Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006047.1 Hibiscus syriacus cultivar Beakdansim tig00014304_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: 680228
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:623115 original size:106 final size:106
Alignment explanation
Indices: 622958--623869 Score: 1455
Period size: 106 Copynumber: 8.6 Consensus size: 106
622948 ATATCGTGCC
* * * * *
622958 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
623023 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
623064 ACTCCAGACGACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
623129 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
623170 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
623235 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* **
623276 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
623341 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
623382 ACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
623447 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
623488 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
623553 AATATCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
623594 ACTCTAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
623659 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
623700 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * *
623765 AATTTCAGAGTCAATTTCAACTTCATAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
623806 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTC
623870 AACTTCACGA
Statistics
Matches: 753, Mismatches: 52, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
106 749 0.99
107 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:624056 original size:84 final size:85
Alignment explanation
Indices: 623923--624099 Score: 248
Period size: 84 Copynumber: 2.1 Consensus size: 85
623913 AAAGACCCCC
* * *
623923 GAGTTCGATTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTAT
* * * *
623988 CTTCTAACCAAAGATCT-TT
66 CTGCCAACCAAAGACCTGAT
* * **
624007 GAGTTCGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTAT
624072 CTGCCAACCAAAGACCTGAT
66 CTGCCAACCAAAGACCTGAT
624092 GAGTTCGA
1 GAGTTCGA
624100 TTTCATTCAG
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 72 0.89
85 9 0.11
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (85 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTAT
CTGCCAACCAAAGACCTGAT
Found at i:624339 original size:3 final size:3
Alignment explanation
Indices: 624328--624396 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
624318 TTAAATAATA
* *
624328 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAC TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * * *
624372 TAT AAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
624397 TTTGCAGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:626946 original size:21 final size:21
Alignment explanation
Indices: 626922--626966 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
626912 TGATTTTAAA
626922 AAAATTAAAAGTTTAAATACT
1 AAAATTAAAAGTTTAAATACT
* * **
626943 AAAATTGATAGTTTACTTACT
1 AAAATTAAAAGTTTAAATACT
626964 AAA
1 AAA
626967 TGCATAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAATACT
Found at i:627432 original size:60 final size:60
Alignment explanation
Indices: 627382--627514 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
627372 TCGATTGACT
* * *
627382 ATTTTATAATTTTTAATAGTTGATGAACTCAACAAAGCAACATTCTATAGTCATAGGACC
1 ATTTTATAACTTTTAATAGTTGAGGAACTCAACAAAGAAACATTCTATAGTCATAGGACC
* * * * *
627442 ATTTTATAACTTTTAATATTTGAGGGACTCAACAAAGAAACA-TCATATAGACATGGGATC
1 ATTTTATAACTTTTAATAGTTGAGGAACTCAACAAAGAAACATTC-TATAGTCATAGGACC
627502 ATTTGTAT-ACTTT
1 ATTT-TATAACTTT
627515 ACCCATAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 58 0.92
61 3 0.05
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTGAGGAACTCAACAAAGAAACATTCTATAGTCATAGGACC
Found at i:631540 original size:36 final size:37
Alignment explanation
Indices: 631468--631541 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
