Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:960638 original size:20 final size:20
Alignment explanation
Indices: 960564--960638 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 20
960554 TCGCGTTGCG
960564 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
960584 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
960597 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
960617 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
960637 AT
1 AT
960639 GTTGCGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
13 3 0.07
14 9 0.21
19 9 0.21
20 22 0.51
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:960644 original size:14 final size:14
Alignment explanation
Indices: 960625--960652 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
960615 TCATTCTCTC
960625 GTTGCGATTTTCAT
1 GTTGCGATTTTCAT
960639 GTTGCGATTTTCAT
1 GTTGCGATTTTCAT
960653 TTCAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
GTTGCGATTTTCAT
Found at i:962581 original size:185 final size:186
Alignment explanation
Indices: 962351--962823 Score: 930
Period size: 185 Copynumber: 2.5 Consensus size: 186
962341 TAGATTGCTT
*
962351 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962416 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
962481 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
962536 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962601 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
962666 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
962722 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962787 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
962824 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.54
186 132 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:962665 original size:93 final size:93
Alignment explanation
Indices: 962351--962823 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
962341 TAGATTGCTT
*
962351 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962416 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
962444 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962508 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
962536 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962601 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
962629 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962694 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
962722 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
962787 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
962815 AGTAAATTT
1 AGTAAATTT
962824 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.24
93 286 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:962907 original size:19 final size:19
Alignment explanation
Indices: 962867--962995 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
962857 TAGTTTACTT
* *
962867 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
962887 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
962906 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAACCAAAA
*
962925 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
962939 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
962958 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
962972 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
962991 TCGCA
1 TCGCA
962996 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:962946 original size:33 final size:32
Alignment explanation
Indices: 962903--962995 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
962893 CGCGAAACCA
**
962903 AAATCGCAACGCGAAATTAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
962935 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
962968 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
962996 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:962993 original size:52 final size:52
Alignment explanation
Indices: 962867--962995 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
962857 TAGTTTACTT
* **
962867 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
962919 TTAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
962972 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
962996 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:963013 original size:19 final size:19
Alignment explanation
Indices: 962991--963125 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
962981 GAAACCAAAA
*
962991 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
963010 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
963026 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
963043 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
963059 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
963076 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
963095 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
963115 TCGTGTTGCGA
1 TCGCGTTGCGA
963126 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:963032 original size:14 final size:14
Alignment explanation
Indices: 963013--963069 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
963003 TTTCATTTCG
963013 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
963027 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
963044 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
963060 CGTTGCGATT
1 CGTTGCGATT
963070 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:963038 original size:33 final size:33
Alignment explanation
Indices: 962996--963088 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
962986 CAAAATCGCA
*
962996 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
963029 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
963062 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
963089 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:965071 original size:14 final size:14
Alignment explanation
Indices: 965052--965087 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
965042 ATTGTTTAAT
965052 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
965066 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
965080 TGATTTGT
1 TGATTTGT
965088 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:965229 original size:20 final size:20
Alignment explanation
Indices: 965194--965243 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
965184 AAAAATGACT
965194 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
965213 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
965233 ATCGCAATGCG
1 ATCGCAATGCG
965244 TTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:965262 original size:19 final size:19
Alignment explanation
Indices: 965234--965424 Score: 144
Period size: 19 Copynumber: 10.8 Consensus size: 19
965224 GAAATGAAAA
*
965234 TCGCAATGCG-TTTATAATT
1 TCGCATTGCGATTT-TAATT
965253 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTAATT
* *
965272 TCGCATTGCGA--TT-CTG
1 TCGCATTGCGATTTTAATT
*
965288 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTAATT
*
965305 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTAATT
* *
965324 TCGCATTGCGA--TT-CTC
1 TCGCATTGCGATTTTAATT
*
965340 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTAATT
*
965357 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTAATT
* *
965376 TCGCATTGCGA--TT-CTC
1 TCGCATTGCGATTTTAATT
*
965392 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTAATT
965409 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
965425 CATGTTGGGA
Statistics
Matches: 142, Mismatches: 13, Indels: 33
0.76 0.07 0.18
Matches are distributed among these distances:
14 18 0.13
16 18 0.13
17 16 0.11
18 2 0.01
19 75 0.53
20 13 0.09
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTAATT
Found at i:965300 original size:33 final size:32
Alignment explanation
Indices: 965258--965455 Score: 177
Period size: 33 Copynumber: 5.8 Consensus size: 32
965248 TAATTTCGCA
*
965258 TTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCT-TCG
*
965291 TTGCGATTTTCATTTCGCATTGCGATT-TTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTCG
* * * *
965322 TTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGA--TTC--TTCG
965360 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCT-TCG
965395 TTGCGATTTTCATTTCCGCATTGCGATT-TTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTTC--G
* *
965429 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
965456 GTATTTTCCG
Statistics
Matches: 137, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
31 9 0.07
32 7 0.05
33 62 0.45
34 28 0.20
35 5 0.04
36 3 0.02
38 12 0.09
39 4 0.03
40 7 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTCG
Found at i:965328 original size:52 final size:52
Alignment explanation
Indices: 965250--965427 Score: 329
Period size: 52 Copynumber: 3.4 Consensus size: 52
965240 TGCGTTTATA
* *
965250 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
965302 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
965354 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
965406 ATTTCCGCATTGCGATTTTCAT
1 ATTT-CGCATTGCGATTTTCAT
965428 GTTGGGATTT
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 106 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:967756 original size:12 final size:12
Alignment explanation
