Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007371.1 Hibiscus syriacus cultivar Beakdansim tig00019787_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: 128172
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4624 original size:4 final size:4
Alignment explanation
Indices: 4617--4641 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4607 GGAAGGGACA
4617 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
4642 CATAAATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5584 original size:17 final size:18
Alignment explanation
Indices: 5562--5598 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5552 TATTTTTTAA
5562 TATTTTTGAT-AAAATAT
1 TATTTTTGATCAAAATAT
*
5579 TATTTTTTATCAAAATAT
1 TATTTTTGATCAAAATAT
5597 TA
1 TA
5599 ATTTCGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTTTGATCAAAATAT
Found at i:5602 original size:19 final size:19
Alignment explanation
Indices: 5558--5602 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5548 AATATATTTT
5558 TTAATATTTTTGATAAAATA
1 TTAAT-TTTTTGATAAAATA
5578 TT-ATTTTTT-ATCAAAATA
1 TTAATTTTTTGAT-AAAATA
5596 TTAATTT
1 TTAATTT
5603 CGTTATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 6 0.26
20 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTAATTTTTTGATAAAATA
Found at i:12166 original size:16 final size:15
Alignment explanation
Indices: 12147--12180 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12137 GTAAAAACAG
12147 TAAATAAAAAGATAAA
1 TAAATAAAAAGA-AAA
*
12163 TAAATAAGAAGAAAA
1 TAAATAAAAAGAAAA
12178 TAA
1 TAA
12181 TCCTCACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAATAAAAAGAAAA
Found at i:22395 original size:17 final size:16
Alignment explanation
Indices: 22373--22406 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
22363 TAAAAACAGT
22373 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
22390 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
22406 A
1 A
22407 TCCTCAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:25431 original size:2 final size:2
Alignment explanation
Indices: 25384--25412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25374 TCTAAAAGAG
25384 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
25413 GAATAGTTGA
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:25724 original size:31 final size:31
Alignment explanation
Indices: 25686--25765 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
25676 AGTTGGGTAG
25686 TGTTCGACTCATGCTCGTTAA-AAAACTTTGT
1 TGTTCGACTCATGCTCGTTAAGAAAAC-TTGT
** * *
25717 T-TCTCGACTTGTGTTTGTTAAGAAAACTTGT
1 TGT-TCGACTCATGCTCGTTAAGAAAACTTGT
25748 TGTTCGACTCGATGCTCG
1 TGTTCGACTC-ATGCTCG
25766 CCTCTCTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
30 1 0.03
31 26 0.70
32 10 0.27
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
TGTTCGACTCATGCTCGTTAAGAAAACTTGT
Found at i:29468 original size:14 final size:14
Alignment explanation
Indices: 29449--29492 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
29439 CTAACCCTTG
29449 GTCAAACATGTTGA
1 GTCAAACATGTTGA
29463 GTCAAAC-TGTTG-
1 GTCAAACATGTTGA
*
29475 GTCAAATATGTTGA
1 GTCAAACATGTTGA
29489 GTCA
1 GTCA
29493 GCTGATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 11 0.41
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (14 bp):
GTCAAACATGTTGA
Found at i:29486 original size:13 final size:13
Alignment explanation
Indices: 29449--29492 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
29439 CTAACCCTTG
29449 GTCAAACATGTTGA
1 GTCAAA-ATGTTGA
*
29463 GTCAAACTGTTG-
1 GTCAAAATGTTGA
29475 GTCAAATATGTTGA
1 GTCAAA-ATGTTGA
29489 GTCA
1 GTCA
29493 GCTGATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 10 0.38
14 10 0.38
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (13 bp):
GTCAAAATGTTGA
Found at i:29752 original size:2 final size:2
Alignment explanation
Indices: 29745--29789 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29735 TGAAACTATC
29745 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
29787 AT A
1 AT A
29790 AAGAAGATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38949 original size:44 final size:44
Alignment explanation
Indices: 38874--38962 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
38864 TCTTACACTT
* * **
38874 AGATGGACACGTATCACTATAGGGTTGAAAGTAAAACTTATAAC
1 AGATGAACACGTATCACCATAGGGTCAAAAGTAAAACTTATAAC
* *
38918 AGATGAACATGTATCACCATATGGTCAAAAGTAAAACTTATAAC
1 AGATGAACACGTATCACCATAGGGTCAAAAGTAAAACTTATAAC
38962 A
1 A
38963 AATTAAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (44 bp):
AGATGAACACGTATCACCATAGGGTCAAAAGTAAAACTTATAAC
Found at i:40322 original size:2 final size:2
Alignment explanation
Indices: 40315--40383 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
40305 ACATATAAGA
40315 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
40357 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
40384 CTAACACACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40703 original size:19 final size:19
Alignment explanation
Indices: 40676--40725 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
40666 TTTTATTTAG
*
40676 GGGTATATCGATGCATTAT
1 GGGTGTATCGATGCATTAT
40695 GGGTGTATCGATGCATTAT
1 GGGTGTATCGATGCATTAT
*
40714 GGGTGCATCGAT
1 GGGTGTATCGAT
40726 ACACAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (19 bp):
GGGTGTATCGATGCATTAT
Found at i:43286 original size:39 final size:40
Alignment explanation
Indices: 43224--43319 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
43214 AGAAACCCAT
* *
43224 TAAAATATTATATATTTGTATAGGAT-CAAGGGTTTAGAA
1 TAAAATATTATATATATGCATAGGATCCAAGGGTTTAGAA
* *
43263 TAAGATATTATATATATGCATAGGATCCATGGGTTTAGAA
1 TAAAATATTATATATATGCATAGGATCCAAGGGTTTAGAA
43303 TAAAATATTATATATAT
1 TAAAATATTATATATAT
