Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008002.1 Hibiscus syriacus cultivar Beakdansim tig00110461_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: 1031338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:249877 original size:21 final size:21
Alignment explanation
Indices: 249837--249901 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
249827 CCCCTTATGC
* *
249837 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
249858 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
249879 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
249900 CT
1 CT
249902 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:252178 original size:20 final size:18
Alignment explanation
Indices: 252124--252169 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
252114 TCCGGTATCA
252124 TTTTACCGGTTTATCATT
1 TTTTACCGGTTTATCATT
*
252142 TTGATACCGGTTTTATCATAT
1 TT-TTACCGG-TTTATCAT-T
252163 TTTTACC
1 TTTTACC
252170 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 12 0.52
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (18 bp):
TTTTACCGGTTTATCATT
Found at i:252317 original size:20 final size:20
Alignment explanation
Indices: 252291--252336 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
252281 CACTTTTAAA
252291 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
252310 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
252331 TTTACC
1 TTTACC
252337 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:254674 original size:21 final size:21
Alignment explanation
Indices: 254650--254695 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
254640 AGTTGATGTT
254650 CGCTAAGCAGGCATATGTGTA
1 CGCTAAGCAGGCATATGTGTA
254671 CGCTAAGCAGGCATATGTGTA
1 CGCTAAGCAGGCATATGTGTA
254692 CGCT
1 CGCT
254696 CGTGTGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (21 bp):
CGCTAAGCAGGCATATGTGTA
Found at i:264814 original size:26 final size:25
Alignment explanation
Indices: 264764--264827 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
264754 ATTAATCTAT
*
264764 TAATTCTGATCGGTACTACAGAGGC
1 TAATTCTGATCGGTACTACAAAGGC
*
264789 TAATTCTGATCGAGTACTATAAAGGC
1 TAATTCTGATCG-GTACTACAAAGGC
264815 TAATTCTGATCGG
1 TAATTCTGATCGG
264828 GCATTGTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 13 0.36
26 23 0.64
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (25 bp):
TAATTCTGATCGGTACTACAAAGGC
Found at i:281093 original size:19 final size:20
Alignment explanation
Indices: 281069--281113 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
281059 TATGAACAAT
281069 TTAAAAGTTTAATAA-TAAA
1 TTAAAAGTTTAATAATTAAA
*
281088 TTAAAATTTTAATAATTAAA
1 TTAAAAGTTTAATAATTAAA
*
281108 ATAAAA
1 TTAAAA
281114 AAATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAAGTTTAATAATTAAA
Found at i:282612 original size:4 final size:4
Alignment explanation
Indices: 282605--282664 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
282595 GGAGGGAAAA
*
282605 AAAT AAAT AAA- AAA- AAAT AAAT AATAT AAAT AAAT ATAAT -AAT AAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT
* *
282652 AAGT AAAG AAAT A
1 AAAT AAAT AAAT A
282665 GGGTAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 9 0.20
4 30 0.65
5 7 0.15
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:282619 original size:13 final size:13
Alignment explanation
Indices: 282601--282640 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
282591 AGAGGGAGGG
282601 AAAAAAATAAATAA
1 AAAAAAATAAAT-A
282615 AAAAAAATAAATA
1 AAAAAAATAAATA
* *
282628 ATATAAATAAATA
1 AAAAAAATAAATA
282641 TAATAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:282620 original size:14 final size:14
Alignment explanation
Indices: 282601--282628 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
282591 AGAGGGAGGG
282601 AAAAAAATAAATAA
1 AAAAAAATAAATAA
282615 AAAAAAATAAATAA
1 AAAAAAATAAATAA
282629 TATAAATAAA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAATAAATAA
Found at i:282724 original size:12 final size:13
Alignment explanation
Indices: 282687--282724 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
282677 AAATGTGTAC
282687 ATATATACATAT-
1 ATATATACATATA
*
282699 ATATATATATATA
1 ATATATACATATA
282712 ATATA-ACATATA
1 ATATATACATATA
282724 A
1 A
282725 GTGAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATATACATATA
Found at i:284387 original size:105 final size:104
Alignment explanation
Indices: 284237--284907 Score: 1085
Period size: 105 Copynumber: 6.4 Consensus size: 104
284227 ATATTGTTCC
* * * * **
284237 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGGAATGTTTGTTGACAGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
284302 CAGCGGTCCCTTCGTCGTGAAGTTGAACCTATAC-TGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAA-CT-TGCGTGTCTG
284342 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
284407 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
284447 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTG-GAAAATTGTTTATTAACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-TGTTTGTTGACA
*
284511 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
284553 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
284618 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
284658 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
284723 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
284763 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAGATTTTTGTGGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
284828 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
284868 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
284908 GGTAAAACCT
Statistics
Matches: 536, Mismatches: 25, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
103 2 0.00
104 3 0.01
105 434 0.81
106 96 0.18
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTGTCTG
Found at i:285765 original size:16 final size:17
Alignment explanation
Indices: 285744--285784 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
285734 GTTCTTCTCT
285744 TTTTGTTTTTTT-TTTG
1 TTTTGTTTTTTTCTTTG
285760 TTTTGTTTTTTTCTTTG
1 TTTTGTTTTTTTCTTTG
285777 TTTT-TTTT
1 TTTTGTTTT
285785 CTTTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTTTTCTTTG
Found at i:285768 original size:12 final size:13
Alignment explanation
Indices: 285743--285795 Score: 69
Period size: 12 Copynumber: 4.4 Consensus size: 13
285733 CGTTCTTCTC
285743 TTTTTGT-TTT-T
1 TTTTTGTCTTTGT
285754 TTTTTGT-TTTGT
1 TTTTTGTCTTTGT
285766 TTTTT-TCTTTGT
1 TTTTTGTCTTTGT
*
285778 TTTTTTTCTTTGT
1 TTTTTGTCTTTGT
285791 TTTTT
1 TTTTT
285796 TCCAACTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.28
12 16 0.41
13 12 0.31
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (13 bp):
TTTTTGTCTTTGT
Found at i:285796 original size:12 final size:12
Alignment explanation
Indices: 285743--285797 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 12
285733 CGTTCTTCTC
*
285743 TTTTTGTTT-TT
1 TTTTTCTTTGTT
*
285754 TTTTTGTTTTGTT
1 TTTTT-CTTTGTT
285767 TTTTTCTTTGTTT
1 TTTTTCTTTG-TT
285780 TTTTTCTTTGTT
1 TTTTTCTTTGTT
285792 TTTTTC
1 TTTTTC
285798 CAACTTAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 5 0.13
12 15 0.38
13 19 0.49
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTGTT
Found at i:295248 original size:10 final size:10
Alignment explanation
Indices: 295223--295256 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
295213 AAGGTTAGTA
*
295223 AAATAGAAAT
1 AAATAAAAAT
*
295233 AGATAAAAAT
1 AAATAAAAAT
295243 AAATAAAAAT
1 AAATAAAAAT
295253 AAAT
1 AAAT
295257 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:296550 original size:9 final size:9
Alignment explanation
Indices: 296536--296581 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
296526 GGGAGGGAAA
296536 AAAATAAAT
1 AAAATAAAT
296545 AAAATAAAT
1 AAAATAAAT
* *
296554 AAATTATAT
1 AAAATAAAT
296563 -AAATAAAT
1 AAAATAAAT
*
296571 ATAAT-AAT
1 AAAATAAAT
296579 AAA
1 AAA
296582 GAAGTAAAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 11 0.37
9 19 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATAAAT
Found at i:296555 original size:13 final size:13
Alignment explanation
Indices: 296533--296581 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
296523 AGAGGGAGGG
296533 AAAA-AAATAAAT
1 AAAATAAATAAAT
