Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 35
Found at i:559818 original size:2 final size:2
Alignment explanation
Indices: 559811--559850 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
559801 ATATTCCACC
*
559811 TA TA TA TA TA TA TA TGA TG TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
559851 CACACACGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:564752 original size:61 final size:60
Alignment explanation
Indices: 564669--564788 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 60
564659 AAATATCTTT
564669 ATATATAAAGAAAGTTAATTATTGTAATTATA-TTTTTAATACATATCCGATAAAACCTAAA
1 ATATATAAAGAAAGTTAATTATTGTAATTATATTTTTTAATACATATCC--TAAAACCTAAA
*
564730 ATATATAAAGAAAGTTAATTATTGTAATTATATTTTTTAATATATATCCTAAAACCTAA
1 ATATATAAAGAAAGTTAATTATTGTAATTATATTTTTTAATACATATCCTAAAACCTAA
564789 TCCAAATTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 10 0.18
61 32 0.56
62 15 0.26
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (60 bp):
ATATATAAAGAAAGTTAATTATTGTAATTATATTTTTTAATACATATCCTAAAACCTAAA
Found at i:564887 original size:12 final size:13
Alignment explanation
Indices: 564872--564901 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
564862 AATATTAATT
564872 TAAATATATAT-A
1 TAAATATATATGA
564884 TAAATATATATGA
1 TAAATATATATGA
564897 TAAAT
1 TAAAT
564902 TCTATTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
TAAATATATATGA
Found at i:568792 original size:5 final size:5
Alignment explanation
Indices: 568782--568814 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
568772 TCGCAAAGAT
*
568782 AAATA AAATA AAATA AAATA AAACA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
568815 AGGAAAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:569266 original size:28 final size:25
Alignment explanation
Indices: 569231--569329 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 25
569221 AAATAGACAT
569231 TTAAGGGACTAAAATCACATAACAAAAC
1 TTAAGGGACTAAAAT-A-A-AACAAAAC
*
569259 TTAAGGGACTAAAATAAAACAAACAT
1 TTAAGGGACTAAAATAAAACAAA-AC
* *
569285 TTAAAGGACTAAAATAGAAAAATAGAAAC
1 TTAAGGGACTAAAAT---AAAACA-AAAC
569314 TTAAGGGACTAAAATA
1 TTAAGGGACTAAAATA
569330 CAAATAAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
25 6 0.10
26 17 0.28
27 1 0.02
28 15 0.25
29 20 0.33
30 2 0.03
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (25 bp):
TTAAGGGACTAAAATAAAACAAAAC
Found at i:570875 original size:3 final size:3
Alignment explanation
Indices: 570861--570905 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
570851 TTGCAAAATG
570861 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T
570906 GTTTTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:575729 original size:42 final size:42
Alignment explanation
Indices: 575613--575831 Score: 260
Period size: 43 Copynumber: 5.1 Consensus size: 42
575603 AACTAAAAAT
* *
575613 GCCGCAATAGGTCAAGAACTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
575656 GTCACAAAAGGCCTAGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
575699 ACCGCAAAAGGTCAGATCTATAGCAGCGTTTTAGGATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
* * **
575742 GCCGCAAAAGGTCAGATCTATAGTGCCGTTTGTTCCAA-AAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTT-TTGGAACAAAC
* *
575784 TCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
575827 GCCGC
1 GCCGC
575832 TAATTACCTT
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
41 3 0.02
42 53 0.36
43 88 0.60
44 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:575772 original size:85 final size:86
Alignment explanation
Indices: 575614--575831 Score: 280
Period size: 85 Copynumber: 2.5 Consensus size: 86
575604 ACTAAAAATG
* * * *
575614 CCGCAATAGGTCAAGAACTATAGCGGCGTTTTTGGA-ACAAACGTCACAAAAGGCCTAGATCTAT
1 CCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGCCTAGATCTAT
* **
575678 AGCGGCGTTT-TTGGAACAAACA
65 AGCGCCGTTTGTTCCAA-AAACA
* * *
575700 CCGCAAAAGGTCAGATCTATAGCAGCGTTTTAGGATACAAACGCCGCAAAAGGTC-AGATCTATA
1 CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGCCTAGATCTATA
* *
575764 GTGCCGTTTGTTCCAAAAACT
66 GCGCCGTTTGTTCCAAAAACA
*
575785 CCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGATACAAACGCCGC
1 CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
575832 TAATTACCTT
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
85 84 0.73
86 31 0.27
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (86 bp):
CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGCCTAGATCTATA
GCGCCGTTTGTTCCAAAAACA
Found at i:578383 original size:43 final size:42
Alignment explanation
Indices: 578268--578461 Score: 221
Period size: 43 Copynumber: 4.6 Consensus size: 42
578258 TATCCAAAAC
* * * * *
578268 TTGCGGCGTTTGTATTTAAAAACGCCGCTACTTCACTTACTTA
1 TTGCGGCGTTTGTA-TTAAAAACGCCACTAATGCACTGATTTA
*
578311 TTGCGGCGTTTGT-TTAAAAATGCCACTAATGCACTGATTTA
1 TTGCGGCGTTTGTATTAAAAACGCCACTAATGCACTGATTTA
* *
578352 TTGCGGCGTTTGTATCTAAAAATGCCACTAATACACTGATTTA
1 TTGCGGCGTTTGTAT-TAAAAACGCCACTAATGCACTGATTTA
* * * *
578395 TTGCAGCGTTTGTATTTAGAAACGTCGCTAATGCACTGATTTA
1 TTGCGGCGTTTGTA-TTAAAAACGCCACTAATGCACTGATTTA
* *
578438 TTGTGGCATTTGT-TTAAAAACGCC
1 TTGCGGCGTTTGTATTAAAAACGCC
578462 GTAAAATATT
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 44 0.34
42 1 0.01
43 84 0.65
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (42 bp):
TTGCGGCGTTTGTATTAAAAACGCCACTAATGCACTGATTTA
Found at i:586414 original size:10 final size:11
Alignment explanation
Indices: 586399--586444 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
586389 CAATCAGAAC
586399 AAAAAAAAG-G
1 AAAAAAAAGAG
586409 AAAAAAAAG-G
1 AAAAAAAAGAG
586419 AAAAACAAAGAG
1 AAAAA-AAAGAG
*
586431 AAAATAAAGAG
1 AAAAAAAAGAG
586442 AAA
1 AAA
586445 CTAAAACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 15 0.45
11 13 0.39
12 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:586445 original size:21 final size:21
Alignment explanation
Indices: 586399--586444 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
586389 CAATCAGAAC
586399 AAAAA-AAAGGAAAAAAAAGG
1 AAAAACAAAGGAAAAAAAAGG
*
586419 AAAAACAAAGAGAAAATAAAGAG
1 AAAAACAAAG-GAAAAAAAAG-G
586442 AAA
1 AAA
586445 CTAAAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 9 0.41
23 4 0.18
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAACAAAGGAAAAAAAAGG
Found at i:588145 original size:33 final size:35
Alignment explanation
Indices: 588071--588150 Score: 119
Period size: 33 Copynumber: 2.3 Consensus size: 35
588061 AATTTACTCA
*
588071 AAACAAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAAC-AAA-TTTGTCTCCCTTGAGATAGTTTCCCTTG
588108 AAACAAATTTGTCTCCCTTGAGA-AGTTT-CCTTG
1 AAACAAATTTGTCTCCCTTGAGATAGTTTCCCTTG
588141 AAACAAATTT
1 AAACAAATTT
588151 TGTTTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 15 0.36
34 5 0.12
35 15 0.36
36 3 0.07
37 4 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (35 bp):
AAACAAATTTGTCTCCCTTGAGATAGTTTCCCTTG
Found at i:588153 original size:34 final size:36
Alignment explanation
Indices: 588071--588153 Score: 127
Period size: 35 Copynumber: 2.4 Consensus size: 36
588061 AATTTACTCA
*
588071 AAACAAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAAC-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTG
588108 AAACAAA-TTTGTCTCCCTTGAGA-AGTTT-CCTTG
1 AAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTG
588141 AAACAAATTTTGT
1 AAACAAATTTTGT
588154 TTATTTCCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 12 0.27
34 10 0.23
35 15 0.34
36 3 0.07
37 4 0.09
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTG
Found at i:588172 original size:24 final size:24
Alignment explanation
Indices: 588133--588179 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
588123 CCTTGAGAAG
* *
588133 TTTCCTTGAAACAAATTTTGTTTA
1 TTTCCTTAAAAAAAATTTTGTTTA
588157 TTTCCTTAAAAAAAATTTTGTTT
1 TTTCCTTAAAAAAAATTTTGTTT
588180 CCCTTAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (24 bp):
TTTCCTTAAAAAAAATTTTGTTTA
Found at i:588709 original size:2 final size:2
Alignment explanation
Indices: 588704--588728 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
588694 CATATTTTTT
588704 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
588729 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:595679 original size:139 final size:139
Alignment explanation
Indices: 595424--595794 Score: 582
Period size: 139 Copynumber: 2.7 Consensus size: 139
595414 GATGGAAAGA
* * * *
595424 AGCTAAGGTTGAGCAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAGATGAGTTCTTCTCA
1 AGCTAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCGGATTAGTTCTTCTCA
* * * * *
595489 TTATGAACTCTCCACTGGAAAGGTTGATCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGT
66 TTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTAACGTGTTGCTGATTCAACTCCATATGT
595554 GACGAATCG
131 GACGAATCG
* * *
595563 AGCTAAGGTTGAACAAATTATTCTCATTATGAACTTATTCTCCTTTATCGGATTCA-TTCTTCTC
1 AGCTAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCGGATT-AGTTCTTCTC
*
595627 ATTATGAACTCTCTATTGGAAATGTTGATCCCTCGAGTAACGTGTTGCTGATTCAACTCCATATG
65 ATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTAACGTGTTGCTGATTCAACTCCATATG
*
595692 TGATGAATCG
130 TGACGAATCG
* *
595702 AGCTAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCCCTCATCGGATTAGTTCTTCTCA
1 AGCTAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCGGATTAGTTCTTCTCA
595767 TTATGAACTCTCCATTGGAAATGTTGAT
66 TTATGAACTCTCCATTGGAAATGTTGAT
595795 TGGTTTTCCC
Statistics
Matches: 210, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
138 1 0.00
139 208 0.99
140 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (139 bp):
AGCTAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCGGATTAGTTCTTCTCA
TTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTAACGTGTTGCTGATTCAACTCCATATGT
GACGAATCG
Found at i:608843 original size:16 final size:16
Alignment explanation
Indices: 608824--608855 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
608814 ATTATCTATC
608824 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
608840 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
608856 CTTGAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:616971 original size:17 final size:18
Alignment explanation
Indices: 616949--616986 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
616939 TTGCCTATTC
616949 TTTAATTATTT-GAT-AAT
1 TTTAATT-TTTCGATGAAT
616966 TTTAATTTTTCGATGAAT
1 TTTAATTTTTCGATGAAT
616984 TTT
1 TTT
616987 GATCTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 10 0.53
18 6 0.32
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTAATTTTTCGATGAAT
Found at i:618429 original size:21 final size:22
Alignment explanation
Indices: 618403--618444 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
618393 TTTTAAGTTC
*
618403 AAGTTT-AGGAATTATCTTTTT
1 AAGTTTAAAGAATTATCTTTTT
*
618424 AAGTTTAAATAATTATCTTTT
1 AAGTTTAAAGAATTATCTTTT
618445 ATATTTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (22 bp):
AAGTTTAAAGAATTATCTTTTT
Found at i:619872 original size:34 final size:32
Alignment explanation
Indices: 619810--619879 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
619800 CCTTACAAAC
* *
619810 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
619842 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
619876 TCCC
1 TCCC
619880 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:619893 original size:30 final size:32
Alignment explanation
Indices: 619832--619894 Score: 76
Period size: 34 Copynumber: 2.0 Consensus size: 32
619822 CCGGGCTAAA
**
619832 CTAGAACCTTTCCCTAGCTTTTACACGGGATAAG
1 CTAGAACCTTTCCC-A-CTTTTACAAAGGATAAG
619866 CTAGAACCTTTCCC-C-TTTACAAAGGATAA
1 CTAGAACCTTTCCCACTTTTACAAAGGATAA
619895 AATAAGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
34 14 0.52
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (32 bp):
CTAGAACCTTTCCCACTTTTACAAAGGATAAG
Found at i:620249 original size:20 final size:21
Alignment explanation
Indices: 620220--620274 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
620210 GCAGCCTTCG
*
620220 TGCATGGATGCACAT-CAGGA
1 TGCATCGATGCACATCCAGGA
**
620240 TGCATCGATGCACATCCTTGA
1 TGCATCGATGCACATCCAGGA
620261 TGCATCGATGCACA
1 TGCATCGATGCACA
620275 GAAGCATCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACATCCAGGA
Found at i:620400 original size:21 final size:21
Alignment explanation
Indices: 620311--620407 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 21
620301 GGTGTTTGAG
* * *
620311 TGCATGAATGCACTGCATGG-
1 TGCATGGATGCACTACAGGGA
*
620331 TGCATCGATGCACTAGTGCA-GG-
1 TGCATGGATGCACTA---CAGGGA
* *
620353 TGCATGTATGCA-TGCAGGGA
1 TGCATGGATGCACTACAGGGA
*
620373 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTACAGGGA
*
620394 TGTATGGATGCACT
1 TGCATGGATGCACT
620408 TTGACACCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
18 2 0.03
19 2 0.03
20 23 0.38
21 20 0.33
22 12 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:620517 original size:29 final size:31
Alignment explanation
Indices: 620485--620544 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
620475 AAACTTTGAA
620485 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
620514 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
620545 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:621751 original size:19 final size:19
Alignment explanation
Indices: 621715--621760 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
621705 CTAAATCCTT
*
621715 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
621735 TTTCAAAATCT-ATTTTGT
1 TTTCAAAATCTCATTTTGC
621753 TTTCAAAA
1 TTTCAAAA
621761 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:622669 original size:34 final size:32
Alignment explanation
Indices: 622607--622676 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
622597 CCTTACAAGC
* *
622607 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
622639 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
622673 TCCC
1 TCCC
622677 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:622690 original size:30 final size:32
Alignment explanation
Indices: 622629--622691 Score: 76
Period size: 34 Copynumber: 2.0 Consensus size: 32
622619 CCGGGCTAAA
**
622629 CTAGAACCTTTCCCTAGCTTTTACACGGGATAAG
1 CTAGAACCTTTCCC-A-CTTTTACAAAGGATAAG
622663 CTAGAACCTTTCCC-C-TTTACAAAGGATAA
1 CTAGAACCTTTCCCACTTTTACAAAGGATAA
622692 AATAAGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
34 14 0.52
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (32 bp):
CTAGAACCTTTCCCACTTTTACAAAGGATAAG
Found at i:622979 original size:20 final size:21
Alignment explanation
Indices: 622942--622988 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
622932 CATAACATGG
622942 TGCATCAGTGCACTATCAAGC
1 TGCATCAGTGCACTATCAAGC
*
622963 TGCATCAGTGC-CTATCAAGG
1 TGCATCAGTGCACTATCAAGC
622983 TGCATC
1 TGCATC
622989 GATACCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
TGCATCAGTGCACTATCAAGC
Found at i:624341 original size:34 final size:32
Alignment explanation
Indices: 624279--624348 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
624269 CCTTACAAAC
* *
624279 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
624311 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
624345 TCCC
1 TCCC
624349 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:624724 original size:20 final size:20
Alignment explanation
Indices: 624699--624769 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
624689 TGCAGCCTTC
* *
624699 ATGCATGGATGCACATCAGG
1 ATGCATCGATGCACAGCAGG
**
624719 ATGCATCGATGCACAGCCTG
1 ATGCATCGATGCACAGCAGG
*
624739 ATGCATCGATGCACAGAAGG
1 ATGCATCGATGCACAGCAGG
*
624759 ATACATCGATG
1 ATGCATCGATG
624770 TACTAATTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.20
Consensus pattern (20 bp):
ATGCATCGATGCACAGCAGG
Found at i:624840 original size:22 final size:23
Alignment explanation
Indices: 624807--624849 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
624797 ATGAATGCAC
624807 TGCATGGTGCATCG-ATGCACTAG
1 TGCATGGTGCAT-GTATGCACTAG
624830 TGCA-GGTGCATGTATGCACT
1 TGCATGGTGCATGTATGCACT
624850 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (23 bp):
TGCATGGTGCATGTATGCACTAG
Found at i:624862 original size:21 final size:20
Alignment explanation
Indices: 624793--624891 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
624783 TGGTCTTTGA
* *
624793 GTGCATGAATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
624813 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
624835 GTGCATGTATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
624855 GATGCATGGATGCACTACAGGG
1 G-TGCATGGATGCACTGCA-GG
*
624877 GTGTATGGATGCACT
1 GTGCATGGATGCACT
624892 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 28 0.42
22 16 0.24
23 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:624889 original size:42 final size:42
Alignment explanation
Indices: 624793--624891 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
624783 TGGTCTTTGA
* * **
624793 GTGCATGAATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAGGGTGCATCGATGCACTACAGCAG
* * *
624835 GTGCATGTATGCACTGCAGGGATGCATGGATGCACTACAG-GG