43320 ATATATATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 23 0.45
40 28 0.55
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39
Consensus pattern (40 bp):
TAAAATATTATATATATGCATAGGATCCAAGGGTTTAGAA
Found at i:43318 original size:2 final size:2
Alignment explanation
Indices: 43307--43339 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43297 TTAGAATAAA
43307 AT AT -T 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
43340 GCATAGGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44993 original size:20 final size:21
Alignment explanation
Indices: 44968--45060 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
44958 TTTTCCCAAT
*
44968 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
44988 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
45009 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
45029 TCGAAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
45050 TCGCAATGCGA
1 TCGCAATGCGA
45061 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:45013 original size:41 final size:41
Alignment explanation
Indices: 44968--45060 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
44958 TTTTCCCAAT
*
44968 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGAAACGCGAATTGGGAAAA
45009 TCGCAATGCGAATAAGTAAATCGAAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGAAACGCGAATTGGGAAAA
45050 TCGCAATGCGA
1 TCGCAATGCGA
45061 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGAAACGCGAATTGGGAAAA
Found at i:45091 original size:41 final size:41
Alignment explanation
Indices: 45046--45123 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
45036 GCGAATTGGG
* * *
45046 AAAATCGCAATGCGATACTTACTATT-GCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACT-TTCGCAACGCGATAATAC
45087 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
45124 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTTTCGCAACGCGATAATAC
Found at i:45139 original size:20 final size:20
Alignment explanation
Indices: 45091--45142 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
45081 TAATACAAAA
* *
45091 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
45111 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
45131 TCGCAACGCGAT
1 TCGCAACGCGAT
45143 TTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:45739 original size:19 final size:19
Alignment explanation
Indices: 45717--45881 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
45707 GAAACCAAAA
*
45717 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45736 TCGCGTTGTGATTTTTATT
1 TCGCGTTGCGATTTTCATT
45755 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
45775 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
45791 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
45808 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
45822 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
45841 CCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
45860 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45880 TC
1 TC
45882 AACCAAAAGA
Statistics
Matches: 115, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 54 0.47
20 33 0.29
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45798 original size:39 final size:39
Alignment explanation
Indices: 45722--45798 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
45712 CAAAATCGCA
* * **
45722 TTGCGATTTTCATTTCGCGTTGTGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
45761 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
45799 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:45807 original size:33 final size:33
Alignment explanation
Indices: 45770--45856 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
45760 GTTGCGATTT
* *
45770 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
45803 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
45836 TCATTCCGCGTTGCGATTCTC
1 TCATTTCGCGTTGCGATTCTC
45857 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:47941 original size:42 final size:42
Alignment explanation
Indices: 47881--48003 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
47871 GCCCGACTCG
* * *
47881 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
47923 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
47965 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
48004 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:47961 original size:21 final size:21
Alignment explanation
Indices: 47937--48003 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
47927 TCATTCCTCG
47937 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
47958 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
47979 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
48000 AGAG
1 AGAG
48004 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:49376 original size:14 final size:14
Alignment explanation
Indices: 49357--49392 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49347 ATTGTTTAAT
49357 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
49371 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
49385 TGATTTGT
1 TGATTTGT
49393 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:49574 original size:19 final size:19
Alignment explanation
Indices: 49552--49702 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
49542 CGAAATTAAA
49552 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
49571 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
49586 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
49604 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
49618 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
49637 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
49652 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