631458 GTTGAAAAAT
* *
631468 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
*
631505 ATTTATATAATTT-TTTAACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAAATT-AAAATCATAAA
631541 A
1 A
631542 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:631543 original size:37 final size:38
Alignment explanation
Indices: 631463--631543 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
631453 AACAAGTTGA
* *
631463 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAA-ATTTATATAATTTCTTTAAAAAAATTAAAATCAT
*
631502 -AAAATTTATATAATTT-TTTAACAAAATTGAAAAT-AT
1 AAAAATTTATATAATTTCTTTAAAAAAATT-AAAATCAT
631538 AAAAAT
1 AAAAAT
631544 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 13 0.35
37 21 0.57
38 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (38 bp):
AAAAATTTATATAATTTCTTTAAAAAAATTAAAATCAT
Found at i:633435 original size:22 final size:22
Alignment explanation
Indices: 633409--633450 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
633399 TATTTTTATC
633409 AATAATAAAGAGTTAAATTTTA
1 AATAATAAAGAGTTAAATTTTA
633431 AATAATAAAGAGTTAAATTT
1 AATAATAAAGAGTTAAATTT
633451 GAAACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (22 bp):
AATAATAAAGAGTTAAATTTTA
Found at i:634801 original size:18 final size:19
Alignment explanation
Indices: 634766--634802 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
634756 CACGGAATGT
634766 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
634786 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
634803 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:637893 original size:22 final size:22
Alignment explanation
Indices: 637868--637912 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
637858 GTAAACACAG
637868 AGCCAAAAAGGAGGAAAAACTA
1 AGCCAAAAAGGAGGAAAAACTA
637890 AGCCAAAAAGGAGGAAAAACTA
1 AGCCAAAAAGGAGGAAAAACTA
637912 A
1 A
637913 TGGAGATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.22, T:0.04
Consensus pattern (22 bp):
AGCCAAAAAGGAGGAAAAACTA
Found at i:641498 original size:28 final size:28
Alignment explanation
Indices: 641439--641509 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
641429 GATTTTGCCG
* **
641439 CCTGATTGATATTTGGTCGATTATATTG
1 CCTGATTGATATATGGTCGATTATATCA
* * *
641467 CCTGATTAATATATGGTCGGTTCTATCA
1 CCTGATTGATATATGGTCGATTATATCA
*
641495 CCTGAATGATATATG
1 CCTGATTGATATATG
641510 ATTGGCCATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (28 bp):
CCTGATTGATATATGGTCGATTATATCA
Found at i:642660 original size:41 final size:41
Alignment explanation
Indices: 642613--642753 Score: 185
Period size: 41 Copynumber: 3.5 Consensus size: 41
642603 ATTCGCGTTG
*
642613 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
642654 CATTTCGTGTTGCGATTGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * ** ** *
642695 CATTTCACGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
642735 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
642754 CCAAGTTGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 33 0.38
41 53 0.62
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:642668 original size:20 final size:20
Alignment explanation
Indices: 642638--642777 Score: 147
Period size: 20 Copynumber: 6.9 Consensus size: 20
642628 TAGTTGAAAA
*
642638 TCGCATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
642658 TCGTGTTGCGATTGTTGAAAA
1 TCGCGTTGCGATT-TTCCATT
642679 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
642699 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
642719 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
** *
642739 TCGCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTCC-ATT
642760 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
642778 AATTCGTTGC
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
20 67 0.69
21 30 0.31
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:642691 original size:21 final size:21
Alignment explanation
Indices: 642617--642691 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