296545 AAAATAAATAAAT
1 AAAATAAATAAAT
* *
296558 TATATAAATAAAT
1 AAAATAAATAAAT
*
296571 ATAAT-AATAAA
1 AAAATAAATAAA
296582 GAAGTAAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:296628 original size:8 final size:8
Alignment explanation
Indices: 296615--296652 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
296605 ACAAAATGTG
296615 TACATATA
1 TACATATA
296623 TACATATA
1 TACATATA
*
296631 TATATATA
1 TACATATA
296639 TA-ATATA
1 TACATATA
296646 -ACATATA
1 TACATATA
296653 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:308565 original size:11 final size:11
Alignment explanation
Indices: 308549--308582 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
308539 TTATATATTG
308549 TATTAATTTAA
1 TATTAATTTAA
308560 TATTAATTTAA
1 TATTAATTTAA
*
308571 -AATAATTTAA
1 TATTAATTTAA
308581 TA
1 TA
308583 AATTCTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:308592 original size:16 final size:17
Alignment explanation
Indices: 308572--308615 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
308562 TTAATTTAAA
308572 ATAATTTAATAAATTCT
1 ATAATTTAATAAATTCT
308589 -TAATGTTAA-AAATTCT
1 ATAAT-TTAATAAATTCT
308605 ATCAATTTAAT
1 AT-AATTTAAT
308616 CCCGATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 11 0.48
17 9 0.39
18 3 0.13
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAATTTAATAAATTCT
Found at i:309326 original size:2 final size:2
Alignment explanation
Indices: 309319--309349 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
309309 AATCGTGAAT
309319 TA 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 TA
309350 GAATCATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:317203 original size:14 final size:15
Alignment explanation
Indices: 317092--317241 Score: 115
Period size: 15 Copynumber: 9.5 Consensus size: 15
317082 TAATAAGGTT
317092 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
317107 ATTTGTTATAAAATA
1 ATTTATTTTAAAATA
*
317122 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
317137 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
317152 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
317171 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
317189 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
317203 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
317221 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
317235 ATTTATT
1 ATTTATT
317242 AGTATGGATT
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
14 22 0.20
15 55 0.50
16 6 0.05
17 3 0.03
18 11 0.10
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:317223 original size:47 final size:46
Alignment explanation
Indices: 317092--317241 Score: 144
Period size: 52 Copynumber: 3.2 Consensus size: 46
317082 TAATAAGGTT
* * * *
317092 ATTTATTTTAAAATAATTTGTTATA--AAATAATTTATTATAAAATA
1 ATTTATTTT-AAATAATTTATTATATGAATTGATTTATTTTAAAATA
* * *
317137 ATTTACTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAATA
1 ATTTA-TTTTAAAT-AA-T-TTAT--TATATGAATTGATTTATTTTAAAATA
317189 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATA
1 ATTTATTTTAAATAATTTATTA-TATGAATTGATTTATTTTAAAATA
317235 ATTTATT
1 ATTTATT
317242 AGTATGGATT
Statistics
Matches: 86, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
45 9 0.10
46 18 0.21
47 18 0.21
48 7 0.08
49 1 0.01
50 5 0.06
51 7 0.08
52 21 0.24
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (46 bp):
ATTTATTTTAAATAATTTATTATATGAATTGATTTATTTTAAAATA
Found at i:317226 original size:18 final size:18
Alignment explanation
Indices: 317203--317259 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
317193 ATTTTAAATA
317203 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
317221 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
317235 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
317253 ATTTATT
1 ATTTATT
317260 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:317228 original size:32 final size:32
Alignment explanation
Indices: 317189--317264 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
317179 TTTTAAAATA
317189 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
317221 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
317253 ATTTATTTTAAA
1 ATTTATTTTAAA
317265 ATATGGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:317281 original size:54 final size:54
Alignment explanation
Indices: 317212--317775 Score: 320
Period size: 54 Copynumber: 10.6 Consensus size: 54
317202 AATTTATTAG
*
317212 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
317266 TATGGATTGATTTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * *
317313 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * *
317367 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATTTATTTTAAAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
317422 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * *
317476 TATGGATTGATTTATTTTAAA-AA--TA-T-GGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTT--AT--TTTA-AAA
* *
317531 TATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
317585 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * ***
317632 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
**
317691 TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
317745 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
317776 TTGTAGTTGT
Statistics
Matches: 404, Mismatches: 65, Indels: 82
0.73 0.12 0.15
Matches are distributed among these distances:
47 8 0.02
48 53 0.13
49 14 0.03
50 14 0.03
51 4 0.01
52 9 0.02
53 14 0.03
54 194 0.48
55 38 0.09
56 9 0.02
57 14 0.03
58 20 0.05
59 5 0.01
60 8 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:317320 original size:80 final size:82
Alignment explanation
Indices: 317165--317760 Score: 700
Period size: 80 Copynumber: 7.5 Consensus size: 82
317155 TATTATAAAA
* * * *
317165 TATGGATTGATTTATTTTAAAATA---ATTTATTT-TAAATAATTTATTAGTATGAATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAAT-ATGTATTAGTATGGATTGATTTA
317226 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
*
317244 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTGTGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
317306 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
*
317324 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGAT
317389 TTATTTT-AA-AA--TA-T-G
62 TTATTTTAAATAATTTATTAG
*
317404 -A---ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGAT
317465 TTA-TTT---TAA---A--A-
62 TTATTTTAAATAATTTATTAG
* *
317476 TATGGATTGATTTATTTTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGA
1 TATGGATTGATTTATTTT-AAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGA
*
317541 TTTATTTTAAATAATTTATTTG
61 TTTATTTTAAATAATTTATTAG
317563 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
317625 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
317643 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
317705 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
**
317723 TATATATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
317761 TTAAATAATT
Statistics
Matches: 473, Mismatches: 14, Indels: 59
0.87 0.03 0.11
Matches are distributed among these distances:
73 2 0.00
74 2 0.00
75 3 0.01
76 76 0.16
77 49 0.10
78 3 0.01
79 25 0.05
80 221 0.47
81 8 0.02
82 15 0.03
83 1 0.00
84 7 0.01
85 4 0.01
86 39 0.08
87 18 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (82 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTATTAGTATGGATTGATTTAT
TTTAAATAATTTATTAG
Found at i:317335 original size:32 final size:29
Alignment explanation
Indices: 317294--317583 Score: 189
Period size: 32 Copynumber: 10.7 Consensus size: 29
317284 TGTAGTTGTG
317294 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAA--TA-TAGTA
317326 TGGATTGATTTA-TTT---TAA-A-A-TA
1 TGGATTGATTTATTTTAAATAATATAGTA
317348 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAA--TA-TAGTA
317380 TGGATTGATTTATTTT-AA-AATAT-G-A
1 TGGATTGATTTATTTTAAATAATATAGTA
317405 ---ATTGATTTATTTT--A-AA-A---TA
1 TGGATTGATTTATTTTAAATAATATAGTA
317424 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAA--TA-TAGTA
317456 TGGATTGATTTA-TTT---TAA-A-A-TA
1 TGGATTGATTTATTTTAAATAATATAGTA
317478 TGGATTGATTTATTTT--A-AA-A-A-TA
1 TGGATTGATTTATTTTAAATAATATAGTA
317501 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAA--TA-TAGTA
