Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007988.1 Hibiscus syriacus cultivar Beakdansim tig00110435_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: 847207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:710499 original size:41 final size:41
Alignment explanation
Indices: 710380--710517 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
710370 CGCTTTGAAA
* * *
710380 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
710421 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
710461 ATCGCGTTGCGATTTTGTATTATCGCGCTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
710502 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
710518 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:710514 original size:20 final size:20
Alignment explanation
Indices: 710400--710513 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
710390 GATTATGTAT
*
710400 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
710420 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
710440 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
710460 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
710481 TATCGCGCTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
710501 TACCGCGTTGCGA
1 TATCGCGTTGCGA
710514 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.04
20 56 0.76
21 13 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:710534 original size:21 final size:21
Alignment explanation
Indices: 710508--710700 Score: 284
Period size: 21 Copynumber: 9.3 Consensus size: 21
710498 CAGTACCGCG
710508 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
710529 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
710550 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
710571 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
710592 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
*
710613 TTGCGATTTTTCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
** *
710634 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTCCAAAT-TCGCA
710654 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* * **
710675 TTGTGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
710695 TTGCGA
1 TTGCGA
710701 ATTGTGAAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.01
20 30 0.19
21 123 0.78
22 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:710735 original size:83 final size:83
Alignment explanation
Indices: 710508--710743 Score: 206
Period size: 83 Copynumber: 2.8 Consensus size: 83
710498 CAGTACCGCG
* * * ** *** *
710508 TTGCGATTTTCCAAATTCGCATTGCG-ATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCAT
1 TTGCGATTTTACAAATTCGCATTGCGAATTGT-CAAAATCGCAACGCGAAAGT-CAAAATCGCAT
710572 TGCGATTTTCCAAATTCGCA
64 TGCGATTTTCCAAATTCGCA
* * * * ** * **
710592 TTGCGATTTTCCAAATTCGCATTGCGATTTTTCAAATTCGCATTGCGATAGTCAGTATCGCATTG
1 TTGCGATTTTACAAATTCGCATTGCGAATTGTCAAAATCGCAACGCGAAAGTCAAAATCGCATTG
710657 CGATTTTCCAAATTCGCA
66 CGATTTTCCAAATTCGCA
* ** * * * *
710675 TTGTGA-TTTACTTATTCGCATTGCGAATTGTGAAAATCGCAACGTGAAATTGGAAAATCGCATT
1 TTGCGATTTTACAAATTCGCATTGCGAATTGTCAAAATCGCAACGCGAAAGT-CAAAATCGCATT
710739 GCGAT
65 GCGAT
710744 AGTCATAATC
Statistics
Matches: 128, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
82 33 0.26
83 47 0.37
84 44 0.34
85 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (83 bp):
TTGCGATTTTACAAATTCGCATTGCGAATTGTCAAAATCGCAACGCGAAAGTCAAAATCGCATTG
CGATTTTCCAAATTCGCA
Found at i:711655 original size:15 final size:16
Alignment explanation
Indices: 711617--711657 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
711607 ACAGAGCCTC
*
711617 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
711633 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
711649 T-AATCATTC
1 TGAATCATTC
711658 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:721696 original size:17 final size:17
Alignment explanation
Indices: 721674--721721 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
721664 AAATGCATGT
721674 TATATTATATTT-TGATA
1 TATATTATATTTATGA-A
*
721691 TATATTGTATTTATGAA
1 TATATTATATTTATGAA
*
721708 TATTTTGATATTTA
1 TATATT-ATATTTA
721722 AATTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TATATTATATTTATGAA
Found at i:721732 original size:27 final size:27
Alignment explanation
Indices: 721680--721735 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
721670 ATGTTATATT
* *
721680 ATATTTTGATATATATTGTATTTATGA
1 ATATTTTGATATATAATGTATATATGA
*
721707 ATATTTTGATATTTAAAT-TATATATGA
1 ATATTTTGATATAT-AATGTATATATGA
721734 AT
1 AT
721736 TGGATGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (27 bp):
ATATTTTGATATATAATGTATATATGA
Found at i:722631 original size:28 final size:29
Alignment explanation
Indices: 722576--722639 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
722566 TTTACATTGG
*
722576 GCTATAAAATAAAAAAGTGAATAATATAA