642607 GCGTTGCATT
*
642617 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTGTTGAAAA
* ** **
642638 TCGCATTGCGATT-TTCCATT
1 TCGCGTTGCGATTGTTGAAAA
*
642658 TCGTGTTGCGATTGTTGAAAA
1 TCGCGTTGCGATTGTTGAAAA
642679 TCGCGTTGCGATT
1 TCGCGTTGCGATT
642692 TTCCATTTCA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATTGTTGAAAA
Found at i:642739 original size:40 final size:41
Alignment explanation
Indices: 642613--642777 Score: 181
Period size: 41 Copynumber: 4.0 Consensus size: 41
642603 ATTCGCGTTG
* * *
642613 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATTGTTCAAAATCGCGTTGCGATTTTC
* *
642654 CATTTCGTGTTGCGATTGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTGTTCAAAATCGCGTTGCGATTTTC
* * ** *
642695 CATTTCACGTTGCGATT-TTCCATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTGTTCAAAATCGCGTTGCGATTTTC
* * * *
642735 CATTTCGCGTTGCGATAG-TCCAAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTGTTCAAAATCG-CGTTGCGATTTTC
642776 CA
1 CA
642778 AATTCGTTGC
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 39 0.37
41 67 0.63
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.41
Consensus pattern (41 bp):
CATTTCGCGTTGCGATTGTTCAAAATCGCGTTGCGATTTTC
Found at i:642767 original size:41 final size:40
Alignment explanation
Indices: 642682--642819 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 40
642672 TTGAAAATCG
** *
642682 CGTTGCGATTTTCCATTTCACGTTGCGATTTTCC-ATTTCG-
1 CGTTGCGATTTTCCATTTC-CGTTGCGATAGTCCAAGTT-GT
*
642722 CGTTGCGATTTTTCATTTCGCGTTGCGATAGTCCAAGTTGT
1 CGTTGCGATTTTCCATTTC-CGTTGCGATAGTCCAAGTTGT
* *
642763 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-ATTTCCGTTGCGATAGTCCA-AGTTGT
*
642804 CATTGCGAATTTTCCA
1 CGTTGCG-ATTTTCCA
642820 AATTCGCAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
40 45 0.54
41 29 0.35
42 10 0.12
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (40 bp):
CGTTGCGATTTTCCATTTCCGTTGCGATAGTCCAAGTTGT
Found at i:642767 original size:61 final size:61
Alignment explanation
Indices: 642643--642777 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
642633 GAAAATCGCA
* ** *
642643 TTGCGATTTTCCATTTCGTGTTGCGATTGTTGAAAATCGCGTTGCGATTTTCCATTTCACG
1 TTGCGATTTTCCATTTCGCGTTGCGATTGTTGAAAATCGCGTTGCGATAGTCCAGTTCACG
** ** **
642704 TTGCGATTTTCCATTTCGCGTTGCGATT-TTTCATTTCGCGTTGCGATAGTCCAAGTTGTCG
1 TTGCGATTTTCCATTTCGCGTTGCGATTGTTGAAAATCGCGTTGCGATAGTCC-AGTTCACG
642765 TTGCGATTTTCCA
1 TTGCGATTTTCCA
642778 AATTCGTTGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 18 0.29
61 45 0.71
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (61 bp):
TTGCGATTTTCCATTTCGCGTTGCGATTGTTGAAAATCGCGTTGCGATAGTCCAGTTCACG
Found at i:642768 original size:21 final size:21
Alignment explanation
Indices: 642742--642811 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
642732 TTTCATTTCG
642742 CGTTGCGATAGTCCAAGTTGT
1 CGTTGCGATAGTCCAAGTTGT
** *
642763 CGTTGCGATTTTCCAA-AT-T
1 CGTTGCGATAGTCCAAGTTGT
*
642782 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCCA-AGTTGT
*
642804 CATTGCGA
1 CGTTGCGA
642812 ATTTTCCAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 15 0.39
22 8 0.21
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTGT
Found at i:643038 original size:14 final size:14
Alignment explanation
Indices: 643021--643052 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
643011 TTTCGCTTTG
643021 CGAAATTCGAGTTA
1 CGAAATTCGAGTTA
*
643035 CGAAATTCGAGTTG
1 CGAAATTCGAGTTA
643049 CGAA
1 CGAA
643053 TTTGACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (14 bp):
CGAAATTCGAGTTA
Found at i:643090 original size:21 final size:20
Alignment explanation
Indices: 643045--643098 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 20
643035 CGAAATTCGA
*
643045 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCAC
643065 GTTGCGAATTTGACTCTTCAC
1 GTTGCGAATTTGACT-TTCAC
643086 GTTGCGAATTTGA
1 GTTGCGAATTTGA
643099 AATTCCGCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCAC
Found at i:643150 original size:20 final size:21
Alignment explanation