49670 TTCGCTTTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
49689 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
49703 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:49598 original size:33 final size:32
Alignment explanation
Indices: 49556--49682 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
49546 ATTAAATTCG
49556 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
49589 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
49622 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
49655 CGTTGCGATTTTCATTTCGCTTTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
49683 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:49639 original size:66 final size:66
Alignment explanation
Indices: 49549--49681 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
49539 ACGCGAAATT
*
49549 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
49614 G
66 G
* *
49615 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCTTTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
49680 G
66 G
49681 A
1 A
49682 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:51870 original size:12 final size:12
Alignment explanation
Indices: 51853--51877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51843 TCTTCGGGGA
51853 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51865 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51877 C
1 C
51878 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:52086 original size:24 final size:24
Alignment explanation
Indices: 52052--52105 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
52042 CTGAAACATC
* *
52052 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
52076 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
52100 ATCAAA
1 ATCAAA
52106 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:53134 original size:20 final size:20
Alignment explanation
Indices: 53109--53166 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
53099 ATTCATTTGA
53109 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
53129 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
53149 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
53167 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:53226 original size:19 final size:19
Alignment explanation
Indices: 53185--53338 Score: 211
Period size: 19 Copynumber: 8.6 Consensus size: 19
53175 GAAATGAAAA
53185 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
53201 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
53218 TCGCATTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATT
53237 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
53253 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53270 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53289 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
53308 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
53327 TCGCGTTGCGAT
1 TCGCATTGCGAT
53339 AGTCTGTTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 17
0.86 0.03 0.12
Matches are distributed among these distances:
14 22 0.18
16 6 0.05
17 6 0.05
19 90 0.73
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:53241 original size:52 final size:52
Alignment explanation
Indices: 53185--53338 Score: 236
Period size: 52 Copynumber: 2.9 Consensus size: 52
53175 GAAATGAAAA
*
53185 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGGTTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
53237 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
53289 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATTTCGCATTGCGAT
53339 AGTCTGTTTT
Statistics
Matches: 94, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
52 67 0.71
55 3 0.03
57 24 0.26
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:55366 original size:20 final size:19
Alignment explanation
Indices: 55331--55397 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
55321 GAAACTTAAA
55331 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
55350 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
55370 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
55389 ATCGCAACG
1 ATCGCAACG
55398 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:55405 original size:14 final size:14
Alignment explanation
Indices: 55386--55443 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55376 ATGCGAAATG
55386 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55400 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
55416 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
55432 AAAATCGCAACG
1 AAAATCGCAACG
55444 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55428 original size:32 final size:33
Alignment explanation
Indices: 55370--55448 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
55360 GGAAATGGCT
*
55370 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
55403 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
55435 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
55449 CACAAATCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:55488 original size:19 final size:19
Alignment explanation
Indices: 55464--55556 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 19
55454 ATCACATTGT
55464 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
55483 GA-TTT--TGT--CGTTGC
1 GATTTTCATTTCGCGTTGC
*
55497 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCGTTGC
***
55516 GATAGCCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
** *
55536 GATAGTCATTTCGTGTTGC
1 GATTTTCATTTCGCGTTGC
55555 GA
1 GA
55557 AAGTAAACTA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.14
15 3 0.05
16 2 0.03
17 2 0.03
18 3 0.05
19 24 0.41
20 17 0.29
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:55537 original size:20 final size:19