1 GCTATGAAATAAAAAAGTGAATAATATAA
* *
722605 GCTATGAAATGAAAAA-TGAA-AATTATAT
1 GCTATGAAATAAAAAAGTGAATAA-TATAA
722633 GCTATGA
1 GCTATGA
722640 CGTTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 15 0.48
29 14 0.45
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (29 bp):
GCTATGAAATAAAAAAGTGAATAATATAA
Found at i:725160 original size:22 final size:22
Alignment explanation
Indices: 725120--725175 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
725110 CTAAATTTCT
* ** *
725120 AATTTTAAAACCATTAACTCTA
1 AATTTTAAATCCAAAAACTATA
725142 AATTTTAAATCCAAAAACTATA
1 AATTTTAAATCCAAAAACTATA
*
725164 AATCTTAAATCC
1 AATTTTAAATCC
725176 TAAACAATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTTTAAATCCAAAAACTATA
Found at i:729572 original size:27 final size:27
Alignment explanation
Indices: 729542--729596 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
729532 AAATAAACTC
*
729542 AGAAAAGTAAAGGAAAAGCATTCTCCA
1 AGAAAAGTAAAGGAAAAGCATTCGCCA
729569 AGAAAAGTAAAGGAAAAGCATTCGCCA
1 AGAAAAGTAAAGGAAAAGCATTCGCCA
729596 A
1 A
729597 CTCTTTGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.53, C:0.15, G:0.20, T:0.13
Consensus pattern (27 bp):
AGAAAAGTAAAGGAAAAGCATTCGCCA
Found at i:745659 original size:63 final size:63
Alignment explanation
Indices: 745580--745721 Score: 221
Period size: 63 Copynumber: 2.2 Consensus size: 63
745570 CTTTAAAAAT
*
745580 GAAACATAGTTATTAATTTATTTAAGCGATTATGAAATAATAATCCAGTCTTATTAAATTATCA
1 GAAA-ATAGTTATTAATTTATTTAAGCGATTATAAAATAATAATCCAGTCTTATTAAATTATCA
* * * *
745644 GAAAATAGTTATTAATTTATTTAAGTGATTATAAAATAATAATCTAGTTTTATTATATTATCA
1 GAAAATAGTTATTAATTTATTTAAGCGATTATAAAATAATAATCCAGTCTTATTAAATTATCA
*
745707 TAAAATAGTTATTAA
1 GAAAATAGTTATTAA
745722 AGTTATTAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 68 0.94
64 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (63 bp):
GAAAATAGTTATTAATTTATTTAAGCGATTATAAAATAATAATCCAGTCTTATTAAATTATCA
Found at i:745758 original size:63 final size:63
Alignment explanation
Indices: 745580--745744 Score: 190
Period size: 63 Copynumber: 2.6 Consensus size: 63
745570 CTTTAAAAAT
* ** * * *
745580 GAAACATAGTTATTAATTTATTTAAGCGATTATGAAATAATAATCCAGTCTTATTAAATTATCA
1 GAAA-ATAGTTATTAAGTTATTTAAATGATTATAAAATAATAATCTAGTTTTATTAAATTATCA
* * *
745644 GAAAATAGTTATTAATTTATTTAAGTGATTATAAAATAATAATCTAGTTTTATTATATTATCA
1 GAAAATAGTTATTAAGTTATTTAAATGATTATAAAATAATAATCTAGTTTTATTAAATTATCA
*
745707 TAAAATAGTTATTAAAGTTA-TTAGAAT-ATTATTAAAAT
1 GAAAATAGTTATT-AAGTTATTTA-AATGATTA-TAAAAT
745745 TTATTATTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
63 73 0.81
64 17 0.19
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (63 bp):
GAAAATAGTTATTAAGTTATTTAAATGATTATAAAATAATAATCTAGTTTTATTAAATTATCA
Found at i:746400 original size:60 final size:60
Alignment explanation
Indices: 746273--746387 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
746263 GTAAAGTACA
* * * * *
746273 TAAATGGTCCCTCGACTATAATACGTTGCTCTGTTGAGTCCCCCGACTATTAAAACTTAC
1 TAAATGGTCCCCCAACTATAAGACATTGCTCTGTTGAATCCCCCGACTATTAAAACTTAC
* * *
746333 TAAATGGTCCCCCAACTATAGGACATTGCTTTGTTGAATCCCTCGACTATTAAAA
1 TAAATGGTCCCCCAACTATAAGACATTGCTCTGTTGAATCCCCCGACTATTAAAA
746388 GTTGTAGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (60 bp):
TAAATGGTCCCCCAACTATAAGACATTGCTCTGTTGAATCCCCCGACTATTAAAACTTAC
Found at i:748176 original size:3 final size:3
Alignment explanation
Indices: 748168--748195 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
748158 GGCAGCTCAC
748168 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
748196 GTACTTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:749926 original size:17 final size:17
Alignment explanation
Indices: 749885--749934 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
749875 ATACAACATT
749885 CAGTAATC--TTATTCC
1 CAGTAATCTTTTATTCC
*
749900 CTGATAATCTTTTATTCC
1 CAG-TAATCTTTTATTCC
*
749918 CAGTAATCTTATATTCC
1 CAGTAATCTTTTATTCC
749935 GTGAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 13 0.45
18 9 0.31
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (17 bp):
CAGTAATCTTTTATTCC
Found at i:755439 original size:24 final size:24
Alignment explanation
Indices: 755409--755502 Score: 170
Period size: 24 Copynumber: 3.9 Consensus size: 24
755399 TCTTCCAGAT
* *
755409 GATGTATAAAACATCTATGTATAT
1 GATGTATAAAACATCTATGTACAC
755433 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
755457 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
755481 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
755503 CATATCATGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:759715 original size:15 final size:15
Alignment explanation
Indices: 759695--759736 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
759685 TTGGTTTCCC
759695 GGAATTTGAATTAAT
1 GGAATTTGAATTAAT
*
759710 GGAATTTGAATTACT
1 GGAATTTGAATTAAT
759725 GGAATTTGAATT