* *
317533 TAGATTGATTTATTTTAAATAATTTATTTGTA
1 TGGATTGATTTATTTTAAATAA--TA-TAGTA
317565 TGGATTGATTTATTTTAAA
1 TGGATTGATTTATTTTAAA
317584 ATATGGATTG
Statistics
Matches: 220, Mismatches: 3, Indels: 70
0.75 0.01 0.24
Matches are distributed among these distances:
19 1 0.00
20 1 0.00
21 3 0.01
22 54 0.25
23 30 0.14
24 1 0.00
25 6 0.03
26 6 0.03
27 1 0.00
28 9 0.04
29 2 0.01
30 2 0.01
31 10 0.05
32 94 0.43
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (29 bp):
TGGATTGATTTATTTTAAATAATATAGTA
Found at i:317349 original size:22 final size:22
Alignment explanation
Indices: 317324--317519 Score: 140
Period size: 22 Copynumber: 8.0 Consensus size: 22
317314 AATTTATTAG
317324 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
317346 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
317370 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
317400 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
317422 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
317446 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
317476 TATGGATTGATTTATTTTAAAAA
1 TATGGATTGATTTATTTT-AAAA
317499 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
317520 TAATTTATTA
Statistics
Matches: 140, Mismatches: 13, Indels: 42
0.72 0.07 0.22
Matches are distributed among these distances:
22 46 0.33
23 26 0.19
24 4 0.03
25 4 0.03
26 20 0.14
27 4 0.03
28 20 0.14
29 4 0.03
30 4 0.03
31 4 0.03
32 4 0.03
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:317502 original size:23 final size:23
Alignment explanation
Indices: 317454--317519 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
317444 AATTTATTAG
317454 TATGGATTGATTTATTTT-AAAA
1 TATGGATTGATTTATTTTAAAAA
317476 TATGGATTGATTTATTTTAAAAA
1 TATGGATTGATTTATTTTAAAAA
317499 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
317520 TAATTTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 18 0.42
23 25 0.58
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (23 bp):
TATGGATTGATTTATTTTAAAAA
Found at i:317527 original size:14 final size:14
Alignment explanation
Indices: 317508--317561 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
317498 ATATGGATTG
317508 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
317522 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
317540 ATTTATTTTAAATA
1 ATTTATTTTAAATA
317554 ATTTATTT
1 ATTTATTT
317562 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:317550 original size:109 final size:112
Alignment explanation
Indices: 317426--317663 Score: 401
Period size: 109 Copynumber: 2.2 Consensus size: 112
317416 TTAAAATATG
317426 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
317490 T-TT-TAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATA
66 TATTGTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATA
*
317535 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
**** *
317600 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATG
66 TATTGTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATA
317647 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
317664 ATATGGATTG
Statistics
Matches: 120, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
109 63 0.52
110 1 0.01
111 2 0.02
112 54 0.45
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (112 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TATTGTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:317657 original size:18 final size:18
Alignment explanation
Indices: 317634--317681 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
317624 ATTTTAAATA
*
317634 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
317652 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
317674 ATTTATTA
1 ATTTATTA
317682 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:317825 original size:31 final size:32
Alignment explanation
Indices: 317790--317869 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
317780 AGTTGTATGG
*
317790 ATTATTTAAATTTCAGTATTGTAAAAC-TAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTTAAA
* *
317821 ATTATTTAAATCTCAGTATTGCAAAACTTCAA
1 ATTATTTAAATTTCAGTATTGCAAAACTTAAA
* *
317853 TTTATTTATATTTCAGT
1 ATTATTTAAATTTCAGT
317870 TTATTTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 25 0.60
32 17 0.40
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (32 bp):
ATTATTTAAATTTCAGTATTGCAAAACTTAAA
Found at i:317872 original size:16 final size:16
Alignment explanation
Indices: 317848--317891 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
317838 ATTGCAAAAC
*
317848 TTCAATTTATTTATAT
1 TTCAGTTTATTTATAT
317864 TTCAGTTTATTTATAT
1 TTCAGTTTATTTATAT
* *
317880 TTTAGTTCATTT
1 TTCAGTTTATTT
317892 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (16 bp):
TTCAGTTTATTTATAT
Found at i:326137 original size:22 final size:22
Alignment explanation
Indices: 326109--326150 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
326099 ATCTTTCATC
326109 TTTCATCTATCTTCTATGTTTT
1 TTTCATCTATCTTCTATGTTTT
326131 TTTCATCTATCTTCTATGTT
1 TTTCATCTATCTTCTATGTT
326151 AGGATCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTCATCTATCTTCTATGTTTT
Found at i:331126 original size:13 final size:13
Alignment explanation
Indices: 331108--331134 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
331098 TATTTTTAGT
331108 TGAACTTAAAATG
1 TGAACTTAAAATG
331121 TGAACTTAAAATG
1 TGAACTTAAAATG
331134 T
1 T
331135 TAATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TGAACTTAAAATG
Found at i:336039 original size:16 final size:17
Alignment explanation
Indices: 336008--336079 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
335998 ATTATCCGGA
336008 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
*
336025 TAAAAAATCGGTTTTTT
1 TAAAAAACCGGTTTTTT
*
336042 AACCGAAAAAATCCGGTTTTTT
1 ----TAAAAAA-CCGGTTTTTT
*
336064 T-TAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
336080 GCAAACCGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
16 10 0.22
17 20 0.44
21 6 0.13
22 9 0.20
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:338707 original size:15 final size:16
Alignment explanation
Indices: 338678--338719 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
338668 ATGGAGTTAT
*
338678 TTTTTATAAATATAATA
1 TTTTTA-AAATATAAAA
338695 TTTTTAAAA-ATAAAA
1 TTTTTAAAATATAAAA
338710 TTTTTAAAAT
1 TTTTTAAAAT
338720 TATCAGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 14 0.61
16 3 0.13
17 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTAAAATATAAAA
Found at i:338971 original size:24 final size:26
Alignment explanation
Indices: 338944--338995 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
338934 TAATTTTATA
* *
338944 TTAAAT-G-GATGAATTTATGAAATT
1 TTAAATGGAGATGAACTTATAAAATT
*
338968 TTAATTGGAGATGAACTTATAAAATT
1 TTAAATGGAGATGAACTTATAAAATT
338994 TT
1 TT
338996 TGGAACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 1 0.04
26 17 0.74
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.42
Consensus pattern (26 bp):
TTAAATGGAGATGAACTTATAAAATT
Found at i:339692 original size:2 final size:2
Alignment explanation
Indices: 339681--339723 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
339671 AAATAGATTT
339681 TA TA -A 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
339722 TA
1 TA
339724 AGTTTATGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:346211 original size:20 final size:20
Alignment explanation
Indices: 346186--346237 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
346176 AAATTTTGAA
346186 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
346206 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
346226 GGTGCATCGATG
1 GGTGCATCGATG
346238 TATGGAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:346659 original size:14 final size:15
Alignment explanation
Indices: 346640--346668 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
346630 TACATGATCT
346640 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
346654 GCATAAAACATAAGA
1 GCATAAAACATAAGA
346669 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:346677 original size:7 final size:7
Alignment explanation
Indices: 346667--346718 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
346657 TAAAACATAA
346667 GATATAT
1 GATATAT
346674 GATATAT
1 GATATAT
346681 GATATGAT
1 GATAT-AT