Indices: 967739--967763 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
967729 TCTTCGGGGA
967739 CTTTTTCTTCTT
1 CTTTTTCTTCTT
967751 CTTTTTCTTCTT
1 CTTTTTCTTCTT
967763 C
1 C
967764 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:968695 original size:20 final size:20
Alignment explanation
Indices: 968667--969035 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
968657 AAATTTCAGT
* * * *
968667 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
968687 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
968707 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
968727 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
968747 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
968767 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
968787 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
968807 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
968827 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
968847 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
968867 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
968887 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
968907 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
968927 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
968947 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
968967 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
968987 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
969007 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
969027 GTTGCGATT
1 GTTGCGATT
969036 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:971911 original size:54 final size:54
Alignment explanation
Indices: 971825--972233 Score: 595
Period size: 54 Copynumber: 7.6 Consensus size: 54
971815 TGCATTTTTT
* *
971825 GTATCGGA-ACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACAACC
1 GTATC-GACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
*
971879 GTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
971933 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
* *
971987 GTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGATC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
* * *
972041 GTATCGACACTAAGTGTGCAACCCATGGAATTCATAATAAGCTTATGAACAACC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
* * *
972095 GTATCTACAGTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
** * * * * *
972149 GTATCGACACTAAGTGTGCAACCCATAGAATTCTTAATGAGCTTATAAATGACC
1 GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
** * * *
972203 GTATCGGTACTACGTGTACACCCCACGGAAT
1 GTATCGACACTAAGTGTGCAACCCACGGAAT
972234 ACTTATAATG
Statistics
Matches: 324, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 323 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (54 bp):
GTATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACC
Found at i:971919 original size:27 final size:27
Alignment explanation
Indices: 971889--971974 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
971879 GTATCGGCAC
971889 TAAGTGTGCAACCCACGGAATTCATAA
1 TAAGTGTGCAACCCACGGAATTCATAA
* * * * * *
971916 TAAGTTTATG-AA-CGACCGTA-TCGACAC
1 TAAG--TGTGCAACCCACGGAATTC-ATAA
971943 TAAGTGTGCAACCCACGGAATTCATAA
1 TAAGTGTGCAACCCACGGAATTCATAA
971970 TAAGT
1 TAAGT
971975 TTATGAACGA
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 3 0.07
26 4 0.10
27 27 0.66
28 4 0.10
29 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
TAAGTGTGCAACCCACGGAATTCATAA
Found at i:973293 original size:2 final size:2
Alignment explanation
Indices: 973286--973312 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
973276 CTTGTTTCCT
973286 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
973313 CAAGTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:973890 original size:17 final size:17
Alignment explanation
Indices: 973851--973892 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
973841 TTGAACACTT
*
973851 ATATTACATTACATTAG
1 ATATTACATTACATTAC
* *
973868 ACATTATATTACATTAC
1 ATATTACATTACATTAC
973885 ATATTACA
1 ATATTACA
973893 AACATTTAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATTACATTACATTAC
Found at i:977304 original size:96 final size:96
Alignment explanation
Indices: 977130--977307 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
977120 CATGAGGAAG
* * * *
977130 GTATCGATACCATTGATTTACAGAATACATAAATGGTATCGATACCATAATAGAGTATCGGTACC
1 GTATCGATACCATTAATTTACAGAATACAGAAATGGTATCGATACCATAAGAGAGTATCGATACC
977195 ATAATACAAAAGTATCGGTACTGAGAGAAAA
66 ATAATACAAAAGTATCGGTACTGAGAGAAAA
* * * *
977226 GTATCGATACCATTAATTTACAGAATGCCGAAATGGTATCGATACTGA-AAGGGAGTATCGATAC
1 GTATCGATACCATTAATTTACAGAATACAGAAATGGTATCGATAC-CATAAGAGAGTATCGATAC
* * *
977290 CATAGTATAGAAGTATCG
65 CATAATACAAAAGTATCG
977308 ATACCATGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
96 69 0.99
97 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (96 bp):
GTATCGATACCATTAATTTACAGAATACAGAAATGGTATCGATACCATAAGAGAGTATCGATACC
ATAATACAAAAGTATCGGTACTGAGAGAAAA
Found at i:977738 original size:45 final size:45
Alignment explanation
Indices: 977678--978091 Score: 621
Period size: 45 Copynumber: 9.2 Consensus size: 45
977668 TTGATGCACC
* * * *
977678 TAAATAAAATACATAATGGTGCATTAAAGGCATTAAAGGATGCCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
*
977723 TAAATGAAATGCATAATGGTGCATTAAAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* * *
977768 TAAATAAAATGCATAACGGTACATTAAAGGCATGAAAGGATACCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* *
977813 TAAATGAAATGTATAACGGTGCATTAAAGGCATGAAAGGATGCCC
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* * * * *
977858 TAAATAAAATGCATAATGGTGCATTAAATGCACGAAAGGATGTCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* * *
977903 TCAATGAAATGCATAACGGTGCATTAAAGGCATAAAAAGATGCCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* * *
977948 TAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATACTA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
977993 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
* *
978038 TAAATGAAATGCATAATGGTGCATTACAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
978083 TAAATGAAA
1 TAAATGAAA
978092 ATAATAAATA
Statistics
Matches: 331, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 331 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCA
Found at i:980379 original size:23 final size:21
Alignment explanation
Indices: 980335--980380 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
980325 TAGTTAATTC
*
980335 AAATTAAAAAAATATTATTTT
1 AAATTAAAAAAATAATATTTT
*
980356 AAATGTAAAAAATTAATATATTT
1 AAAT-TAAAAAAATAATAT-TTT
980379 AA
1 AA
980381 TAGAATTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTAAAAAAATAATATTTT
Found at i:980718 original size:37 final size:37
Alignment explanation
Indices: 980668--980741 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
980658 ACCCAACCCA
980668 AAATTTACTCCTTTCATATTGGAAAAGAAAGCCACAT
1 AAATTTACTCCTTTCATATTGGAAAAGAAAGCCACAT
980705 AAATTTACTCCTTTCATATTGGAAAAGAAAGCCACAT
1 AAATTTACTCCTTTCATATTGGAAAAGAAAGCCACAT
980742 TAGAAAACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (37 bp):
AAATTTACTCCTTTCATATTGGAAAAGAAAGCCACAT
Found at i:981635 original size:35 final size:35
Alignment explanation
Indices: 981588--981673 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
981578 AAAACATTCA
* * *
981588 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
981623 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
981658 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
981674 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:981667 original size:21 final size:21
Alignment explanation
Indices: 981642--981684 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
981632 TTCTAAACCC
981642 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
981663 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
981684 T
1 T
981685 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:981839 original size:16 final size:18
Alignment explanation
Indices: 981807--981840 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
981797 TATTAATGTA
981807 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
981825 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
981841 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:982514 original size:130 final size:130
Alignment explanation
Indices: 982324--982558 Score: 425
Period size: 130 Copynumber: 1.8 Consensus size: 130
982314 TTAAGAGGTG
* *
982324 ACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGATCCTGATTAAATGA
1 ACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAATGA
982389 TTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGGTA
66 TTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGGTA
* * *
982454 ACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGATCCTAATTAAATGA
1 ACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAATGA
982519 TTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 TTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
982559 TATATAAATA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 100 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (130 bp):
ACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTAATTAAATGA
TTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAATTAGGTGGTA
Found at i:988619 original size:126 final size:126
Alignment explanation
Indices: 988427--988671 Score: 436
Period size: 126 Copynumber: 1.9 Consensus size: 126
988417 ACCATCTACA
*
988427 CCGGCCCCTTCATGTCCGGTCGTTGCTAGACTGCTTTCTTCAGTGGGAACAGCATTATCTGTTTC
1 CCGGCCCCTTCATGTCCGGTCGTTGCTAGACTGCTTTCTTCAGTGGGAACAGCATTATCCGTTTC
* * *
988492 CTGCTTTTTATCTTCTGTTTCTGGTGCAGCCGGTGCGGATTCCAGTTCAGCAGTGTTGGTG
66 CTGCTTTTTATCTTCTGTTTCTGGTGCAACCGGAGCGGATTCCAGTTCAACAGTGTTGGTG
988553 CCGGCCCCTTCATGTCCGGTCGTTGCTAGACTGCTTTCTTCAGTGGGAACAGCATTATCCGTTTC
1 CCGGCCCCTTCATGTCCGGTCGTTGCTAGACTGCTTTCTTCAGTGGGAACAGCATTATCCGTTTC
* *
988618 CTGCTTTTTATCTTCTGTTTCTGGTGCAACCGGAGTGGATTCCGGTTCAACAGT
66 CTGCTTTTTATCTTCTGTTTCTGGTGCAACCGGAGCGGATTCCAGTTCAACAGT
988672 ATCGGTGCTT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.36
Consensus pattern (126 bp):
CCGGCCCCTTCATGTCCGGTCGTTGCTAGACTGCTTTCTTCAGTGGGAACAGCATTATCCGTTTC
CTGCTTTTTATCTTCTGTTTCTGGTGCAACCGGAGCGGATTCCAGTTCAACAGTGTTGGTG
Found at i:993191 original size:16 final size:16
Alignment explanation
Indices: 993165--993226 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
993155 ATTTGGGTAA
*
993165 GGTTATATTCGGTTCG
1 GGTTATTTTCGGTTCG
* *
993181 GGTTTTTTTCGGATCG
1 GGTTATTTTCGGTTCG
*
993197 GGTTGCTTTT-GGTTCG
1 GGTT-ATTTTCGGTTCG
*
993213 GGTTAATTTCGGTT
1 GGTTATTTTCGGTT
993227 TCGGTTCGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 3 0.08
16 30 0.81
17 4 0.11
ACGTcount: A:0.08, C:0.11, G:0.32, T:0.48
Consensus pattern (16 bp):
GGTTATTTTCGGTTCG
Found at i:993229 original size:38 final size:38
Alignment explanation
Indices: 993187--993267 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
993177 TTCGGGTTTT
** * * *
993187 TTTCGGATCGGGTTGCTTTTGGTTCGGGTTAATTTCGG
1 TTTCGGATCGGGTTAATTTAGGTTCAGGTTAATTTCGA
* *
993225 TTTCGGTTCGGGTTAATTTAGGTTCAGGTTGATTTCGA
1 TTTCGGATCGGGTTAATTTAGGTTCAGGTTAATTTCGA
993263 TTTCG
1 TTTCG
993268 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.11, C:0.12, G:0.31, T:0.46
Consensus pattern (38 bp):
TTTCGGATCGGGTTAATTTAGGTTCAGGTTAATTTCGA
Found at i:993254 original size:22 final size:22
Alignment explanation
Indices: 993207--993248 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
993197 GGTTGCTTTT
*
993207 GGTTCGGGTTAATTTCGGTTTC
1 GGTTCGGGTTAATTTAGGTTTC
993229 GGTTCGGGTTAATTTAGGTT
1 GGTTCGGGTTAATTTAGGTT
993249 CAGGTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.10, G:0.33, T:0.45
Consensus pattern (22 bp):
GGTTCGGGTTAATTTAGGTTTC
Found at i:997682 original size:27 final size:27
Alignment explanation
Indices: 997652--997711 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
997642 AGTTGTGTGG
997652 GGGAAAGTTCTGATGGTTGAAGAACTT
1 GGGAAAGTTCTGATGGTTGAAGAACTT
997679 GGGAAAGTTCTGATGGTTGAAGAACTT
1 GGGAAAGTTCTGATGGTTGAAGAACTT
*
997706 GAGAAA
1 GGGAAA
997712 CTACAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (27 bp):
GGGAAAGTTCTGATGGTTGAAGAACTT
Found at i:1000968 original size:21 final size:21
Alignment explanation
Indices: 1000944--1000987 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1000934 ATTTATTATA
* *
1000944 ATGGATTTAAAGTTGGTTTTT
1 ATGGAATTAAAGTTGGTTGTT
*
1000965 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
1000986 AT
1 AT
1000988 AGATGTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:1001611 original size:12 final size:12
Alignment explanation
Indices: 1001594--1001643 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1001584 TGATTCTACT
1001594 ATATAAAATATA
1 ATATAAAATATA
1001606 ATATAAAA-ATA
1 ATATAAAATATA
1001617 AT-TAAAATGA-A
1 ATATAAAAT-ATA
* *
1001628 ATATATAATAAA
1 ATATAAAATATA
1001640 ATAT
1 ATAT
1001644 GAATAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 5 0.15
11 9 0.27
12 19 0.58
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:1004798 original size:17 final size:17
Alignment explanation
Indices: 1004776--1004808 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1004766 ATTTTACCTT
1004776 TACCAT-ATCCATTTCTA
1 TACCATAAT-CATTTCTA
1004793 TACCATAATCATTTCT
1 TACCATAATCATTTCT
1004809 TTTAGCCGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TACCATAATCATTTCTA
Found at i:1008903 original size:2 final size:2
Alignment explanation
Indices: 1008892--1008958 Score: 51
Period size: 2 Copynumber: 37.0 Consensus size: 2
1008882 GAATATTAAC
1008892 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TCA T- TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* *
1008930 TT TA -A AA TA -A TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1008959 ATTTTAATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
1 8 0.15
2 44 0.81
3 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1010955 original size:2 final size:2
Alignment explanation
Indices: 1010950--1010990 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1010940 TGTGTGTATG
1010950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1010991 TTAATTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1012872 original size:2 final size:2
Alignment explanation
Indices: 1012865--1012911 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1012855 TCGTAAATTA
1012865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1012907 AT AT A
1 AT AT A
1012912 CCCACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1016682 original size:55 final size:53
Alignment explanation
Indices: 1016599--1016738 Score: 142
Period size: 52 Copynumber: 2.6 Consensus size: 53
1016589 TTGATAGAGG
* * * **
1016599 TATCGATACC-TGAAGGATGGTATTGATACCCTTAAAAACATCGAATGTAATTTTGA
1 TATCGGTACCTTG-AGGA-GGTATCGATACCCTT-AAAACATAGAACATAA-TTTGA
* *
1016655 TATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATAGAACATAATTTGG
1 TATCGGTACCTTGAGGAGGTATCGATACCCTTAAAACATAGAACATAATTTGA
*
1016708 TATCGGTACATGTGA--AGGTATCGATACCCTT
1 TATCGGTACCT-TGAGGAGGTATCGATACCCTT
1016739 GAAAGGGGTG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
52 16 0.22
53 14 0.19
54 15 0.20
55 14 0.19
56 13 0.18
57 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (53 bp):
TATCGGTACCTTGAGGAGGTATCGATACCCTTAAAACATAGAACATAATTTGA
Found at i:1016734 original size:52 final size:53
Alignment explanation
Indices: 1016617--1016742 Score: 148
Period size: 52 Copynumber: 2.4 Consensus size: 53
1016607 CCTGAAGGAT
* * * ** *
1016617 GGTATTGATACCCTTAAAAACATCGAATGTAATTTTGATATCGGTACCTTGAGGA
1 GGTATCGATACCCTT-GAAACATAGAACATAATTTTGATATCGGTACATTGA-GA
*
1016672 GGTATCGATACCCTTGAAACATAGAACATAA-TTTGGTATCGGTACATGTGA-A
1 GGTATCGATACCCTTGAAACATAGAACATAATTTTGATATCGGTACAT-TGAGA
1016724 GGTATCGATACCCTTGAAA
1 GGTATCGATACCCTTGAAA
1016743 GGGGTGGTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
52 20 0.32
53 14 0.22
54 15 0.24
55 14 0.22
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (53 bp):
GGTATCGATACCCTTGAAACATAGAACATAATTTTGATATCGGTACATTGAGA
Found at i:1017315 original size:21 final size:22
Alignment explanation
Indices: 1017289--1017343 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
1017279 ATCGAGGGTC
* *
1017289 TATGTGGCCCTTC-AGGATAAT
1 TATGTGGCACTTCTAGGACAAT
* *
1017310 TATGTGG-TCTTCTGGGACAAT
1 TATGTGGCACTTCTAGGACAAT
1017331 TATGTGGCACTTC
1 TATGTGGCACTTC
1017344 GGTGCAACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (22 bp):
TATGTGGCACTTCTAGGACAAT
Found at i:1017358 original size:23 final size:22
Alignment explanation
Indices: 1017331--1017386 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1017321 CTGGGACAAT
* *
1017331 TATGTGG-CACTTCGGTGCAACCC
1 TATGTGGTC-CTTCGGTACAA-AC
1017354 TATGTGGTCCTTCGGTACAAAC
1 TATGTGGTCCTTCGGTACAAAC
1017376 TATGTGGTCCT
1 TATGTGGTCCT
1017387 CCGGGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 12 0.40
23 17 0.57
24 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (22 bp):
TATGTGGTCCTTCGGTACAAAC
Found at i:1017381 original size:22 final size:22
Alignment explanation
Indices: 1017310--1017386 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
1017300 TCAGGATAAT
* *
1017310 TATGTGGT-CTTCTGGGAC-AAT
1 TATGTGGTCCTTC-GGTACAAAC
* *
1017331 TATGTGG-CACTTCGGTGCAACCC
1 TATGTGGTC-CTTCGGTACAA-AC
1017354 TATGTGGTCCTTCGGTACAAAC
1 TATGTGGTCCTTCGGTACAAAC
1017376 TATGTGGTCCT
1 TATGTGGTCCT
1017387 CCGGGATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 10 0.22
22 17 0.38
23 17 0.38
24 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (22 bp):
TATGTGGTCCTTCGGTACAAAC
Found at i:1019451 original size:76 final size:79
Alignment explanation
Indices: 1019299--1019456 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 79
1019289 CTGAATATAG
* *
1019299 TAAATAAACATTGAAATAATGTAATTCTGATTACAACTCTTTTAATGGATATTTAATTCAGAATA
1 TAAATAAACATTGAAAGAATGTAATTCTGATTACAACTCTTTTAATGAATATTTAATTCAGAATA
1019364 ATTAAATAAGAATT
66 ATTAAATAAGAATT
* * * * *
1019378 TAAATAAACGTT-AAAGAGTGTAATT-TGAATTATAAGTC-TTTAATGAATATTT-ATT-TGAAT
1 TAAATAAACATTGAAAGAATGTAATTCTG-ATTACAACTCTTTTAATGAATATTTAATTCAGAA-
1019438 TAATTAAATAAGAATT
64 TAATTAAATAAGAATT
1019454 TAA
1 TAA
1019457 TTAATTCGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
75 3 0.04
76 22 0.31
77 15 0.21
78 19 0.27
79 11 0.16
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (79 bp):
TAAATAAACATTGAAAGAATGTAATTCTGATTACAACTCTTTTAATGAATATTTAATTCAGAATA