1 GGAATTTGAATT
759737 CTGGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (15 bp):
GGAATTTGAATTAAT
Found at i:759742 original size:29 final size:30
Alignment explanation
Indices: 759695--759752 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
759685 TTGGTTTCCC
**
759695 GGAATTTGAATTAATGGAATTTGAATTACT
1 GGAATTTGAATTAATGGAAAATGAATTACT
*
759725 GGAATTTGAATT-CTGGAAAATGAATTAC
1 GGAATTTGAATTAATGGAAAATGAATTAC
759753 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
GGAATTTGAATTAATGGAAAATGAATTACT
Found at i:759748 original size:14 final size:15
Alignment explanation
Indices: 759701--759752 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
759691 TCCCGGAATT
* **
759701 TGAATTAATGGAATT
1 TGAATTACTGGAAAA
**
759716 TGAATTACTGGAATT
1 TGAATTACTGGAAAA
759731 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
759745 TGAATTAC
1 TGAATTAC
759753 ATTTCTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:759758 original size:20 final size:20
Alignment explanation
Indices: 759735--759784 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
759725 GGAATTTGAA
759735 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
759755 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
759775 TTATGGAAAA
1 TTCTGGAAAA
759785 CATCTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:759978 original size:49 final size:50
Alignment explanation
Indices: 759881--759979 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
759871 TACAAATATT
*
759881 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
759931 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
759980 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:760085 original size:90 final size:86
Alignment explanation
Indices: 759929--760098 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
759919 ATTATTATTT
* * * * *
759929 TAAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATT
1 TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
*
759994 AATATTGGTATATTTTAGTGAAA
66 -A-ATTAGTATATTTTAGTGAAA
* *
760017 TAAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-TTAAAAA
1 TAAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTATATTAATAAAAA
760080 TATTAATTAGTATATTTTA
62 TATTAATTAGTATATTTTA
760099 AATATATTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 23 0.33
89 7 0.10
90 16 0.23
91 15 0.21
92 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
AATTAGTATATTTTAGTGAAA
Found at i:760117 original size:23 final size:24
Alignment explanation
Indices: 760067--760130 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
760057 AGTGTTATAT
* *
760067 TATATTTTAAAAATA-TTAATTAG
1 TATATTTTAAATATATTTAATAAG
*
760090 TATATTTTAAATATATTTACTAAG
1 TATATTTTAAATATATTTAATAAG
760114 -ATATTATTTAAATATAT
1 TATA-T-TTTAAATATAT
760131 AAATAATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.49
24 7 0.20
25 11 0.31
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (24 bp):
TATATTTTAAATATATTTAATAAG
Found at i:760171 original size:30 final size:29
Alignment explanation
Indices: 760114--760217 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 29
760104 ATTTACTAAG
*
760114 ATATTATTTAAATATAT-AAATAATATTAT
1 ATATTA-TTAAATATATAAAAAAATATTAT
760143 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAAAA-TATTAT
760173 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAA-A-AATAT-TAT
760202 ATATTATTATAATATA
1 ATATTATTA-AATATA
760218 ATTGATTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
28 15 0.23
29 26 0.40
30 20 0.31
31 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTATTAAATATATAAAAAAATATTAT
Found at i:760246 original size:30 final size:30
Alignment explanation
Indices: 760167--760270 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
760157 ATAAAAAAAT
* * *
760167 TATTATATATTATTAAAATAAAAATATAATA
1 TATTATATAATATTAAAAT-ATAATATTATA
* *
760198 TCTTATAT--TATTATAATATAATTGATTAT-
1 TATTATATAATATTAAAATATAA-T-ATTATA
760227 T-TTATATAATATTAAAATATAATATTATA
1 TATTATATAATATTAAAATATAATATTATA
760256 TATTATA-AATATTAA
1 TATTATATAATATTAA
760271 TAAATATATT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
28 14 0.23
29 20 0.32
30 21 0.34
31 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTATATAATATTAAAATATAATATTATA
Found at i:760278 original size:23 final size:22
Alignment explanation
Indices: 760230--760289 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
760220 TGATTATTTT
760230 ATATAATATTA-AAATA-TAATA
1 ATAT-ATATTATAAATATTAATA
*
760251 TTATATATTATAAATATTAATA
1 ATATATATTATAAATATTAATA
*
760273 A-ATATATTTTAAATATT
1 ATATATATTATAAATATT
760290 TTAATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 23 0.68
22 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATTATAAATATTAATA
Found at i:760279 original size:28 final size:28
Alignment explanation
Indices: 760118--760280 Score: 82