1 GTGCATGGATGCACTGCAGGG-TGCATCGATGCACTACAGCAG
*
624877 GTGTATGGATGCACT
1 GTGCATGGATGCACT
624892 TTGACACCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 33 0.69
43 15 0.31
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGGTGCATCGATGCACTACAGCAG
Found at i:624992 original size:29 final size:29
Alignment explanation
Indices: 624971--625028 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
624961 AAACTTTGAA
624971 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
625000 TAAATTCAATTCAAGTCCAAAAATCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
625029 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:625018 original size:30 final size:30
Alignment explanation
Indices: 624971--625030 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
624961 AAACTTTGAA
624971 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
625000 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
625031 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:626317 original size:19 final size:19
Alignment explanation
Indices: 626281--626326 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
626271 CTAAATCCTT
*
626281 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
626301 TTTCAAAATCT-ATTTTGT
1 TTTCAAAATCTCATTTTGC
626319 TTTCAAAA
1 TTTCAAAA
626327 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:628504 original size:21 final size:21
Alignment explanation
Indices: 628478--628525 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
628468 CATAACATGG
628478 TGCATCAGTGCACTATCAAGC
1 TGCATCAGTGCACTATCAAGC
*
628499 TGCATCAGTGCACTATCAAGG
1 TGCATCAGTGCACTATCAAGC
628520 TGCATC
1 TGCATC
628526 GAACCCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (21 bp):
TGCATCAGTGCACTATCAAGC
Found at i:628692 original size:20 final size:19
Alignment explanation
Indices: 628667--628770 Score: 106
Period size: 20 Copynumber: 5.4 Consensus size: 19
628657 TGAGTGCATA
*
628667 ATGCACTGCATGGTGCATCG
1 ATGCACTGCA-GGTGCATGG
*
628687 ATGCACT--A-GTGCATCG
1 ATGCACTGCAGGTGCATGG
*
628703 ATGCATAGTGCAGGTGCATGG
1 ATGC--ACTGCAGGTGCATGG
*
628724 ATGCACTACAGGATGCATGG
1 ATGCACTGCAGG-TGCATGG
628744 ATGCACTGCAGGGTGCATGG
1 ATGCACTGCA-GGTGCATGG
628764 ATGCACT
1 ATGCACT
628771 TTGACACCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
16 12 0.17
18 3 0.04
19 6 0.08
20 38 0.53
21 13 0.18
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (19 bp):
ATGCACTGCAGGTGCATGG
Found at i:628713 original size:15 final size:15
Alignment explanation
Indices: 628673--628714 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
628663 CATAATGCAC
*
628673 TGCATGGTGCATCGA
1 TGCATAGTGCATCGA
628688 TGCACTAGTGCATCGA
1 TGCA-TAGTGCATCGA
628704 TGCATAGTGCA
1 TGCATAGTGCA
628715 GGTGCATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (15 bp):
TGCATAGTGCATCGA
Found at i:628875 original size:26 final size:29
Alignment explanation
Indices: 628845--628900 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 29
628835 AAACTTTGAA
628845 TAAATTCAATT-AA-TCCAAAAA-CATTT
1 TAAATTCAATTCAAGTCCAAAAACCATTT
628871 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAACCATTT
628900 T
1 T
628901 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 11 0.41
27 2 0.07
28 8 0.30
29 6 0.22
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACCATTT
Found at i:631412 original size:21 final size:21
Alignment explanation
Indices: 631386--631433 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
631376 CATAACATGG
*
631386 TGCATCAGTGCACTATCAAGC
1 TGCATCAATGCACTATCAAGC
*
631407 TGCATCAATGCACTATCAAGG
1 TGCATCAATGCACTATCAAGC
631428 TGCATC
1 TGCATC
631434 GATACCCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (21 bp):
TGCATCAATGCACTATCAAGC
Found at i:631634 original size:21 final size:21
Alignment explanation
Indices: 631608--631747 Score: 235
Period size: 21 Copynumber: 6.7 Consensus size: 21
631598 CTAGTGCAAG
631608 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
*
631629 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGA
631650 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
*
631671 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGA
631692 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
* * *
631713 TGCATAGATGCACTGCAGGGG
1 TGCATGGATGCACTACAGGGA
631734 TGCATGGATGCACT
1 TGCATGGATGCACT
631748 TTGACACCCT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 111 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:631657 original size:42 final size:42
Alignment explanation
Indices: 631608--631747 Score: 262
Period size: 42 Copynumber: 3.3 Consensus size: 42
631598 CTAGTGCAAG
631608 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
631650 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
* *
631692 TGCATGGATGCACTACAGGGATGCATAGATGCACTGCAGGGG
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
631734 TGCATGGATGCACT
1 TGCATGGATGCACT
631748 TTGACACCCT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (42 bp):
TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
Found at i:631848 original size:29 final size:29
Alignment explanation
Indices: 631827--631884 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
631817 AAACTTTGAA
631827 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
631856 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
631885 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:631874 original size:30 final size:30
Alignment explanation
Indices: 631827--631886 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
631817 AAACTTTGAA
631827 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
631856 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
631887 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:634445 original size:21 final size:21
Alignment explanation
Indices: 634419--634465 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
634409 TAACATTGTG
634419 CATCGGTGCACTATCAAGGTA
1 CATCGGTGCACTATCAAGGTA
*
634440 CATCGGTGCACTATCAAGGTG
1 CATCGGTGCACTATCAAGGTA
634461 CATCG
1 CATCG
634466 ATACCCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (21 bp):
CATCGGTGCACTATCAAGGTA
Found at i:634619 original size:42 final size:42
Alignment explanation
Indices: 634573--634713 Score: 207
Period size: 42 Copynumber: 3.4 Consensus size: 42
634563 TGGTCTTTGA
*
634573 GTGCATGGATGCACTGCATGGTGCGTCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
634615 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
* *
634657 GTGCATGGATGCACTGCAGGGATGCATAGATGCAC---TGCAGGG
1 GTGCATGGATGCACTGCATGG-TGCATCGATGCACTAGTGCA--G
634699 GTGCATGGATGCACT
1 GTGCATGGATGCACT
634714 TTGACACCCT
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
40 4 0.04
42 77 0.83
43 12 0.13
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (42 bp):
GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
Found at i:634625 original size:22 final size:21
Alignment explanation
Indices: 634573--634714 Score: 134
Period size: 22 Copynumber: 6.8 Consensus size: 21
634563 TGGTCTTTGA
634573 GTGCATGGATGCAC-TGCATG
1 GTGCATGGATGCACTTGCATG
* *
634593 GTGCGTCGATGCACTAGTGCA-G
1 GTGCATGGATGCACT--TGCATG
634615 GTGCATGGATGCAC-TGCATG
1 GTGCATGGATGCACTTGCATG
*
634635 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACT--TGCATG
*
634657 GTGCATGGATGCAC-TGCAGG
1 GTGCATGGATGCACTTGCATG
* *
634677 GATGCATAGATGCAC-TGCAGGG
1 G-TGCATGGATGCACTTGCA-TG
634699 GTGCATGGATGCACTT
1 GTGCATGGATGCACTT
634715 TGACACCCTT
Statistics
Matches: 103, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.08
20 28 0.27
21 28 0.27
22 31 0.30
23 8 0.08
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTTGCATG
Found at i:634824 original size:29 final size:30
Alignment explanation
Indices: 634791--634849 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
634781 AAACTTTGAA
634791 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
*
634820 TAAATTCAATTCAAGTCCAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
634850 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:635959 original size:3 final size:3
Alignment explanation
Indices: 635935--635974 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
635925 TGGACATGTA
* * *
635935 GGT GAT GGT AGT GGT AGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
635975 TTGATGTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.07, C:0.00, G:0.60, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:636145 original size:28 final size:28
Alignment explanation
Indices: 636106--636165 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