ATTAAATAAGAATT
Found at i:1020458 original size:186 final size:186
Alignment explanation
Indices: 1020144--1020519 Score: 716
Period size: 186 Copynumber: 2.0 Consensus size: 186
1020134 TACATCCCCT
*
1020144 TCTTGTAACAGAGGGCAATTATTAAGTTTGGAAAGATTAAGGGGCTTGACTTCCTCTTGAGGCAT
1 TCTTGTAACAGAGGGCAATTATTAAGTTTGGAAAGATTAAGAGGCTTGACTTCCTCTTGAGGCAT
1020209 GCACATACCTCATCGATAATGATATTTCCAATATCGATTGGGCGTCCCACAATAATAGAATGAAA
66 GCACATACCTCATCGATAATGATATTTCCAATATCGATTGGGCGTCCCACAATAATAGAATGAAA
*
1020274 CAACATCATCTACTACAAGAAAACGATTGTATGATGTGATGTGGGCATCAACCTTA
131 CAACATCACCTACTACAAGAAAACGATTGTATGATGTGATGTGGGCATCAACCTTA
1020330 TCTTGTAACAGAGGGCAATTATTAAGTTTGGAAAGATTAAGAGGCTTGACTTCCTCTTGAGGCAT
1 TCTTGTAACAGAGGGCAATTATTAAGTTTGGAAAGATTAAGAGGCTTGACTTCCTCTTGAGGCAT
*
1020395 GCACATACCTCATCGATAATGATATTTCCAATGTCGATTGGGCGTCCCACAATAATAGAATGAAA
66 GCACATACCTCATCGATAATGATATTTCCAATATCGATTGGGCGTCCCACAATAATAGAATGAAA
*
1020460 CAACATCACCTACTACAAGAAAACGATTGTATGATGTGATGTGGGCATCAACCTTG
131 CAACATCACCTACTACAAGAAAACGATTGTATGATGTGATGTGGGCATCAACCTTA
1020516 TCTT
1 TCTT
1020520 AAGGAAGTGA
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 186 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (186 bp):
TCTTGTAACAGAGGGCAATTATTAAGTTTGGAAAGATTAAGAGGCTTGACTTCCTCTTGAGGCAT
GCACATACCTCATCGATAATGATATTTCCAATATCGATTGGGCGTCCCACAATAATAGAATGAAA
CAACATCACCTACTACAAGAAAACGATTGTATGATGTGATGTGGGCATCAACCTTA
Found at i:1021467 original size:50 final size:51
Alignment explanation
Indices: 1021312--1021555 Score: 302
Period size: 50 Copynumber: 4.8 Consensus size: 51
1021302 TTCATACTAC
* *
1021312 AAAAAAAT-TAGCACTTAACACATACTTACATC-AGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGA-TGTAAGTAAATAAAAT
* * * *
1021362 AAACAAA-TATAGCACTTAATACATACTTACACC-AGTGTAAGTGAATAAAAC
1 AAA-AAAGTGTAGCACTTAACACATACTTACACCGA-TGTAAGTAAATAAAAT
*
1021413 AAAAAAGTGTAGCACTTAACACATAC-TACACCGATGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAAT
* * * *
1021463 AAAAAAGTGTAACACTTAACACATACTTACAACGGTGTAAATAAAT-AAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAAT
* *
1021513 AAAAAAGTGTAGCACATAATACATACTTACACCGATGTAAGTA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTA
1021556 TGTACATCTC
Statistics
Matches: 171, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
50 94 0.55
51 77 0.45
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (51 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAAT
Found at i:1021487 original size:101 final size:101
Alignment explanation
Indices: 1021310--1021555 Score: 320
Period size: 101 Copynumber: 2.4 Consensus size: 101
1021300 AATTCATACT
* *
1021310 ACAAAAAAAT-TAGCACTTAACACATACTTACATC-AGTGTAAGTAAATAAAATAAACAAATATA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGA-TGTAAGTAAATAAAATAAACAAATATA
* * * * *
1021373 GCACTTAATACATACTTACACCAGTGTAAGTGAATAAA
65 ACACTTAACACATACTTACAACAGTGTAAATAAAT-AA
* *
1021411 ACAAAAAAGTGTAGCACTTAACACATAC-TACACCGATGTAAGTGAATAAAATAAA-AAAGTGTA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAATAAACAAA-TATA
*
1021474 ACACTTAACACATACTTACAACGGTGTAAATAAATAA
65 ACACTTAACACATACTTACAACAGTGTAAATAAATAA
* * *
1021511 ATAAAAAAGTGTAGCACATAATACATACTTACACCGATGTAAGTA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTA
1021556 TGTACATCTC
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 30 0.24
101 79 0.62
102 18 0.14
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (101 bp):
ACAAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTAAATAAAATAAACAAATATAA
CACTTAACACATACTTACAACAGTGTAAATAAATAA
Found at i:1021657 original size:16 final size:16
Alignment explanation
Indices: 1021636--1021666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1021626 TTTTTAAAGA
*
1021636 AATAAAAATTAAAAAT
1 AATAAAAAATAAAAAT
1021652 AATAAAAAATAAAAA
1 AATAAAAAATAAAAA
1021667 ATATATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAAAAAATAAAAAT
Found at i:1027338 original size:17 final size:17
Alignment explanation
Indices: 1027316--1027350 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1027306 CCAGAGCTAA
*
1027316 TGGATAAAGCACAAATT
1 TGGATAAAGCAAAAATT
1027333 TGGATAAAGCAAAAATT
1 TGGATAAAGCAAAAATT
1027350 T
1 T
1027351 TCGAGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (17 bp):
TGGATAAAGCAAAAATT
Found at i:1030179 original size:12 final size:12
Alignment explanation
Indices: 1030162--1030206 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1030152 AGAATTGGAA
*
1030162 GACATTCTAACT
1 GACATTCTGACT
1030174 GACATTCTGACT
1 GACATTCTGACT
* *
1030186 GATATTCTGATT
1 GACATTCTGACT
1030198 GACATTCTG
1 GACATTCTG
1030207 GCATCTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (12 bp):
GACATTCTGACT
Found at i:1030327 original size:17 final size:16
Alignment explanation
Indices: 1030305--1030357 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
1030295 AATTAAGAGT
1030305 TAGTTTAAGAAATGAAC
1 TAGTTTAAG-AATGAAC
*
1030322 TAGTTTGATGAATGAAC
1 TAGTTT-AAGAATGAAC
*
1030339 TAGTTTAATTAATGAAC
1 TAGTTTAA-GAATGAAC
1030356 TA
1 TA
1030358 ACTTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 28 0.90
18 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (16 bp):
TAGTTTAAGAATGAAC
Found at i:1030366 original size:17 final size:17
Alignment explanation
Indices: 1030315--1030367 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1030305 TAGTTTAAGA
* * *
1030315 AATGAACTAGTTTGATG
1 AATGAACTACTTTAATT
*
1030332 AATGAACTAGTTTAATT
1 AATGAACTACTTTAATT
1030349 AATGAACTAACTTT-ATT
1 AATGAACT-ACTTTAATT
1030366 AA
1 AA
1030368 ATAAACTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 28 0.88
18 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (17 bp):
AATGAACTACTTTAATT
Found at i:1032731 original size:41 final size:41
Alignment explanation
Indices: 1032673--1032789 Score: 144
Period size: 41 Copynumber: 2.9 Consensus size: 41
1032663 AAATAGTTTT
* *
1032673 ATCGTAGTTAAACGGTGTCAGGTCAACAGTTAATCCATCAG
1 ATCGTAGTTAAATGGTGTCAGGTCAACAGTTAATCCATCAC
* * * * *
1032714 ATCGTAATTAAATGGTGTTAGGTTAACAGTTAACCCGTCAC
1 ATCGTAGTTAAATGGTGTCAGGTCAACAGTTAATCCATCAC
* * *
1032755 ATTGTAGTTAAATGGTATCAAGTCAACAGTTAATC
1 ATCGTAGTTAAATGGTGTCAGGTCAACAGTTAATC
1032790 TGCCATATCA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (41 bp):
ATCGTAGTTAAATGGTGTCAGGTCAACAGTTAATCCATCAC
Found at i:1035822 original size:3 final size:3
Alignment explanation
Indices: 1035810--1035857 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1035800 GCAATAATTG
**
1035810 TAA T-A TAA TAA TAA TAA TAA TAA TTT TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1035856 TA
1 TA
1035858 TATAGTCTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1035839 original size:26 final size:26
Alignment explanation
Indices: 1035802--1035857 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
1035792 TATTATTTGC
1035802 AATAATTGTAATATAATAATAATAAT
1 AATAATTGTAATATAATAATAATAAT
*
1035828 AATAATTTTAATATAATAATAATAAT
1 AATAATTGTAATATAATAATAATAAT
1035854 AATA
1 AATA
1035858 TATAGTCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAATTGTAATATAATAATAATAAT
Found at i:1036069 original size:21 final size:20
Alignment explanation
Indices: 1036028--1036074 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1036018 ATGACCCAGA
*
1036028 GGTTTTACAATTTACCCGGG
1 GGTTTTACAAATTACCCGGG
1036048 GGTTTTACAAATTACCCGGG
1 GGTTTTACAAATTACCCGGG
1036068 GGTTTTA
1 GGTTTTA
1036075 ATTTTCTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GGTTTTACAAATTACCCGGG
Found at i:1036165 original size:20 final size:20
Alignment explanation
Indices: 1036140--1036193 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1036130 AAAACATCCT
*
1036140 ACCCTGAGGTTTTACAGATG
1 ACCCTGAGGTTTTACAAATG
* *
1036160 ACCCTGTGGTTTTACAAATT
1 ACCCTGAGGTTTTACAAATG
*
1036180 ACCCAGAGGTTTTA
1 ACCCTGAGGTTTTA
1036194 ATTTTATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
ACCCTGAGGTTTTACAAATG
Found at i:1036406 original size:119 final size:119
Alignment explanation
Indices: 1036021--1036772 Score: 1161
Period size: 119 Copynumber: 6.3 Consensus size: 119
1036011 TTTATAGATG
* * * * *
1036021 ACCCAGAGGTTTTACA-ATTTACCCGGGGGTTTTACAAATTACCCGGGGGTTTTAATTTTCTAGA
1 ACCCTGAGGTTTTACAGA-TGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGA
* * * *
1036085 ACATTAAATGAGAAACTTTATTTATTACTTTCCCATTTTCGTGCGAAAACATCCT
65 ACATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
* * * * *
1036140 ACCCTGAGGTTTTACAGATGACCCTGTGGTTTTACAAATTACCCAGAGGTTTTAATTTTATAGAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
* * *
1036205 CATTAAATGAGAAACTTTGGTTATTA--CTCTTATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
* * * * *
1036257 ACCCTGAGGTTTTACAGATGACTCGAAGGATTTATAAATTACTCGGAGATTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
* *
1036322 TATTAAATGAGAAACTTTGTTTATTATTTTCACATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
* * *
1036376 ACCTTGAGGTTTTACAGATGACCCGGAGGATTTATAAATTACCTGGAGGTTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
1036441 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
*
1036495 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCAGAGGTTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
* *
1036560 CTTTAAATGAGAAACTTTGATTATTATTTTCTCATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