Period size: 30 Copynumber: 5.9 Consensus size: 28
760108 ACTAAGATAT
760118 TATT-TAAATA-T-ATAAATAATATTAT-
1 TATTATAAATATTAATAAAT-ATATTATA
*
760143 TCATTATTAAATATATAA-AAAAATTATTATA
1 T-ATTA-TAAATAT-TAATAAATA-TATTATA
** *
760174 TATTATTAAAATAAAAATATAATATCTTATA
1 TATTA-T-AAATATTAATA-AATATATTATA
**
760205 TTATTAT-AATA-TAATTGAT-TATT-T-
1 -TATTATAAATATTAATAAATATATTATA
760229 TA-TAT-AATATTAA-AATATAATATTATA
1 TATTATAAATATTAATAA-AT-ATATTATA
760256 TATTATAAATATTAATAAATATATT
1 TATTATAAATATTAATAAATATATT
760281 TTAAATATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 39
0.68 0.07 0.25
Matches are distributed among these distances:
22 7 0.07
23 7 0.07
25 6 0.06
26 7 0.07
27 4 0.04
28 17 0.16
29 15 0.14
30 20 0.19
31 15 0.14
32 8 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTATAAATATTAATAAATATATTATA
Found at i:760285 original size:11 final size:11
Alignment explanation
Indices: 760235--760288 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
760225 ATTTTATATA
760235 ATATTA-AAAT
1 ATATTATAAAT
* *
760245 ATAATAT-TAT
1 ATATTATAAAT
760255 ATATTATAAAT
1 ATATTATAAAT
*
760266 AT-TAATAAAT
1 ATATTATAAAT
*
760276 ATATTTTAAAT
1 ATATTATAAAT
760287 AT
1 AT
760289 TTTAATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
10 22 0.65
11 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTATAAAT
Found at i:760289 original size:30 final size:31
Alignment explanation
Indices: 760228--760302 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
760218 ATTGATTATT
*
760228 TTATATAATATT-A-AAATATAATATTATATA
1 TTATA-AATATTAATAAATATAATATTAAATA
*
760258 TTATAAATATTAATAAATAT-ATTTTAAATA
1 TTATAAATATTAATAAATATAATATTAAATA
*
760288 TT-TTAATAATTAATA
1 TTATAAAT-ATTAATA
760303 TTTTGATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 10 0.26
30 23 0.59
31 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TTATAAATATTAATAAATATAATATTAAATA
Found at i:760541 original size:42 final size:42
Alignment explanation
Indices: 760479--760596 Score: 175
Period size: 41 Copynumber: 2.8 Consensus size: 42
760469 ATGAATTACG
760479 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
* *
760521 TTTCGGAAAACGAATTACGTGAAACAAACACG-GAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
** * *
760562 TTCCAAAAAATGAATTACATGAAACAAACACGAGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGA
760597 TTTCGGAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 35 0.51
42 33 0.49
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
Found at i:769527 original size:2 final size:2
Alignment explanation
Indices: 769520--769544 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
769510 CACAAAAATG
769520 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 A
769545 AGCAAGTGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:773087 original size:108 final size:108
Alignment explanation
Indices: 772920--773206 Score: 355
Period size: 108 Copynumber: 2.7 Consensus size: 108
772910 ATATTATGAG
* * *
772920 AGTTTAAGCTGATAGGGCTTTAGAAATCTCACGATAACAAAATAAATTAATTACTTATTTTGTTA
1 AGTTTAAACTGATAGGGCTTTAGAAATCTCACAATAACAAAATAAGTTAATTACTTATTTTGTTA
* * *
772985 TTAATATTATCAACATATTTGGTTGCG-CTTAAAATGTTACCAA
66 TAAATATTATCAACATATTAGATTGCGTC-TAAAATGTTACCAA
* * * *
773028 AGTTTAAACTGATAGGGTTTTAGAAATCTCACAATAATAAAATATGTTAATTATTTATTTTGTTA
1 AGTTTAAACTGATAGGGCTTTAGAAATCTCACAATAACAAAATAAGTTAATTACTTATTTTGTTA
* * *
773093 TAAATATTATCAACATATTAGATTGTGTCTAATATGTTATCAA
66 TAAATATTATCAACATATTAGATTGCGTCTAAAATGTTACCAA
* * * * * *
773136 AG-TTAAAGCTGA-CGAGGCCTTAGAAATCTCACAACAACAAAATAGGTTAAATACTTATTTTAT
1 AGTTTAAA-CTGATAG-GGCTTTAGAAATCTCACAATAACAAAATAAGTTAATTACTTATTTTGT
773199 TATAAATA
64 TATAAATA
773207 AATATTAATA
Statistics
Matches: 154, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
107 6 0.04
108 147 0.95
109 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (108 bp):
AGTTTAAACTGATAGGGCTTTAGAAATCTCACAATAACAAAATAAGTTAATTACTTATTTTGTTA
TAAATATTATCAACATATTAGATTGCGTCTAAAATGTTACCAA
Found at i:774021 original size:76 final size:75
Alignment explanation
Indices: 773920--774228 Score: 433
Period size: 76 Copynumber: 4.1 Consensus size: 75
773910 AAGTTGTAAA
* * *
773920 TATTTTACCGTTTATATTATTATTATACCTTTAAACTAACAGGTAGTTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAAC-GGTAGCTAGTTTAACGTAATAGGT
*
773985 TGCGCCTACTT
65 TGCGCCTATTT
* *
773996 TATTTTACCGTTTACATTATTATTATACCTTAAAACAAACCGGTAGCTAGTTTAACGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAA-CGGTAGCTAGTTTAACGTAATAGGT
774061 TGCGCCTATTT
65 TGCGCCTATTT
*
774072 TATTTTACCGTTTATATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGT--TAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAAC-GGTAGCTAGTTTAACGTAATAGGT
*
774135 TGCGACTATTT
65 TGCGCCTATTT
* * * *
774146 TATTTTACCGTTTGCATTAATATTATATCTTTAAACAAATCGGTACCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAA-CGGTAGCTAGTTTAACGTAATAGGT