636096 ATTTGTAATA
* * *
636106 TTTTTATTTAATTGAACTTTATTTTCTT
1 TTTTTAGTTAATCGAACTCTATTTTCTT
*
636134 TTTTTAGTTAATCGAACTCTGTTTTCTT
1 TTTTTAGTTAATCGAACTCTATTTTCTT
636162 TTTT
1 TTTT
636166 CTTTAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.10, G:0.07, T:0.65
Consensus pattern (28 bp):
TTTTTAGTTAATCGAACTCTATTTTCTT
Found at i:646852 original size:25 final size:25
Alignment explanation
Indices: 646807--646855 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
646797 ACCTTTACAC
*
646807 TTGGACTGAATCTTTGCTGGACCTT
1 TTGGACTGAATCTTTACTGGACCTT
*
646832 TTGGACTGAA-CTTTTATTGGACCT
1 TTGGACTGAATC-TTTACTGGACCT
646856 GAAAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (25 bp):
TTGGACTGAATCTTTACTGGACCTT
Found at i:646924 original size:2 final size:2
Alignment explanation
Indices: 646917--646955 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
646907 TTTCAAAAAT
646917 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA -A 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
646956 ACATACACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:647019 original size:27 final size:25
Alignment explanation
Indices: 646966--647025 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 25
646956 ACATACACTG
646966 TATATTTTAAAATATATATATTATA
1 TATATTTTAAAATATATATATTATA
646991 TATATTTTCAAAAACTATATTATATTATA
1 TATATTTT--AAAA-TATA-TATATTATA
647020 TTATAT
1 -TATAT
647026 ATACTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 8 0.27
27 4 0.13
28 4 0.13
29 9 0.30
30 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTTAAAATATATATATTATA
Found at i:647021 original size:34 final size:35
Alignment explanation
Indices: 646977--647051 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 35
646967 ATATTTTAAA
*
646977 ATATA-TATATTATATATATTTTCAAAAACTATAT
1 ATATATTATATTATATATACTTTCAAAAACTATAT
*
647011 -TATATTATATTATATATACTTTCAAAATCTATAT
1 ATATATTATATTATATATACTTTCAAAAACTATAT
647045 ATATATT
1 ATATATT
647052 TTCGAAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 4 0.11
34 27 0.73
35 6 0.16
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (35 bp):
ATATATTATATTATATATACTTTCAAAAACTATAT
Found at i:647068 original size:23 final size:23
Alignment explanation
Indices: 647017--647074 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
647007 ATATTATATT
* *
647017 ATATTATATATACTTTCAAAATC
1 ATATTATATATATTTTCAAAACC
*
647040 -TA-TATATATATTTTCGAAACC
1 ATATTATATATATTTTCAAAACC
*
647061 ATATTATACATATT
1 ATATTATATATATT
647075 ATACTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.55
22 4 0.14
23 9 0.31
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTATATATATTTTCAAAACC
Found at i:647113 original size:21 final size:22
Alignment explanation
Indices: 647065--647114 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
647055 GAAACCATAT
*
647065 TATACATATTATACTATATATAA
1 TATAAATATTATAC-ATATATAA
647088 TATAAATATTATAC-TATATAA
1 TATAAATATTATACATATATAA
647109 TATAAA
1 TATAAA
647115 GATAGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.50
23 13 0.50
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAATATTATACATATATAA
Found at i:647783 original size:21 final size:21
Alignment explanation
Indices: 647757--647807 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
647747 ATGTTGCTTC
*
647757 TCTCGCTTCTCGTTCTACTTA
1 TCTCGCTTCTCATTCTACTTA
*
647778 TCTCGCTTTTCATTCTACTTA
1 TCTCGCTTCTCATTCTACTTA
647799 TCTCGCTTC
1 TCTCGCTTC
647808 AACTTCGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.33, G:0.08, T:0.49
Consensus pattern (21 bp):
TCTCGCTTCTCATTCTACTTA
Found at i:653600 original size:2 final size:2
Alignment explanation
Indices: 653593--653642 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
653583 CAATTAAGTA
653593 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
653635 AT A- AT AT A
1 AT AT AT AT A
653643 GCCCTTGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:653622 original size:25 final size:25
Alignment explanation
Indices: 653593--653643 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
653583 CAATTAAGTA
653593 ATATATATATATATATATATATATAGT
1 ATATATATATATA-ATATA-ATATAGT
653620 ATATATATATATAATATAATATAG
1 ATATATATATATAATATAATATAG
653644 CCCTTGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATATATATATAATATAATATAGT
Found at i:653687 original size:2 final size:2
Alignment explanation
Indices: 653680--653733 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
653670 AATCTACTTT
653680 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
*
653722 TA -A TA TG TA TA T
1 TA TA TA TA TA TA T
653734 TAATGTATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:653815 original size:2 final size:2
Alignment explanation
Indices: 653808--653844 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
653798 GTATGTACAA
653808 AT AT 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 AT AT A
653845 AGTATAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:655082 original size:13 final size:13
Alignment explanation
Indices: 655054--655133 Score: 79
Period size: 13 Copynumber: 5.8 Consensus size: 13
655044 AATATAAGTT
*
655054 TATATATAAATTA
1 TATATATAAACTA
655067 TATATATAAACTA
1 TATATATAAACTA
655080 TATAATTATTATAAGCTA
1 TAT-A-TA-TA-AA-CTA
*
655098 TATATATAAATTA
1 TATATATAAACTA
*
655111 TGTATATAAACTA
1 TATATATAAACTA
*
655124 TATATGTAAA
1 TATATATAAA
655134 AACTATAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
13 36 0.64
14 3 0.05
15 4 0.07
16 4 0.07
17 3 0.05
18 6 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:655202 original size:19 final size:18
Alignment explanation
Indices: 655155--655209 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
655145 TTATATAGTT
655155 TATAAACTATA-ATT-TA
1 TATAAACTATATATTATA
* *
655171 TTTAATACAATATATATATA
1 TATAA-ACTATATAT-TATA
655191 TATAAACTATATATGTATA
1 TATAAACTATATAT-TATA
655210 AACTATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.13
17 5 0.17
18 2 0.07
19 13 0.43
20 6 0.20
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TATAAACTATATATTATA
Found at i:655203 original size:13 final size:14
Alignment explanation
Indices: 655185--655218 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
655175 ATACAATATA
655185 TATATA-TATAAAC
1 TATATAGTATAAAC
655198 TATATATGTATAAAC
1 TATATA-GTATAAAC
655213 TATATA
1 TATATA
655219 AAATATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (14 bp):
TATATAGTATAAAC
Found at i:655240 original size:74 final size:76
Alignment explanation
Indices: 655113--655258 Score: 226
Period size: 76 Copynumber: 1.9 Consensus size: 76
655103 ATAAATTATG
655113 TATATAAACTATATATGTAAAAACTATAAAAATTATATAGTTTATAAACTATAATTTAT-TTA-A
1 TATATAAACTATATATGTAAAAACTATAAAAA-TATATAGTTTATAAACTATAATTTATATTATA
655176 TACAATATATATA
65 TA-AATATATATA
* * *
655189 TATATAAACTATATATGTATAAACTATATAAA-ATATAGTTTATAAATTATAATTTATATTATAT
1 TATATAAACTATATATGTAAAAACTATAAAAATATATAGTTTATAAACTATAATTTATATTATAT
655253 AAATAT
66 AAATAT
655259 TTGTATGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
74 24 0.37
75 8 0.12
76 33 0.51
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (76 bp):
TATATAAACTATATATGTAAAAACTATAAAAATATATAGTTTATAAACTATAATTTATATTATAT
AAATATATATA
Found at i:655273 original size:74 final size:75
Alignment explanation
Indices: 655087--655283 Score: 235
Period size: 74 Copynumber: 2.7 Consensus size: 75
655077 CTATATAATT
**
655087 ATTATAAGCTATA-TATATAAAT-TATGTATATA-AACTATATATGTAAAAACTATAAAAATTAT
1 ATTATAATTTATATTATATAAATATATGTATATATAACTATATATGTAAAAACTATAAAAA-TAT
655149 ATAGTTTATAA
65 ATAGTTTATAA
* * * *
655160 ACTATAATTTAT-TTA-ATACAATATATATATATATAAACTATATATGTATAAACTATATAAA-A
1 ATTATAATTTATATTATATA-AATATATGTATATAT-AACTATATATGTAAAAACTATAAAAATA
655222 TATAGTTTATAA
64 TATAGTTTATAA
* * *
655234 ATTATAATTTATATTATATAAATATTTGTATGTATAACTAATATAAGTAA
1 ATTATAATTTATATTATATAAATATATGTATATATAACT-ATATATGTAA
655284 TCTATAGATT
Statistics
Matches: 104, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
72 3 0.03
73 14 0.13
74 37 0.36
75 23 0.22
76 27 0.26
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (75 bp):
ATTATAATTTATATTATATAAATATATGTATATATAACTATATATGTAAAAACTATAAAAATATA
TAGTTTATAA
Found at i:655339 original size:21 final size:21
Alignment explanation
Indices: 655310--655376 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
655300 ATAGTTTATA
* * *
655310 AAAACCCTAAATCCTACACCTT
1 AAAA-CCTAAATCATAAACCCT
*
655332 AAATCCTAAATCATAAACCCT
1 AAAACCTAAATCATAAACCCT
* *
655353 AAAACCTAAATCGTAAACACT
1 AAAACCTAAATCATAAACCCT
655374 AAA