* *
1036614 ACCCTAAGGTTTTACAGATGACCCGGAGGATTTATAAATTACCCGGAGGTTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
*
1036679 CTTTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
1036733 A-CCTGGAGGTTTTACAGATGACCCGGAGGATTTACAAATT
1 ACCCT-GAGGTTTTACAGATGACCCGGAGGATTTACAAATT
1036773 TGTGGGAAAT
Statistics
Matches: 581, Mismatches: 48, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
117 101 0.17
118 3 0.01
119 476 0.82
120 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (119 bp):
ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
CATTAAATGAGAAACTTTGTTTATTATTTTCTCATTTTCATGCGAAAACATCCT
Found at i:1036523 original size:20 final size:20
Alignment explanation
Indices: 1036495--1036548 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1036485 AAAACATCCT
* *
1036495 ACCCTGAGGTTTTACAGATG
1 ACCCAGAGGTTTTACAAATG
* * *
1036515 ACCCGGAGGATTTACAAATT
1 ACCCAGAGGTTTTACAAATG
1036535 ACCCAGAGGTTTTA
1 ACCCAGAGGTTTTA
1036549 ATTTTCTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (20 bp):
ACCCAGAGGTTTTACAAATG
Found at i:1036647 original size:20 final size:20
Alignment explanation
Indices: 1036624--1036667 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1036614 ACCCTAAGGT
*
1036624 TTTACAGATGACCCGGAGGA
1 TTTACAAATGACCCGGAGGA
* * *
1036644 TTTATAAATTACCCGGAGGT
1 TTTACAAATGACCCGGAGGA
1036664 TTTA
1 TTTA
1036668 ATTTTCTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
TTTACAAATGACCCGGAGGA
Found at i:1039390 original size:11 final size:11
Alignment explanation
Indices: 1039374--1039416 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
1039364 CTTGATTCAA
*
1039374 TTTTCTTCTTC
1 TTTTCTTTTTC
1039385 TTTTCTTTTTTC
1 TTTTC-TTTTTC
1039397 TTTTCTTTTTC
1 TTTTCTTTTTC
1039408 TTTTCTTTT
1 TTTTCTTTT
1039417 GGATGAGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1039392 original size:5 final size:5
Alignment explanation
Indices: 1039374--1039416 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
1039364 CTTGATTCAA
1039374 TTTTC TTCTTC TTTTC TTTTTTC TTTTC TTTTTC TTTTC TTTT
1 TTTTC TT-TTC TTTTC --TTTTC TTTTC -TTTTC TTTTC TTTT
1039417 GGATGAGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 19 0.56
6 10 0.29
7 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:1046618 original size:2 final size:2
Alignment explanation
Indices: 1046611--1046639 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1046601 TTATAATAAT
1046611 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1046640 GTTATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1046945 original size:35 final size:33
Alignment explanation
Indices: 1046888--1046952 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
1046878 ATAAAAGGTA
*
1046888 AAAATAAAATAAAGTTGTAATTAAATAATAACC
1 AAAATAAAATAAAGTTGTAATTAAAAAATAACC
1046921 AAAATAATAATATAAGTT-TAAATTAAAAAATA
1 AAAATAA-AATA-AAGTTGT-AATTAAAAAATA
1046953 TAAATTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (33 bp):
AAAATAAAATAAAGTTGTAATTAAAAAATAACC
Found at i:1047666 original size:13 final size:13
Alignment explanation
Indices: 1047650--1047675 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1047640 AGTTTGTGTT
1047650 CTTTGTATGAATG
1 CTTTGTATGAATG
1047663 CTTTGTATGAATG
1 CTTTGTATGAATG
1047676 TTTTTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
CTTTGTATGAATG
Found at i:1048106 original size:3 final size:3
Alignment explanation
Indices: 1048100--1048153 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
1048090 GTATTATTTG
**
1048100 TAA TAA TAAA TATA TAA TAA TAA TAA TAA TTG TAA T-A TAA TAA TAA
1 TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1048146 TAA TAA TA
1 TAA TAA TA
1048154 TATAGTCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1060945 original size:3 final size:3
Alignment explanation
Indices: 1060937--1060969 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1060927 TTTAATTGTA
1060937 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1060970 TCTTATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1062077 original size:2 final size:2
Alignment explanation
Indices: 1062070--1062100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1062060 GGTCATTGCC
1062070 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 A
1062101 AGGTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1076515 original size:35 final size:35
Alignment explanation
Indices: 1076462--1076635 Score: 213
Period size: 35 Copynumber: 4.9 Consensus size: 35
1076452 AAGTAATACA
* * * * * *
1076462 AATTTAGCCATCAAAAAAGAGTAGTAAATCAATGT
1 AATTCAGCCTTCACAAAAGAGTAGTGAAGCAATGC
1076497 AATTCAGCCTTCACAAAAGAGTAGTGAAGCAATGC
1 AATTCAGCCTTCACAAAAGAGTAGTGAAGCAATGC
* * *
1076532 ATTTTAGCCTTCACAAAAGAGTAGTGAAGCGATGC
1 AATTCAGCCTTCACAAAAGAGTAGTGAAGCAATGC
* *
1076567 AAATCTAGCCTTCACAAAAGAGTAGTGAAGCGATGC
1 AATTC-AGCCTTCACAAAAGAGTAGTGAAGCAATGC
* *
1076603 AAATCCAGCCTTTACAAAAGAGTAGTGAAGCAA
1 -AATTCAGCCTTCACAAAAGAGTAGTGAAGCAA
1076636 CAGAAGAGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
35 63 0.52
36 55 0.45
37 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (35 bp):
AATTCAGCCTTCACAAAAGAGTAGTGAAGCAATGC
Found at i:1076583 original size:36 final size:36
Alignment explanation
Indices: 1076460--1076635 Score: 221
Period size: 36 Copynumber: 4.9 Consensus size: 36
1076450 TCAAGTAATA
* * * * *
1076460 CAAATTTAGCCATCAAAAAAGAGTAGTAAATCAATG
1 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAATG
* *
1076496 TAATTC-AGCCTTCACAAAAGAGTAGTGAAGCAATG
1 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAATG
* * *
1076531 C-ATTTTAGCCTTCACAAAAGAGTAGTGAAGCGATG
1 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAATG
*
1076566 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCGATG
1 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAATG
* *
1076602 CAAATCCAGCCTTTACAAAAGAGTAGTGAAGCAA
1 CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAA
1076636 CAGAAGAGCA
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
34 3 0.02
35 54 0.44
36 66 0.54
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (36 bp):
CAAATCTAGCCTTCACAAAAGAGTAGTGAAGCAATG
Found at i:1077950 original size:22 final size:20
Alignment explanation
Indices: 1077902--1077950 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
1077892 TAAAAGCATG
*
1077902 TTTTTGTATTTTTTAATTTA
1 TTTTTGCATTTTTTAATTTA
*
1077922 TTCTTTGCATTTTATTTATTTA
1 TT-TTTGCATTTT-TTAATTTA
1077944 TATTTTG
1 T-TTTTG
1077951 GTCAGTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 12 0.50
23 1 0.04
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (20 bp):
TTTTTGCATTTTTTAATTTA
Found at i:1077967 original size:2 final size:2
Alignment explanation
Indices: 1077960--1078011 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1077950 GGTCAGTTCC
1077960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1078002 AT AT AT AT AT
1 AT AT AT AT AT
1078012 CTTAAGGTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1079495 original size:19 final size:19
Alignment explanation
Indices: 1079441--1079495 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1079431 AACCAATAAT
1079441 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
1079460 GATGAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
1079479 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1079496 AAAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1079525 original size:22 final size:21
Alignment explanation
Indices: 1079478--1079527 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1079468 AAATGAAATT
1079478 GAATAAAATAAAATAAATAAA
1 GAATAAAATAAAATAAATAAA
*
1079499 G-ATAAAATATATATACAAT-AA
1 GAATAAAATA-AAATA-AATAAA
1079520 GAATAAAA
1 GAATAAAA
1079528 AAGGTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (21 bp):
GAATAAAATAAAATAAATAAA
Found at i:1079604 original size:21 final size:20
Alignment explanation
Indices: 1079580--1079722 Score: 62
Period size: 22 Copynumber: 6.7 Consensus size: 20
1079570 GCAAAGAAAC
1079580 TAAAAATATAATGAAAATAAA
1 TAAAAATATAAT-AAAATAAA
*
1079601 TAAATAGTATAAATAAAAT-AA
1 TAAA-AATAT-AATAAAATAAA
1079622 TAAAAAATATATATATAAA-AATA
1 T-AAAAATATA-ATA-AAATAA-A
* * *
1079645 TAAAAATGTATGTATAATATAA
1 TAAAAATATA-ATAAAATA-AA
1079667 T-AAAATACTAAATAATAAT-AA
1 TAAAAATA-T-AATAA-AATAAA
1079688 TAATAAATA-AATGAAAAATAAA
1 TAA-AAATATAAT--AAAATAAA
* *
1079710 TATACATATAATA
1 TAAAAATATAATA
1079723 TTAACTAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 37
0.67 0.07 0.26
Matches are distributed among these distances:
20 5 0.05
21 31 0.33
22 43 0.46
23 15 0.16
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAATATAATAAAATAAA
Found at i:1079615 original size:28 final size:27
Alignment explanation
Indices: 1079598--1079713 Score: 68
Period size: 24 Copynumber: 4.4 Consensus size: 27
1079588 TAATGAAAAT
1079598 AAATAAATAGTATAAATAAAATAATAAA
1 AAATAAATA-TATAAATAAAATAATAAA
*
1079626 AAAT--ATATATATA-AAAAT-ATAAA
1 AAATAAATATATAAATAAAATAATAAA
* ** *
1079649 AATGTATGTATAATATAATAAAATACTAAA
1 AA-ATAAATAT-ATA-AATAAAATAATAAA
* *
1079679 TAAT-AATA-AT-AAT-AAATAAATGAA
1 AAATAAATATATAAATAAAAT-AATAAA
1079703 AAATAAATATA
1 AAATAAATATA
1079714 CATATAATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 22
0.66 0.12 0.22