* **
774211 AGTTCCTATTT
65 TGCGCCTATTT
774222 TATTTTA
1 TATTTTA
774229 ATCGGTTAAG
Statistics
Matches: 209, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
74 65 0.31
75 2 0.01
76 141 0.67
77 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (75 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACGGTAGCTAGTTTAACGTAATAGGTT
GCGCCTATTT
Found at i:774196 original size:150 final size:151
Alignment explanation
Indices: 773920--774228 Score: 467
Period size: 150 Copynumber: 2.0 Consensus size: 151
773910 AAGTTGTAAA
* *
773920 TATTTTACCGTTTATATTATTATTATACCTTTAAACTAACAGGTAGTTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTATATTATTATTATACCTTTAAACAAACAGGTAGCTAGTTTAACGT-ATAGGT
* * *
773985 TGCGCCTACTTTATTTTACCGTTTACATTATTATTATACCTTAAAACAAACCGGTAGCTAGTTTA
65 TGCGACTACTTTATTTTACCGTTTACATTAATATTATACCTTAAAACAAACCGGTACCTAGTTTA
* *
774050 ACGTAATATGTTGCGCCTATTT
130 ACGTAATAGGTAGCGCCTATTT
*
774072 TATTTTACCGTTTATATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGT-TAGGTT
1 TATTTTACCGTTTATATTATTATTATACCTTTAAACAAACAGGTAGCTAGTTTAACGTATAGGTT
* * * * *
774136 GCGACTATTTTATTTTACCGTTTGCATTAATATTATATCTTTAAACAAATCGGTACCTAGTTTAA
66 GCGACTACTTTATTTTACCGTTTACATTAATATTATACCTTAAAACAAACCGGTACCTAGTTTAA
**
774201 CGTAATAGGTAGTTCCTATTT
131 CGTAATAGGTAGCGCCTATTT
774222 TATTTTA
1 TATTTTA
774229 ATCGGTTAAG
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
150 87 0.61
152 55 0.39
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (151 bp):
TATTTTACCGTTTATATTATTATTATACCTTTAAACAAACAGGTAGCTAGTTTAACGTATAGGTT
GCGACTACTTTATTTTACCGTTTACATTAATATTATACCTTAAAACAAACCGGTACCTAGTTTAA
CGTAATAGGTAGCGCCTATTT
Found at i:774282 original size:100 final size:100
Alignment explanation
Indices: 774146--774330 Score: 271
Period size: 100 Copynumber: 1.9 Consensus size: 100
774136 GCGACTATTT
* * * * * **
774146 TATTTTACCGTTTGCATTAATATTATATCTTTAAACAAATCGGTACCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTAATATTATACCTTCAAACAAACCGGTAACTAGTTTAAAATAATAGGT
***
774211 AGTTCCTATTTTATTTTAATCGGTTAAGTTGTAAA
66 AACGCCTATTTTATTTTAATCGGTTAAGTTGTAAA
*
774246 TATTTTACCGTTTACATTAGTATTATACCTTCAAACAAACCGGTAACTAGTTTAAAATAATAGGT
1 TATTTTACCGTTTACATTAATATTATACCTTCAAACAAACCGGTAACTAGTTTAAAATAATAGGT
774311 AACGCCTATTTTATTTTAAT
66 AACGCCTATTTTATTTTAAT
774331 GTTAACTAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 74 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (100 bp):
TATTTTACCGTTTACATTAATATTATACCTTCAAACAAACCGGTAACTAGTTTAAAATAATAGGT
AACGCCTATTTTATTTTAATCGGTTAAGTTGTAAA
Found at i:774394 original size:21 final size:21
Alignment explanation
Indices: 774368--774407 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
774358 AAAGATCAAA
774368 AGTATAGGTATCGATACATAT
1 AGTATAGGTATCGATACATAT
*
774389 AGTATAGGTATGGATACAT
1 AGTATAGGTATCGATACAT
774408 TTTCAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (21 bp):
AGTATAGGTATCGATACATAT
Found at i:774934 original size:100 final size:99
Alignment explanation
Indices: 774813--775040 Score: 348
Period size: 100 Copynumber: 2.3 Consensus size: 99
774803 TATGCCAGTA
* * * * * *
774813 TAATAATAATGTAAACAGTAAAATATTTATAATCTAACATGTTAAAACAATTTTGGCGCAACCTA
1 TAATAATAATGTAAACGGTAAAATATTTAAAACCTAACAGGTTAAAAAAATTTAGGCGCAACCTA
774878 TTACTTTAAACTTGCTACCCGCTTGTTTATAGGGT
66 TTACTTTAAACTTGCTA-CCGCTTGTTTATAGGGT
* * *
774913 TAATGATAATGTAAACGGTAAAATATTTAAAACCTAACCGGTTAAAAAAATTTAGGTGCAACCTA
1 TAATAATAATGTAAACGGTAAAATATTTAAAACCTAACAGGTTAAAAAAATTTAGGCGCAACCTA
*
774978 TTACTTTAAACTTGCTACCGTTTGTTTATAGGGT
66 TTACTTTAAACTTGCTACCGCTTGTTTATAGGGT
*
775012 TAATAATAATGTAACCGGTAAAATATTTA
1 TAATAATAATGTAAACGGTAAAATATTTA
775041 CAACATAATC
Statistics
Matches: 116, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 43 0.37
100 73 0.63
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (99 bp):
TAATAATAATGTAAACGGTAAAATATTTAAAACCTAACAGGTTAAAAAAATTTAGGCGCAACCTA
TTACTTTAAACTTGCTACCGCTTGTTTATAGGGT
Found at i:775316 original size:144 final size:144
Alignment explanation
Indices: 775056--775352 Score: 348
Period size: 144 Copynumber: 2.1 Consensus size: 144
775046 TAATCGGTTA
* * * *
775056 ATACTTTTTTTCAGTATGTTCTCTTAAACATTTTGCATGAAAATGTATCGATACACATAGATAAC
1 ATACTTTTTTCCAGTATGTTCTCTTAAACATTTTGCAAGAAAACGTATCGATACACATAGATAAA
* * * * ** ** * *
775121 GTATCAATATTGCTTATTTCGAAACAAAATATGCAATATCTTCAACGTCAAAGTATTGATGCTTG
66 ATATCAATATTACTAATTTCAAAACAAAATATGCAATATCTAAAACGTCAAAGTATCAATACATG
* *
775186 TTATGACAATATTG
131 TTATAACAATATCG
* ** *
775200 ATACTTTTTTCCATTATGCTT-TCTTAAACATTTTGCAAGAGGACGTATCGATACACATATATAA
1 ATACTTTTTTCCAGTATG-TTCTCTTAAACATTTTGCAAGAAAACGTATCGATACACATAGATAA
* *
775264 AATATCGACCT-TTAC-AATTTCAAAACAAAATATGCAATATCTAAAATGTCAAAGTATCAATAC
65 AATATC-A-ATATTACTAATTTCAAAACAAAATATGCAATATCTAAAACGTCAAAGTATCAATAC
775327 ATGTTATAACAATATCG
128 ATGTTATAACAATATCG
775344 ATACTTTTT
1 ATACTTTTT