Alignment explanation
Indices: 55503--55556 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
55493 TTGCGATTTT
*
55503 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
55522 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
55542 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
55557 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:56055 original size:18 final size:18
Alignment explanation
Indices: 56029--56073 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
56019 GTCGATCAGA
* *
56029 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
56047 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
56065 TGATGGCTC
1 TGATGGCTC
56074 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:57609 original size:22 final size:22
Alignment explanation
Indices: 57584--57627 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
57574 GATTTAGATA
57584 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
57606 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
57628 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:57908 original size:20 final size:20
Alignment explanation
Indices: 57795--57908 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
57785 CGCTTTGAAA
57795 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
57815 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * *
57835 ATCGCGTTACGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
57855 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
57876 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
57896 ATCGCATTGCGAT
1 ATCGCATTGCGAT
57909 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 54 0.72
21 12 0.16
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:57926 original size:21 final size:21
Alignment explanation
Indices: 57897--57989 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
57887 ATAGTAAGTA
57897 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
57918 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
57938 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
57959 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
57979 TCGCATTGCGA
1 TCGCATTGCGA
57990 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:57927 original size:41 final size:41
Alignment explanation
Indices: 57836--57970 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
57826 AAAGTCAGTA
* * * * ** *
57836 TCGCGTTACGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
57876 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
57918 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
57959 TCGCGTTGCGAT
1 TCGCGTTGCGAT
57971 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:57971 original size:41 final size:41
Alignment explanation
Indices: 57897--57989 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
57887 ATAGTAAGTA
57897 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
57938 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
57979 TCGCATTGCGA
1 TCGCATTGCGA
57990 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:58227 original size:6 final size:6
Alignment explanation
Indices: 58216--58257 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
58206 AAACTCCAAT
58216 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC
58258 AATCAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCCCC
Found at i:60075 original size:60 final size:60
Alignment explanation
Indices: 59994--60159 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 60
59984 ATTGGAAGAA
** ** *
59994 TCAAAAGTTTGGGGACCAATTTAAAATGAGAGTCATAGCTTGAGGGTGAAA-TTAGAATGT
1 TCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGCTTGAGAATAAAATTTA-AATGT
* * * * *
60054 TCAAAAGTTTAAGGACTAATTTAGAATGAGAATCATAGGTT-ATGAATAAAATTTAAATTT
1 TCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGCTTGA-GAATAAAATTTAAATGT
* * *
60114 TTAAAGGTTTAAGGACCAATTTAAAATGAG-GATCATAGTTTGAGAA
1 TCAAAAGTTTAAGGACCAATTTAAAATGAGAG-TCATAGCTTGAGAA
60160 CATATGATAC
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 1 0.01
60 81 0.94
61 4 0.05
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (60 bp):
TCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGCTTGAGAATAAAATTTAAATGT
Found at i:64106 original size:29 final size:29
Alignment explanation
Indices: 64074--64130 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
64064 TTTTAAAAAA
64074 TTAAGGCTT-TTTTTAAAAATAAAATATTT
1 TTAA-GCTTCTTTTTAAAAATAAAATATTT
**
64103 TTAATTTTCTTTTTAAAAATAAAATATT
1 TTAAGCTTCTTTTTAAAAATAAAATATT
64131 AAAATTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (29 bp):
TTAAGCTTCTTTTTAAAAATAAAATATTT
Found at i:64696 original size:16 final size:17
Alignment explanation
Indices: 64675--64726 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
64665 TTTTTAATTT
64675 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
64691 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
64706 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
64723 AATT
1 AATT
64727 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:65032 original size:29 final size:30
Alignment explanation
Indices: 64967--65045 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
64957 TGGATTTTCG
*
64967 AAAAAATGACC-AGAAACATTATTAGACGCT
1 AAAAAATGACCGA-AAATATTATTAGACGCT
*
64997 AAAAAATGACCGAAAATATTATTAGGCGCT
1 AAAAAATGACCGAAAATATTATTAGACGCT
* *
65027 -AAAAATAATCGAAAATATT
1 AAAAAATGACCGAAAATATT
65046 TATAAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 26 0.59
31 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (30 bp):
AAAAAATGACCGAAAATATTATTAGACGCT
Found at i:73804 original size:15 final size:16
Alignment explanation
Indices: 73784--73816 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
73774 TAGACTTAAA
