 733089--733140 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
733079 CTTCTTTTCC
* *
733089 TTTTTGCTACAAAAATGAAAG
1 TTTTTGCCATAAAAATGAAAG
733110 TTTTTGCCATAAAAATGAAAG
1 TTTTTGCCATAAAAATGAAAG
733131 TTTTTGCCAT
1 TTTTTGCCAT
733141 GGTGAAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (21 bp):
TTTTTGCCATAAAAATGAAAG
Found at i:734012 original size:174 final size:173
Alignment explanation
Indices: 733662--734012 Score: 537
Period size: 174 Copynumber: 2.0 Consensus size: 173
733652 TAACAAGCCA
*
733662 AAAATGTTGGGAGACTATTACACCAAAGCCAAGCAAATATTTTAAAGTTCATTTACCAGTAAGGA
1 AAAATGTTGGGAGACTATTACACCAAAGCCAAGCAAATAATTTAAAGTTCATTTACCAGTAAGGA
* * **
733727 ACACTTAACTAATTTTCTGGTAATGCAAAAACCAGTATAGTGCAATTCTTAATCCTCTAAAATGT
66 ACACTTAACTAATTATCTAGTAATGCAAAAAAAAGTATAGTGCAATTCTTAATCCTCTAAAATGT
* * *
733792 AAGAGGAAAATGATCAAGACAACTTTTCCGATGCAACATCAAC
131 AAGAAGAAAATGATCAAGACAACTTTTACGAAGCAACATCAAC
733835 AAAA-GTTGGGAGACTATTACACCAAAGCCAAGCAAATAATTTAAAGTTCATTTACCAGTAAAGG
1 AAAATGTTGGGAGACTATTACACCAAAGCCAAGCAAATAATTTAAAGTTCATTTACCAGT-AAGG
*
733899 AAGACTTAAACTAATTATCTAGTAATGCAAAAAAAAGTATAGTGCAATTCTTAATCCTCTAAAAT
65 AACACTT-AACTAATTATCTAGTAATGCAAAAAAAAGTATAGTGCAATTCTTAATCCTCTAAAAT
* * *
733964 GTGAAGAAGAAAATTATCAAGCCAAC-TTTACTAAGACAACAT-AAC
129 GT-AAGAAGAAAATGATCAAGACAACTTTTACGAAG-CAACATCAAC
734009 AAAA
1 AAAA
734013 CAACTGAATA
Statistics
Matches: 162, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
172 54 0.33
173 14 0.09
174 68 0.42
175 26 0.16
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (173 bp):
AAAATGTTGGGAGACTATTACACCAAAGCCAAGCAAATAATTTAAAGTTCATTTACCAGTAAGGA
ACACTTAACTAATTATCTAGTAATGCAAAAAAAAGTATAGTGCAATTCTTAATCCTCTAAAATGT
AAGAAGAAAATGATCAAGACAACTTTTACGAAGCAACATCAAC
Found at i:741800 original size:2 final size:2
Alignment explanation
Indices: 741793--741821 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
741783 ACAATTTTTG
741793 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 T
741822 TAACTAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:743841 original size:185 final size:184
Alignment explanation
Indices: 743488--743876 Score: 611
Period size: 185 Copynumber: 2.1 Consensus size: 184
743478 TTTTCTAATT
* * * * * *
743488 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTCAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
*
743552 TATAAAATAAAAATCTCAGATAATTTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTTATT
66 TATAAAATAAAAATCTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
** *
743617 GGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTTAA-CCCATATTTTA
131 AAATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGC-TAAGCCCATATGTTA
*
743671 TATATAATATATTTAGTATTTTTCAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTCAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
743736 TTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
65 TTATAAAATAAAAATCTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
743801 TAAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
130 TAAATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTAAGCCCATATGTTA
743856 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
743877 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
183 7 0.04
184 24 0.13
185 156 0.83
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTCAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATCTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
AAATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTAAGCCCATATGTTA
Found at i:744300 original size:25 final size:23
Alignment explanation
Indices: 744258--744308 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 23
744248 CAACAACATT
744258 AAATTTTAAAAATATAAATTTATTA
1 AAATTTTAAAAATATAAA--TATTA
*
744283 AAATGTTTAAAAA-GTAAATATTA
1 AAAT-TTTAAAAATATAAATATTA
744306 AAA
1 AAA
744309 ATTAAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
25 8 0.33
26 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATTTTAAAAATATAAATATTA
Found at i:747497 original size:39 final size:39
Alignment explanation
Indices: 747454--747536 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
747444 CTCATGATTT
* *
747454 TATCAAAACCATGATAAACAATATTATATATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
*** * *
747493 TATCAAGGTCATGATAAATAATATCATACATAATAGTTA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