1 AAA
655377 CTTTATAAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.21
Consensus pattern (21 bp):
AAAACCTAAATCATAAACCCT
Found at i:655590 original size:19 final size:18
Alignment explanation
Indices: 655560--655614 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
655550 GTATAAATAG
655560 TATAGTATATAACTATATA
1 TATA-TATATAACTATATA
655579 TATATATCATAA-TACTATA
1 TATATAT-ATAACTA-TATA
655598 TATATATATAAACTATA
1 TATATATAT-AACTATA
655615 AAGTAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.22
19 23 0.72
20 2 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (18 bp):
TATATATATAACTATATA
Found at i:655714 original size:2 final size:2
Alignment explanation
Indices: 655707--655735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
655697 ACCCTAAACA
655707 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 A
655736 GACACAATTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:655974 original size:16 final size:16
Alignment explanation
Indices: 655953--655986 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
655943 TAGATATTAT
655953 TTTAAAAAAATTAAAA
1 TTTAAAAAAATTAAAA
* *
655969 TTTAAATAGATTAAAA
1 TTTAAAAAAATTAAAA
655985 TT
1 TT
655987 AATAGTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTTAAAAAAATTAAAA
Found at i:656529 original size:24 final size:24
Alignment explanation
Indices: 656499--656545 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
656489 GCCAAAATTA
*
656499 TAATTTACATAAATTAAACTATAT
1 TAATTTACATAAATGAAACTATAT
656523 TAATTTACATAAATGAAACTATA
1 TAATTTACATAAATGAAACTATA
656546 ATTTACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATTTACATAAATGAAACTATAT
Found at i:656601 original size:27 final size:25
Alignment explanation
Indices: 656543--656635 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 25
656533 AAATGAAACT
* *
656543 ATAATTTACATTAAT-ATTTTCAATTCA
1 ATAATTT-TATTAATAATTTT--ATTAA
656570 ATAATTTTATTAATAATTTTA-T--
1 ATAATTTTATTAATAATTTTATTAA
*
656592 ATAATTTAATTTAAATAATTTTATTAA
1 ATAATTTTA-TT-AATAATTTTATTAA
656619 ATAATTTTATATAATAA
1 ATAATTTTAT-TAATAA
656636 GTCTATTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
22 8 0.14
23 2 0.04
24 11 0.20
25 2 0.04
26 12 0.21
27 21 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTTTATTAATAATTTTATTAA
Found at i:656609 original size:14 final size:14
Alignment explanation
Indices: 656587--656625 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
656577 TATTAATAAT
*
656587 TTTATATAATTTAA
1 TTTAAATAATTTAA
*
656601 TTTAAATAATTTTA
1 TTTAAATAATTTAA
656615 -TTAAATAATTT
1 TTTAAATAATTT
656626 TATATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAATAATTTAA
Found at i:656620 original size:13 final size:12
Alignment explanation
Indices: 656569--656635 Score: 75
Period size: 13 Copynumber: 5.4 Consensus size: 12
656559 TTTTCAATTC
656569 AATAATTTTATT
1 AATAATTTTATT
656581 AATAATTTTA-T
1 AATAATTTTATT
*
656592 -ATAATTTAATTT
1 AATAATTTTA-TT
656604 AAATAATTTTATT
1 -AATAATTTTATT
656617 AAATAATTTTATAT
1 -AATAATTTTAT-T
656631 AATAA
1 AATAA
656636 GTCTATTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
10 8 0.17
11 1 0.02
12 11 0.23
13 19 0.40
14 9 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATAATTTTATT
Found at i:656849 original size:16 final size:16
Alignment explanation
Indices: 656823--656861 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
656813 CGGATCATTT
656823 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * *
656839 ATAGGTTAGGTTGAAA
1 ACAGGTCAGGTTAAAA
656855 ACAGGTC
1 ACAGGTC
656862 GGGTAATATC
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:657240 original size:19 final size:20
Alignment explanation
Indices: 657202--657241 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
657192 TCTTTCTTTT
657202 AATCAATTTTCCCTTCAAAA
1 AATCAATTTTCCCTTCAAAA
657222 AATCAATTTTCCC-TCAAAA
1 AATCAATTTTCCCTTCAAAA
657241 A
1 A
657242 CAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
AATCAATTTTCCCTTCAAAA
Found at i:657355 original size:22 final size:23
Alignment explanation
Indices: 657308--657355 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
657298 AAATATTTTA
*
657308 AAATTTTAAATTAAGTTATACTT
1 AAATTTTAAATTAAGTTATACAT
657331 AAATTTT-AATTAA-TTATTACAT
1 AAATTTTAAATTAAGTTA-TACAT
657353 AAA
1 AAA
657356 AATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 3 0.13
22 13 0.57
23 7 0.30
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTTAAATTAAGTTATACAT
Found at i:657477 original size:21 final size:22
Alignment explanation
Indices: 657435--657482 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
657425 TTATTAAAAC
* *
657435 AAATTTAAAAATATTATTATTA
1 AAATTTAAAAATATAATGATTA
*
657457 AAATTT-ATAATATAATGATTA
1 AAATTTAAAAATATAATGATTA
*
657478 TAATT
1 AAATT
657483 AATATAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTTAAAAATATAATGATTA
Found at i:657631 original size:56 final size:57
Alignment explanation
Indices: 657564--657671 Score: 173
Period size: 56 Copynumber: 1.9 Consensus size: 57
657554 GTTAATTGTC
* * *
657564 ATAATTTATTATAATTTCAAAATCTTACAACTACAT-CATTGTAACTTATAAATACT
1 ATAATTTATTATAAATTCAAAATCTCACAACTACATCCATTATAACTTATAAATACT
*
657620 ATAATTTATTATAAATTCAAAATCTCACAACTTCATCCATTATAACTTATAA
1 ATAATTTATTATAAATTCAAAATCTCACAACTACATCCATTATAACTTATAA
657672 GTAAGGTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 33 0.70
57 14 0.30
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.40
Consensus pattern (57 bp):
ATAATTTATTATAAATTCAAAATCTCACAACTACATCCATTATAACTTATAAATACT
Found at i:658761 original size:3 final size:3
Alignment explanation
Indices: 658755--658785 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
658745 TAATAATAAG
*
658755 AGA AGA AGA AGA ATA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
658786 AGTTGTTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:658865 original size:25 final size:25
Alignment explanation
Indices: 658818--658865 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
658808 AGCTTATTTA
* *
658818 TACTAGGTTTTCATCCAAGTAAAAT
1 TACTAGGCTTTCATCCAAATAAAAT
* *
658843 TACTAGGCTTTCTTGCAAATAAA
1 TACTAGGCTTTCATCCAAATAAA
658866 GTTTTATTCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (25 bp):
TACTAGGCTTTCATCCAAATAAAAT
Found at i:660728 original size:183 final size:183
Alignment explanation
Indices: 660410--660775 Score: 653
Period size: 183 Copynumber: 2.0 Consensus size: 183
660400 ATAAAATTTT
* *
660410 AAATATATTATATATAACATATGGGCTCAGCCCAAACTATTTAAAACCTAATTAATAATTTAAGA
1 AAATATATTATATATAAAATATGGGCTCAGCCCAAACCATTTAAAACCTAATTAATAATTTAAGA
*
660475 TCTAATAACTTTTACACCTAAATTAATATTAATTAATTAAAAAATTTATATAAAATTTATATTTT
66 TCTAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATATAAAATTTATATTTT
*
660540 ATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAAAAATA
131 ATAATTATATATTATTTAAATTAATTATAAACTA-TTTTTTGAATTAAAAAATA
660594 AAATATATTATATATAAAATATGGGCTCAGCCCAAACCATTTAAAACCTAATTAATAATTTAAGA
1 AAATATATTATATATAAAATATGGGCTCAGCCCAAACCATTTAAAACCTAATTAATAATTTAAGA
* *
660659 TC-AATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAATTTTATATAAAATTTTTATTTT
66 TCTAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATATAAAATTTATATTTT
*
660723 ATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTATAAAATA
131 ATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAAAAATA
660776 TTTAATTTTT
Statistics
Matches: 175, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 18 0.10
183 92 0.53
184 65 0.37
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (183 bp):
AAATATATTATATATAAAATATGGGCTCAGCCCAAACCATTTAAAACCTAATTAATAATTTAAGA
TCTAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATATAAAATTTATATTTT
ATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAAAAATA
Found at i:660758 original size:20 final size:20
Alignment explanation
Indices: 660724--660780 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
660714 TTTTATTTTA
* *
660724 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* *
660744 TAATTATAAACTATTT--TT
1 TAATTATAAAATATTTAAAT
660762 TGAATTATAAAATATTTAA
1 T-AATTATAAAATATTTAA
660781 TTTTTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:661243 original size:35 final size:34
Alignment explanation
Indices: 661204--661285 Score: 78
Period size: 34 Copynumber: 2.4 Consensus size: 34
661194 ATATATCAAT
*
661204 TTAAAAAATATTTAT-TATTTTTTAAAATTTGAATA
1 TTAAAAAATATTTATATA-CTTTTAAAATTTGAA-A
* * * *
661239 TT-AAAGATAATTATATACTTTTAATATTTTAAA
1 TTAAAAAATATTTATATACTTTTAAAATTTGAAA
661272 TTAAAATAATATTT
1 TTAAAA-AATATTT