*
73784 ATTTAATAT-TTCTTT
1 ATTTAAAATATTCTTT
73799 ATTTAAAATATTCTTT
1 ATTTAAAATATTCTTT
73815 AT
1 AT
73817 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAAAATATTCTTT
Found at i:73861 original size:10 final size:10
Alignment explanation
Indices: 73833--73894 Score: 70
Period size: 11 Copynumber: 5.9 Consensus size: 10
73823 AATTATAAAA
*
73833 AATATAAAATA
1 AATA-AAAATG
73844 AATAAAAATG
1 AATAAAAATG
73854 CAATAAAAATG
1 -AATAAAAATG
73865 AATTAAAAATG
1 AA-TAAAAATG
* *
73876 AATAAAATTC
1 AATAAAAATG
73886 AATAAAAAT
1 AATAAAAAT
73895 ATAATGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
10 21 0.47
11 24 0.53
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (10 bp):
AATAAAAATG
Found at i:73872 original size:21 final size:21
Alignment explanation
Indices: 73833--73893 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
73823 AATTATAAAA
73833 AATATAAAATAAAT-AAAAATG
1 AATA-AAAATAAATAAAAAATG
* *
73854 CAATAAAAATGAATTAAAAATG
1 -AATAAAAATAAATAAAAAATG
* *
73876 AATAAAATTCAATAAAAA
1 AATAAAAATAAATAAAAA
73894 TATAATGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.68
22 11 0.32
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAAAAATAAATAAAAAATG
Found at i:73967 original size:28 final size:29
Alignment explanation
Indices: 73930--73986 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
73920 CTCTTTATTT
**
73930 AAAATAATTATTTATAATATT-AATTTTAA
1 AAAATAATTAAATA-AATATTAAATTTTAA
73959 AAAAT-ATTAAATAAATATTAAATTTTAA
1 AAAATAATTAAATAAATATTAAATTTTAA
73987 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 14 0.56
29 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATAATTAAATAAATATTAAATTTTAA
Found at i:78170 original size:14 final size:12
Alignment explanation
Indices: 78135--78171 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
78125 CAAGCAAAGA
78135 ATGTGAAGAGAG
1 ATGTGAAGAGAG
78147 ATGTGAAGAGAG
1 ATGTGAAGAGAG
78159 ATGTGAAGAGAG
1 ATGTGAAGAGAG
78171 A
1 A
78172 AGAAGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.41, T:0.16
Consensus pattern (12 bp):
ATGTGAAGAGAG
Found at i:81927 original size:2 final size:2
Alignment explanation
Indices: 81920--81976 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
81910 TTTTTAAAAC
81920 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
81962 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
81977 CCCCCATCCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83343 original size:18 final size:18
Alignment explanation
Indices: 83322--83357 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
83312 CTTCCATCCG
*
83322 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
83340 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
83358 GTCCTTTCGA
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:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:84368 original size:3 final size:3
Alignment explanation
Indices: 84360--84404 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
84350 AAACCATTAT
84360 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
84405 CGGAAGCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:89393 original size:2 final size:2
Alignment explanation
Indices: 89386--89412 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
89376 CTGAAAATTA
89386 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
89413 ATCAACTTTA
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:89783 original size:2 final size:2
Alignment explanation
Indices: 89776--89822 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
89766 TGCCCGAAAT
89776 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
89818 TA TA T
1 TA TA T
89823 TAACCTAGCA
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:101510 original size:21 final size:21
Alignment explanation
Indices: 101486--101532 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
101476 AGTACCCAAC
101486 AATAACAAAACCGATAGAAAA
1 AATAACAAAACCGATAGAAAA
*
101507 AATAACAAAATCGATAGAAAA
1 AATAACAAAACCGATAGAAAA
101528 AATAA
1 AATAA
101533 TGTTTTCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.68, C:0.11, G:0.09, T:0.13
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:104124 original size:3 final size:3
Alignment explanation
Indices: 104116--104142 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
104106 GAATAGGGTT
104116 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
104143 ATATAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:108503 original size:21 final size:22
Alignment explanation
Indices: 108473--108518 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
108463 GTTTTATGTT
* * *
108473 TTTTTAAAATATATATTTTTAA
1 TTTTTAAAATAAAAATTTTAAA
108495 TTTTT-AAATAAAAATTTTAAA
1 TTTTTAAAATAAAAATTTTAAA
108516 TTT
1 TTT
108519 ATCAGGTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAAAATAAAAATTTTAAA
Found at i:110275 original size:16 final size:16
Alignment explanation
Indices: 110254--110284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
110244 GAATAAGATC
110254 AAATTTATATTATAAT
1 AAATTTATATTATAAT
*
110270 AAATTTATTTTATAA
1 AAATTTATATTATAA
110285 AAAGTTTCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTATATTATAAT
Found at i:111153 original size:40 final size:36
Alignment explanation
Indices: 111080--111162 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 36
111070 TGAGCAGCTC
*
111080 AAAAATATAATATATTAAGATTTTATTTTATTTTTT
1 AAAAATATAATATATTAACATTTTATTTTATTTTTT
111116 AAAAATATTAATAATATTAACA-TTTATGTATTGATTTTTT
1 AAAAATA-TAAT-ATATTAACATTTTAT-T-TT-ATTTTTT
*
111156 TAAAATA
1 AAAAATA
111163 CAGTACGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 7 0.17
37 9 0.22
38 9 0.22
39 2 0.05
40 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