747532 TATCA
1 TATCA
747537 TATTATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:747586 original size:13 final size:13
Alignment explanation
Indices: 747566--747643 Score: 77
Period size: 13 Copynumber: 5.9 Consensus size: 13
747556 ACAATACAAA
*
747566 ACTTTCATATCTC
1 ACTTTCATATTTC
* *
747579 ATTTTCATCTTTC
1 ACTTTCATATTTC
747592 ACTTTCATA-TTC
1 ACTTTCATATTTC
*
747604 ACTTTCACATTTC
1 ACTTTCATATTTC
*
747617 ATTTTCATAATTTGC
1 ACTTTCAT-ATTT-C
*
747632 ACTTTCACATTT
1 ACTTTCATATTT
747644 TAGAACTCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
12 11 0.21
13 26 0.50
14 8 0.15
15 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.01, T:0.51
Consensus pattern (13 bp):
ACTTTCATATTTC
Found at i:747642 original size:28 final size:25
Alignment explanation
Indices: 747566--747643 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
747556 ACAATACAAA
*
747566 ACTTTCATATCTCATTTTCATC-TTTC
1 ACTTTCATAT-TCACTTTCA-CATTTC
747592 ACTTTCATATTCACTTTCACATTTC
1 ACTTTCATATTCACTTTCACATTTC
*
747617 ATTTTCATAATTTGCACTTTCACATTT
1 ACTTTCAT-A-TT-CACTTTCACATTT
747644 TAGAACTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.02
25 19 0.41
26 11 0.24
27 2 0.04
28 13 0.28
ACGTcount: A:0.23, C:0.24, G:0.01, T:0.51
Consensus pattern (25 bp):
ACTTTCATATTCACTTTCACATTTC
Found at i:747743 original size:19 final size:18
Alignment explanation
Indices: 747681--747730 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
747671 GTGTCCGGAC
747681 TCATAACTTATTTCAGAT
1 TCATAACTTATTTCAGAT
747699 TCATAACTTAATTTCAGAT
1 TCATAACTT-ATTTCAGAT
*
747718 TCATAGCTTATTT
1 TCATAACTTATTT
747731 TCAAGTTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (18 bp):
TCATAACTTATTTCAGAT
Found at i:751294 original size:21 final size:23
Alignment explanation
Indices: 751264--751324 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
751254 CGTAAGCTAC
*
751264 CAAAGGCAGAGA-AAA-ATGCCA
1 CAAAGACAGAGATAAACATGCCA
* *
751285 CAAAGACAGAGATAAACTTGTCA
1 CAAAGACAGAGATAAACATGCCA
*
751308 TAAAGACAGAGATAAAC
1 CAAAGACAGAGATAAAC
751325 TTGTAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.32
22 3 0.09
23 20 0.59
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.11
Consensus pattern (23 bp):
CAAAGACAGAGATAAACATGCCA
Found at i:751314 original size:23 final size:23
Alignment explanation
Indices: 751286--751342 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
751276 AAAATGCCAC
*
751286 AAAGACAGAGATAAACTTGTCAT
1 AAAGACAGAGATAAACTTGTAAT
751309 AAAGACAGAGATAAACTTGTAAT
1 AAAGACAGAGATAAACTTGTAAT
*
751332 AAAGGCAGAGA
1 AAAGACAGAGA
751343 ACATGTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.18
Consensus pattern (23 bp):
AAAGACAGAGATAAACTTGTAAT
Found at i:756332 original size:4 final size:4
Alignment explanation
Indices: 756323--756357 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
756313 TCTCAAAGAG
756323 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
756358 AAGAACCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:761130 original size:3 final size:3
Alignment explanation
Indices: 761124--761203 Score: 153
Period size: 3 Copynumber: 27.0 Consensus size: 3
761114 GTAGTAGTTG
761124 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
761171 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
761204 GATTTAATGT
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:761653 original size:22 final size:21
Alignment explanation
Indices: 761606--761653 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
761596 TTTTAATACC
761606 CAAATCCCTAAATCAAAATCT
1 CAAATCCCTAAATCAAAATCT
761627 CAAATCCCTAAAAATCAAAA-CT
1 CAAATCCCT--AAATCAAAATCT
761649 CAAAT
1 CAAAT
761654 TGCAAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (21 bp):
CAAATCCCTAAATCAAAATCT
Found at i:762230 original size:16 final size:16
Alignment explanation
Indices: 762209--762269 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
762199 ACAGAGCCTC
762209 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
762225 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
762241 TGAATCATTCAACATT
1 TGAATCATTCAGCATT
762257 TGAATCATTCAGC
1 TGAATCATTCAGC
762270 GCTTAATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:769130 original size:21 final size:22
Alignment explanation
Indices: 769084--769130 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