*
346689 -ATACAT
1 GATATAT
346695 GATTATAT
1 GA-TATAT
*
346703 GCATATGT
1 G-ATATAT
346711 GATATAT
1 GATATAT
346718 G
1 G
346719 CTATGAGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 2 0.05
7 22 0.59
8 12 0.32
9 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (7 bp):
GATATAT
Found at i:348111 original size:65 final size:64
Alignment explanation
Indices: 347961--348122 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
347951 TCCCTTGACG
* * * * *
347961 GGTGCATCGATGCACTACTCATTCATCGGTGCATAAATCCTATTCGATGTTTATATTTTAAGCA
1 GGTGCATCGATGCACTACTTATGCATCGATGCATAAATCCTATTCGATGTTCATATTTAAAGCA
* * * *
348025 GGTGCATTGATGCACTTCTTATGCATCGATGCATTAATGGC-ATTCGATGTTCATTAATTTAAAT
1 GGTGCATCGATGCACTACTTATGCATCGATGCATAAAT-CCTATTCGATGTTCA-T-ATTTAAA-
348089 G-A
62 GCA
*
348091 -GTGCATCGATGCACTCCTTATGCATCGATGCA
1 GGTGCATCGATGCACTACTTATGCATCGATGCA
348123 CCTTCAACAG
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 43 0.52
65 32 0.39
66 7 0.08
67 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
GGTGCATCGATGCACTACTTATGCATCGATGCATAAATCCTATTCGATGTTCATATTTAAAGCA
Found at i:353086 original size:38 final size:38
Alignment explanation
Indices: 353038--353133 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
353028 TGTAAGACAT
* * *
353038 ATGATAGGTCCTACGGGACACATATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
353076 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
353114 ATGATAGGTCATTCGGGACA
1 ATGATAGGTCCTTCGGGACA
353134 TTTATACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:356431 original size:18 final size:18
Alignment explanation
Indices: 356408--356443 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
356398 GTTCAGTATT
356408 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
356426 TGTCCCGAATGACCACTA
1 TGTCCCAAAGGACCACTA
356444 GATACGTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:356455 original size:22 final size:22
Alignment explanation
Indices: 356427--356509 Score: 112
Period size: 22 Copynumber: 3.8 Consensus size: 22
356417 GGACCACTAT
*
356427 GTCCCGAATGACCACTAGATAC
1 GTCCCGAAGGACCACTAGATAC
* *
356449 GTCCCGAAGAACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
* *
356471 GTCTCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
*
356493 GTCCCGAAGGATCACTA
1 GTCCCGAAGGACCACTA
356510 TGTCCCGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCACTAGATAC
Found at i:356516 original size:18 final size:18
Alignment explanation
Indices: 356408--356540 Score: 95
Period size: 22 Copynumber: 6.7 Consensus size: 18
356398 GTTCAGTATT
*
356408 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
356426 TGTCCCGAATGACCACTAGA
1 TGTCCCGAAGGACCACT--A
*
356446 TACGTCCCGAAGAACCACTGGA
1 T--GTCCCGAAGGACCACT--A
*
356468 TACGTCTCGAAGGACCACTGGA
1 T--GTCCCGAAGGACCACT--A
*
356490 TACGTCCCGAAGGATCACTA
1 T--GTCCCGAAGGACCACTA
*
356510 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
356528 TGTCCTGAAGGAC
1 TGTCCCGAAGGAC
356541 TAATATACCC
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
18 41 0.42
20 4 0.04
22 53 0.54
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:359615 original size:29 final size:29
Alignment explanation
Indices: 359574--359735 Score: 234
Period size: 29 Copynumber: 5.6 Consensus size: 29
359564 CACATTCAAA
*
359574 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
** * *
359603 AATTCTTATAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
359632 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
*
359661 AATTCCCAAAATGACACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
359690 AATTCCCAAAATATCACATGTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
359719 AATTTCCAAAATATCAC
1 AATTCCCAAAATGTCAC
359736 CGGGTCGGGT
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 121 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:359759 original size:13 final size:13
Alignment explanation
Indices: 359741--359765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359731 ATCACCGGGT
359741 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
359754 CGGGTCGGGTCA
1 CGGGTCGGGTCA
359766 GACCGGTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:360626 original size:23 final size:23
Alignment explanation
Indices: 360586--360648 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
360576 ATCTACATGC
* *
360586 TTACATG-AATATGCAATATGTA
1 TTACATGTTATATGAAATATGTA
360608 TTACATGTTATATGAAATATGTA
1 TTACATGTTATATGAAATATGTA
360631 TTACATGTTATATGAAAT
1 TTACATGTTATATGAAAT
360649 GATATAGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 7 0.18
23 31 0.82
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (23 bp):
TTACATGTTATATGAAATATGTA
Found at i:367139 original size:59 final size:60
Alignment explanation
Indices: 367074--367195 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
367064 AAGGAATATG
*
367074 ATTTAAATTATTATTTATTTTAAAAG-AGTTTTAAATAAACGATAATTAAGTTCATTCTA
1 ATTTAAATTATTATTTATTTTAAAAGAAGTTTTAAATAAACGATAATTAAGTTAATTCTA
* * *
367133 ATTTAAATTATTATTTATTTTAAAAGAAGTTTTAAATAAATGATATTTACGTTAATTCTA
1 ATTTAAATTATTATTTATTTTAAAAGAAGTTTTAAATAAACGATAATTAAGTTAATTCTA
367193 ATT
1 ATT
367196 AAGTTATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 26 0.45
60 32 0.55
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (60 bp):
ATTTAAATTATTATTTATTTTAAAAGAAGTTTTAAATAAACGATAATTAAGTTAATTCTA
Found at i:369037 original size:20 final size:20
Alignment explanation
Indices: 369008--369102 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 20
368998 ACTTGGACTA
*
369008 TCGCAATGCGATTTACATA-T
1 TCGCATTGCGATTTACA-AGT
*
369028 TCGCATTGCGATTGTCCAAGT
1 TCGCATTGCGATT-TACAAGT
* * *
369049 TCGCGTTGCGATTTTTCAAAT
1 TCGCATTGCGA-TTTACAAGT
*
369070 TCG--TTGCGATAGT-CGAAGT
1 TCGCATTGCGAT-TTAC-AAGT
369089 TCGCATTGCGATTT
1 TCGCATTGCGATTT
369103 TCTAAATTCG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 14 0.23
21 29 0.48
22 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAGT
Found at i:369057 original size:21 final size:21
Alignment explanation
Indices: 369027--369223 Score: 122
Period size: 21 Copynumber: 9.7 Consensus size: 21
369017 GATTTACATA
*
369027 TTCGCATTGCGATTGTCCAAG
1 TTCGCGTTGCGATTGTCCAAG
* * *
369048 TTCGCGTTGCGATTTTTCAAA
1 TTCGCGTTGCGATTGTCCAAG
* *
369069 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTGTCCAAG
* * * *
369088 TTCGCATTGCGATTTTCTAAA
1 TTCGCGTTGCGATTGTCCAAG
* *
369109 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTGTCCAAG
* * *
369128 TTCGTGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATTGTCCAAG
* * *
369149 TT--CGTTACGATAGTCGAAG
1 TTCGCGTTGCGATTGTCCAAG
* * *
369168 TTCGCGTTGCGATTTATTCAAAA
1 TTCGCGTTGCGA-TT-GTCCAAG
*
369191 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATTGTCCAAG
369210 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
369224 TATTCCAAAT
Statistics
Matches: 126, Mismatches: 40, Indels: 20
0.68 0.22 0.11
Matches are distributed among these distances:
19 47 0.37
20 1 0.01
21 71 0.56
22 1 0.01
23 6 0.05
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATTGTCCAAG
Found at i:369089 original size:40 final size:40
Alignment explanation
Indices: 369033--369247 Score: 306
Period size: 40 Copynumber: 5.3 Consensus size: 40
369023 CATATTCGCA
* *
369033 TTGCGATTGTCCAAGTTCGCGTTGCGATTTTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCG
*
369073 TTGCGATAGTCGAAGTTCGCATTGCGA-TTTTCTAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTC-AAATTCG
* *
369113 TTGCGATAGTCGAAGTTCGTGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCG
*
369153 TTACGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTT-TTC-AAATTCG
* *
369195 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCA
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTT-TT-CAAATTCG
369237 TTGCGATAGTC
1 TTGCGATAGTC
369248 CAAAATCGCA
Statistics
Matches: 158, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 5 0.03
40 91 0.58
41 6 0.04
42 55 0.35
43 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCG
Found at i:369240 original size:21 final size:21
Alignment explanation
Indices: 369052--369243 Score: 79
Period size: 21 Copynumber: 9.4 Consensus size: 21
369042 TCCAAGTTCG
369052 CGTTGCGATTT-TT-CAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