AAAAATATAATATATTAACATTTTATTTTATTTTTT
Found at i:113206 original size:32 final size:33
Alignment explanation
Indices: 113168--113257 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 33
113158 GGGTACAATA
* *
113168 ATTATAAAATTAATTATT-AATTTTATCTAATT
1 ATTATAAAATTAATTATTAAATTTTATCAAAAT
113200 ATTAT-AAATTAATTATTAAATTTTATCAAAAT
1 ATTATAAAATTAATTATTAAATTTTATCAAAAT
* *
113232 GTTATAAAA-TAATCATTAAATTTTAT
1 ATTATAAAATTAATTATTAAATTTTAT
113258 TAGATCGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.23
32 37 0.71
33 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
ATTATAAAATTAATTATTAAATTTTATCAAAAT
Found at i:113270 original size:32 final size:32
Alignment explanation
Indices: 113170--113293 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
113160 GTACAATAAT
* * *
113170 TATAAAATTAATTATT-AATTTTATC-TAATTA
1 TATAAAA-TAATCATTAAATTTTATCAAAATGA
* * *
113201 TTATAAATTAATTATTAAATTTTATCAAAATGT
1 -TATAAAATAATCATTAAATTTTATCAAAATGA
* *
113234 TATAAAATAATCATTAAATTTTAT-TAGATCGA
1 TATAAAATAATCATTAAATTTTATCAAAAT-GA
* *
113266 TATAAACTAATCATTCAA-TTTATCAAAA
1 TATAAAATAATCATTAAATTTTATCAAAA
113294 CTTTTATACT
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 16 0.21
32 56 0.75
33 3 0.04
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
TATAAAATAATCATTAAATTTTATCAAAATGA
Found at i:113301 original size:64 final size:64
Alignment explanation
Indices: 113169--113293 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
113159 GGTACAATAA
* * * *
113169 TTATAAAATTAATTATTAATTTTATCTAATTATTATAAATTAATTATTAAATTTTATCAAAATG
1 TTATAAAATTAATCATTAATTTTATCTAATGATTATAAACTAATCATTAAATTTTATCAAAATG
*
113233 TTATAAAA-TAATCATTAAATTTTAT-TAGATCGA-TATAAACTAATCATTCAA-TTTATCAAAA
1 TTATAAAATTAATCATT-AATTTTATCTA-AT-GATTATAAACTAATCATTAAATTTTATCAAAA
113294 CTTTTATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
63 19 0.36
64 33 0.62
65 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (64 bp):
TTATAAAATTAATCATTAATTTTATCTAATGATTATAAACTAATCATTAAATTTTATCAAAATG
Found at i:122434 original size:15 final size:15
Alignment explanation
Indices: 122416--122445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
122406 AAAACCATGT
*
122416 TAGATAAAAAGGTAA
1 TAGATAAAAAAGTAA
122431 TAGATAAAAAAGTAA
1 TAGATAAAAAAGTAA
122446 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAAGTAA
Found at i:122541 original size:4 final size:4
Alignment explanation
Indices: 122534--122676 Score: 51
Period size: 4 Copynumber: 34.8 Consensus size: 4
122524 ATAGTAAGTA
* * * * * * *
122534 AAAT AAAT ATAAA AAAT AAAG AAAA AGAAG AAAT AAAT ATAG AAAT AAAAC
1 AAAT AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT -AAAT
* * *
122585 AAAT AAAT AAA- ATAAT -AAT AAA- AAAGT AAAA ATAAT ATAT ATAT AAAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT A-AAT AAAT AAAT -AAAT
* * * * *
122634 AAA- AAAT AAAA AAAGT AAAT ATAT ATAT ATAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAA
122677 ACTGATAATA
Statistics
Matches: 105, Mismatches: 22, Indels: 24
0.70 0.15 0.16
Matches are distributed among these distances:
3 10 0.10
4 74 0.70
5 21 0.20
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:122572 original size:21 final size:21
Alignment explanation
Indices: 122534--122595 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
122524 ATAGTAAGTA
*
122534 AAATAAATATAAA-AAATAAAG
1 AAATAAA-ACAAATAAATAAAG
* *
122555 AAA-AAGAAGAAATAAATATAG
1 AAATAA-AACAAATAAATAAAG
122576 AAATAAAACAAATAAATAAA
1 AAATAAAACAAATAAATAAA
122596 ATAATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.18
21 26 0.76
22 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
AAATAAAACAAATAAATAAAG
Found at i:122592 original size:25 final size:23
Alignment explanation
Indices: 122555--122643 Score: 65
Period size: 25 Copynumber: 3.7 Consensus size: 23
122545 AAAAATAAAG
*
122555 AAAAAGAAGAAATAAATATAGAAAT
1 AAAAA-AATAAATAAATATA-AAAT
122580 AAAACAAATAAATAAA-ATAATAAT
1 AAAA-AAATAAATAAATATAA-AAT
* * *
122604 AAAAAAGTAAAAATAATATATATAT
1 AAAAAAATAAATA-AATATA-AAAT
122629 AAAATAAA-AAATAAA
1 AAAA-AAATAAATAAA
122644 AAAAGTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
23 8 0.15
24 14 0.27
25 26 0.50
26 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAAATAAATAAATATAAAAT
Found at i:122618 original size:29 final size:29
Alignment explanation
Indices: 122534--122645 Score: 88
Period size: 30 Copynumber: 3.7 Consensus size: 29
122524 ATAGTAAGTA
* * *
122534 AAATAAATATAAAAAATAAAGAAAAAGA-AG
1 AAATAAA-ATAAAAAATAAA-AATAATATAT
122564 AAATAAATATAGAAATAA-AACAAATAA-ATA-
1 AAATAAA-ATA-AAA-AATAA-AAATAATATAT
122594 AAATAATAATAAAAAAGTAAAAATAATATAT
1 AAATAA-AATAAAAAA-TAAAAATAATATAT
*
122625 ATATAAAATAAAAAATAAAAA
1 AAATAAAATAAAAAATAAAAA
122646 AAGTAAATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
28 2 0.03
29 15 0.21
30 35 0.49
31 16 0.23
32 3 0.04
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (29 bp):
AAATAAAATAAAAAATAAAAATAATATAT
Found at i:122618 original size:38 final size:38
Alignment explanation
Indices: 122576--122662 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
122566 ATAAATATAG
122576 AAATAA-A-ACAAAT-AAATAAAATAATAATAAAAAAGTAA
1 AAATAATATACAAATAAAATAAAA-AAT-A-AAAAAAGTAA
* *
122614 AAATAATATATATATAAAATAAAAAATAAAAAAAGTAA
1 AAATAATATACAAATAAAATAAAAAATAAAAAAAGTAA
*
122652 ATATATATATA
1 AAATA-ATATA
122663 TATAAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 20 0.48
39 7 0.17
40 7 0.17
41 8 0.19
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (38 bp):
AAATAATATACAAATAAAATAAAAAATAAAAAAAGTAA
Found at i:122655 original size:29 final size:29
Alignment explanation
Indices: 122576--122677 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 29
122566 ATAAATATAG
*
122576 AAATAAAACAAATAAATAAAATAATAATAAA