769074 ACCGCCGTCG
*
769084 TTTCAGATGACATAACAACCGA
1 TTTCAGATGACACAACAACCGA
**
769106 -TTCAGATGACACCGCAACC-A
1 TTTCAGATGACACAACAACCGA
769126 TTTCA
1 TTTCA
769131 TAAGCCATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (22 bp):
TTTCAGATGACACAACAACCGA
Found at i:769433 original size:15 final size:15
Alignment explanation
Indices: 769413--769451 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
769403 TAGCCGCTAC
* *
769413 TGATGATGACGACGA
1 TGATGATGAAGAAGA
769428 TGATGATGAAGAAGA
1 TGATGATGAAGAAGA
769443 TGATGATGA
1 TGATGATGA
769452 GAATGAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.23
Consensus pattern (15 bp):
TGATGATGAAGAAGA
Found at i:775858 original size:115 final size:114
Alignment explanation
Indices: 775728--776006 Score: 427
Period size: 115 Copynumber: 2.4 Consensus size: 114
775718 TGGGGTTGGT
** *
775728 TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGATCTAGTTTGAATCTAGTTTAGG
1 TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGAT-TAGTTCAAATCTAGTTCAGG
*
775793 TGTATGGTAAATC-GAGTCGAGG-ATCGGGTCAGTCAATTTTCGAGGTCAGG
65 TGTATGATAAATCGGA-TCG-GGTATCGGGTCAGTCAATTTTCGAGGTCAGG
* *
775843 TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGATTTGGTTCAAATCTAGTTCGGG
1 TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGA-TTAGTTCAAATCTAGTTCAGG
*
775908 TGTATGATAAATCGGATCGGGTATCGGGTCAGTCAATTTTCGAGGTCATG
65 TGTATGATAAATCGGATCGGGTATCGGGTCAGTCAATTTTCGAGGTCAGG
* *
775958 TGATTATCGGATCGGTTATTTTTCGGTTTGGATCAATATCATATTAGTT
1 TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGATTAGTT
776007 GATTTTTGGT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
114 7 0.05
115 141 0.93
116 3 0.02
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (114 bp):
TGATTATCGGATCGGTTGTTTTTCGGTTTGGATCAATATCAGATTAGTTCAAATCTAGTTCAGGT
GTATGATAAATCGGATCGGGTATCGGGTCAGTCAATTTTCGAGGTCAGG
Found at i:776354 original size:25 final size:24
Alignment explanation
Indices: 776326--776374 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
776316 TGTGTTAGAA
*
776326 TTTGTTATCAAAAGTTTATATTGAT
1 TTTG-TATCAAAAGTTTATAATGAT
*
776351 TTTGTATGAAAAGTTTATAATGAT
1 TTTGTATCAAAAGTTTATAATGAT
776375 AACTATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTGTATCAAAAGTTTATAATGAT
Found at i:781261 original size:39 final size:39
Alignment explanation
Indices: 781153--781266 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
781143 CTCGACTCAA
*
781153 CCTTGTCCTCTTCAACAGTCTTCTCCCCCACAAACTCGC
1 CCTTGTCCTCTTCAACAGTCTTCTCCTCCACAAACTCGC
* * *
781192 CCTTGTCCTCTTCAACAGTCTTATCCTCCACAAATTCGT
1 CCTTGTCCTCTTCAACAGTCTTCTCCTCCACAAACTCGC
* * * *
781231 CCTTGTCTTCTCCAACAGTCTTCTCTTCCACGAACT
1 CCTTGTCCTCTTCAACAGTCTTCTCCTCCACAAACT
781267 TATTGCATCT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.18, C:0.40, G:0.08, T:0.33
Consensus pattern (39 bp):
CCTTGTCCTCTTCAACAGTCTTCTCCTCCACAAACTCGC
Found at i:784744 original size:15 final size:15
Alignment explanation
Indices: 784724--784755 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
784714 ATCTGGTAAT
*
784724 TTAAAAATATTAAAA
1 TTAAAAAAATTAAAA
784739 TTAAAAAAATTAAAA
1 TTAAAAAAATTAAAA
784754 TT
1 TT
784756 CTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAAAAATTAAAA
Found at i:785226 original size:29 final size:27
Alignment explanation
Indices: 785184--785241 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
785174 ACAGAATGAT
*
785184 ACGTTAAGCACTAAACTGAAACGAAATAA
1 ACGTTAAGCACTAAACTAAAAC-AAA-AA
*
785213 ACGTTAGGCACTAAACTAAAACAAAAA
1 ACGTTAAGCACTAAACTAAAACAAAAA
785240 AC
1 AC
785242 ATACGTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 20 0.74
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (27 bp):
ACGTTAAGCACTAAACTAAAACAAAAA
Found at i:787259 original size:72 final size:71
Alignment explanation
Indices: 787096--787271 Score: 207
Period size: 72 Copynumber: 2.5 Consensus size: 71
787086 TTCGTTCTAG
* *
787096 TTGAATCGGAAGTGCGATGCTTCCTT-CAGTTCAACTTGAATCGAAAGTGCCGATGCTTCATTCT
1 TTGAATCGAAAGTGCGATGCTTCCTTCCA-TTCAACTTGAATCGAAAGTGCCGATGCTTCATTCC
*
787160 GTTCGAT
65 GTTCGAC
* * * *
787167 TTAAATC-AGAAGTACTGATGCTTCCTTCCATTCAACTTGAATC-AGAAGTGTCGATGCTTCCTT
1 TTGAATCGA-AAGTGC-GATGCTTCCTTCCATTCAACTTGAATCGA-AAGTGCCGATGCTTCATT
787230 CCGTTCGAC
63 CCGTTCGAC
787239 TTGAATCGAAAGTGTCGATGCTTCAC-TCCATTC
1 TTGAATCGAAAGTG-CGATGCTTC-CTTCCATTC