369071 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
*
369090 CGCATTGCGA-TT-TTCTAAATT
1 CG--TTGCGATTTATTCCAAATT
* * *
369111 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
369130 CGTGTTGCGA-TT-TTCCAAATT
1 C--GTTGCGATTTATTCCAAATT
* * * *
369151 CGTTACGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
*
369170 CGCGTTGCGATTTATTCAAAATT
1 --CGTTGCGATTTATTCCAAATT
* *
369193 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
369212 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
*
369235 CATTGCGAT
1 CGTTGCGAT
369244 AGTCCAAAAT
Statistics
Matches: 129, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
17 1 0.01
18 3 0.02
19 47 0.36
21 59 0.46
22 2 0.02
23 17 0.13
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:369347 original size:6 final size:6
Alignment explanation
Indices: 369336--369366 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
369326 GACAAGTATT
369336 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
369367 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:369883 original size:6 final size:6
Alignment explanation
Indices: 369872--369924 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
369862 TCTCGTCTCG
* * *
369872 GGTCGT GGTCGT -CTCG- GGTCGT GGTCGT GGTCGT -CTCG- GGTCAT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
369916 GGTCGT GGT
1 GGTCGT GGT
369925 AATACGTGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
5 11 0.30
6 26 0.70
ACGTcount: A:0.02, C:0.21, G:0.45, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:369900 original size:22 final size:22
Alignment explanation
Indices: 369859--369924 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
369849 CGCCGTCGTC
**
369859 TCGTCTCGTCTCG-GGTCGTGG
1 TCGTCTCGGGTCGTGGTCGTGG
369880 TCGTCTCGGGTCGTGGTCGTGG
1 TCGTCTCGGGTCGTGGTCGTGG
*
369902 TCGTCTCGGGTCATGGTCGTGG
1 TCGTCTCGGGTCGTGGTCGTGG
369924 T
1 T
369925 AATACGTGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 11 0.27
22 30 0.73
ACGTcount: A:0.02, C:0.24, G:0.41, T:0.33
Consensus pattern (22 bp):
TCGTCTCGGGTCGTGGTCGTGG
Found at i:369919 original size:16 final size:16
Alignment explanation
Indices: 369864--369899 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
369854 TCGTCTCGTC
369864 TCGTCTCGGGTCGTGG
1 TCGTCTCGGGTCGTGG
369880 TCGTCTCGGGTCGTGG
1 TCGTCTCGGGTCGTGG
369896 TCGT
1 TCGT
369900 GGTCGTCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.42, T:0.33
Consensus pattern (16 bp):
TCGTCTCGGGTCGTGG
Found at i:370092 original size:23 final size:23
Alignment explanation
Indices: 370065--370132 Score: 63
Period size: 25 Copynumber: 3.0 Consensus size: 23
370055 CTTCGACTAT
370065 CGCAACGAATTTGGAATAAATCG
1 CGCAACGAATTTGGAATAAATCG
* *
370088 CGCAACGCGAACTTGGACT--AT--
1 CGCAA--CGAATTTGGAATAAATCG
*
370109 CGCAACGAATTTAGAATAAATCG
1 CGCAACGAATTTGGAATAAATCG
370132 C
1 C
370133 AAAGCGAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
19 9 0.26
21 7 0.21
23 8 0.24
25 10 0.29
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (23 bp):
CGCAACGAATTTGGAATAAATCG
Found at i:370107 original size:44 final size:42
Alignment explanation
Indices: 370017--370191 Score: 282
Period size: 42 Copynumber: 4.2 Consensus size: 42
370007 TGCGATTTTG
370017 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
370059 GACTATCGCAACGAATTTGGAATAAATCGCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAAT--CGCAACGCGAACTTC
* *
370103 GACTATCGCAACGAATTTAGAATAAATCGCAAAGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
370145 GACTATCGTAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
370185 GACTATC
1 GACTATC
370192 TCAATGCGAA
Statistics
Matches: 124, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
40 25 0.20
41 1 0.01
42 58 0.47
44 40 0.32
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:370159 original size:86 final size:82
Alignment explanation
Indices: 370014--370191 Score: 284
Period size: 86 Copynumber: 2.1 Consensus size: 82
370004 CGTTGCGATT
* *
370014 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
1 TTGGACTATCGCAACGAATTTAGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGAATTTGG
370079 AATAAATCGCGCAACGCGAAC
66 -A-AAAT--CGCAACGCGAAC
*
370100 TTGGACTATCGCAACGAATTTAGAATAAATCGCAAAGCGAACTTCGACTATCGTAACGAATTTGG
1 TTGGACTATCGCAACGAATTTAGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGAATTTGG
370165 AAAATCGCAACGCGAAC
66 AAAATCGCAACGCGAAC
*
370182 TTCGACTATC
1 TTGGACTATC
370192 TCAATGCGAA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
82 21 0.24
84 4 0.05
85 1 0.01
86 62 0.70
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (82 bp):
TTGGACTATCGCAACGAATTTAGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGAATTTGG
AAAATCGCAACGCGAAC
Found at i:371390 original size:28 final size:29
Alignment explanation
Indices: 371350--371412 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
371340 AACCTATACT
* *
371350 TTATCCAATTGCTTAGATTTCATGG-GCC
1 TTATCCAACTGCTCAGATTTCATGGAGCC
*
371378 TTATCCAACTGCTCAGGTTTCATGGAGCC
1 TTATCCAACTGCTCAGATTTCATGGAGCC
371407 TT-TCCA
1 TTATCCA
371413 TAGAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (29 bp):
TTATCCAACTGCTCAGATTTCATGGAGCC
Found at i:373973 original size:24 final size:23
Alignment explanation
Indices: 373946--373990 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
373936 AAGGGTAAAC
*
373946 TTTTAAAATTTTAAGGAGACAAGT
1 TTTTAAAATTATAA-GAGACAAGT
373970 TTTTAAAATTATAAGAGACAA
1 TTTTAAAATTATAAGAGACAA
373991 AAACAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (23 bp):
TTTTAAAATTATAAGAGACAAGT
Found at i:375263 original size:23 final size:21
Alignment explanation
Indices: 375236--375287 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
375226 TTTCTTAATC
*
375236 AAAAAGAATATTTATATTTTT
1 AAAAAAAATATTTATATTTTT
*
375257 ATAAAAAAATATTTTTTATTTTT
1 A-AAAAAAATA-TTTATATTTTT
375280 AAAAAAAA
1 AAAAAAAA
375288 ATTATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 15 0.56
23 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAAAAATATTTATATTTTT
Found at i:375288 original size:23 final size:23
Alignment explanation
Indices: 375236--375297 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
375226 TTTCTTAATC
*
375236 AAAAAGAATA-TTTATATTTTTA
1 AAAAAAAATATTTTATATTTTTA
* *
375258 TAAAAAAATATTTTTTATTTTTA
1 AAAAAAAATATTTTATATTTTTA
375281 AAAAAAAATTATTTTAT
1 AAAAAAAA-TATTTTAT
375298 GTTATATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 8 0.24
23 18 0.55
24 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAAAAAATATTTTATATTTTTA
Found at i:377464 original size:2 final size:2
Alignment explanation
Indices: 377459--377513 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
377449 AACAAGCGGC
377459 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
377501 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
377514 GAATGAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:380138 original size:2 final size:2
Alignment explanation
Indices: 380131--380160 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
380121 TGTTGACTTG
380131 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
380161 GAGTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386748 original size:27 final size:28
Alignment explanation
Indices: 386718--386770 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
386708 AATTTAGTAT
386718 TTTTATAGC-TTTTAAAAT-ATTTTTAGA
1 TTTT-TAGCGTTTTAAAATAATTTTTAGA
**
386745 TTTTTTTCGTTTTAAAATAATTTTTA
1 TTTTTAGCGTTTTAAAATAATTTTTA
386771 AAATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 13 0.59
28 7 0.32
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTTTAGCGTTTTAAAATAATTTTTAGA
Found at i:386748 original size:28 final size:29
Alignment explanation
Indices: 386710--386770 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
386700 AAAAAAACAA
386710 TTTAGTATTTTTATAGCTTTTAAAAT-ATT
1 TTTAGTATTTTTATAG-TTTTAAAATAATT
* *
386739 TTTAG-ATTTTTTTCGTTTTAAAATAATT
1 TTTAGTATTTTTATAGTTTTAAAATAATT
386767 TTTA
1 TTTA
386771 AAATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.31
28 15 0.52
29 5 0.17
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (29 bp):
TTTAGTATTTTTATAGTTTTAAAATAATT
Found at i:388058 original size:22 final size:22
Alignment explanation