Indices: 643127--643182 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
643117 TGGAAACTGG
* *
643127 GTTGCGAAATTGGAG-TTCGC
1 GTTGCGAATTTGGAGATTCAC
643147 GTTGCGAATTTGGAGAATTCAC
1 GTTGCGAATTTGGAG-ATTCAC
643169 GTTGCGAATTTGGA
1 GTTGCGAATTTGGA
643183 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.32
Consensus pattern (21 bp):
GTTGCGAATTTGGAGATTCAC
Found at i:643174 original size:22 final size:21
Alignment explanation
Indices: 643036--643189 Score: 120
Period size: 20 Copynumber: 7.4 Consensus size: 21
643026 TTCGAGTTAC
*
643036 GAAATTCGAGTTGCGAATTT-
1 GAAATTCGCGTTGCGAATTTG
**
643056 GACTTTCGCGTTGCGAATTT-
1 GAAATTCGCGTTGCGAATTTG
** *
643076 GACTCTTCACGTTGCGAATTT-
1 GA-AATTCGCGTTGCGAATTTG
* *
643097 GAAATTCCGCGTAGCGAAATTG
1 GAAATT-CGCGTTGCGAATTTG
* * *
643119 GAAACT-GGGTTGCGAAATTG
1 GAAATTCGCGTTGCGAATTTG
*
643139 G-AGTTCGCGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
*
643159 GAGAATTCACGTTGCGAATTTG
1 GA-AATTCGCGTTGCGAATTTG
*
643181 GAAAATCGC
1 GAAATTCGC
643190 AACACGAATT
Statistics
Matches: 106, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.02
20 47 0.44
21 33 0.31
22 24 0.23
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:643295 original size:63 final size:63
Alignment explanation
Indices: 643194--643640 Score: 351
Period size: 63 Copynumber: 7.1 Consensus size: 63
643184 AATCGCAACA
* *
643194 CGAATTTCGTTTTCGCAACGCTAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGCTG
1 CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
* * * *
643257 CTAATTTCGTTTTCGCAACACTAATTACCTATATAGGTAATT-AGCGTTGTGAAATTCGTGTTG
1 CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAG-GTTGAGAAATTCGAGTTG
*
643320 CGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
1 CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
* ** *** * * **** * *
643383 CGAATTTGGAGAATTCGCGTTGCGAATTTGA-CT-T-TCGCGTTGCGAA-TTTG-GAAAATCGCA
1 CGAATTT--CGTTTTCGCAACGCTAA-TT-ACCTATATAG-GTAATTAAGGTTGAGAAATTCG-A
**
643443 -ACG
60 GTTG
*
643446 CGAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
1 CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
* * **** * * * ** * * *
643509 CGAATTT-GACTTTCGCAACGCGAATTTGGAAAAT-CGCAACGCGAA-TTTG-GAAAATCGCA-A
1 CGAATTTCG-TTTTCGCAACGCTAATTACCTATATAGGTAA--TTAAGGTTGAGAAATTCG-AGT
*
643569 CG
62 TG
*
643571 CGAATTTTGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
1 CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
643634 CGAATTT
1 CGAATTT
643641 GGAAAATTCG
Statistics
Matches: 285, Mismatches: 76, Indels: 46
0.70 0.19 0.11
Matches are distributed among these distances:
59 1 0.00
60 4 0.01
61 16 0.06
62 48 0.17
63 187 0.66
64 10 0.04
65 14 0.05
66 4 0.01
67 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (63 bp):
CGAATTTCGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTG
Found at i:643398 original size:22 final size:21
Alignment explanation
Indices: 643370--643441 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 21
643360 TTAAGGTTGA
*
643370 GAAATTCGAGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
643391 GAGAATTCGCGTTGCGAATTT-
1 GA-AATTCGCGTTGCGAATTTG
**
643412 GACTTTCGCGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
*
643433 GAAAATCGC
1 GAAATTCGC
643442 AACGCGAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 16 0.37
21 10 0.23
22 17 0.40
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:643444 original size:252 final size:252
Alignment explanation
Indices: 643127--643651 Score: 695
Period size: 252 Copynumber: 2.1 Consensus size: 252
643117 TGGAAACTGG
*
643127 GTTGCGAAATTGGAG--TTCGCGTTGCGAATTTGGAGAATTCACGTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTTGGAGAATTCGCGTTGCGAATTTGGAGAATTCACGTTGCGAATTTGGAAAATCGC
*
643190 AACACGAATTTCGTTTTCGCAACGCTAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGC
66 AACACGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGC
* * * * * * * * **
643255 TGCTAATTTCG-TTTTCGCAACACTAATTACCTATATAGGTAATTAGCG--TTGTGAAATTCGTG
131 TGCGAATTT-GACTTTCGCAACACGAATTACCAAAAT-CGCAA--AGCGATTTG-GAAAATCGCA