661286 GTTTAAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
33 3 0.08
34 25 0.68
35 9 0.24
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (34 bp):
TTAAAAAATATTTATATACTTTTAAAATTTGAAA
Found at i:661329 original size:61 final size:62
Alignment explanation
Indices: 661219--661345 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 62
661209 AAATATTTAT
* *
661219 TATTTTTTAAAATTTGAATATTAAAGATAATTATATACTTTTAATATTTT-AAATTAAAATAA
1 TATTTTTTAAAATTTGAATAATAAAGAGAATTATATACTTTTAATATTTTAAAATTAAAA-AA
661281 TATTTGTTT-AAATTTGAATAAT-AAG-GAATGTATAT-CTCTTTAATATTTTAAAATTAAAAAA
1 TATTT-TTTAAAATTTGAATAATAAAGAGAAT-TATATACT-TTTAATATTTTAAAATTAAAAAA
661342 TATT
1 TATT
661346 ATTATCTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
60 5 0.08
61 25 0.42
62 26 0.44
63 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (62 bp):
TATTTTTTAAAATTTGAATAATAAAGAGAATTATATACTTTTAATATTTTAAAATTAAAAAA
Found at i:664350 original size:11 final size:11
Alignment explanation
Indices: 664334--664366 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
664324 TTATTATACA
664334 TATATATTTTT
1 TATATATTTTT
664345 TATATATTTTT
1 TATATATTTTT
664356 T-TACTATTTTT
1 TATA-TATTTTT
664367 ATTTTTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 2 0.10
11 19 0.90
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (11 bp):
TATATATTTTT
Found at i:664494 original size:10 final size:10
Alignment explanation
Indices: 664445--664514 Score: 65
Period size: 10 Copynumber: 7.1 Consensus size: 10
664435 ATATTTCATT
*
664445 TATACATTTA
1 TATATATTTA
*
664455 TATATATCTA
1 TATATATTTA
664465 TATAT-TTTA
1 TATATATTTA
664474 TACTAATATTTA
1 TA-T-ATATTTA
664486 TATATATTT-
1 TATATATTTA
664495 TAT-TATTTA
1 TATATATTTA
* *
664504 TTTTTATTTA
1 TATATATTTA
664514 T
1 T
664515 TTAATACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
8 5 0.10
9 10 0.20
10 27 0.53
11 3 0.06
12 6 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATATTTA
Found at i:664610 original size:2 final size:2
Alignment explanation
Indices: 664598--664637 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
664588 CATTAAATAC
*
664598 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
664638 CACCTCACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:664845 original size:14 final size:14
Alignment explanation
Indices: 664826--664907 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
664816 TAGTTATATA
664826 TTTTCATTTTTATT
1 TTTTCATTTTTATT
*
664840 TTTTCATTATTATT
1 TTTTCATTTTTATT
**
664854 TTTTC-TTTTTGGT
1 TTTTCATTTTTATT
* *
664867 TTTT-ACTTATTGTT
1 TTTTCA-TTTTTATT
664881 TTTTC-TTTTTATT
1 TTTTCATTTTTATT
664894 TCTTT-A-TTTTATT
1 T-TTTCATTTTTATT
664907 T
1 T
664908 ATTTGTTTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
13 24 0.44
14 31 0.56
ACGTcount: A:0.12, C:0.07, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTTCATTTTTATT
Found at i:664856 original size:27 final size:25
Alignment explanation
Indices: 664826--664907 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 25
664816 TAGTTATATA
664826 TTTTCATTTTTATTTTTTCATTATTATT
1 TTTTC-TTTTTATTTTTT-ATTATTA-T
** *
664854 TTTTCTTTTTGGTTTTTACTTATTGTT
1 TTTTCTTTTTATTTTTTA-TTATT-AT
664881 TTTTCTTTTTATTTCTTTATT-TTAT
1 TTTTCTTTTTATTT-TTTATTATTAT
664906 TT
1 TT
664908 ATTTGTTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 30 0.67
28 9 0.20
ACGTcount: A:0.12, C:0.07, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTCTTTTTATTTTTTATTATTAT
Found at i:666702 original size:18 final size:18
Alignment explanation
Indices: 666679--666721 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
666669 TCAACCTGTC
*
666679 AGAAGACATTTGGGGTCT
1 AGAAGACATTCGGGGTCT
**
666697 AGAAGATGTTCGGGGTCT
1 AGAAGACATTCGGGGTCT
666715 AGAAGAC
1 AGAAGAC
666722 TTATTTAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (18 bp):
AGAAGACATTCGGGGTCT
Found at i:670687 original size:85 final size:85
Alignment explanation
Indices: 670458--671557 Score: 1171
Period size: 85 Copynumber: 13.0 Consensus size: 85
670448 AAACCATTCG
* * * * *
670458 CAGCATAGCTCAAGGTGAGAAGGGCTA----T--ATCAAGACCTTCAAGTTCGATTATATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
*
670517 TCAAAGGCATATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* * * *
670537 CAGCATAGCTCAAGGCGAGAATGACTATTTGT----CAAGA-CTATCGAGTTTGATTACACTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCT-TCGAGTTCGATTACACTCAG
*
670597 CTCAAAGGCACATCAAATTTG
65 CTCAAAGGCACATCAAATTTA
* * * * *
670618 CAGTATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAGACCTTCGAGTTCGATTACACTCAAC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
*
670683 TCAAAGGTACATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* * *
670703 CAGCATAGCTAAAGGCGAGAAGGGCTATCTGCCAACCAAGACCTTTGAGTTCGATTACACTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
*
670768 TCAAAGGCACATCAAATTTG
66 TCAAAGGCACATCAAATTTA
* * * *
670788 CAGCATAGATCAAGGCGAGAAGGGCTATTTGTCAACCAAGACCTTCGACTTCAATTACACTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
* *
670853 TCAAAGACACATCAAATCTA
66 TCAAAGGCACATCAAATTTA
* * * ** * *
670873 CAACATAGCTCAAGGCTAGAAGGGCTATCTGTAAAAAAAGACCTTCGAGTTCAATTACACTCAGG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
**
670938 TCAAAGGCACATCAAATTCG
66 TCAAAGGCACATCAAATTTA
* * * * * * * *
670958 TAGTATAACTCAAGGTGAGAAGGGTTATCT-TCCAATCAAGACCTTCGAGTTCAATTACACTCAT
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGT-CAACCAAGACCTTCGAGTTCGATTACACTCAG
* * *
671022 CTCGAAGACACATCAAATTTG
65 CTCAAAGGCACATCAAATTTA
* * **
671043 CAGCATAGGTTAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
* *
671108 TCAAAGACACATCAAATCTA
66 TCAAAGGCACATCAAATTTA
** * * * * * * *
671128 CAGTGTAGCTCAAGGCGAGAAGGTCTATATGTCAACAAAAGACCTTCAAGTTCAATTACATTTAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAG
* *
671193 CTCAAAGGCATATCCAATTTA
65 CTCAAAGGCACATCAAATTTA
* * * * * * * * *
671214 CAACATAACTCAAGGCGATAAGGGTTATCTATCAGCAAAGACCTTCAAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
671279 TCAAAGGCACATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* * * * * * * * *
671299 CAGCATAGTTCAAGGCGAGAATGACTATCTGTCAACAAAAAACCTTCGAGTTTGATTATATTTAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAG
* *
671364 CTCAAAGGCATATCCAATTTA
65 CTCAAAGGCACATCAAATTTA
* * * * *** * * *
671385 CAACATAACTCAAGGCGAGAAGGGTTATCTATCAGTAAAGTCCTTCGAGTTCGATTACATTTAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
*
671450 TTAAAGGCACATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* * * *
671470 CAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAG
*
671535 CTCAAAGGCATATCAAATTTA
65 CTCAAAGGCACATCAAATTTA
671556 CA
1 CA
671558 ACTTAGCTTA
Statistics
Matches: 856, Mismatches: 150, Indels: 23
0.83 0.15 0.02
Matches are distributed among these distances:
79 24 0.03
80 2 0.00
81 65 0.08
83 1 0.00
84 1 0.00
85 578 0.68
86 185 0.22
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCACATCAAATTTA
Found at i:671267 original size:171 final size:171
Alignment explanation
Indices: 670489--671565 Score: 1170
Period size: 171 Copynumber: 6.3 Consensus size: 171
670479 GGGCTATATC
* * *
670489 AAGACCTTCAAGTTCGATTATATTCAGCTCAAAGGCATATCAAATTTACAGCATAGCTCAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
* ** ** *
670554 AGAATGACTAT-T-T-GTC-AAGA-CTATCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAA
66 AGAAGGGTTATCTATCAACAAAGACCT-TCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAA
* * * * *
670614 TTTGCAGTATAACTCAAGGCGAGAAGGGT-TATCTGCCAAC-C
130 TTTACAGCATAGCTCAAGGCGAGAA-GGTCTATCTGTCAACAA
* * * * * *
670655 AAGACCTTCGAGTTCGATTACACTCAACTCAAAGGTACATCAAATTTACAGCATAGCTAAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
* ** * *
670720 AGAAGGGCTATCTGCCAACCAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
66 AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
* * * * *
670785 TTGCAGCATAGATCAAGGCGAGAAGGGCTATTTGTCAAC-C
131 TTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
* * * * * * *
670825 AAGACCTTCGACTTCAATTACACTCAGCTCAAAGACACATCAAATCTACAACATAGCTCAAGGCT
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
* * * * * *
670890 AGAAGGGCTATCTGTAAAAAAAGACCTTCGAGTTCAATTACACTCAGGTCAAAGGCACATCAAAT
66 AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
*** * * *
670955 TCGTAGTATAACTCAAGGTGAGAAGGGT-TATCT-TC--CAA
131 TTACAGCATAGCTCAAGGCGAGAA-GGTCTATCTGTCAACAA
* * * * * * * * * *
670993 TCAAGACCTTCGAGTTCAATTACACTCATCTCGAAGACACATCAAATTTGCAGCATAGGTTAAGG
1 --AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGG
* * * *