Indices: 388031--388078 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
388021 CGGCGATATC
* *
388031 CGTCCCCATCTCTAGTGAAATT
1 CGTCCCCATCTCCAGCGAAATT
*
388053 CGTCCCCATCTCCGGCGAAATT
1 CGTCCCCATCTCCAGCGAAATT
388075 CGTC
1 CGTC
388079 TATCTCCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.27
Consensus pattern (22 bp):
CGTCCCCATCTCCAGCGAAATT
Found at i:388440 original size:20 final size:20
Alignment explanation
Indices: 388417--388455 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
388407 TTTGAAACTT
388417 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
388437 AAATTTGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
388456 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:389871 original size:42 final size:42
Alignment explanation
Indices: 389812--389908 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
389802 CCCCACTTCG
* * *
389812 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCAACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCAACAACC
* *
389854 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCAACAACC
389896 AGAGCCATCACCT
1 AGAGCCATCACCT
389909 ATTCCATCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTCAACAACC
Found at i:390052 original size:21 final size:21
Alignment explanation
Indices: 390023--390072 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
390013 GTTTGGGGAG
* *
390023 TTACATGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
390044 TTGCGTGATGGGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
390065 TTACGTGA
1 TTACGTGA
390073 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:390285 original size:2 final size:2
Alignment explanation
Indices: 390278--390380 Score: 76
Period size: 2 Copynumber: 55.0 Consensus size: 2
390268 CAATTATTAT
*
390278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
390318 TT TA AA T- TA AA T- TA -A AA TA TA TA TA TA TA TA TA -A TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
390356 TA TA TA TT TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
390381 CCCGACCCGA
Statistics
Matches: 77, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
1 7 0.09
2 70 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:390675 original size:21 final size:21
Alignment explanation
Indices: 390637--390677 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
390627 CTTTATGCGG
* * *
390637 TGAGGTATCTACTTTACGTGT
1 TGAGGTAGCCACTCTACGTGT
390658 TGAGGTAGCCACTCTACGTG
1 TGAGGTAGCCACTCTACGTG
390678 AGATTGTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TGAGGTAGCCACTCTACGTGT
Found at i:390987 original size:21 final size:21
Alignment explanation
Indices: 390963--391013 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
390953 CCTATTATCA
390963 TTCAAGAGGCCCCTACCACCG
1 TTCAAGAGGCCCCTACCACCG
** *
390984 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTACCACCG
391005 TTCAAGAGG
1 TTCAAGAGG
391014 TTTCTCCCAC
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:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTACCACCG
Found at i:392607 original size:20 final size:20
Alignment explanation
Indices: 392582--392621 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
392572 TTCGCGTTGG
392582 GATTTTCGCGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
* *
392602 GATTTTTGTGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
392622 TACATTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
GATTTTCGCGTTGCGAATTT
Found at i:395266 original size:24 final size:24
Alignment explanation
Indices: 395175--395258 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
395165 CTGAAACATC
* *
395175 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAATTTCGAGTATTGACCAAG
*
395199 ATCAAAGTTCGAGTATTGACCAAG
1 ATCAAATTTCGAGTATTGACCAAG
395223 ATCAAATTTCGAGTATTGACCAAG
1 ATCAAATTTCGAGTATTGACCAAG
395247 ATCAAATTTCGA
1 ATCAAATTTCGA
395259 ATACTGACTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAATTTCGAGTATTGACCAAG
Found at i:396269 original size:40 final size:40
Alignment explanation
Indices: 396189--396314 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 40
396179 ATAAAACCTA
* *
396189 TTGCGAAATTAAAATTTGTGTTTGTGAATTCGAAAATCGAG
1 TTGCGAAATTAAAATTAGTG-TTGCGAATTCGAAAATCGAG
**
396230 TTGCGAAAACAAAATTAGTGTTGCGAATTC-AGAAATCGAG
1 TTGCGAAATTAAAATTAGTGTTGCGAATTCGA-AAATCGAG
* * *
396270 TTGC-AAATTTGAAATTCAGTGTTGCGAATTTGGAAAATCGCG
1 TTGCGAAA-TTAAAATT-AGTGTTGCGAA-TTCGAAAATCGAG
396312 TTG
1 TTG
396315 TAAAATTAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.06
40 26 0.37
41 28 0.39
42 12 0.17
43 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (40 bp):
TTGCGAAATTAAAATTAGTGTTGCGAATTCGAAAATCGAG
Found at i:396272 original size:20 final size:19
Alignment explanation
Indices: 396214--396278 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
396204 TTGTGTTTGT
396214 GAATTCGAAAATCGAGTTGC
1 GAATTC-AAAATCGAGTTGC
** * *
396234 GAAAACAAAATTAGTGTTGC
1 GAATTCAAAA-TCGAGTTGC
396254 GAATTCAGAAATCGAGTTGC
1 GAATTCA-AAATCGAGTTGC
*
396274 AAATT
1 GAATT
396279 TGAAATTCAG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 4 0.12
20 27 0.79
21 3 0.09
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (19 bp):
GAATTCAAAATCGAGTTGC
Found at i:396314 original size:21 final size:20
Alignment explanation
Indices: 396249--396314 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
396239 CAAAATTAGT
*
396249 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATCGA
* * *
396269 GTTGCAAATTTGAAATTCAGT
1 GTTGCGAATTTGAAAATC-GA
*
396290 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAAATCGA
396311 GTTG
1 GTTG
396315 TAAAATTAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 11 0.31
21 19 0.53
22 6 0.17
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGA
Found at i:401295 original size:21 final size:21
Alignment explanation
Indices: 401253--401305 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
401243 ATTCTGACTA
401253 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
401274 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
401295 TTGCAATGCGA
1 TCGCATTGCGA
401306 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:401325 original size:20 final size:20
Alignment explanation
Indices: 401297--401388 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
401287 TTCCTAATTT
401297 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* *
401317 GCAACGCGATTACGTAAATC
1 GCAATGCGAATACGTAAATC
* * *
401337 GCAATACGAATTAGGAAAATC
1 GCAATGCGAA-TACGTAAATC
401358 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
401378 GCAATGCGAAT
1 GCAATGCGAAT
401389 CTGATTATCG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:401957 original size:21 final size:21
Alignment explanation
Indices: 401931--401974 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
401921 CGTAACATGA
401931 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
*
401952 AAATGAAAATCTCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
401973 AA
1 AA
401975 TCGCAACGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:402012 original size:19 final size:19
Alignment explanation
Indices: 401973--402015 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
401963 TCAACGAGAG
**
401973 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
401992 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
402011 AATCG
1 AATCG
402016 TATTGCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:402110 original size:20 final size:19
Alignment explanation
Indices: 402068--402135 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
402058 GCGATTCTCT
**
402068 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
402087 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
** *
402107 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATAGTCATT-TCG
402127 CGTTGCGAT
1 CGTTGCGAT
402136 TTTCATTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.36
20 26 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:402136 original size:20 final size:19
Alignment explanation
Indices: 402018--402144 Score: 138
Period size: 19 Copynumber: 6.8 Consensus size: 19
402008 CAAAATCGTA
402018 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* * *
402037 TTGTGATTTTAATTTCGTG
1 TTGCGATTTTCATTTCGCG
*
402056 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