**
643317 TTGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGA
191 ACGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGA
** *
643379 GTTGCGAATTTGGAGAATTCGCGTTGCGAATTT-GA-CTTTCGCGTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTTGGAGAATTCGCGTTGCGAATTTGGAGAATTCACGTTGCGAATTTGGAAAATCGC
* * *
643442 AACGCGAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGT
66 AACACGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGC
* *** *
643507 TGCGAATTTGACTTTCGCAACGCGAATTTGGAAAATCGCAACGCGAATTTGGAAAATCGCAACGC
131 TGCGAATTTGACTTTCGCAACACGAATTACCAAAATCGCAAAGCG-ATTTGGAAAATCGCAACGC
* *
643572 GAATTTTGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGA
195 GAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGA
*
643630 GTTGCGAATTTGGAAAATTCGC
1 GTTGCGAATTTGGAGAATTCGC
643652 AATGACAACT
Statistics
Matches: 239, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
249 3 0.01
251 90 0.38
252 128 0.54
253 2 0.01
254 16 0.07
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (252 bp):
GTTGCGAATTTGGAGAATTCGCGTTGCGAATTTGGAGAATTCACGTTGCGAATTTGGAAAATCGC
AACACGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGC
TGCGAATTTGACTTTCGCAACACGAATTACCAAAATCGCAAAGCGATTTGGAAAATCGCAACGCG
AATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGA
Found at i:643449 original size:126 final size:128
Alignment explanation
Indices: 643150--643653 Score: 559
Period size: 126 Copynumber: 4.0 Consensus size: 128
643140 AGTTCGCGTT
* * *
643150 GCGAATTTGGAGAATTCACGTTGCGAATTTGGAAAATCGCAACACGAATTTCGTTTTCGCAACGC
1 GCGAATTTGGACAATTCGCGTTGCGAATTTGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGC
* * * * **
643215 TAATTACATATATAGGTAATTAAGGTTGAGAAATTCGAGCTGCTAATTT--CGTTTTCGCAAC
66 TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTCGCAAC
* * * * * ****
643276 ACTAA-TT--ACCTATATAG-GTAATTAGCG---TTGTGAAATTCGTGTTGCGAATTTCGTTTTC
1 GCGAATTTGGA-CAAT-TCGCG---TT-GCGAATTTG-GAAAATCGCAACGCGAATTTCGTTTTC
*
643334 ACAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTC
59 GCAACGCTAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTC
***
643399 GCGTT
124 GCAAC
* *
643404 GCGAATTT-GAC-TTTCGCGTTGCGAATTTGGAAAATCGCAACGCGAATTTCATTTTCGCAACGC
1 GCGAATTTGGACAATTCGCGTTGCGAATTTGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGC
**
643467 TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTT-GA-CTTTCGCAAC
66 TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTCGCAAC
* *** *
643528 GCGAATTTGGA-AAATCGCAACGCGAATTTGGAAAATCGCAACGCGAATTTTGTTTTCGCAACGC
1 GCGAATTTGGACAATTCGCGTTGCGAATTTGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGC
*
643592 TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAAAATTCGCAA
66 TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTCGCAA
643654 TGACAACTGT
Statistics
Matches: 312, Mismatches: 47, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
123 1 0.00
124 19 0.06
125 106 0.34
126 154 0.49
127 14 0.04
128 14 0.04
129 3 0.01
130 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (128 bp):
GCGAATTTGGACAATTCGCGTTGCGAATTTGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGC
TAATTACCTATATAGGTAATTAAGGTTGAGAAATTCGAGTTGCGAATTTGGAGAATTCGCAAC
Found at i:643461 original size:41 final size:42
Alignment explanation
Indices: 643374--643461 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
643364 GGTTGAGAAA
* * *** *
643374 TTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGGAGAAATCGCAACGCGAATTTCACT
*
643416 TTCGCGTTGCGAATTTGGA-AAATCGCAACGCGAATTTCATT
1 TTCGCGTTGCGAATTTGGAGAAATCGCAACGCGAATTTCACT
643457 TTCGC
1 TTCGC
643462 AACGCTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 21 0.54
42 18 0.46
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (42 bp):
TTCGCGTTGCGAATTTGGAGAAATCGCAACGCGAATTTCACT
Found at i:643547 original size:21 final size:21
Alignment explanation
Indices: 643521--643577 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
643511 AATTTGACTT
643521 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGGAAAA
643542 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGGAAAA
643563 TCGCAACGCGAATTT
1 TCGCAACGCGAATTT
643578 TGTTTTCGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAATTTGGAAAA
Found at i:643694 original size:251 final size:250
Alignment explanation
Indices: 643173--643696 Score: 655
Period size: 251 Copynumber: 2.1 Consensus size: 250
643163 ATTCACGTTG
* *
643173 CGAATTTGGAAAATCGCAACACGAATTTCGTTTTCGCAACGCTAATTACATATATAGGTAATTAA
1 CGAATTTGGAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAA
* * * * * * *
643238 GGTTGAGAAATTCGAGCTGCTAATTTCGTTTTCGCAACACTAATTACCTATATAGGTAATTAGCG
66 GGTTGAGAAATTCGAGCTGCGAATTTCGCTTTCGCAACACGAATTACCAAAATACGCAA-TAGCG
* ****
643303 TTGTGAAATTCGTGTTGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTT
130 TTGTGAAAATCGCAACGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTT
* ** * * **
643368 GAGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGAATTTGACTTTCGCGTTG
195 GAGAAATTCGAGTTGCGAATTTGGAAAATTCGCAATGCGAATTAGACTATCGCG-AA
*
643425 CGAATTTGGAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAA
1 CGAATTTGGAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAA
* * *** *
643490 GGTTGAGAAATTCGAGTTGCGAATTT-GACTTTCGCAACGCGAATTTGGAAAAT-CGCAA-CGCG
66 GGTTGAGAAATTCGAGCTGCGAATTTCG-CTTTCGCAACACGAATTACCAAAATACGCAATAGCG
* *
643552 AATT-TGGAAAATCGCAACGCGAATTTTGTTTTCGCAACGCTAATTACCTATATAGGTAATTAAG
130 --TTGT-GAAAATCGCAACGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAG
643616 GTTGAGAAATTCGAGTTGCGAATTTGGAAAATTCGCAATGAC-AACTGTAGACTATCGC-AA
192 GTTGAGAAATTCGAGTTGCGAATTTGGAAAATTCGCAATG-CGAA-T-TAGACTATCGCGAA
643676 CGAATTTGGAAAATCGCAACG
1 CGAATTTGGAAAATCGCAACG
643697 ACAACTGTAG
Statistics
Matches: 235, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
249 3 0.01
250 1 0.00
251 117 0.50
252 105 0.45
253 9 0.04
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (250 bp):
CGAATTTGGAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACATATATAGGTAATTAA
GGTTGAGAAATTCGAGCTGCGAATTTCGCTTTCGCAACACGAATTACCAAAATACGCAATAGCGT
TGTGAAAATCGCAACGCGAATTTCGTTTTCACAACGCTAATTACCTATATAGGTAATTAAGGTTG
AGAAATTCGAGTTGCGAATTTGGAAAATTCGCAATGCGAATTAGACTATCGCGAA
Found at i:643728 original size:42 final size:41
Alignment explanation
Indices: 643640--643779 Score: 194
Period size: 41 Copynumber: 3.4 Consensus size: 41
643630 GTTGCGAATT
* *
643640 TGGAAAATTCGCAATGACAACTGTAGACTATCGCAA-CGAATT
1 TGGAAAA-TCGCAACGACAACTGTAGACTATCGCAAGCGAA-A
643682 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA-GCGAAA
*
643724 TGGAAAATCGCAACGACAACT-TGGACTATCGCAAAGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGC-AAGCGAAA
*
643765 TGAAAAATCGCAACG
1 TGGAAAATCGCAACG
643780 CGAATTTGCT
Statistics
Matches: 91, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
41 57 0.63
42 30 0.33
43 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAAGCGAAA
Found at i:643735 original size:20 final size:20
Alignment explanation
Indices: 643710--643783 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
643700 ACTGTAGACT
643710 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
643730 ATCGCAACGAC-AACTTGGACT
1 ATCGCAACG-CGAA-ATGGAAA
* *
643751 ATCGCAAAGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
643771 ATCGCAACGCGAA
1 ATCGCAACGCGAA
643784 TTTGCTATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:645516 original size:31 final size:31
Alignment explanation
Indices: 645468--645528 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
645458 ACAAATACTA
645468 ACAATCACAGTTAAGAAAACACATCGTTCAG
1 ACAATCACAGTTAAGAAAACACATCGTTCAG
* * * *
645499 ACAATCATAGTTCAGAAAACATATTGTTCA
1 ACAATCACAGTTAAGAAAACACATCGTTCA
645529 AACATCTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (31 bp):
ACAATCACAGTTAAGAAAACACATCGTTCAG
Found at i:654323 original size:31 final size:31
Alignment explanation
Indices: 654199--654323 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
654189 GTTGAGGGTA
*
654199 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
654231 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