775353 CGGCAGTATG
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
144 121 0.95
145 6 0.05
146 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (144 bp):
ATACTTTTTTCCAGTATGTTCTCTTAAACATTTTGCAAGAAAACGTATCGATACACATAGATAAA
ATATCAATATTACTAATTTCAAAACAAAATATGCAATATCTAAAACGTCAAAGTATCAATACATG
TTATAACAATATCG
Found at i:776204 original size:145 final size:143
Alignment explanation
Indices: 775717--776335 Score: 713
Period size: 144 Copynumber: 4.3 Consensus size: 143
775707 AAAATTGATA
* * * *
775717 CATAACAAGTATTGATACTTTGACATTTTAGATATTGCACATTTTGTTTCGAAATTATAAATATT
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
* * *
775782 GATACTTTATATATGTGTATTGATA-TATTTTCCATGCGAATTGTTTGAGAAGCATATTGGAAAA
66 GATACTTTATATATGTGTATCGATACT-TTTT-CATGCAAATTATTTGAGAAGCATATTGGAAAA
*
775846 AAATATTGATATTGT
129 AAATATTGATACTGT
* * * * * * * *
775861 TATAACAAATATCAATACTTTAACGTTGAAGATATTGTATATTTTGTTTCGAAATTATAAACATC
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
* * * * * *
775926 GATACTTTATATACGTGTATCGATGCATTTTCGTGCAAATTATTTGAGAAACATAGTGGAATAAA
66 GATACTTTATATATGTGTATCGATACTTTTTCATGCAAATTATTTGAGAAGCATATTGGAA-AAA
* * *
775991 AGTATTAATATTGT
130 AATATTGATACTGT
* *
776005 CATAACAAGTATCGATACTTTGACATTTCAGATATTGCATATTTTGTTTTGAAATTATAAATATC
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
* * * * * *
776070 AATACTCTATATATGTGTATCGATACTTTTTCATGCAAATTGTTTTAGAGAGCATACTGCAACAA
66 GATACTTTATATATGTGTATCGATACTTTTTCATGCAAATTATTTGAGA-AGCATATTGGAA-AA
*
776135 AAATATTGATACTAT
129 AAATATTGATACTGT
* * * * *
776150 TATAACTAGTATCGATACTTTGACATTTCAGATATTGCATATTTTGTATCGAAA-TAAACAATAT
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATA-AATAT
* * * *
776214 CGATACTTGATATGTATGTATCGATACCTTTTCATGCAAATTATTTGAGAGAGCATATTGGAAAA
65 CGATACTTTATATATGTGTATCGATACTTTTTCATGCAAATTATTTGAGA-AGCATATTGGAAAA
776279 AAAGTATTGATACTGT
129 AAA-TATTGATACTGT
* * * *
776295 CATAACTATTATCGATACATAT-ACATTGAAGATATTGCATA
1 CATAACAAGTATCGATAC-TTTGACATTTAAGATATTGCATA
776336 AAACTCAATA
Statistics
Matches: 399, Mismatches: 70, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
143 25 0.06
144 198 0.50
145 174 0.44
146 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (143 bp):
CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
GATACTTTATATATGTGTATCGATACTTTTTCATGCAAATTATTTGAGAAGCATATTGGAAAAAA
ATATTGATACTGT
Found at i:776254 original size:289 final size:289
Alignment explanation
Indices: 775717--776335 Score: 780
Period size: 289 Copynumber: 2.1 Consensus size: 289
775707 AAAATTGATA
* * * *
775717 CATAACAAGTATTGATACTTTGACATTTTAGATATTGCACATTTTGTTTCGAAATTATAAATATT
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
* * * * * *
775782 GATACTTTATATATGTGTATTGATATATTTTCCATGCGAATTGTTTGAGAAGCATATTGGAAAAA
66 AATACTCTATATATGTGTATCGATATATTTTCCATGCAAATTGTTTGAGAAGCATACTGCAAAAA
* * * * *
775847 AATATTGATATTGTTATAACAAATATCAATACTTTAACGTTGAAGATATTGTATATTTTGTTTCG
131 AATATTGATACTATTATAACAAATATCAATACTTTAACATTGAAGATATTGCATATTTTGTATCG
* * * * *
775912 AAATTATAAACATCGATACTTTATATACGTGTATCGATGCATTTTCGTGCAAATTATTTGAGA-A
196 AAATTAAAAACATCGATACTTGATATACATGTATCGATACATTTTCATGCAAATTATTTGAGAGA
* *
775976 ACATAGTGGAATAAAAGTATTAATATTGT
261 ACATAGTGGAAAAAAAGTATTAATACTGT
* *
776005 CATAACAAGTATCGATACTTTGACATTTCAGATATTGCATATTTTGTTTTGAAATTATAAATATC
1 CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
*
776070 AATACTCTATATATGTGTATCGATACT-TTTT-CATGCAAATTGTTTTAGAGAGCATACTGCAAC
66 AATACTCTATATATGTGTATCGATA-TATTTTCCATGCAAATTGTTTGAGA-AGCATACTGCAA-
* * * * **
776133 AAAAATATTGATACTATTATAACTAGTATCGATACTTTGACATTTCAGATATTGCATATTTTGTA
128 AAAAATATTGATACTATTATAACAAATATCAATACTTTAACATTGAAGATATTGCATATTTTGTA
* ** *
776198 TCGAAA-TAAACAATATCGATACTTGATATGTATGTATCGATACCTTTTCATGCAAATTATTTGA
193 TCGAAATTAAA-AACATCGATACTTGATATACATGTATCGATACATTTTCATGCAAATTATTTGA
* * *
776262 GAGAGCATATTGGAAAAAAAGTATTGATACTGT
257 GAGAACATAGTGGAAAAAAAGTATTAATACTGT
* * * *
776295 CATAACTATTATCGATACATAT-ACATTGAAGATATTGCATA
1 CATAACAAGTATCGATAC-TTTGACATTTAAGATATTGCATA
776336 AAACTCAATA
Statistics
Matches: 283, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
287 16 0.06
288 99 0.35
289 108 0.38
290 58 0.20
291 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (289 bp):
CATAACAAGTATCGATACTTTGACATTTAAGATATTGCATATTTTGTTTCGAAATTATAAATATC
AATACTCTATATATGTGTATCGATATATTTTCCATGCAAATTGTTTGAGAAGCATACTGCAAAAA
AATATTGATACTATTATAACAAATATCAATACTTTAACATTGAAGATATTGCATATTTTGTATCG
AAATTAAAAACATCGATACTTGATATACATGTATCGATACATTTTCATGCAAATTATTTGAGAGA
ACATAGTGGAAAAAAAGTATTAATACTGT
Found at i:777158 original size:10 final size:10
Alignment explanation
Indices: 777122--777160 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
777112 ACAGTACTGT
777122 ATGAACAATA
1 ATGAACAATA
777132 ATGAA-AATA
1 ATGAACAATA
777141 CTATGAACAATA
1 --ATGAACAATA
777153 ATGAACAA
1 ATGAACAA