402070 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
402089 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
*
402109 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
402129 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
402145 AACCAAAAGA
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 2 0.02
19 40 0.45
20 33 0.38
21 1 0.01
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:402142 original size:40 final size:39
Alignment explanation
Indices: 402068--402144 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
402058 GCGATTCTCT
402068 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCG
* **
402107 CGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATT-TCGCGTTGCGATAGTCATTTC
402145 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 16 0.47
40 18 0.53
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (39 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCG
Found at i:403992 original size:14 final size:14
Alignment explanation
Indices: 403972--404008 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
403962 AATTGTTTAA
403972 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
403985 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
404000 TTGATTTGT
1 TTGATTTGT
404009 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:404152 original size:14 final size:14
Alignment explanation
Indices: 404131--404170 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
404121 ATGCGAAATG
*
404131 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
404145 AGAATCGCAACGAC
1 AAAATCGCAACGAC
404159 AAAATCGCAACG
1 AAAATCGCAACG
404171 CGAAACTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.20, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:404209 original size:19 final size:18
Alignment explanation
Indices: 404187--404298 Score: 69
Period size: 19 Copynumber: 6.4 Consensus size: 18
404177 TAAATTCACG
404187 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
404205 TTTGCGA--TTC-CCTCG-
1 -TTGCGATTTTCATTTCGC
404220 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
404238 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
404253 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
* **
404271 ATTACGATAGTCATTTCCGC
1 -TTGCGATTTTCATTT-CGC
404291 GTTGCGAT
1 -TTGCGAT
404299 AGACATTAAG
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 12 0.17
16 13 0.18
17 13 0.18
19 24 0.34
20 9 0.13
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:404227 original size:33 final size:33
Alignment explanation
Indices: 404185--404278 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
404175 ACTAAATTCA
*
404185 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
404218 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
404251 CGTTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
404279 AGTCATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:404300 original size:20 final size:20
Alignment explanation
Indices: 404251--404344 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
404241 GCGATTCTCT
**
404251 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
404270 CATTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
404290 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
404309 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
404331 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
404345 AATGAATGCC
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
19 16 0.29
20 25 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:407741 original size:21 final size:21
Alignment explanation
Indices: 407717--407757 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
407707 TATTCGCATT
407717 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
407738 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
407758 TGTGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:411626 original size:19 final size:19
Alignment explanation
Indices: 411602--411640 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
411592 ATATATTTTA
411602 ATTTTT-ATATAAAATATAT
1 ATTTTTAATATAAAA-ATAT
*
411621 ATTTTTAATTTAAAAATAT
1 ATTTTTAATATAAAAATAT
411640 A
1 A
411641 ATAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTAATATAAAAATAT
Found at i:411647 original size:27 final size:26
Alignment explanation
Indices: 411589--411651 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
411579 TAGCATAATT
** *
411589 TATATATATTTTAATTTTTATATAAAA
1 TATATAT-TTTTAATTTAAAAATAAAA
*
411616 TATATATTTTTAATTTAAAAATATAA
1 TATATATTTTTAATTTAAAAATAAAA
411642 TAATATATTT
1 T-ATATATTT
411652 GAATTAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATATTTTTAATTTAAAAATAAAA
Found at i:415969 original size:21 final size:22
Alignment explanation
Indices: 415919--415969 Score: 59
Period size: 26 Copynumber: 2.2 Consensus size: 22
415909 CCAACCAAAC
415919 TATCTCTAAGAGTAATTAGCTTTTCT
1 TATCTCTAAGAGTAATTAG----TCT
415945 TATCTCTAAGAGTAATTAG-CT
1 TATCTCTAAGAGTAATTAGTCT
415966 TATC
1 TATC
415970 CTCATCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
26 19 0.76
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (22 bp):
TATCTCTAAGAGTAATTAGTCT
Found at i:418536 original size:13 final size:13
Alignment explanation
Indices: 418515--418559 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
418505 GAAAACTTTA
418515 ATTATCTTTGACT
1 ATTATCTTTGACT
*
418528 ATTAACTTT-A--
1 ATTATCTTTGACT
418538 ATTATCTTTGACT
1 ATTATCTTTGACT
*
418551 ATTAGCTTT
1 ATTATCTTT
418560 AAAAATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.31
11 1 0.04
12 1 0.04
13 16 0.62
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (13 bp):
ATTATCTTTGACT
Found at i:418538 original size:23 final size:23
Alignment explanation
Indices: 418508--418561 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
418498 AACAAGTGAA
418508 AACTTTAATTATCTTTGACTATT
1 AACTTTAATTATCTTTGACTATT
418531 AACTTTAATTATCTTTGACTATT
1 AACTTTAATTATCTTTGACTATT
*
418554 AGCTTTAA
1 AACTTTAA
418562 AAATGACACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (23 bp):
AACTTTAATTATCTTTGACTATT
Found at i:418738 original size:21 final size:21
Alignment explanation
Indices: 418700--418740 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
418690 CTTGACATTT
*
418700 TAGTTTCTATATCTTTGTAAG
1 TAGTTTCTAGATCTTTGTAAG
418721 TAGTTTCT-GATCTGTTGTAA
1 TAGTTTCTAGATCT-TTGTAA
418741 ATTCATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (21 bp):
TAGTTTCTAGATCTTTGTAAG
Found at i:429270 original size:2 final size:2
Alignment explanation
Indices: 429225--429251 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
429215 CATTTGAATA
429225 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 A
429252 AACTTATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:433597 original size:23 final size:23
Alignment explanation
Indices: 433540--433608 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
433530 AAATATGAAA
* *
433540 TATAATAAA-TAATTTTATTTAT
1 TATAAAAAATTAATATTATTTAT
*
433562 TATAAAAACTTAATATTA-TTAT
1 TATAAAAAATTAATATTATTTAT
* * *
433584 TTTAAAAATATTAAAATAATTTAT
1 TATAAAAA-ATTAATATTATTTAT
433608 T
1 T
433609 TAATATTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 18 0.49
23 14 0.38
24 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAAAAAATTAATATTATTTAT
Found at i:433628 original size:15 final size:14
Alignment explanation
Indices: 433602--433633 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
433592 TATTAAAATA
433602 ATTTATTTAATATT
1 ATTTATTTAATATT
433616 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
433631 ATT
1 ATT
433634 ATTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:449832 original size:2 final size:2
Alignment explanation
Indices: 449821--449855 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
449811 ATACTGATTC
449821 TA TA TA -A 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
449856 AAAGATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:457348 original size:29 final size:29
Alignment explanation
Indices: 457316--457375 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
457306 ATTTATTTAA
* *
457316 TATTTTAAAGTTATAATAATTTTAATATT
1 TATTTTAAAGATATAATAATATTAATATT
* *
457345 TATTTTATAGATATAATAATATTAATGTT
1 TATTTTAAAGATATAATAATATTAATATT