654262 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
654293 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
654324 GCCGAGGATC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:656616 original size:31 final size:32
Alignment explanation
Indices: 656505--656617 Score: 97
Period size: 31 Copynumber: 3.6 Consensus size: 32
656495 TTTCGATAAA
* * * * * *
656505 TTTAAGGATCA-TTTGTAACAATTTGATAAAT
1 TTTAATGATCATTTTATAATAATTTAATGAAG
* *
656536 TTTAATGATCATTTTGTACTAATTTAATGAAG
1 TTTAATGATCATTTTATAATAATTTAATGAAG
* **
656568 TTTAATG-TTATACTATAATAATTTAAT-AAG
1 TTTAATGATCATTTTATAATAATTTAATGAAG
*
656598 TTTAATGATGATTTTATAAT
1 TTTAATGATCATTTTATAAT
656618 TCCCAGAACT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
30 10 0.15
31 34 0.52
32 22 0.33
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (32 bp):
TTTAATGATCATTTTATAATAATTTAATGAAG
Found at i:657121 original size:2 final size:2
Alignment explanation
Indices: 657114--657138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
657104 TTATAATGGC
657114 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
657139 CCTCCTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:657233 original size:4 final size:4
Alignment explanation
Indices: 657224--657253 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
657214 AATTTTTCGG
657224 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
657254 CCGTCGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:667462 original size:51 final size:51
Alignment explanation
Indices: 667407--667698 Score: 332
Period size: 51 Copynumber: 5.5 Consensus size: 51
667397 CATAAAACAA
* * *
667407 GTCCGTTCTCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAACGT
* *
667458 GTCCGCTCCCCATTCCTTCAGAGAGTATAGGACTCAATCTTCAATCAAACGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAA-CAAACGT
* * *
667510 GTCCGCTCCCTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC-T--A-AATCTTCAACAAACGT
* * * *
667565 GTCCTCTCCCTATTCCTTCAGAAAGTATAGGACTCAATCTTCAACAAATGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAACGT
* * * **
667616 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAACGT
* *
667671 GTCTGCTCCCTATTTCTTCAGAGAGTAT
1 GTCCGCTCCCTATTCCTTCAGAGAGTAT
667699 TAGACTCGAA
Statistics
Matches: 205, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
51 84 0.41
52 36 0.18
53 1 0.00
54 1 0.00
55 75 0.37
56 8 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAACGT
Found at i:667574 original size:55 final size:55
Alignment explanation
Indices: 667416--667827 Score: 404
Period size: 55 Copynumber: 7.7 Consensus size: 55
667406 AGTCCGTTCT
* *
667416 CTATTCCTTCAGAGAGTATAGGAC-T--A-AATCTTCAACAAATGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* *
667467 CCATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAATCAAACGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAA-CAAACGTGTCTGCTCC
* * *
667519 CTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCCT-CTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGT-CTGCTCC
* *
667574 CTATTCCTTCAGAAAGTATAGGAC-T---CAATCTTCAACAAATGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * * **
667625 CTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * * ** *
667680 CTATTTCTTCAGAGAGTATTA-GACTCGAACAATTTTCAATATTCATGTCTGCTCC
1 CTATTCCTTCAGAGAGTA-TAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * *
667735 CTATTGCTTAAGAGAGTAT-GAGACTTGAACAATCTTCAACAATCGTGTCTGCTCT
1 CTATTCCTTCAGAGAGTATAG-GACTTGAACAATCTTCAACAAACGTGTCTGCTCC
** * * *
667790 CTATTTGTTCTGAGAGTATAAGACTCGAACAATCTTCA
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCA
667828 TTTGCTTCAC
Statistics
Matches: 307, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.01
51 76 0.25
52 36 0.12
53 1 0.00
54 2 0.01
55 178 0.58
56 12 0.04
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
Found at i:667644 original size:158 final size:158
Alignment explanation
Indices: 667356--667711 Score: 443
Period size: 158 Copynumber: 2.2 Consensus size: 158
667346 CATTGGGTTT