777161 CATCGTGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.15
10 13 0.50
11 5 0.19
12 4 0.15
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (10 bp):
ATGAACAATA
Found at i:777246 original size:21 final size:21
Alignment explanation
Indices: 777207--777249 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
777197 ATTGTAATAG
777207 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATT-CCCTGCTACA
777229 GGGAACCGATAT-CCTGCTACA
1 GGGAACCGAT-TCCCTGCTACA
777250 ATACTGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 10 0.50
23 1 0.05
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
GGGAACCGATTCCCTGCTACA
Found at i:778002 original size:18 final size:18
Alignment explanation
Indices: 777979--778013 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
777969 CACTGAAATT
777979 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
777997 TGTCCCGTAGGACCACT
1 TGTCCCGAAGGACCACT
778014 GTAACTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:783501 original size:21 final size:21
Alignment explanation
Indices: 783450--783548 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
783440 GCACTAAAAT
*
783450 TTGTCCCGAATGACCAC--TA
1 TTGTCCCGAAGGACCACTGTA
* *
783469 -TCTCCCGTAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
783489 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
* *
783510 TTATCCCGAATGACCAC--TA
1 TTGTCCCGAAGGACCACTGTA
*
783529 -TGTCCCGTAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
783549 ACCTTAGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
18 26 0.40
19 2 0.03
20 4 0.06
21 33 0.51
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:789105 original size:75 final size:75
Alignment explanation
Indices: 789009--789147 Score: 233
Period size: 75 Copynumber: 1.9 Consensus size: 75
788999 TTTGCAAATA
* *
789009 AAATGGTTTCTTACCGTGTCACAATTGGTTAATTTGGCATAGTATTTCAATATGGACTTCCAAAT
1 AAATGGTATCTTACCGTGTCACAATTGGTTAATTTCGCATAGTATTTCAATATGGACTTCCAAAT
789074 ATCGTGTCAC
66 ATCGTGTCAC
* * *
789084 AAATGGTATCTTACCGTGTCACAATTGGTTAATTTCGTATAGTCTTTCAATATGGACTTTCAAA
1 AAATGGTATCTTACCGTGTCACAATTGGTTAATTTCGCATAGTATTTCAATATGGACTTCCAAA
789148 AGTCCACAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (75 bp):
AAATGGTATCTTACCGTGTCACAATTGGTTAATTTCGCATAGTATTTCAATATGGACTTCCAAAT
ATCGTGTCAC
Found at i:792196 original size:13 final size:13
Alignment explanation
Indices: 792178--792207 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
792168 TCGAACCGTT
792178 TTTTTTTCAATTC
1 TTTTTTTCAATTC
792191 TTTTTTTCAATTC
1 TTTTTTTCAATTC
792204 TTTT
1 TTTT
792208 AAATTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTCAATTC
Found at i:792354 original size:20 final size:19
Alignment explanation
Indices: 792303--792397 Score: 86
Period size: 20 Copynumber: 4.9 Consensus size: 19
792293 GGTAGAGCTT
*
792303 AACCGGTTTTGTCCAATTTC
1 AACCGGTTTTGT-CAAATTC
* * *
792323 AATCGATATTGTCAAATTCC
1 AACCGGTTTTGTCAAATT-C
* *
792343 TACCGGTTTTGTC--CTTC
1 AACCGGTTTTGTCAAATTC
*
792360 AACCGATTTTGTCAAATTGC
1 AACCGGTTTTGTCAAATT-C
792380 AACCGGTTTTGTCAAATT
1 AACCGGTTTTGTCAAATT
792398 TTAACATATT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
17 12 0.21
18 2 0.03
19 7 0.12
20 37 0.64
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (19 bp):
AACCGGTTTTGTCAAATTC
Found at i:792372 original size:37 final size:38
Alignment explanation
Indices: 792303--792392 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 38
792293 GGTAGAGCTT
*
792303 AACCGGTTTTGTCCAATTTCAATCGATATTGTCAAATTCC
1 AACCGGTTTTGTCC-A-TTCAACCGATATTGTCAAATTCC
* * *
792343 TACCGGTTTTGTCC-TTCAACCGATTTTGTCAAATTGC
1 AACCGGTTTTGTCCATTCAACCGATATTGTCAAATTCC
792380 AACCGGTTTTGTC
1 AACCGGTTTTGTC
792393 AAATTTTAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 32 0.71
40 13 0.29
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (38 bp):
AACCGGTTTTGTCCATTCAACCGATATTGTCAAATTCC
Found at i:793277 original size:26 final size:25
Alignment explanation
Indices: 793238--793302 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
793228 GATCACATTT
*
793238 TTTCTTAACCTTATATTAATAT-GTC
1 TTTCTTAACATTATATTAAT-TCGTC
793263 TTTCTTTAACATTATATTAATTCGTC
1 TTTC-TTAACATTATATTAATTCGTC
793289 TTTCCTTATACATT
1 TTT-CTTA-ACATT
793303 CCCGATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 5 0.14
26 24 0.69
27 6 0.17
ACGTcount: A:0.26, C:0.17, G:0.03, T:0.54
Consensus pattern (25 bp):
TTTCTTAACATTATATTAATTCGTC
Found at i:802960 original size:2 final size:2
Alignment explanation
Indices: 802953--803004 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
802943 AATTTTGAGT
802953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
802995 TA TA TA TA TA
1 TA TA TA TA TA
803005 GTAAAAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:803307 original size:13 final size:13
Alignment explanation
Indices: 803289--803317 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