457374 TA
1 TA
457376 GTATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TATTTTAAAGATATAATAATATTAATATT
Found at i:459213 original size:50 final size:50
Alignment explanation
Indices: 459138--459263 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
459128 GTAGTAGTAA
* * * *
459138 AGCGTGCCCCCTGAACCGCGCTATACGCTAATTTGGCGCCACGTGGGTAT
1 AGCGTGCCCCCTGAACCGCGATATACGCTAATCTGGAGCCACGCGGGTAT
** * *
459188 AGCGTGCCCCCTGTCCCGCGATATACGGTGATCTGGAGCCACGCGGGTAT
1 AGCGTGCCCCCTGAACCGCGATATACGCTAATCTGGAGCCACGCGGGTAT
* ** * *
459238 AACACGCCCCCTGATCCGCGCTATAC
1 AGCGTGCCCCCTGAACCGCGATATAC
459264 CTGGGTATCT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (50 bp):
AGCGTGCCCCCTGAACCGCGATATACGCTAATCTGGAGCCACGCGGGTAT
Found at i:459401 original size:10 final size:10
Alignment explanation
Indices: 459386--459425 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
459376 TTTATCACAC
459386 CAAATTCTCT
1 CAAATTCTCT
459396 CAAATTCTCT
1 CAAATTCTCT
459406 -AAATTTCTCT
1 CAAA-TTCTCT
*
459416 CAAATACTCT
1 CAAATTCTCT
459426 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:459698 original size:106 final size:108
Alignment explanation
Indices: 459552--459768 Score: 321
Period size: 111 Copynumber: 2.0 Consensus size: 108
459542 TGAAAATCAT
* * *
459552 ATATCTCTACACTTTGCTGATACGATAACATTTTAACG-T-TTTAATTTAAATTATTAGTAATAT
1 ATATCTCGACACTTTGCTGATACGATAACATTTCAACGTTATTTAATTTAAATTATTAGTAATAA
* *
459615 TTAGTTGATTTATTTAATGTATCATTATTAGATTAATAATTAA
66 TTAGTTGATTTATTTAATGCATCATTATTAGATTAAGAATTAA
* *
459658 ATATCTCGACACTTTGTTGATACGGTAACATTTCAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTCAACG--TT-ATTTAATTTAAATTATTAGTAA
*
459723 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
63 TAATTAGTTGATTTATTTAATGCATCATTATTAGATTAAGAATTAA
459769 TTTTTGTAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 34 0.35
109 1 0.01
111 63 0.64
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (108 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTCAACGTTATTTAATTTAAATTATTAGTAATAA
TTAGTTGATTTATTTAATGCATCATTATTAGATTAAGAATTAA
Found at i:464847 original size:2 final size:2
Alignment explanation
Indices: 464840--464886 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
464830 ACGAATTATG
464840 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
464882 TA TA T
1 TA TA T
464887 TGAAACTATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:479142 original size:14 final size:14
Alignment explanation
Indices: 479125--479166 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
479115 CGTTTGTGAA
479125 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
479139 CGTTCGGTTATGTT
1 CGTTCGTTTATGTT
* *
479153 CATTCATTTATGTT
1 CGTTCGTTTATGTT
479167 TAACCCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.55
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:480258 original size:16 final size:16
Alignment explanation
Indices: 480234--480297 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
480224 CAACGTTTAC
480234 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
* *
480250 GTTCATTTATGTTCAT
1 GTTCGTTTATGTTCGT
480266 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
480282 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
480298 TTATTTGTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
GTTCGTTTATGTTCGT
Found at i:480277 original size:10 final size:10
Alignment explanation
Indices: 480227--480301 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
480217 GGGTCTCCAA
*
480227 CGTTTACGTT
1 CGTTTATGTT
480237 CGTTTATGTT
1 CGTTTATGTT
480247 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
480258 ATGTTCATGTT
1 -CGTTTATGTT
480269 CGTTTATGTT
1 CGTTTATGTT
480279 CG----TGTT
1 CGTTTATGTT
480285 CGTTTATGTT
1 CGTTTATGTT
480295 CGTTTAT
1 CGTTTAT
480302 TTGTTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:480388 original size:16 final size:16
Alignment explanation
Indices: 480367--480399 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
480357 AAAAAAATTT
*
480367 TGTTCGTTTATGTTCG
1 TGTTCGTTTAAGTTCG
480383 TGTTCGTTTAAGTTCG
1 TGTTCGTTTAAGTTCG
480399 T
1 T
480400 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTAAGTTCG
Found at i:486384 original size:16 final size:17
Alignment explanation
Indices: 486363--486398 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
486353 TGTTTAATTC
*
486363 AAATTG-ATTCGATTTA
1 AAATTGAATTCGACTTA
486379 AAATTGAATTCGACTTA
1 AAATTGAATTCGACTTA
486396 AAA
1 AAA
486399 CCTTAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (17 bp):
AAATTGAATTCGACTTA
Found at i:486610 original size:43 final size:43
Alignment explanation
Indices: 486549--486666 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
486539 ATTGTAATAT
* *
486549 GTTAGTTTGGGGTGTTTGTGAATTGTTACTTTAATTATAACAC
1 GTTAGTTTGGTGTATTTGTGAATTGTTACTTTAATTATAACAC
* * * *
486592 GTTAGTTTGGTATATTTGTGAATTGTTATTTTGATTATAATAC
1 GTTAGTTTGGTGTATTTGTGAATTGTTACTTTAATTATAACAC
* *
486635 GTTCGTTTGGTGTATATGT-ACATTGTTACTTT
1 GTTAGTTTGGTGTATTTGTGA-ATTGTTACTTT
486667 GGAATTTAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.22, C:0.06, G:0.21, T:0.51
Consensus pattern (43 bp):
GTTAGTTTGGTGTATTTGTGAATTGTTACTTTAATTATAACAC
Found at i:490214 original size:51 final size:52
Alignment explanation
Indices: 490155--490449 Score: 170
Period size: 57 Copynumber: 5.4 Consensus size: 52
490145 CATCCATACC
*
490155 TGCATGCTCT-TTGTTGGTGTTGATTTGAACAGCACTGTTCTCATTCTGACT
1 TGCATTCTCTGTTGTTGGTGTTGATTTGAACAGCACTGTTCTCATTCTGACT
* * * * * * *
490206 TGCATGCTCACTGTTATTGCTGTTGTAGTTCTGGGA-AGCATTATTCTCATTCTGACC
1 TGCAT--TCTCTGTTGTTGGTGTTG-A-TT-T-GAACAGCACTGTTCTCATTCTGACT
* ** * * * * *
490263 TGCATTTTCT-TTGTTGGTAATGCTCTT-AGCAACATTGTTCTCATTCTCACT
1 TGCATTCTCTGTTGTTGGTGTTGAT-TTGAACAGCACTGTTCTCATTCTGACT
* *
490314 TGCATTCTCGTTGTTGTTGGT-TTGAATCTGAACAGCATCATTGTTCTCAATCTGACT
1 TGCATTCTC--TGTTGTTGGTGTTG-ATTTGAACAGCA-C--TGTTCTCATTCTGACT
* * *
490371 TGTATTCTCATTGTTGTTGGTATTGATCTGAACAGCAGCGTTGTTCTCATTCTGACT
1 TGCATTCTC--TGTTGTTGGTGTTGATTTGAACAGCA-C--TGTTCTCATTCTGACT
* * *
490428 TGTATTCTC-ATTGTTGCTGTTG
1 TGCATTCTCTGTTGTTGGTGTTG
490450 TTGCTCTGGG
Statistics
Matches: 188, Mismatches: 38, Indels: 33
0.73 0.15 0.13
Matches are distributed among these distances:
51 30 0.16
52 2 0.01
53 8 0.04
54 42 0.22
55 4 0.02
56 2 0.01
57 95 0.51
58 5 0.03
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (52 bp):
TGCATTCTCTGTTGTTGGTGTTGATTTGAACAGCACTGTTCTCATTCTGACT
Found at i:490264 original size:108 final size:107
Alignment explanation
Indices: 490022--490488 Score: 325
Period size: 108 Copynumber: 4.4 Consensus size: 107
490012 TCGTTGTTTA
* * * * * * * *
490022 AGTTCTGGGAAGCATTATTC-CTATTCTGGCCCGCATTTTCTTTGTCGATAATGCTCTGAGA-AG
1 AGTTCTGGGAAGCATTATTCTC-ATTCTGACCTGCATTCTCTTTGTTGGTATTGATTTGA-ACAG
* ** * *
490085 CATTGTTCTCATTAAGACTTGCATTCTC--GCT-AT--TGTTGT
64 CACTGTTCTCATTCTGACTTGCATTCTCATGTTGTTGCTGTTGT
* * * * *
490124 AGTTCTGGGAAGCATTGTTTTCATCCAT-ACCTGCATGCTCTTTGTTGGTGTTGATTTGAACAGC
1 AGTTCTGGGAAGCATTATTCTCATTC-TGACCTGCATTCTCTTTGTTGGTATTGATTTGAACAGC
* *
490188 ACTGTTCTCATTCTGACTTGCATGCTCACTGTTATTGCTGTTGT
65 ACTGTTCTCATTCTGACTTGCATTCTCA-TGTTGTTGCTGTTGT
* * * * *
490232 AGTTCTGGGAAGCATTATTCTCATTCTGACCTGCATTTTCTTTGTTGGTAATGCTCTT-AGCAAC
1 AGTTCTGGGAAGCATTATTCTCATTCTGACCTGCATTCTCTTTGTTGGTATTGAT-TTGAACAGC
* * * *
490296 ATTGTTCTCATTCTCACTTGCATTCTCGTTGTTGTTGGT-TTG-
65 ACTGTTCTCATTCTGACTTGCATTCTC-ATGTTGTTGCTGTTGT
* * * * * * *
490338 A-ATCT-GAACAGCATCATTGTTCTCAATCTGACTTGTATTCTCATTGTTGTTGGTATTGATCTG
1 AGTTCTGGGA-AG---CATTATTCTCATTCTGACCTGCATTCTC--T-TTGTTGGTATTGATTTG
*
490401 AACAGCAGCGTTGTTCTCATTCTGACTTGTATTCTCA--TTGTTGCTGTTGT
59 AACAGCA-C--TGTTCTCATTCTGACTTGCATTCTCATGTTGTTGCTGTTGT
* * *
490451 TGCTCTGGGAAGCATTATTCTCATTCTGACCAGCATTC
1 AGTTCTGGGAAGCATTATTCTCATTCTGACCTGCATTC
490489 CGTTTGTCGT
Statistics
Matches: 278, Mismatches: 60, Indels: 45
0.73 0.16 0.12
Matches are distributed among these distances:
101 1 0.00
102 68 0.24
103 2 0.01
104 2 0.01
105 7 0.03
106 2 0.01
107 4 0.01
108 110 0.40
109 2 0.01
110 2 0.01
111 45 0.16
112 3 0.01
114 28 0.10
115 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (107 bp):
AGTTCTGGGAAGCATTATTCTCATTCTGACCTGCATTCTCTTTGTTGGTATTGATTTGAACAGCA
CTGTTCTCATTCTGACTTGCATTCTCATGTTGTTGCTGTTGT
Done.