787272 GACTCAAATC
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
71 12 0.13
72 72 0.81
73 5 0.06
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (71 bp):
TTGAATCGAAAGTGCGATGCTTCCTTCCATTCAACTTGAATCGAAAGTGCCGATGCTTCATTCCG
TTCGAC
Found at i:787283 original size:36 final size:35
Alignment explanation
Indices: 787096--787275 Score: 152
Period size: 36 Copynumber: 5.0 Consensus size: 35
787086 TTCGTTCTAG
* * *
787096 TTGAATCGGAAGTG-CGATGCTTCCTTCAGTTCAAC
1 TTGAATCGAAAGTGTCGATGCTTCCTCCA-TTCGAC
* * ** *
787131 TTGAATCGAAAGTGCCGATGCTTCATTCTGTTCGAT
1 TTGAATCGAAAGTGTCGATGCTTC-CTCCATTCGAC
* * *
787167 TTAAATC-AGAAGT-ACTGATGCTTCCTTCCATTCAAC
1 TTGAATCGA-AAGTGTC-GATGCTTCC-TCCATTCGAC
*
787203 TTGAATC-AGAAGTGTCGATGCTTCCTTCCGTTCGAC
1 TTGAATCGA-AAGTGTCGATGCTTCC-TCCATTCGAC
787239 TTGAATCGAAAGTGTCGATGCTTCACTCCATTCGAC
1 TTGAATCGAAAGTGTCGATGCTTC-CTCCATTCGAC
787275 T
1 T
787276 CAAATCGATG
Statistics
Matches: 118, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
35 15 0.13
36 99 0.84
37 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTCCATTCGAC
Found at i:789161 original size:44 final size:45
Alignment explanation
Indices: 789111--789199 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
789101 TAACGTTAAA
789111 TATCATATATATTA-TTTTTTATATTTATTAAATCATATAAAATT
1 TATCATATATATTATTTTTTTATATTTATTAAATCATATAAAATT
789155 TATCATATATATTATTTTTTTATATTTATTAAATCATATAAAATT
1 TATCATATATATTATTTTTTTATATTTATTAAATCATATAAAATT
789200 GAACCTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 14 0.32
45 30 0.68
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (45 bp):
TATCATATATATTATTTTTTTATATTTATTAAATCATATAAAATT
Found at i:789171 original size:16 final size:16
Alignment explanation
Indices: 789111--789171 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 16
789101 TAACGTTAAA
789111 TATCATATATATTATT
1 TATCATATATATTATT
*
789127 T-T-TTATAT-TTATT
1 TATCATATATATTATT
* *
789140 AAATCATATA-A-AATT
1 -TATCATATATATTATT
789155 TATCATATATATTATT
1 TATCATATATATTATT
789171 T
1 T
789172 TTTTATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
13 5 0.15
14 13 0.39
15 6 0.18
16 9 0.27
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TATCATATATATTATT
Found at i:790949 original size:15 final size:15
Alignment explanation
Indices: 790929--790986 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
790919 ATATTTAGTT
790929 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGTG
790944 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGTG
* * *
790959 GGGCGAGCGGATGCG
1 GGGCGGGTGGATGTG
790974 GGGCGGGTGGATG
1 GGGCGGGTGGATG
790987 CGGTGCGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.09, C:0.10, G:0.66, T:0.16
Consensus pattern (15 bp):
GGGCGGGTGGATGTG
Found at i:790987 original size:15 final size:15
Alignment explanation
Indices: 790929--790994 Score: 87
Period size: 15 Copynumber: 4.4 Consensus size: 15
790919 ATATTTAGTT
*
790929 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGCG
*
790944 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGCG
* *
790959 GGGCGAGCGGATGCG
1 GGGCGGGTGGATGCG
790974 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
*
790989 GTGCGG
1 GGGCGG
790995 ATGGGGGGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.08, C:0.12, G:0.65, T:0.15
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:796369 original size:16 final size:17
Alignment explanation
Indices: 796348--796380 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
796338 TTTGAAATCT
*
796348 AATTTA-ATTATTCTAA
1 AATTTACATTATACTAA
796364 AATTTACATTATACTAA
1 AATTTACATTATACTAA
796381 TTTAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTACATTATACTAA
Found at i:796918 original size:56 final size:56
Alignment explanation
Indices: 796821--796953 Score: 171
Period size: 56 Copynumber: 2.3 Consensus size: 56
796811 ACACAATTCG
* *
796821 TGCGTATGTGTTTGTTCTTGTTTTTTTCTTTCTTTTCTAAGTATACAGTTATTCGTAAT
1 TGCGTA-GTGTCTGTTCTTGTTTTTTTCTTCCTTTTCTAAGTATACAGTTATTCGT--T
* * *
796880 TTCGTA-TGTCTGTTCTTGTTTTTTT-TTCCTTTTTTAAGTATGCAGTTATTCGTT
1 TGCGTAGTGTCTGTTCTTGTTTTTTTCTTCCTTTTCTAAGTATACAGTTATTCGTT
796934 TGCGTATGTGTCTGTTCTTG
1 TGCGTA-GTGTCTGTTCTTG
796954 ATAATCACAG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
54 6 0.09
56 37 0.56
57 18 0.27
59 5 0.08
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.58