803279 CATTCTATAA
803289 TAAAAATTAAAAT
1 TAAAAATTAAAAT
803302 TAAAAATTAAAAT
1 TAAAAATTAAAAT
803315 TAA
1 TAA
803318 TACATAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:808288 original size:14 final size:14
Alignment explanation
Indices: 808266--808312 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
808256 TGCTCCAGAT
808266 GCATGTGTTGCATA
1 GCATGTGTTGCATA
*
808280 GCATATGTTGCATA
1 GCATGTGTTGCATA
808294 GCATGTGTTGCATA
1 GCATGTGTTGCATA
808308 GCATG
1 GCATG
808313 ATGCACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (14 bp):
GCATGTGTTGCATA
Found at i:809635 original size:162 final size:163
Alignment explanation
Indices: 809367--809697 Score: 646
Period size: 162 Copynumber: 2.0 Consensus size: 163
809357 TGCCGTCATC
809367 AGCGATAGGAGAAAAAACACCCATTGGAGGTATGGTCTGGAAAACCTGCTACTGATTATGATTCC
1 AGCGATAGGAGAAAAAACACCCATTGGAGGTATGGTCTGGAAAACCTGCTACTGATTATGATTCC
809432 TTACATGTATTTGGATCCACTGCTTATTATCATGTGAAGGAATCCAATCTTGATCCGAGAGCAAA
66 TTACATGTATTTGGATCCACTGCTTATTATCATGTGAAGGAATCCAATCTTGATCCGAGAGCAAA
809497 GAAGGCTCTCTTTATGGGAATCTCCGAGGTACA
131 GAAGGCTCTCTTTATGGGAATCTCCGAGGTACA
809530 AGCGATAGGAGAAAAAACA-CCATTGGAGGTATGGTCTGGAAAACCTGCTACTGATTATGATTCC
1 AGCGATAGGAGAAAAAACACCCATTGGAGGTATGGTCTGGAAAACCTGCTACTGATTATGATTCC
*
809594 TTACATGTATTTGGATCCACTGCTTATTATCATGTGAAGGAATCCAATCTTGATCCTAGAGCAAA
66 TTACATGTATTTGGATCCACTGCTTATTATCATGTGAAGGAATCCAATCTTGATCCGAGAGCAAA
809659 GAAGGCTCTCTTTATGGGAATCTCCGAGGTACA
131 GAAGGCTCTCTTTATGGGAATCTCCGAGGTACA
809692 AGCGAT
1 AGCGAT
809698 TTGATAGCTT
Statistics
Matches: 167, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
162 148 0.89
163 19 0.11
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (163 bp):
AGCGATAGGAGAAAAAACACCCATTGGAGGTATGGTCTGGAAAACCTGCTACTGATTATGATTCC
TTACATGTATTTGGATCCACTGCTTATTATCATGTGAAGGAATCCAATCTTGATCCGAGAGCAAA
GAAGGCTCTCTTTATGGGAATCTCCGAGGTACA
Found at i:814864 original size:36 final size:36
Alignment explanation
Indices: 814817--814924 Score: 137
Period size: 36 Copynumber: 3.0 Consensus size: 36
814807 CGGCCATGTT
814817 GCAGCAGCCTATTGTCGGA-TGCCCTAACCAGTTGCA
1 GCAGCAGCCTATTGTCGGAGT-CCCTAACCAGTTGCA
* * * *
814853 GCAGCATCCTATTGTTGGAGTCCCTAATCAGTTTCA
1 GCAGCAGCCTATTGTCGGAGTCCCTAACCAGTTGCA
* * *
814889 GCAGCAGCCTATTGTAGCAGTCCCTAACCCGTTGCA
1 GCAGCAGCCTATTGTCGGAGTCCCTAACCAGTTGCA
814925 AGCTCCACTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 60 0.98
37 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (36 bp):
GCAGCAGCCTATTGTCGGAGTCCCTAACCAGTTGCA
Found at i:821175 original size:2 final size:2
Alignment explanation
Indices: 821168--821200 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
821158 ACGGATTGCT
821168 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 T
821201 TTAGTATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:842969 original size:21 final size:19
Alignment explanation
Indices: 842943--842994 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
842933 TTCCATTTCG
*
842943 CGTTGCGATAGTCTATAATGT
1 CGTTGCGATAGTCCA-AAT-T
**
842964 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
842983 CGTTGCGATAGT
1 CGTTGCGATAGT
842995 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 12 0.46
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:843591 original size:6 final size:6
Alignment explanation
Indices: 843580--843606 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
843570 AGTCGGGTCA
843580 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
843607 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:843765 original size:19 final size:19
Alignment explanation
Indices: 843705--843768 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
843695 GAATTTTTGT
843705 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
* * **
843724 AACGATAACTGTAGACTATCGC
1 AACG--AA-TTTGGAAAATCGC
843746 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
843765 AACG
1 AACG
843769 CGATTTTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.50
20 2 0.06
21 2 0.06
22 13 0.38
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (19 bp):
AACGAATTTGGAAAATCGC
Found at i:844029 original size:2 final size:2
Alignment explanation
Indices: 844022--844054 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
844012 TTCGAACATC
844022 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
844055 AGAATATAAA
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:845198 original size:24 final size:24
Alignment explanation
Indices: 845166--845221 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
845156 TGAACGGTTC
845166 AGCGGTTCTGGCCGGTTCACTAAT
1 AGCGGTTCTGGCCGGTTCACTAAT
845190 AGCGGTTCTGGCCGGTTCACTAAT
1 AGCGGTTCTGGCCGGTTCACTAAT
845214 AGCGGTTC
1 AGCGGTTC
845222 AACCGATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (24 bp):
AGCGGTTCTGGCCGGTTCACTAAT
Done.