Matches are distributed among these distances:
23 11 0.17
24 16 0.24
25 9 0.14
26 9 0.14
27 3 0.05
28 7 0.11
29 6 0.09
30 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
AAATAAATATATAAATAAAATAATAAA
Found at i:1079642 original size:24 final size:23
Alignment explanation
Indices: 1079595--1079699 Score: 81
Period size: 24 Copynumber: 4.4 Consensus size: 23
1079585 ATATAATGAA
*
1079595 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATATAAAAT
1079620 AATAAAAAATATATATAT-AAA-
1 AATAAAAAATATATATATAAAAT
* * *
1079641 AATATAAAAATGTATGTATAATAT
1 AATA-AAAAATATATATATAAAAT
* *
1079665 AATAAAATACTAAATA-ATAATAAT
1 AATAAAA-AATATATATATAA-AAT
1079689 AATAAATAAAT
1 AATAAA-AAAT
1079700 GAAAAATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.06
22 15 0.23
23 15 0.23
24 23 0.36
25 7 0.11
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAAAAAATATATATATAAAAT
Found at i:1079660 original size:22 final size:21
Alignment explanation
Indices: 1079581--1079671 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
1079571 CAAAGAAACT
*
1079581 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
1079600 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
1079625 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* *
1079647 AAAATGTATGTATAATATAATAA
1 AAAATATATATATAA-A-AATAA
1079670 AA
1 AA
1079672 TACTAAATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 5 0.08
22 21 0.36
23 12 0.20
24 11 0.19
25 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:1079694 original size:16 final size:15
Alignment explanation
Indices: 1079587--1079711 Score: 57
Period size: 15 Copynumber: 8.2 Consensus size: 15
1079577 AACTAAAAAT
1079587 ATAATGAAAATAAATAA
1 ATAAT-AAAAT-AATAA
*
1079604 ATAGTATAAAT-A-AA
1 ATAATA-AAATAATAA
*
1079618 ATAATAAAA-AATAT
1 ATAATAAAATAATAA
1079632 ATATATAAAA-ATATAA
1 ATA-ATAAAATA-ATAA
** *
1079648 A-AAT-GTATGTATAA
1 ATAATAAAAT-AATAA
*
1079662 TATAATAAAATACTAA
1 -ATAATAAAATAATAA
1079678 ATAATAATAATAATAA
1 ATAATAA-AATAATAA
*
1079694 ATAAATGAAA-AATAA
1 AT-AATAAAATAATAA
1079709 ATA
1 ATA
1079712 TACATATAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
13 5 0.06
14 18 0.22
15 24 0.29
16 22 0.27
17 14 0.17
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAAAATAATAA
Found at i:1079882 original size:21 final size:21
Alignment explanation
Indices: 1079841--1079889 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1079831 AGATAAAAAA
* *
1079841 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
1079862 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
1079886 ATAA
1 ATAA
1079890 CGCAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 4 0.17
24 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:1079928 original size:27 final size:29
Alignment explanation
Indices: 1079898--1079955 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
1079888 AACGCAAAGA
1079898 AAAATGAAAA-TAAATAAATA-A-ATAAAT
1 AAAAT-AAAATTAAATAAATACATATAAAT
*
1079925 AAAATAAAATTAAATATATACATATAAAT
1 AAAATAAAATTAAATAAATACATATAAAT
1079954 AA
1 AA
1079956 TAAGGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 14 0.52
28 1 0.04
29 8 0.30
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAATAAAATTAAATAAATACATATAAAT
Found at i:1080442 original size:37 final size:37
Alignment explanation
Indices: 1080349--1080450 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
1080339 ATGCTTGTGG
* * ** * *
1080349 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
1080386 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
1080423 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1080451 TAGGATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:1081386 original size:106 final size:106
Alignment explanation
Indices: 1081203--1082054 Score: 1310
Period size: 106 Copynumber: 8.0 Consensus size: 106
1081193 GCATTGTTTC
* * * * * * * *
1081203 GAGTCAAATATCCTCCGTCGTAAAGTTGAAATTGGCTCTGGAATCGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1081268 CCAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* ** *
1081309 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1081374 CCAGCGGTCCCTTCATCGTTAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* *
1081415 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1081480 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* *
1081521 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1081586 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* *
1081627 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1081692 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* *
1081733 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* **
1081798 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAAGTTGTCTG
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* * *
1081839 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1081904 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTATG
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
* *
1081945 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1082010 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
1082051 GAGT
1 GAGT
1082055 GGTACGATAT
Statistics
Matches: 687, Mismatches: 58, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 1 0.00
106 686 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
Found at i:1083045 original size:22 final size:22
Alignment explanation
Indices: 1083017--1083071 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1083007 TTGTGTTTGG
1083017 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1083039 TTAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1083061 TCAAAGGTTTG
1 TCAAAGGTTTG
1083072 ATGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1083696 original size:16 final size:15
Alignment explanation
Indices: 1083674--1083742 Score: 66
Period size: 17 Copynumber: 4.3 Consensus size: 15
1083664 TTTTTGTCCC
*
1083674 TTTTTCTTTTTTATT
1 TTTTTCTTTTTTCTT
*
1083689 TTTGTTCTTTTTTTTTGT
1 TTT-TTC-TTTTTTCT-T
1083707 TTTCTTCTTTTTTGCTT
1 TTT-TTCTTTTTT-CTT
*
1083724 CTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
1083739 TTTT
1 TTTT
1083743 ACCCTTTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
15 9 0.20
16 12 0.27
17 16 0.36
18 8 0.18
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:1083701 original size:18 final size:18
Alignment explanation
Indices: 1083688--1083741 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1083678 TCTTTTTTAT
*
1083688 TTTTGTTCTTTTTTTTTG
1 TTTTCTTCTTTTTTTTTG
* *
1083706 TTTTCTTCTTTTTTGCTTC
1 TTTTCTTCTTTTTT-TTTG
1083725 TTTTCTT-TTTTCTTTTT
1 TTTTCTTCTTTT-TTTTT
1083742 TACCCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTTTTTTTTG
Found at i:1083717 original size:26 final size:25
Alignment explanation
Indices: 1083675--1083742 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
1083665 TTTTGTCCCT
* *
1083675 TTTTCTTTTTTATTTTTGTT-CTT-
1 TTTTCTTTTTTCTTTTTTTTGCTTC
*
1083698 TTTTTTTGTTTTCTTCTTTTTTGCTTC
1 TTTTCTT-TTTTCTT-TTTTTTGCTTC
1083725 TTTTCTTTTTTCTTTTTT
1 TTTTCTTTTTTCTTTTTT
1083743 ACCCTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 6 0.16
24 6 0.16
25 9 0.24
26 10 0.27
27 6 0.16
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.82
Consensus pattern (25 bp):
TTTTCTTTTTTCTTTTTTTTGCTTC
Found at i:1087995 original size:20 final size:19
Alignment explanation
Indices: 1087944--1088000 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1087934 AACCAATAAT
1087944 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
1087963 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1087984 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1088001 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1088147 original size:24 final size:24
Alignment explanation
Indices: 1088100--1088176 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 24
1088090 ATATAATGAA
*
1088100 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATAGTATATATAAAAT
1088125 AATAAAAAATATGTATATA-AAAAT
1 AATAAAAAATA-GTATATATAAAAT
* *
1088149 -AT-AAAAAT-GTATGTATAATAT
1 AATAAAAAATAGTATATATAAAAT
1088170 AATAAAA
1 AATAAAA
1088177 TACTAAATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.13
21 4 0.09
22 8 0.18
23 5 0.11
24 10 0.22
25 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (24 bp):
AATAAAAAATAGTATATATAAAAT
Found at i:1088357 original size:2 final size:2
Alignment explanation
Indices: 1088350--1088374 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1088340 AGATAAAATA
1088350 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1088375 ATAATAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1088453 original size:10 final size:9
Alignment explanation
Indices: 1088419--1088451 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
1088409 AAATGAAAAA
1088419 TAAATAAA-
1 TAAATAAAT
1088427 TAAATAAAT
1 TAAATAAAT
1088436 TAAATATAAT
1 TAAATA-AAT
1088446 TAAATA
1 TAAATA
1088452 TATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAATAAAT
Found at i:1088962 original size:37 final size:37
Alignment explanation
Indices: 1088869--1088970 Score: 134
Period size: 37 Copynumber: 2.8 Consensus size: 37
1088859 ATGCTTGTGG
* * ** * *
1088869 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATTT
1088906 ATCCTATTTTTAGGAGTTTGAATCCTAGCA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATT-T
1088943 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1088971 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 4 0.07
37 54 0.93
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATTT
Found at i:1092152 original size:2 final size:2
Alignment explanation
Indices: 1092107--1092134 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1092097 AGTAATCATA
1092107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1092135 CAAATATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1093464 original size:22 final size:22
Alignment explanation
Indices: 1093436--1093484 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1093426 AATACCTGCC
1093436 AAAATCCAAAGGAAATTTCTAA
1 AAAATCCAAAGGAAATTTCTAA
*
1093458 CAAATCCAAAGGAAATTTCTAA
1 AAAATCCAAAGGAAATTTCTAA
1093480 AAAAT
1 AAAAT
1093485 TGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.22
Consensus pattern (22 bp):
AAAATCCAAAGGAAATTTCTAA
Found at i:1093496 original size:23 final size:22
Alignment explanation
Indices: 1093436--1093500 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
1093426 AATACCTGCC
*
1093436 AAAATCCAAAGGAAATTTCTAA
1 AAAATCAAAAGGAAATTTCTAA
* *
1093458 CAAATCCAAAGGAAATTTCTAA
1 AAAATCAAAAGGAAATTTCTAA
* *
1093480 AAAATTGAAAAGAAAATTTCT
1 AAAA-TCAAAAGGAAATTTCT
1093501 CTCACCTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 24 0.65
23 13 0.35
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (22 bp):
AAAATCAAAAGGAAATTTCTAA
Found at i:1096903 original size:54 final size:54
Alignment explanation
Indices: 1096845--1097235 Score: 498
Period size: 54 Copynumber: 7.2 Consensus size: 54
1096835 GATACAATTA
* * * * * *
1096845 TTCATAAACACATTATGAATTTCGTGGGTTACACACTTAGTGCCTTTATGGTTG
1 TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
*
1096899 TTCATCAACATATGAT-AGATTTCGTGGGTTGCACACTTAGTGCCTATACAGTTG
1 TTCATCAACATATGATGA-ATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
* * *
1096953 TTCATCAACATATGATGAATTAT-GTGGGTTGCACACTTAGTGCCTATATGATTT
1 TTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTGCCTATACGGTTG
* ** * *
1097007 TTCGTCAACATATGATGAATTTAATGGGTTACACACTTAGTGCCTATATGGTTG
1 TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
* * * *
1097061 TTCATCAACATATGATGAATTCCCTGGCTTGCACACTTTGTGCCTATACGGTTG
1 TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
* * *
1097115 TTCATCAACATATGATGAATTACGTGGGTTGCACACTTAGTGCTTATACAGTTG
1 TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
* * * * *
1097169 TTCATCAACATATGATGAATTTCGTGGGTTGCACGCTTAGTGCCGATAAGATCG
1 TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
*
1097223 TTCGTCAACATAT
1 TTCATCAACATAT
1097236 ACCTTTAACA
Statistics
Matches: 294, Mismatches: 39, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 290 0.99
55 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTTG
Found at i:1097095 original size:162 final size:162
Alignment explanation
Indices: 1096815--1097235 Score: 549
Period size: 162 Copynumber: 2.6 Consensus size: 162
1096805 ATTAGTTTTT
* * * * * * * * *
1096815 TGGGGTGCACACGTAGTGTCGATACAATTATTCATAAACACATTATGAATTTCGTGGGTTACACA
1 TGGGTTGCACACTTAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTCGTGGGTTACACA
* * * *
1096880 CTTAGTGCCTTTATGGTTGTTCATCAACATATGATAGATTTCGTGGGTTGCACACTTAGTGCCTA
66 CTTAGTGCCTATATGGTTGTTCATCAACATATGATAGATTCCCTGGCTTGCACACTTAGTGCCTA
*
1096945 TACAGTTGTTCATCAACATATGATGAATTATG
131 TACAGTTGTTCATCAACATATGATGAATTACG
* * * **
1096977 TGGGTTGCACACTTAGTGCCTATA-TGATTTTTCGTCAACATATGATGAATTTAATGGGTTACAC
1 TGGGTTGCACACTTAGTGCCTATACAG-TTGTTCATCAACATATGATGAATTTCGTGGGTTACAC
*
1097041 ACTTAGTGCCTATATGGTTGTTCATCAACATATGAT-GAATTCCCTGGCTTGCACACTTTGTGCC
65 ACTTAGTGCCTATATGGTTGTTCATCAACATATGATAG-ATTCCCTGGCTTGCACACTTAGTGCC
*
1097105 TATACGGTTGTTCATCAACATATGATGAATTACG
129 TATACAGTTGTTCATCAACATATGATGAATTACG
* * *
1097139 TGGGTTGCACACTTAGTGCTTATACAGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACG
1 TGGGTTGCACACTTAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTCGTGGGTTACACA
* * * * *
1097204 CTTAGTGCCGATAAGATCGTTCGTCAACATAT
66 CTTAGTGCCTATATGGTTGTTCATCAACATAT
1097236 ACCTTTAACA
Statistics
Matches: 223, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
161 1 0.00
162 221 0.99
163 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (162 bp):
TGGGTTGCACACTTAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTCGTGGGTTACACA
CTTAGTGCCTATATGGTTGTTCATCAACATATGATAGATTCCCTGGCTTGCACACTTAGTGCCTA
TACAGTTGTTCATCAACATATGATGAATTACG
Found at i:1098083 original size:70 final size:70
Alignment explanation
Indices: 1098004--1098143 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 70
1097994 GTAGACATCA
* *
1098004 ATAAAACTCATATTCCAACATATCATTGAAAAAACTACTTCATTCAAGCTCAAATATTTCCCTAA
1 ATAAAACTCATATTCCAACATATCATTCAAAAAACCACTTCATTCAAGCTCAAATATTTCCCTAA
1098069 TTACT
66 TTACT
* *
1098074 ATAAAACTCATATTCCAACATATCATTCAAAAAACCACTTCATTCAATCTCAAATATTTCGCTAA
1 ATAAAACTCATATTCCAACATATCATTCAAAAAACCACTTCATTCAAGCTCAAATATTTCCCTAA
1098139 TTACT
66 TTACT
1098144 TAGTTTTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (70 bp):
ATAAAACTCATATTCCAACATATCATTCAAAAAACCACTTCATTCAAGCTCAAATATTTCCCTAA
TTACT
Found at i:1107958 original size:19 final size:19
Alignment explanation
Indices: 1107891--1107950 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
1107881 TAAGTTAGAA
1107891 TGTTGATTTGGGACCGAAG
1 TGTTGATTTGGGACCGAAG
1107910 TGTTGATTTGGGACCGAAG
1 TGTTGATTTGGGACCGAAG
*
1107929 TGTTGATTTGGGACCAAAG
1 TGTTGATTTGGGACCGAAG
1107948 TGT
1 TGT
1107951 AAATTTGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33
Consensus pattern (19 bp):
TGTTGATTTGGGACCGAAG
Found at i:1116714 original size:2 final size:2
Alignment explanation
Indices: 1116709--1116737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1116699 TGTGTGTGTG
1116709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1116738 TATGTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1125694 original size:26 final size:26
Alignment explanation
Indices: 1125664--1125716 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1125654 AGGAAATAAA
1125664 TCGACTCACAGAAGACTTGTGAAAGG
1 TCGACTCACAGAAGACTTGTGAAAGG
1125690 TCGACTCACAGAAGACTTGTGAAAGG
1 TCGACTCACAGAAGACTTGTGAAAGG
1125716 T
1 T
1125717 AAAAGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (26 bp):
TCGACTCACAGAAGACTTGTGAAAGG
Found at i:1126304 original size:30 final size:30
Alignment explanation
Indices: 1126235--1126305 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
1126225 AAATTTTTTA
** *
1126235 TAGT-GACCAAAATATATGTTTTGAGAATT
1 TAGTGGACCAAAATATAAATTTTGAAAATT
1126264 TAGTGG-CCAAAATATAAATTTTGAAAAGTT
1 TAGTGGACCAAAATATAAATTTTGAAAA-TT
1126294 TAG-GGACCAAAA
1 TAGTGGACCAAAA
1126306 ATGTAAAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.31
Consensus pattern (30 bp):
TAGTGGACCAAAATATAAATTTTGAAAATT
Found at i:1148164 original size:44 final size:44
Alignment explanation
Indices: 1148071--1148157 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
1148061 ATAAAAACAA
1148071 GGTACACTTGTCGCAAGTCTTCCTGATGATGTATAAAACATCTT
1 GGTACACTTGTCGCAAGTCTTCCTGATGATGTATAAAACATCTT
1148115 GGTACACTTGTCGCAAGTCTTCCTGATGATGTATAAAACATCT
1 GGTACACTTGTCGCAAGTCTTCCTGATGATGTATAAAACATCT
1148158 ATGTACAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
GGTACACTTGTCGCAAGTCTTCCTGATGATGTATAAAACATCTT
Found at i:1148660 original size:43 final size:47
Alignment explanation
Indices: 1148558--1148663 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 47
1148548 AGGATCAGAT
*
1148558 TTATTATTTTATTAGGAATTAAGGTTAGGTTAAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGG-TAGGTTAAAAC-A-ATGTTTAGTTA
1148608 TTATTATTTTATTAGGAATT-A-G-A-GTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGTAGGTTAAAACAATGTTTAG-TTA
1148651 TTATTATTTTATT
1 TTATTATTTTATT
1148664 CTCTAGTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 7 0.13
43 16 0.30
45 8 0.15
46 1 0.02
48 1 0.02
49 1 0.02
50 20 0.37
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAAGGTAGGTTAAAACAATGTTTAGTTA
Found at i:1152125 original size:8 final size:9
Alignment explanation
Indices: 1152101--1152128 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1152091 AATAACTCGA
1152101 ATATTTTTG
1 ATATTTTTG
1152110 ATATTTTTG
1 ATATTTTTG
1152119 ATATTTTTG
1 ATATTTTTG
1152128 A
1 A
1152129 ACATATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (9 bp):
ATATTTTTG
Found at i:1155354 original size:15 final size:16
Alignment explanation
Indices: 1155334--1155363 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1155324 GTTCAAAAAA
1155334 AATATGAAAG-GAAAG
1 AATATGAAAGTGAAAG
1155349 AATATGAAAGTGAAA
1 AATATGAAAGTGAAA
1155364 ATGAAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (16 bp):
AATATGAAAGTGAAAG
Found at i:1155873 original size:18 final size:20
Alignment explanation
Indices: 1155852--1155894 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1155842 AAATTAGGCA
*
1155852 ATATTTCGGTTG-GTT-TAT
1 ATATTTCGGGTGTGTTATAT
*
1155870 ATATTTTGGGTGTGTTATAT
1 ATATTTCGGGTGTGTTATAT
1155890 ATATT
1 ATATT
1155895 GGGAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (20 bp):
ATATTTCGGGTGTGTTATAT