Consensus pattern (56 bp):
TGCGTAGTGTCTGTTCTTGTTTTTTTCTTCCTTTTCTAAGTATACAGTTATTCGTT
Found at i:797079 original size:161 final size:160
Alignment explanation
Indices: 796879--797200 Score: 619
Period size: 161 Copynumber: 2.0 Consensus size: 160
796869 TTATTCGTAA
796879 TTTCGTATGTCTGTTCTTGTTTTTTTTTCCTTTTTTAAGTATGCAGTTATTCGTTTGCGTATGTG
1 TTTCGTATGTCTGTTCTTGTTTTTTTTTCCTTTTTTAAGTATGCAGTTATTCGTTTGCGTATGTG
796944 TCTGTTCTTGATAATCACAGTTTCTCTTATTTAATTTTCTGTTTTCATTTTTCTGGCTTCTGGGA
66 TCTGTTCTTGATAATCACAGTTTCTCTTATTTAATTTTCTGTTTTCATTTTTCTGGCTTCTGGGA
797009 CAATATTGCAGCTGTTAATCATCAATATTT
131 CAATATTGCAGCTGTTAATCATCAATATTT
797039 TTTCGTATGTGTCTGTTCTTG-TTTTTTTTCCTTTTTTAAGTATGCAGTTATTCGTTTGCGTATG
1 TTTCGTA--TGTCTGTTCTTGTTTTTTTTTCCTTTTTTAAGTATGCAGTTATTCGTTTGCGTATG
797103 TGTCTGTTCTTGATAATCACAGTTTCTCTTATTTAATTTTCTGTTTTCATTTTTCTGGCTTCTGG
64 TGTCTGTTCTTGATAATCACAGTTTCTCTTATTTAATTTTCTGTTTTCATTTTTCTGGCTTCTGG
797168 GACAATATTGCAGCTGTTAATCATCAATATTT
129 GACAATATTGCAGCTGTTAATCATCAATATTT
797200 T
1 T
797201 GCTTTTGGAA
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 7 0.04
161 141 0.88
162 12 0.08
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (160 bp):
TTTCGTATGTCTGTTCTTGTTTTTTTTTCCTTTTTTAAGTATGCAGTTATTCGTTTGCGTATGTG
TCTGTTCTTGATAATCACAGTTTCTCTTATTTAATTTTCTGTTTTCATTTTTCTGGCTTCTGGGA
CAATATTGCAGCTGTTAATCATCAATATTT
Found at i:802706 original size:56 final size:56
Alignment explanation
Indices: 802631--802821 Score: 131
Period size: 56 Copynumber: 3.4 Consensus size: 56
802621 ATAAAATATT
* *
802631 TTAAATTAAAATTAAATTAATATATTATATAGGTTTTAAGAATTAAAATTATTATG
1 TTAAAATAATATTAAATTAATATATTATATAGGTTTTAAGAATTAAAATTATTATG
* * * * *
802687 TTAAAATAATATTTAATTAA-ATAATGTATTCATA--TCTGAAAAATGTAACTATT-TTATTG
1 TTAAAATAATATTAAATTAATAT-AT-TA-T-ATAGGTTTTAAGAAT-TAA-AATTATTA-TG
* * * **** *
802746 TTAAAATTATAATTAAATGACT-TGGCGTATAGGGTTTAAGAATTAAAATTATTATG
1 TTAAAATAAT-ATTAAATTAATATATTATATAGGTTTTAAGAATTAAAATTATTATG
*
802802 TTAAAATAATATTTAATTAA
1 TTAAAATAATATTAAATTAA
802822 ATAATGTATT
Statistics
Matches: 99, Mismatches: 24, Indels: 25
0.67 0.16 0.17
Matches are distributed among these distances:
55 9 0.09
56 36 0.36
57 16 0.16
58 13 0.13
59 17 0.17
60 8 0.08
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (56 bp):
TTAAAATAATATTAAATTAATATATTATATAGGTTTTAAGAATTAAAATTATTATG
Found at i:802787 original size:115 final size:115
Alignment explanation
Indices: 802658--802887 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 115
802648 TAATATATTA
* *
802658 TATAGGTTTTAAGAATTAAAATTATTATGTTAAAATAATATTTAATTAAATAATGTATTCATATC
1 TATAGGGTTTAAGAATTAAAATTATTATGTTAAAATAATATTTAATTAAATAATGTATTCATATA
802723 TGAAAAATGTAACTATTTTATTGTTAAAATTATAATTAAATGACTTGGCG
66 TGAAAAATGTAACTATTTTATTGTTAAAATTATAATTAAATGACTTGGCG
802773 TATAGGGTTTAAGAATTAAAATTATTATGTTAAAATAATATTTAATTAAATAATGTATTCATATA
1 TATAGGGTTTAAGAATTAAAATTATTATGTTAAAATAATATTTAATTAAATAATGTATTCATATA
* * *
802838 TGAAAAATGTAACTATTTTTTTTTTGAAATTATAATTAAATGACTTGGCG
66 TGAAAAATGTAACTATTTTATTGTTAAAATTATAATTAAATGACTTGGCG
802888 AGACAAATTG
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (115 bp):
TATAGGGTTTAAGAATTAAAATTATTATGTTAAAATAATATTTAATTAAATAATGTATTCATATA
TGAAAAATGTAACTATTTTATTGTTAAAATTATAATTAAATGACTTGGCG
Found at i:805620 original size:30 final size:30
Alignment explanation
Indices: 805584--805643 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
805574 ATATATTTTT
*
805584 ACCCTACTGAAATTTTATGAGTTCAAATTC
1 ACCCTACTAAAATTTTATGAGTTCAAATTC
805614 ACCCTACTAAAATTTTATGAGTTCAAATTC
1 ACCCTACTAAAATTTTATGAGTTCAAATTC
805644 GTCCCACTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (30 bp):
ACCCTACTAAAATTTTATGAGTTCAAATTC
Found at i:807561 original size:17 final size:17
Alignment explanation
Indices: 807539--807592 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
807529 TTTAATAGAA
807539 AAATTATTTAATTAAAT
1 AAATTATTTAATTAAAT
*
807556 AAATTA--AAATT-AAT
1 AAATTATTTAATTAAAT
**
807570 AAAAAATTTAATTAAAT
1 AAATTATTTAATTAAAT
807587 AAATTA
1 AAATTA
807593 AAACTAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 7 0.25
15 4 0.14
16 4 0.14
17 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATTTAATTAAAT
Found at i:807581 original size:31 final size:31
Alignment explanation
Indices: 807544--807605 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
807534 TAGAAAAATT
*
807544 ATTTAATTAAATAAATTAAAATTAATAAAAA