671058 CGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACATCAA
64 CGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA
* ** *
671123 ATCTACAGTGTAGCTCAAGGCGAGAAGGTCTATATGTCAACAA
129 ATTTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
* * * * *
671166 AAGACCTTCAAGTTCAATTACATTTAGCTCAAAGGCATATCCAATTTACAACATAACTCAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
* * * *
671231 ATAAGGGTTATCTATCAGCAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCACATCAAAT
66 AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
* * *
671296 TTACAGCATAGTTCAAGGCGAGAATGACTATCTGTCAACAA
131 TTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
* * * * * *
671337 AAAACCTTCGAGTTTGATTATATTTAGCTCAAAGGCATATCCAATTTACAACATAACTCAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
** * * * *
671402 AGAAGGGTTATCTATCAGTAAAGTCCTTCGAGTTCGATTACATTTAGCTTAAAGGCACATCAAAT
66 AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
* * *
671467 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAA
131 TTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
*
671508 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACTTAGCT
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCT
671566 TAAGTCAAGA
Statistics
Matches: 776, Mismatches: 121, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
166 67 0.09
167 2 0.00
169 8 0.01
170 341 0.44
171 355 0.46
173 3 0.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (171 bp):
AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCG
AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
TTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
Found at i:673192 original size:15 final size:16
Alignment explanation
Indices: 673169--673202 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
673159 GCCCTTTTAT
673169 TATTATTATATATATA
1 TATTATTATATATATA
673185 TATT-TTATATATATA
1 TATTATTATATATATA
673200 TAT
1 TAT
673203 AAATTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATATATATA
Found at i:673193 original size:13 final size:13
Alignment explanation
Indices: 673163--673200 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
673153 ACATTAGCCC
673163 TTTTAT-TAT-TA
1 TTTTATATATATA
*
673174 TTATATATATATA
1 TTTTATATATATA
673187 TTTTATATATATA
1 TTTTATATATATA
673200 T
1 T
673201 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 5 0.22
12 3 0.13
13 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTATATATATA
Found at i:673208 original size:19 final size:18
Alignment explanation
Indices: 673171--673210 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
673161 CCTTTTATTA
*
673171 TTATTATATATATATATT
1 TTATTATATATATAAATT
673189 TTATATATATATATAAATT
1 TTAT-TATATATATAAATT
673208 TTA
1 TTA
673211 CTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATATATATAAATT
Found at i:673238 original size:3 final size:3
Alignment explanation
Indices: 673230--673272 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
673220 TTTTTGGGTT
*
673230 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTTA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TT
673273 TTCTTTTCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:673263 original size:7 final size:7
Alignment explanation
Indices: 673229--673273 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
673219 ATTTTTGGGT
673229 TTTATTA
1 TTTATTA
673236 -TTATTA
1 TTTATTA
673242 TTACTATTA
1 TT--TATTA
673251 -TTATTA
1 TTTATTA
673257 TTTATTA
1 TTTATTA
673264 TTTATTA
1 TTTATTA
673271 TTT
1 TTT
673274 TCTTTTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 11 0.32
7 17 0.50
8 1 0.03
9 5 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:673824 original size:14 final size:14
Alignment explanation
Indices: 673805--673840 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
673795 GTTTTTTTGT
*
673805 TTTTATTTCTTTTA
1 TTTTATTTATTTTA
673819 TTTTATTTATTTTA
1 TTTTATTTATTTTA
*
673833 TTTGATTT
1 TTTTATTT
673841 GTTTCCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:673831 original size:29 final size:28
Alignment explanation
Indices: 673739--673831 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 28
673729 TAGTTATATA
* *
673739 TTTTCCTTTTTATTTTTTCATTATTATTAT
1 TTTTTCTTTTTATTTTTTTATT-TTATT-T
* * *
673769 TTTTTCTTTTTCTTTTTTTAATTAATGTT
1 TTTTTCTTTTTATTTTTTTATTTTAT-TT
*
673798 TTTTTGTTTTTATTTCTTTTATTTTATTT
1 TTTTTCTTTTTATTT-TTTTATTTTATTT
*
673827 ATTTT
1 TTTTT
673832 ATTTGATTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.45
30 28 0.55
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTTTCTTTTTATTTTTTTATTTTATTT
Found at i:675639 original size:21 final size:21
Alignment explanation
Indices: 675612--675717 Score: 102
Period size: 21 Copynumber: 5.3 Consensus size: 21
675602 TTATAGTATT
675612 GATACCCTAGGGTCAAATATC
1 GATACCCTAGGGTCAAATATC
* * *
675633 AATACCCTTA---T-GAGTATC
1 GATACCC-TAGGGTCAAATATC
675651 GATACCCTAGGGTCAAATATC
1 GATACCCTAGGGTCAAATATC
*
675672 GATACCCCTA---T-AAGTATC
1 GATA-CCCTAGGGTCAAATATC
675690 GATACCCTAGGGTCAAATATC
1 GATACCCTAGGGTCAAATATC
675711 GATACCC
1 GATACCC
675718 CTATGAGTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
17 7 0.10
18 21 0.31
19 2 0.03
20 2 0.03
21 28 0.42
22 7 0.10
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
GATACCCTAGGGTCAAATATC
Found at i:675655 original size:18 final size:17
Alignment explanation
Indices: 675629--675734 Score: 68
Period size: 18 Copynumber: 5.6 Consensus size: 17
675619 TAGGGTCAAA
* *
675629 TATCAATACCCTTATGAG
1 TATCGATACCC-TATAAG
*
675647 TATCGATACCCTAGGGTCAAA
1 TATCGATACCCTA---T-AAG
675668 TATCGATACCCCTATAAG
1 TATCGATA-CCCTATAAG
*
675686 TATCGATACCCTAGGGTCAAA
1 TATCGATACCCTA---T-AAG
*
675707 TATCGATACCCCTATGAG
1 TATCGATA-CCCTATAAG
675725 TATCGATACC
1 TATCGATACC
675735 AAAAAATACA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
17 9 0.13
18 29 0.41
19 2 0.03
20 2 0.03
21 19 0.27
22 10 0.14
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (17 bp):
TATCGATACCCTATAAG
Found at i:675655 original size:39 final size:39
Alignment explanation
Indices: 675606--675734 Score: 222
Period size: 39 Copynumber: 3.3 Consensus size: 39
675596 CTTTTCTTAT
* * *
675606 AGTATTGATACCCTAGGGTCAAATATCAATACCCTTATG
1 AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATG
*
675645 AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATA
1 AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATG
675684 AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATG
1 AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATG
675723 AGTATCGATACC
1 AGTATCGATACC
675735 AAAAAATACA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
AGTATCGATACCCTAGGGTCAAATATCGATACCCCTATG
Found at i:679299 original size:14 final size:15
Alignment explanation
Indices: 679272--679301 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
679262 CCTGATACTC
679272 TAATACCACTAAATA
1 TAATACCACTAAATA
679287 TAATACC-CTAAATA
1 TAATACCACTAAATA
679301 T
1 T
679302 GAATGGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATACCACTAAATA
Found at i:689206 original size:18 final size:18
Alignment explanation
Indices: 689183--689224 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
689173 CCTTAGCTTG
*
689183 CTAGCTCCTCTCGGACGC
1 CTAGCTCCTCTCAGACGC
689201 CTAGCTCCTCTCAGACGC
1 CTAGCTCCTCTCAGACGC
689219 CTAGCT
1 CTAGCT
689225 TGCCACTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.43, G:0.19, T:0.24
Consensus pattern (18 bp):
CTAGCTCCTCTCAGACGC
Found at i:704930 original size:138 final size:137
Alignment explanation
Indices: 704682--704964 Score: 410
Period size: 138 Copynumber: 2.1 Consensus size: 137
704672 CACTGAAGTG
* * *
704682 TCGAAATGGAAATTCACAAACTTATTATGAATTCCATGGATGTACACATAGTGCCAAAAGTACAC
1 TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACAC
* * *
704747 ACAGTACTGATACGAAAATGCACCGTTATGCATTAAACAAAATCGA-TCGATAACTTTTATACAT
66 ACAGTACTGATACGAAAAGGCACCGTTATGCATTAAACAAAATCGACT-GATAACTTTTATAAAC
704811 AATTGTATA
130 AATT-TATA
* *
704820 TCGAAATGGTAATTCACAAAGTCATTATGAATACCAT-GATTGCACATC-TAGTGCCAAAAGTAC
1 TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGA-TGCACA-CATAGTGCCAAAAGTAC
* *
704883 ACACAGTACTGATACGAAAAGGCACTGTTATGCATTAAACAAAATCGACTGATGACTTTTATAAA
64 ACACAGTACTGATACGAAAAGGCACCGTTATGCATTAAACAAAATCGACTGATAACTTTTATAAA
*
704948 CAATTTATG
129 CAATTTATA
704957 TCGAAATG
1 TCGAAATG
704965 CACCTTTGAA
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
137 13 0.10
138 116 0.89
139 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (137 bp):
TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACAC
ACAGTACTGATACGAAAAGGCACCGTTATGCATTAAACAAAATCGACTGATAACTTTTATAAACA
ATTTATA
Found at i:710572 original size:46 final size:44
Alignment explanation
Indices: 710512--710598 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 44
710502 AAATAGCCTG
*
710512 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGT-ATGTGCATCGATGCAT-AAATGCACTA
710558 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCA
1 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCA
710599 TTCGATGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 7 0.17
45 15 0.38
46 18 0.45
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
AGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCACTA
Found at i:713857 original size:22 final size:20
Alignment explanation
Indices: 713815--713860 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
713805 CTTACTCTCA
*
713815 TTATAAATACAATTACATCC
1 TTATAAATACAATAACATCC
713835 TTATAAATACAATACAACATCC
1 TTATAAATACAAT--AACATCC
713857 TTAT
1 TTAT
713861 CTAACGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
22 10 0.43
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (20 bp):
TTATAAATACAATAACATCC
Found at i:725563 original size:183 final size:184
Alignment explanation
Indices: 725255--725625 Score: 735
Period size: 183 Copynumber: 2.0 Consensus size: 184
725245 CACCTAAAGG
725255 TCAGAAAATAAATAAAAGTTTATATAGACGTTTGTTATATCAAAAATACTTTGGAAACAAATATA
1 TCAGAAAATAAATAAAAGTTTATATAGACGTTTGTTATATCAAAAATACTTTGGAAACAAATATA
725320 AAGAAATGCAGGGGCTCTTTTAGTTTTACACATATTTAATACTGTTGCATGCATGAAAATAAAAA
66 AAGAAATGCAGGGGCTCTTTTAGTTTTACACATATTTAATACTGTTGCATGCATGAAAATAAAAA
725385 GTTAA-TTCTTGTTTTTTTTCCAATGAATATCTTTTCATTTCCTACAGTTAATC
131 GTTAACTTCTTGTTTTTTTTCCAATGAATATCTTTTCATTTCCTACAGTTAATC
725438 TCAGAAAATAAATAAAAGTTTATATAGACGTTTGTTATATCAAAAATACTTTGGAAACAAATATA
1 TCAGAAAATAAATAAAAGTTTATATAGACGTTTGTTATATCAAAAATACTTTGGAAACAAATATA
725503 AAGAAATGCAGGGGCTCTTTTAGTTTTACACATATTTAATACTGTTGCATGCATGAAAATAAAAA
66 AAGAAATGCAGGGGCTCTTTTAGTTTTACACATATTTAATACTGTTGCATGCATGAAAATAAAAA
725568 GTTAACTTCTTGTTTTTTTTCCAATGAATATCTTTTCATTTCCTACAGTTAATC
131 GTTAACTTCTTGTTTTTTTTCCAATGAATATCTTTTCATTTCCTACAGTTAATC
725622 TCAG
1 TCAG
725626 CTTTCTATTT
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 135 0.72
184 52 0.28
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (184 bp):
TCAGAAAATAAATAAAAGTTTATATAGACGTTTGTTATATCAAAAATACTTTGGAAACAAATATA
AAGAAATGCAGGGGCTCTTTTAGTTTTACACATATTTAATACTGTTGCATGCATGAAAATAAAAA
GTTAACTTCTTGTTTTTTTTCCAATGAATATCTTTTCATTTCCTACAGTTAATC
Found at i:730022 original size:89 final size:89
Alignment explanation
Indices: 729871--730053 Score: 312
Period size: 89 Copynumber: 2.1 Consensus size: 89
729861 ATATTAAACC
* *
729871 ATCATCCCAAGAGCTGGAAAACCAGTAGCCATTAAGTATTAAACAGTTGTACTTAATGCGATTCA
1 ATCATCCCAAGAGCTGGAAAACCAGTAGCCATTAAGTATTAAACAGTTATACTTAACGCGATTCA
729936 TAACTCTTCTATTCTTATATTCAT
66 TAACTCTTCTATTCTTATATTCAT
* * *
729960 ATCATCCCAAGAGCTGTAAAACCAGTAGCCATTACGTATTAAACAGTTATATTTAACGCGATTCA
1 ATCATCCCAAGAGCTGGAAAACCAGTAGCCATTAAGTATTAAACAGTTATACTTAACGCGATTCA
*
730025 TAACTCTTCTTTTCTTATATTCAT
66 TAACTCTTCTATTCTTATATTCAT
730049 ATCAT
1 ATCAT
730054 AAACTTTTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (89 bp):
ATCATCCCAAGAGCTGGAAAACCAGTAGCCATTAAGTATTAAACAGTTATACTTAACGCGATTCA
TAACTCTTCTATTCTTATATTCAT
Found at i:734916 original size:20 final size:21
Alignment explanation
Indices: 734879--734917 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
734869 AGGTCATTGT
734879 GACACCGCAAGCCACAACCAG
1 GACACCGCAAGCCACAACCAG
*
734900 GACACCGC-AGTCACAACC
1 GACACCGCAAGCCACAACC
734918 GCAATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.44, G:0.18, T:0.03
Consensus pattern (21 bp):
GACACCGCAAGCCACAACCAG
Found at i:735975 original size:3 final size:3
Alignment explanation
Indices: 735965--736000 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
735955 ATATGTCAGC
735965 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
736001 ACGAATGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:736292 original size:31 final size:31
Alignment explanation
Indices: 736257--736367 Score: 204
Period size: 31 Copynumber: 3.6 Consensus size: 31
736247 ATGTTATTGG
736257 TTTGTAACAAAATAATCATTAATATTATCGA
1 TTTGTAACAAAATAATCATTAATATTATCGA
736288 TTTGTAACAAAATAATCATTAATATTATCGA
1 TTTGTAACAAAATAATCATTAATATTATCGA
*
736319 TTTGTAACAAAATAATCATTAATATTATTGA
1 TTTGTAACAAAATAATCATTAATATTATCGA
*
736350 TTTGTAACAAAATGATCA
1 TTTGTAACAAAATAATCA
736368 CTCTATTGTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTGTAACAAAATAATCATTAATATTATCGA
Found at i:737299 original size:3 final size:3
Alignment explanation
Indices: 737291--737332 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
737281 TCTGGATACC
737291 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
737333 ATTTGTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:739073 original size:53 final size:52
Alignment explanation
Indices: 739011--739114 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 52
739001 AAATATTACT
739011 CCAGTTTTTCAAAGTTCAATTTCAATCCTTACTAAAGTGGTAAAATTATGTTC
1 CCAGTTTTTCAAAGTTCAATTTCAATCCTTACTAAAGT-GTAAAATTATGTTC
739064 CCAGTTTTTCAAAGTTCAATTTCAATCCTTACTAAAGTGTAAAATTATGTT
1 CCAGTTTTTCAAAGTTCAATTTCAATCCTTACTAAAGTGTAAAATTATGTT
739115 TTATACTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 13 0.25
53 38 0.75
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (52 bp):
CCAGTTTTTCAAAGTTCAATTTCAATCCTTACTAAAGTGTAAAATTATGTTC
Found at i:749184 original size:131 final size:131
Alignment explanation
Indices: 749020--749275 Score: 383
Period size: 131 Copynumber: 2.0 Consensus size: 131
749010 CACTCGGATT
* *
749020 AATATTGAATTTTAGGATGAAATACTAATATCTCTTCATTTCAATTGGAGTAATAAAT-GACTGC
1 AATATTGAATTTTAGGATGAAATACTAATATCTCTTCATTTCAATTAGAGTAATAAATGGA-TAC
* *
749084 TTTAAGGCACGAG-AGAT-ATTTTATTCTAGATTGGAAATAATCAGATATTATCGTTTCCTCTTG
65 TTTAAGGCACGAGAAG-TCATTAT-TTCTAGATTGGAAATAATCAGATATTATCGCTTCCTCTTG
749147 AATC
128 AATC
* *
749151 AATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTCGATTAGAGTAATAAATGGATACT
1 AATATTGAATTTTAGGATGAAATACTAATATCTCTTCATTTCAATTAGAGTAATAAATGGATACT
* * *
749216 TTAAGGCATGAGAAGTCATTATTTCTCGATTGGAAATAATTAGATATTATCGCTTCCTCT
66 TTAAGGCACGAGAAGTCATTATTTCTAGATTGGAAATAATCAGATATTATCGCTTCCTCT
749276 CTTAAATTCA
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
131 105 0.93
132 8 0.07
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (131 bp):
AATATTGAATTTTAGGATGAAATACTAATATCTCTTCATTTCAATTAGAGTAATAAATGGATACT
TTAAGGCACGAGAAGTCATTATTTCTAGATTGGAAATAATCAGATATTATCGCTTCCTCTTGAAT
C
Found at i:758743 original size:18 final size:17
Alignment explanation
Indices: 758711--758763 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
758701 TACTTCACAT
*
758711 AAAGAAAGAAAAATGAA
1 AAAGAAAAAAAAATGAA
758728 AAAGAAAAAGAAAATGAA
1 AAAGAAAAA-AAAATGAA
*
758746 AGAA-AAATAAAAAT-AA
1 A-AAGAAAAAAAAATGAA
758762 AA
1 AA
758764 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 13 0.41
18 13 0.41
19 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAGAAAAAAAAATGAA
Found at i:760485 original size:3 final size:3
Alignment explanation
Indices: 760477--760533 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
760467 TCTGGATACC
760477 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
760525 ATT -TT ATT A
1 ATT ATT ATT A
760534 ATTTTTTAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:761867 original size:108 final size:108
Alignment explanation
Indices: 761678--761931 Score: 303
Period size: 108 Copynumber: 2.3 Consensus size: 108
761668 TCATGCATAG
* * * * *
761678 GTCCCCTTAATTTAGCATGTTTTTGCATGTTGGTCACTTGTAGGGACCAAAGTTATAATTTACCC
1 GTCCCCTT-ATTTAGCGTGTTTTTTCATCTTGGTCACCTATAGGGACCAAAGTTATAATTTACCC
* * ** *
761743 ATTTTTATGCAAGTTATATA-TATTTTGGGTTATTTTTTGTTTA
65 ATTTTCATGCAAGTTATATATTATTTTAGAATATTTGTTGTTTA
* *
761786 GTCCCCATAGTTTAGCGTGTTTTTTCATCTTGGTCACCTATAGGGACCAAAGTTATTATTTACCC
1 GTCCCCTTA-TTTAGCGTGTTTTTTCATCTTGGTCACCTATAGGGACCAAAGTTATAATTTACCC
* ** * *
761851 GTTTTCATGCCTGTTATGTATTTTTTTAGAATATTTGTTGTTTA
65 ATTTTCATGCAAGTTATATATTATTTTAGAATATTTGTTGTTTA
*
761895 GTCCCCCTTATTTAAGCGTGTTTTTTCATTTTGGTCA
1 GT-CCCCTTATTT-AGCGTGTTTTTTCATCTTGGTCA
761932 TGTGTAGAGA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
107 1 0.01
108 71 0.58
109 23 0.19
110 28 0.23
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (108 bp):
GTCCCCTTATTTAGCGTGTTTTTTCATCTTGGTCACCTATAGGGACCAAAGTTATAATTTACCCA
TTTTCATGCAAGTTATATATTATTTTAGAATATTTGTTGTTTA
Done.