* * * * * ** *
667356 GCTCCCT-TTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTCCGT-TCTCT
1 GCTCCCTATTT-CTTCAGAGAGTATTAGACTCGAACAACCTTCA-ACAAACGTGTCC-TCTCCCT
*
667418 ATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCCCCATTCCTTCAGAGAG
63 ATTCCTTCAGAAAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCCCCATTCCTTCAGAGAG
*
667483 TATAGGACTC-AATCTTCAATCAAACGTGTCC
128 TATAAGACTCAAATCTTCAA-CAAACGTGTCC
*
667514 GCTCCCTATTTCTTCAGAGAGTA-TATGACTTGAACAACCTTCAACAAACGTGTCCTCTCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATTA-GACTCGAACAACCTTCAACAAACGTGTCCTCTCCCTAT
* * *
667578 TCCTTCAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTA
65 TCCTTCAGAAAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCCCCATTCCTTCAGAGAGTA
* ** *
667643 TAAGACTCGAATAATTTTCAACATTCGTGTCT
130 TAAGACTC--A-AATCTTCAACAAACGTGTCC
667675 GCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAA
1 GCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAA
667712 TTTTCAATAT
Statistics
Matches: 170, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
157 3 0.02
158 113 0.66
159 3 0.02
161 41 0.24
162 10 0.06
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (158 bp):
GCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAACCTTCAACAAACGTGTCCTCTCCCTATT
CCTTCAGAAAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCCCCATTCCTTCAGAGAGTAT
AAGACTCAAATCTTCAACAAACGTGTCC
Found at i:667773 original size:110 final size:109
Alignment explanation
Indices: 667330--667827 Score: 404
Period size: 106 Copynumber: 4.6 Consensus size: 109
667320 TCCCTCTTCT
* * * * * * * * *
667330 TTGAACAATCTTCGACCATTGGGTTTGCTCCCT-TTTGCTTCAGGGAGTATAAAACTCAAACAAT
1 TTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT-CTTCAGAGAGTATTAGACTCGAACAAT
* * * * *
667394 CTTCATA-AAACAAGTCCGTTCTCTATTCCTTCAGAGAGTATAGGAC
65 CTTCA-ACAAATATGTCTGCTCCCTATTCCTTCAGAGAGTATA-GAC
* * *
667440 -T--A-AATCTTCAACAAAT-GTGTCCGCTCCCCATTCCTTCAGAGAGTA-TAGGACT----CAA
1 TTGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATTA-GACTCGAACAA
** * *
667495 TCTTCAATCAAACGTGTCCGCTCCCTATTTCTTCAGAGAGTATATGAC
64 TCTTCAA-CAAATATGTCTGCTCCCTATTCCTTCAGAGAGTATA-GAC
* * * *
667543 TTGAACAACCTTCAACAAACGTGTCCT-CTCCCTATTCCTTCAGAAAGTA-TAGGACT----CAA
1 TTGAACAATCTTCAACAATCGTGT-CTGCTCCCTATTTCTTCAGAGAGTATTA-GACTCGAACAA
*
667602 TCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
64 TCTTCAACAAATATGTCTGCTCCCTATTCCTTCAGAGAGTAT-AGAC
* * * * *
667649 TCGAATAATTTTCAACATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATT
1 TTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATC
* * * *
667714 TTCAA-TATTCATGTCTGCTCCCTATTGCTTAAGAGAGTATGAGAC
66 TTCAACAAAT-ATGTCTGCTCCCTATTCCTTCAGAGAGTAT-AGAC
* * * *
667759 TTGAACAATCTTCAACAATCGTGTCTGCTCTCTATTTGTTCTGAGAGTATAAGACTCGAACAATC
1 TTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATC
667824 TTCA
66 TTCA
667828 TTTGCTTCAC
Statistics
Matches: 321, Mismatches: 48, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
101 1 0.00
102 9 0.03
103 33 0.10
104 1 0.00
105 3 0.01
106 112 0.35
107 58 0.18
108 1 0.00
109 3 0.01
110 100 0.31
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (109 bp):
TTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATC
TTCAACAAATATGTCTGCTCCCTATTCCTTCAGAGAGTATAGAC
Found at i:669130 original size:23 final size:24
Alignment explanation
Indices: 669104--669148 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
669094 AACCCTCCCT
669104 TTTTCTTTTTC-TTCCTTTTTTCG
1 TTTTCTTTTTCTTTCCTTTTTTCG
*
669127 TTTTTTTTTTCTTTCCTTTTTT
1 TTTTCTTTTTCTTTCCTTTTTT
669149 AAGCAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTCTTTTTCTTTCCTTTTTTCG
Found at i:669130 original size:24 final size:24
Alignment explanation
Indices: 669103--669148 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
669093 GAACCCTCCC
669103 TTTTTCTTTTTC-TTCCTTTTTTCG
1 TTTTT-TTTTTCTTTCCTTTTTTCG
669127 TTTTTTTTTTCTTTCCTTTTTT
1 TTTTTTTTTTCTTTCCTTTTTT
669149 AAGCAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTTTTTTCTTTCCTTTTTTCG
Done.