1 ATTTAATTAAATAAATTAAAACTAATAAAAA
807575 ATTTAATTAAATAAATTAAAACTAATAAAAA
1 ATTTAATTAAATAAATTAAAACTAATAAAAA
807606 TTTCTCCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (31 bp):
ATTTAATTAAATAAATTAAAACTAATAAAAA
Found at i:817029 original size:2 final size:2
Alignment explanation
Indices: 817022--817070 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
817012 ATGTGGTAGA
817022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
817064 AT AT AT A
1 AT AT AT A
817071 AAGAATGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:821724 original size:23 final size:23
Alignment explanation
Indices: 821644--821724 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
821634 TCTTGCCCTA
*
821644 GGATGCCCTCGCATAGCTCGCTC
1 GGATGGCCTCGCATAGCTCGCTC
* * * *
821667 GGATGGCCTAG-GTCAGATGGCCTC
1 GGATGGCCTCGCAT-AGCTCG-CTC
*
821691 GGAT-GCTCTCGCATAGCTTGCTC
1 GGATGGC-CTCGCATAGCTCGCTC
821714 GGATGGCCTCG
1 GGATGGCCTCG
821725 GATGCCCAGC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
22 1 0.02
23 26 0.59
24 16 0.36
25 1 0.02
ACGTcount: A:0.14, C:0.31, G:0.32, T:0.23
Consensus pattern (23 bp):
GGATGGCCTCGCATAGCTCGCTC
Found at i:822420 original size:20 final size:20
Alignment explanation
Indices: 822397--822468 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
822387 GTTTCCAGAT
*
822397 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
822417 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
822437 TCACAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
822457 TCGCAACGCGAT
1 TCGCAACGCGAT
822469 AATACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:822489 original size:41 final size:40
Alignment explanation
Indices: 822400--822490 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
822390 TCCAGATTCG
* * **
822400 CAACGCGATTTTGACTATCGCAATGCGAATATGTAAATCA
1 CAACGCGATTCTGACTATCGCAACGCGAATATCAAAATCA
822440 CAACGCGATTCTGACTATCGCAACGCG-ATAATACAAAATCA
1 CAACGCGATTCTGACTATCGCAACGCGAAT-AT-CAAAATCA
*
822481 CAATGCGATT
1 CAACGCGATT
822491 TTCAAAGCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
39 2 0.05
40 27 0.61
41 15 0.34
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (40 bp):
CAACGCGATTCTGACTATCGCAACGCGAATATCAAAATCA
Found at i:823105 original size:42 final size:42
Alignment explanation
Indices: 823059--823152 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
823049 CCTCTCATAT
*
823059 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* * ** *
823101 CGTTCAAAAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
*
823143 CATTCAAGAG
1 CGTTCAAGAG
823153 CCCGATTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 38 0.88
43 5 0.12
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:823916 original size:203 final size:198
Alignment explanation
Indices: 823574--823961 Score: 699
Period size: 203 Copynumber: 1.9 Consensus size: 198
823564 TCACGTCTTC
823574 TAATAAGGAAAATGAGGAAAATAAAAAAAATACGCGATACAATTATGCTAACGTCTTCACGTAGT
1 TAATAAGGAAAATGAGGAAAATAAAAAAAATACGCGATACAATTATGCTAACGTCTTCACGTAGT
823639 TCACTTGAAGAACAACGAGAAGAATCATATGTGTTGAGTAATGGACAAGCTAAACTTTATCCTGC
66 TCACTTGAAGAACAACGAGAAGAATCATATGTGTTGAGTAATGGACAAGCTAAACTTTATCCTGC
823704 ATGGTAGGAGATCGATAATGTTAGTATTTA-TTTTTAAATA-TTTAAAGGTGTTCTCACGTCTTC
131 ATGGTAGGAGATCGATAATGTTAGTATTTATTTTTTAAATATTTTAAAGGTGTTCTCACGTCTTC
823767 TAA
196 TAA
823770 TAATAAGGAAAATGAGGAAAAATTAAAAAAAATACGCGATATACAATTATGCTAACGTCTTTTCA
1 TAATAAGGAAAATGAGG-AAAA-TAAAAAAAATACGCG--ATACAATTATGCTAACGTC--TTCA
823835 CGTAGTTCACTTGAAGAATCAACGAGAAGAATCATATGTGTTGAGTAATGGACAAGCTAAACTTT
60 CGTAGTTCACTTGAAGAA-CAACGAGAAGAATCATATGTGTTGAGTAATGGACAAGCTAAACTTT
823900 ATCCTGCATGGTAGGAGATCGATAATGTTAGTATTTATTTTTTAAATATTTTAAAGGTGTTC
124 ATCCTGCATGGTAGGAGATCGATAATGTTAGTATTTATTTTTTAAATATTTTAAAGGTGTTC
823962 ATAAATAAGT
Statistics
Matches: 183, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
196 17 0.09
197 4 0.02
198 15 0.08
200 19 0.10
202 22 0.12
203 83 0.45
204 10 0.05
205 13 0.07
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (198 bp):
TAATAAGGAAAATGAGGAAAATAAAAAAAATACGCGATACAATTATGCTAACGTCTTCACGTAGT
TCACTTGAAGAACAACGAGAAGAATCATATGTGTTGAGTAATGGACAAGCTAAACTTTATCCTGC
ATGGTAGGAGATCGATAATGTTAGTATTTATTTTTTAAATATTTTAAAGGTGTTCTCACGTCTTC
TAA
Found at i:824725 original size:14 final size:14
Alignment explanation