Found at i:1158577 original size:13 final size:13
Alignment explanation
Indices: 1158559--1158584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1158549 CACGAGTCTG
1158559 GAACTTATTTAAA
1 GAACTTATTTAAA
1158572 GAACTTATTTAAA
1 GAACTTATTTAAA
1158585 TAGGAAGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GAACTTATTTAAA
Found at i:1162516 original size:20 final size:20
Alignment explanation
Indices: 1162469--1162586 Score: 96
Period size: 20 Copynumber: 5.8 Consensus size: 20
1162459 AATGACCAAC
* *
1162469 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
1162488 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
1162508 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* *
1162528 AAGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
1162548 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
1162569 AAGAATCGCAACGCGATT
1 AA-AATCGCAACGCGATT
1162587 CTTGGAAGAT
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 18 0.23
20 40 0.51
21 6 0.08
22 14 0.18
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1162598 original size:22 final size:22
Alignment explanation
Indices: 1162527--1162615 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 22
1162517 ACGTTGAAAA
*
1162527 GAAGATCGCAACGCGATTC--A
1 GAAGATCGCAACGCGATTCTTG
* *
1162547 GAAAATCGCAACGCGA-TCTTC
1 GAAGATCGCAACGCGATTCTTG
*
1162568 CAAGAATCGCAACGCGATTCTTG
1 GAAG-ATCGCAACGCGATTCTTG
***
1162591 GAAGATCGCGTTGCGATTCTTG
1 GAAGATCGCAACGCGATTCTTG
1162613 GAA
1 GAA
1162616 TCGCGTTGCG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 15 0.27
21 2 0.04
22 30 0.54
23 7 0.12
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (22 bp):
GAAGATCGCAACGCGATTCTTG
Found at i:1162646 original size:40 final size:42
Alignment explanation
Indices: 1162595--1162838 Score: 376
Period size: 40 Copynumber: 6.0 Consensus size: 42
1162585 TTCTTGGAAG
*
1162595 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGG
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
1162635 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
1162675 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
* *
1162717 ATCGCGTTGCGATT-TTCTG-A-ACCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTCTGA
*
1162757 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
1162799 ATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1162839 TTTCAACGTT
Statistics
Matches: 188, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
40 91 0.48
41 7 0.04
42 90 0.48
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (42 bp):
ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
Found at i:1162700 original size:62 final size:60
Alignment explanation
Indices: 1162581--1162893 Score: 314
Period size: 62 Copynumber: 5.1 Consensus size: 60
1162571 GAATCGCAAC
* *
1162581 GCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTG-GATCGCGTT
1 GCGATTCTTGG-A-ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTT-GGAGATCGCGTT
*
1162643 GCGATTCTTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTT
1 GCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTGG-AGATCGCGTT
* * *
1162705 GCGATT-TTCTGAATCGCGTTGCGATTTTCTGAACCGCGTTGCGATTTTCTGA-ATCGCGTT
1 GCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTT-GGAGATCGCGTT
* *
1162765 GCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTT
1 GCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTGG-AGATCGCGTT
**** * * * * *
1162829 GCGATT-TTCTTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTTTT-GATATCGCGTT
1 GCGATTCTTGGAATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATTTTGGAGATCGCGTT
1162888 GCGATT
1 GCGATT
1162894 TTGTTGGTCA
Statistics
Matches: 215, Mismatches: 23, Indels: 29
0.81 0.09 0.11
Matches are distributed among these distances:
59 17 0.08
60 46 0.21
61 15 0.07
62 118 0.55
63 5 0.02
64 14 0.07
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.37
Consensus pattern (60 bp):
GCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTGGAGATCGCGTT
Found at i:1162868 original size:20 final size:20
Alignment explanation
Indices: 1162595--1162895 Score: 259
Period size: 20 Copynumber: 14.8 Consensus size: 20
1162585 TTCTTGGAAG
**
1162595 ATCGCGTTGCGATTCTT-GGA
1 ATCGCGTTGCGATT-TTCTAA
**
1162615 ATCGCGTTGCGATTTTCTGG
1 ATCGCGTTGCGATTTTCTAA
**
1162635 ATCGCGTTGCGATTCTT-GGA
1 ATCGCGTTGCGATT-TTCTAA
1162655 ATCGCGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTTTCTAA
**
1162675 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
*
1162696 GATCGCGTTGCGATTTTCTGA
1 -ATCGCGTTGCGATTTTCTAA
*
1162717 ATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTTTCTAA
* *
1162737 ACCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTTTCTAA
**
1162757 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
* *
1162778 GATCGCGTTGCGATTTTATGA
1 -ATCGCGTTGCGATTTTCTAA
* **
1162799 ATCGCATTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
*
1162820 GATCGCGTTGCGATTTTCT-T
1 -ATCGCGTTGCGATTTTCTAA
* * *
1162840 TTCAACGTTGCGCTTTTCTAA
1 ATC-GCGTTGCGATTTTCTAA
* * *
1162861 ATCGCGTTGCGGTTTT-GAT
1 ATCGCGTTGCGATTTTCTAA
1162880 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1162896 GTTGGTCATT
Statistics
Matches: 233, Mismatches: 37, Indels: 23
0.80 0.13 0.08
Matches are distributed among these distances:
19 22 0.09
20 148 0.64
21 22 0.09
22 41 0.18
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:1162871 original size:82 final size:82
Alignment explanation
Indices: 1162595--1162838 Score: 386
Period size: 82 Copynumber: 3.0 Consensus size: 82
1162585 TTCTTGGAAG
*
1162595 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGGATCGCGTTGCGATTCTTGGAATC
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATC
1162658 GCGTTGCGATTTTCTAA
66 GCGTTGCGATTTTCTAA
* *
1162675 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTGAAC
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GGAAT
*
1162739 CGCGTTGCGATTTTCTGA
65 CGCGTTGCGATTTTCTAA
* *
1162757 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG-A-A
1162822 TCGCGTTGCGATTTTCT
64 TCGCGTTGCGATTTTCT
1162839 TTTCAACGTT
Statistics
Matches: 150, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
80 19 0.13
81 3 0.02
82 108 0.72
83 3 0.02
84 17 0.11
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (82 bp):
ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATC
GCGTTGCGATTTTCTAA
Found at i:1166257 original size:3 final size:3
Alignment explanation
Indices: 1166249--1166274 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1166239 CACCAAACAC
1166249 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1166275 CTCTCTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1173892 original size:43 final size:48
Alignment explanation
Indices: 1173789--1173895 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 48
1173779 AAGATCAGAT
1173789 TTATTATTTTTATTAGGAATTAAGGTTAGGTTAAAACAATATTTTTAAATA
1 TTATTA-TTTTATTAGGAATTAAGG-TAGGTTAAAACAATA-TTTTAAATA
*
1173840 TTATTATTTTATTAGGAATT-A-G-A-GTTAAAAC-ATA-TTTAATTTA
1 TTATTATTTTATTAGGAATTAAGGTAGGTTAAAACAATATTTTAA-ATA
1173883 TTATTATTTTATT
1 TTATTATTTTATT
1173896 CTCTAGTAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
42 5 0.09
43 15 0.28
44 3 0.06
45 8 0.15
46 1 0.02
48 1 0.02
49 1 0.02
50 14 0.26
51 6 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (48 bp):
TTATTATTTTATTAGGAATTAAGGTAGGTTAAAACAATATTTTAAATA
Found at i:1175379 original size:31 final size:31
Alignment explanation
Indices: 1175341--1175541 Score: 183
Period size: 31 Copynumber: 6.5 Consensus size: 31
1175331 TAAGTTTAAA
* * * * *
1175341 GACCATTTTGTAATAGTTTGATTAGTGCAAT
1 GACCATTTTGTAACAATTAGATAAGTGAAAT
*
1175372 GACCATTTTGTAACAATTAGATAAGTTAAAT
1 GACCATTTTGTAACAATTAGATAAGTGAAAT
* **
1175403 GACCATTTTTTTAACAATTCA-ATAAGTTTAAT
1 GACCA-TTTTGTAACAATT-AGATAAGTGAAAT
**
1175435 GACCATTTTGTAACAATTAGATAAGTTTAAT
1 GACCATTTTGTAACAATTAGATAAGTGAAAT
* *
1175466 GACCATTTTGTAACAATTCA-ACAAGTTCAAA-
1 GACCATTTTGTAACAATT-AGATAAG-TGAAAT
* * **
1175497 GATCATTTTGTAACAATTCGATAAGTTTAAT
1 GACCATTTTGTAACAATTAGATAAGTGAAAT
*
1175528 GATCATTTTGTAAC
1 GACCATTTTGTAAC
1175542 TTTCAAAACT
Statistics
Matches: 146, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.03
31 110 0.75
32 31 0.21
33 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
GACCATTTTGTAACAATTAGATAAGTGAAAT
Found at i:1175511 original size:62 final size:62
Alignment explanation
Indices: 1175330--1175541 Score: 280
Period size: 62 Copynumber: 3.4 Consensus size: 62
1175320 ATAAATTTCC
* * * ** * *
1175330 ATAAGTTTAAAGACCATTTTGTAATAGTTTGATTAGTGCAATGACCATTTTGTAACAATTAG
1 ATAAGTTTAATGACCATTTTGTAACAATTCAATAAGTTCAATGACCATTTTGTAACAATTAG
* * *
1175392 ATAAGTTAAATGACCATTTTTTTAACAATTCAATAAGTTTAATGACCATTTTGTAACAATTAG
1 ATAAGTTTAATGACCA-TTTTGTAACAATTCAATAAGTTCAATGACCATTTTGTAACAATTAG
* * * *
1175455 ATAAGTTTAATGACCATTTTGTAACAATTCAACAAGTTCAAAGATCATTTTGTAACAATTCG
1 ATAAGTTTAATGACCATTTTGTAACAATTCAATAAGTTCAATGACCATTTTGTAACAATTAG
*
1175517 ATAAGTTTAATGATCATTTTGTAAC
1 ATAAGTTTAATGACCATTTTGTAAC
1175542 TTTCAAAACT
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
62 78 0.60
63 53 0.40
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (62 bp):
ATAAGTTTAATGACCATTTTGTAACAATTCAATAAGTTCAATGACCATTTTGTAACAATTAG
Done.