1 AAATAAAA-AAATAAAT-ATATAATAATAAA
*
122607 AAAGTAAAAATAATATATATATAA-AATAAA
1 AAA-TAAAAA-AATAAATATATAATAATAAA
122637 AAATAAAAAAAGTAAATATATATATATATAAA
1 AAATAAAAAAA-TAAATATATA-ATA-ATAAA
*
122669 TTAATAAAA
1 -AAATAAAA
122678 CTGATAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.03
29 15 0.25
30 10 0.17
31 10 0.17
32 16 0.27
33 7 0.12
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (29 bp):
AAATAAAAAAATAAATATATAATAATAAA
Found at i:122660 original size:37 final size:39
Alignment explanation
Indices: 122589--122727 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 39
122579 TAAAACAAAT
*
122589 AAATAAAATAATAATAAAAAAGTAAAAATAATATATATATA
1 AAATAAAA-AATAATAAAAAAGTAAATAT-ATATATATATA
122630 AAATAAAAAAT-A-AAAAAAGTAAATATATATATATATA
1 AAATAAAAAATAATAAAAAAGTAAATATATATATATATA
* * * *
122667 AATTAATAAAACTGATAATAAAAATAATATATTTATATATATA
1 AAATAA-AAAA-TAATAA-AAAAGTAA-ATATATATATATATA
**
122710 ATCTAAAAAA-AATAAAAA
1 AAATAAAAAATAATAAAAA
122728 TATATACTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
37 16 0.19
38 17 0.20
39 5 0.06
40 8 0.09
41 10 0.12
42 11 0.13
43 18 0.21
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (39 bp):
AAATAAAAAATAATAAAAAAGTAAATATATATATATATA
Found at i:122777 original size:22 final size:21
Alignment explanation
Indices: 122723--122783 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
122713 TAAAAAAAAT
122723 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
122743 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
122766 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
122784 AAAAGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 10 0.31
23 12 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:123129 original size:37 final size:36
Alignment explanation
Indices: 123086--123187 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
123076 ATAGTAGAAC
123086 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
123123 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
123157 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
123188 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:123948 original size:105 final size:105
Alignment explanation
Indices: 123734--124188 Score: 597
Period size: 105 Copynumber: 4.3 Consensus size: 105
123724 CATTGTTCCA
* ** * *
123734 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAACCGGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
123798 CCAGCCGTCCCTTCGTTGTGAAGTCGAACTTGTGTTGTCTCG
64 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
123840 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
123905 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
123945 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGA
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
124010 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
124050 AGTCCAATATCCTTTGTTGTGAAGTTGAAATAGGCTCTGAAATTGAGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* * * *
124115 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
124155 AGTGCCACGATATCCTCCTTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTCGTGAAGTTGAAAT
124189 CGCAGATGGC
Statistics
Matches: 312, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
105 242 0.78
106 48 0.15
107 2 0.01
108 20 0.06
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:124927 original size:67 final size:67
Alignment explanation
Indices: 124749--124949 Score: 219
Period size: 68 Copynumber: 3.0 Consensus size: 67
124739 TGTCTTGAAA
* * * * * *
124749 GAGATAGAATTTGTTTCAAGGGAAA-CAATCTCAAAGATATCTGTTGTTTCATGAGAAACGGTCT
1 GAGATAAAATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCT
124813 CAAGG
63 CAAGG
* * ** *
124818 GAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCA
1 GAGATAAAATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCA
124883 AGG
65 AGG
* * *
124886 GAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAA
1 GAGATAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
124949 G
66 G
124950 ATAGACGAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
65 22 0.20
66 3 0.03
67 22 0.20
68 31 0.28
69 11 0.10
70 19 0.17
71 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (67 bp):
GAGATAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
GG
Found at i:124965 original size:65 final size:67
Alignment explanation
Indices: 124756--124975 Score: 189
Period size: 65 Copynumber: 3.3 Consensus size: 67
124746 AAAGAGATAG
* * * * *
124756 AATTTGTTTCAAGGGAAA-CAATCTCAAAGA-TATCTGTTGTTTCATGAGAAACGGTCTCAAGGG
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAGT-T-TG-TGTTTCAAGAGAAACTGTCTCAAGAG
* *
124819 AAACAA
62 AGAGAA
** * * *
124825 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
*
124890 TAA
65 GAA
* * *
124893 AATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAAGATAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA-
124956 GAA
65 GAA
* *
124959 AA-TTGTTTCAAGAGAAA
1 AATTTGTTTTAAGGGAAA
124976 CTGTCTCAAG
Statistics
Matches: 126, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
65 37 0.29
66 7 0.06
67 22 0.17
68 31 0.25
69 6 0.05
70 19 0.15
71 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAG
AA
Found at i:124976 original size:36 final size:35
Alignment explanation
Indices: 124925--125203 Score: 254
Period size: 36 Copynumber: 8.0 Consensus size: 35
124915 TTCAAAGGTT
* *
124925 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
124961 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
124996 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
125034 TTGTTTCAA-AGAAAACATAT-T--A-A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
125063 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
125098 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