Indices: 824704--824742 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
824694 TTTTTTATTT
824704 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
824718 AGTTGATTTGTAAA
1 AATTGATTTGTAAA
824732 AATTGATTTGT
1 AATTGATTTGT
824743 TTAATTGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:824763 original size:28 final size:29
Alignment explanation
Indices: 824703--824763 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
824693 ATTTTTTATT
*
824703 TAATTGATTTGTAAAAGTTGATTTGTAAA
1 TAATTGATTTGTAAAAGTTGATGTGTAAA
**
824732 -AATTGATTTGTTTAA-TTGATGTGTAAA
1 TAATTGATTTGTAAAAGTTGATGTGTAAA
824759 TAATT
1 TAATT
824764 TTTATTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (29 bp):
TAATTGATTTGTAAAAGTTGATGTGTAAA
Found at i:827148 original size:14 final size:14
Alignment explanation
Indices: 827129--827165 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
827119 TCACGTGGTA
827129 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
827143 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
827157 TTCTTCTTC
1 TT-TTCTTC
827166 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:827382 original size:24 final size:24
Alignment explanation
Indices: 827348--827401 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
827338 TTCTGAAATC
827348 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
827372 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
827396 ATCAAA
1 ATCAAA
827402 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:828297 original size:19 final size:19
Alignment explanation
Indices: 828273--828309 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
828263 TTGGATACTG
* *
828273 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
828292 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
828310 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:833911 original size:143 final size:143
Alignment explanation
Indices: 833653--833939 Score: 574
Period size: 143 Copynumber: 2.0 Consensus size: 143
833643 CCAAATAGGC
833653 TTAGATGATATACAGGACTTGCTCTGTAAATCACTTCTCTTGGAACTTGTTAGCGCCGAGCTTGA
1 TTAGATGATATACAGGACTTGCTCTGTAAATCACTTCTCTTGGAACTTGTTAGCGCCGAGCTTGA
833718 CCCCAGTAAGTGATGAAACTAAGCTCACAGTTCTTTTTCTTTTTTCGTTCTTCAACTTTAACGTT
66 CCCCAGTAAGTGATGAAACTAAGCTCACAGTTCTTTTTCTTTTTTCGTTCTTCAACTTTAACGTT
833783 ACATCTAGTTGCG
131 ACATCTAGTTGCG
833796 TTAGATGATATACAGGACTTGCTCTGTAAATCACTTCTCTTGGAACTTGTTAGCGCCGAGCTTGA
1 TTAGATGATATACAGGACTTGCTCTGTAAATCACTTCTCTTGGAACTTGTTAGCGCCGAGCTTGA
833861 CCCCAGTAAGTGATGAAACTAAGCTCACAGTTCTTTTTCTTTTTTCGTTCTTCAACTTTAACGTT
66 CCCCAGTAAGTGATGAAACTAAGCTCACAGTTCTTTTTCTTTTTTCGTTCTTCAACTTTAACGTT
833926 ACATCTAGTTGCG
131 ACATCTAGTTGCG
833939 T
1 T
833940 ATAAATGTTG
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 144 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (143 bp):
TTAGATGATATACAGGACTTGCTCTGTAAATCACTTCTCTTGGAACTTGTTAGCGCCGAGCTTGA
CCCCAGTAAGTGATGAAACTAAGCTCACAGTTCTTTTTCTTTTTTCGTTCTTCAACTTTAACGTT
ACATCTAGTTGCG
Found at i:835510 original size:15 final size:15
Alignment explanation
Indices: 835458--835524 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
835448 CTAATGAGTA
*
835458 AATTAAT-AGTTAGAT
1 AATTAATAATTTA-AT
*
835473 AATTAA-AATTAAAAT
1 AATTAATAATT-TAAT
835488 AATTTAATAATTTAAT
1 AA-TTAATAATTTAAT
*
835504 AATTAATGATTTAAT
1 AATTAATAATTTAAT
*
835519 ATTTAA
1 AATTAA
835525 CTTTTTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 29 0.67
16 10 0.23
17 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
AATTAATAATTTAAT
Found at i:835522 original size:7 final size:8
Alignment explanation
Indices: 835485--835524 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
835475 TTAAAATTAA
835485 AATAATTT
1 AATAATTT
835493 AATAATTT
1 AATAATTT
835501 AATAA-TT
1 AATAATTT
*
835508 AATGATTT
1 AATAATTT
835516 AAT-ATTT
1 AATAATTT
835523 AA
1 AA
835525 CTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 12 0.40
8 18 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
AATAATTT
Found at i:842677 original size:23 final size:23
Alignment explanation
Indices: 842517--842669 Score: 234
Period size: 23 Copynumber: 6.7 Consensus size: 23
842507 CTCGTATAAA
*
842517 TGCACCGAAGTGCCACGTAGAGT
1 TGCACCGAAGTGCCACGTAGAAT
*
842540 TGCACCGAAGTGCCACGTAGAGT
1 TGCACCGAAGTGCCACGTAGAAT
*
842563 TGCACCGAAGTGCCACGTAGAGT
1 TGCACCGAAGTGCCACGTAGAAT
*
842586 TGCACCGAAGTGCCACTTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
842609 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
842632 TGCACCGAAGTGCCGCGTAAAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
842655 TGCACCAAAGTGCCA
1 TGCACCGAAGTGCCA
842670 TATAAAATGT
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 121 1.00
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:844322 original size:13 final size:13
Alignment explanation
Indices: 844288--844331 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
844278 ACTGGTCACA
*
844288 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
844301 ACCCAACCCGTTG
1 ACCCGACCCGTTG
*
844314 ACTCGACCCGTTG
1 ACCCGACCCGTTG
844327 ACCCG
1 ACCCG
844332 TTGAGCGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:848685 original size:64 final size:63
Alignment explanation
Indices: 848597--848734 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 63
848587 TTAACATGTA
* * * *
848597 CATCGATGCACTACCTATGCATCGATACACCAATCACCTTCGATGTTTTCAT-TTTAAGGGGGTG
1 CATCGATACACTACCTATGCATCGATACACCAATCACATTCGATG-TTTCATCTTTAA-AGAGTG
* * ** *
848661 CATCGATACACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTCTTCTTTAAAGAGTG
1 CATCGATACACTACC-TATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGAGTG
848724 CATCGATACAC
1 CATCGATACAC
848735 CTTGCCCAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 22 0.35
64 41 0.65
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (63 bp):
CATCGATACACTACCTATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGAGTG
Found at i:852861 original size:20 final size:20
Alignment explanation
Indices: 852833--852876 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
852823 TTTTTCAAGA
*
852833 AAAATATTTTATTATTAAAC
1 AAAACATTTTATTATTAAAC
852853 AAAACATTTTATTATTAAAC
1 AAAACATTTTATTATTAAAC
852873 AAAA
1 AAAA
852877 AACTTGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAACATTTTATTATTAAAC
Found at i:859506 original size:21 final size:21
Alignment explanation
Indices: 859482--859529 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
859472 GGTTTACATT
*
859482 CCACA-ACAGTTTCAGATGCCA
1 CCACAGACA-TTTCAGACGCCA
*
859503 CCACAGTCATTTCAGACGCCA
1 CCACAGACATTTCAGACGCCA
859524 CCACAG
1 CCACAG
859530 CCGATTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.17
Consensus pattern (21 bp):
CCACAGACATTTCAGACGCCA
Found at i:859544 original size:21 final size:21
Alignment explanation
Indices: 859491--859544 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
859481 TCCACAACAG
*
859491 TTTCAGATGCCACCACAGTCA
1 TTTCAGATGCCACCACAGCCA
*
859512 TTTCAGACGCCACCACAGCCGA
1 TTTCAGATGCCACCACAGCC-A
*
859534 -TTCATATGCCA
1 TTTCAGATGCCA
859545 ACGCTGCAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.22
Consensus pattern (21 bp):
TTTCAGATGCCACCACAGCCA
Found at i:861624 original size:13 final size:13
Alignment explanation
Indices: 861606--861632 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
861596 GTCTCCAGTA
861606 TCGCTAATTCGCG
1 TCGCTAATTCGCG
861619 TCGCTAATTCGCG
1 TCGCTAATTCGCG
861632 T
1 T
861633 TGCGATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (13 bp):
TCGCTAATTCGCG
Found at i:861935 original size:41 final size:41
Alignment explanation
Indices: 861869--862024 Score: 269
Period size: 41 Copynumber: 3.8 Consensus size: 41
861859 ACTATAGACT
*
861869 ATCGCAACGACACTGTATG-CTATCGCAACGCGAGATGGAAA
1 ATCGCAACGACACTGTA-GACTATCGCAACGCGAAATGGAAA
* *
861910 ATCGTAACAACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
861951 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
861992 ATCGCAACGACACTGTAGACTATCGCAACGCGA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA
862025 TTTTCAACCA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 1 0.01
41 108 0.99
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:861956 original size:20 final size:20
Alignment explanation
Indices: 861931--862000 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
861921 ACTGTAGACT
861931 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
861951 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
861972 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
861992 ATCGCAACG
1 ATCGCAACG
862001 ACACTGTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 18 0.46
21 9 0.23
22 3 0.08
23 3 0.08
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Done.