125135 TTGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
125168 TTATTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
125204 CTCTTCTAGT
Statistics
Matches: 200, Mismatches: 25, Indels: 36
0.77 0.10 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.00
31 2 0.01
32 2 0.01
33 6 0.03
34 25 0.12
35 9 0.05
36 101 0.50
37 33 0.17
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:125034 original size:138 final size:137
Alignment explanation
Indices: 124873--125177 Score: 384
Period size: 138 Copynumber: 2.2 Consensus size: 137
124863 TTTCAAGAGT
* * ** * * * *
124873 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
* *
124938 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
125002 TCCAAAAGA
129 TCCAAAAGA
* * *
125011 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTAAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
* * * * *
125076 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
125141 CAAGAGA
131 CAAAAGA
125148 AACTGTCTCAA--GAGACAAAATTAT-TTTCAA
1 AACTGTCTCAAGGGAGACAAAATT-TGTTTCAA
125178 GGGAAACTGT
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
135 16 0.11
136 1 0.01
137 26 0.18
138 102 0.70
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:125149 original size:102 final size:102
Alignment explanation
Indices: 124961--125149 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
124951 TAGACGAAAA
*
124961 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
125026 GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
* * * ** *
125063 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
125127 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
125150 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 37 0.47
102 42 0.53
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
Found at i:125187 original size:70 final size:72
Alignment explanation
Indices: 125062--125199 Score: 228
Period size: 70 Copynumber: 1.9 Consensus size: 72
125052 ATTAAAATAT
* *
125062 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
125127 GACGAAA
66 GACGAAA
125134 TTTGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAA-TTATTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGAG
125196 AGAC
65 AGAC
125200 AAAACTCTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
69 3 0.05
70 37 0.59
71 1 0.02
72 22 0.35
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (72 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
GACGAAA
Found at i:126123 original size:22 final size:22
Alignment explanation
Indices: 126098--126146 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
126088 TTGTGTTTGG
126098 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
126120 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
126142 TCAAA
1 TCAAA
126147 AGATTGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:126781 original size:20 final size:21
Alignment explanation
Indices: 126758--126817 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
126748 TTTGTCCCTT
*
126758 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
126778 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
126799 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
126818 TTTCTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:126804 original size:8 final size:7
Alignment explanation
Indices: 126791--126834 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 7
126781 TTTGTTCTTG
126791 TTTTTTCC
1 TTTTTT-C
126799 TTTTTTGC
1 TTTTTT-C
126807 TTCTTTTC
1 TT-TTTTC
126815 TTTTTTC
1 TTTTTTC
126822 TTTTTTTC
1 -TTTTTTC
126830 TTTTT
1 TTTTT
126835 GCCTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 10 0.30
8 19 0.58
9 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:126819 original size:6 final size:7
Alignment explanation
Indices: 126755--126834 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
126745 CTTTTTGTCC
126755 CTTTTTT
1 CTTTTTT
*
126762 TTATTTTT
1 CT-TTTTT
* *
126770 GTTCTTT
1 CTTTTTT
126777 CTTTTTT
1 CTTTTTT
* *
126784 GTTCTTGT
1 CTT-TTTT
*
126792 -TTTTTC
1 CTTTTTT
126798 CTTTTTT
1 CTTTTTT
126805 GCTTCTTTT
1 -CTT-TTTT
126814 CTTTTTT
1 CTTTTTT
126821 CTTTTTTT
1 C-TTTTTT
126829 CTTTTT
1 CTTTTT
126835 GCCTTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
6 2 0.04
7 29 0.51
8 22 0.39
9 4 0.07
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:126840 original size:16 final size:15
Alignment explanation
Indices: 126778--126844 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
126768 TTGTTCTTTC
* *
126778 TTTTTTGTTCTTG-T
1 TTTTTTCTTTTTGCT
*
126792 TTTTTCCTTTTTTGCT
1 TTTTTTC-TTTTTGCT
* *
126808 TCTTTTCTTTTTTCT
1 TTTTTTCTTTTTGCT
126823 TTTTTTCTTTTTGCCT
1 TTTTTTCTTTTTG-CT
126839 TTTTTT
1 TTTTTT
126845 GTTCTGATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 5 0.12
15 23 0.55
16 14 0.33
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTTTTGCT
Found at i:126840 original size:23 final size:24
Alignment explanation
Indices: 126791--126843 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
126781 TTTGTTCTTG
*
126791 TTTTTTCCTTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTTGCTTCTTTCC
*
126815 TTTTTT-CTTTTTTTCTT-TTTGCC
1 TTTTTTCCTTTTTTGCTTCTTT-CC
126838 TTTTTT
1 TTTTTT
126844 TGTTCTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 17 0.65
24 6 0.23
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TTTTTTCCTTTTTTGCTTCTTTCC
Found at i:128031 original size:15 final size:15
Alignment explanation
Indices: 128011--128041 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128001 AATGTAGATG
128011 AAAATGCAAAAATGC
1 AAAATGCAAAAATGC
*
128026 AAAATGCAAGAATGC
1 AAAATGCAAAAATGC
128041 A
1 A
128042 CGAAATGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAATGCAAAAATGC
Done.