Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007774.1 Hibiscus syriacus cultivar Beakdansim tig00110055_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: 176222
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:195 original size:21 final size:21
Alignment explanation
Indices: 170--213 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
160 CCCCTTATGC
170 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
191 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
212 CT
1 CT
214 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2456 original size:19 final size:19
Alignment explanation
Indices: 2401--2447 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
2391 ATCCGGTATC
2401 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
2420 -TTTGATACCGGTTTTATCAT
1 ATTT--TACCGGTTTTATCAT
2440 ATTTTACC
1 ATTTTACC
2448 TGTTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:2608 original size:20 final size:20
Alignment explanation
Indices: 2582--2627 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
2572 TCCGGTAACG
2582 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
2601 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
2622 TTTACC
1 TTTACC
2628 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:3167 original size:224 final size:228
Alignment explanation
Indices: 2680--3380 Score: 1217
Period size: 228 Copynumber: 3.1 Consensus size: 228
2670 TTATACGTAT
2680 ACTTTTAT--AAATGATATATACTTTTTTTAAAGTTATGTAA--TATGTTTCAATTTTTTTTAAT
1 ACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAT
*
2741 AGCGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTATTTGAT
66 AGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTATTTGAT
*
2806 TTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATATAATAAT
131 TTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
2871 AAATATGTTTTCCACAGTG-AATAAGTATGGAC
196 AAATATGTTTTCCACAGTGAAATAAGTATGGAC
*
2903 ACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCATTTTTTTTTTAA
1 ACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA-ATTTTTTTTAA
*
2968 TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTTTTTGA
65 TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTATTTGA
*
3033 TTTTTT-TTATTTT-T-AAA-ATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAA
130 TTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAA
3094 TAAATATGTTTTCCACAGTGAAATAAGTATGGAC
195 TAAATATGTTTTCCACAGTGAAATAAGTATGGAC
*
3128 ACTTTTATAAAAATGATATATAC-TTTTTTAAAGTTATGTAATTTATGTTTGAATTTTTTTTAAT
1 ACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAT
*
3192 AGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACATAATTATTTGA
66 AGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA-AAAATTATTTGA
3257 TTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAA
130 TTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAA
*
3322 TAAATATATTTT-CACAGTGAAATAAGTATGGAC
195 TAAATATGTTTTCCACAGTGAAATAAGTATGGAC
* *
3355 ACTTTTATAAAAAAGATAGATACTTT
1 ACTTTTATAAAAATGATATATACTTT
3381 ACATAACAGG
Statistics
Matches: 453, Mismatches: 13, Indels: 19
0.93 0.03 0.04
Matches are distributed among these distances:
223 71 0.16
224 107 0.24
225 77 0.17
226 2 0.00
227 60 0.13
228 136 0.30
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (228 bp):
ACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAT
AGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTATTTGAT
TTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
AAATATGTTTTCCACAGTGAAATAAGTATGGAC
Found at i:8729 original size:21 final size:22
Alignment explanation
Indices: 8700--8741 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
8690 TTAACTTAAG
*
8700 TAATAATTTTA-ATTTTTTTAT
1 TAATAATTTTATATATTTTTAT
*
8721 TAATGATTTTATATATTTTTA
1 TAATAATTTTATATATTTTTA
8742 ACTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TAATAATTTTATATATTTTTAT
Found at i:10251 original size:20 final size:20
Alignment explanation
Indices: 10226--10275 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
10216 TTGTCTTATG
10226 GTATCGATACTATTCATGAA
1 GTATCGATACTATTCATGAA
* *
10246 GTATCGATATTGTTCATGAA
1 GTATCGATACTATTCATGAA
10266 GTATCGATAC
1 GTATCGATAC
10276 CCACACATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
GTATCGATACTATTCATGAA
Found at i:11652 original size:44 final size:44
Alignment explanation
Indices: 11603--11688 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
11593 ATAAATCAAG
* *
11603 ATCTCCTTATAACATAGGTAATATATTTTCCTTCATGCTCTCTA
1 ATCTCCTCATAACATAGGCAATATATTTTCCTTCATGCTCTCTA
*
11647 ATCTCCTCATAACATAGGCAATATCTTTTCCTTCATGCTCTC
1 ATCTCCTCATAACATAGGCAATATATTTTCCTTCATGCTCTC
11689 CTACTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.26, C:0.27, G:0.07, T:0.41
Consensus pattern (44 bp):
ATCTCCTCATAACATAGGCAATATATTTTCCTTCATGCTCTCTA
Found at i:13543 original size:21 final size:21
Alignment explanation
Indices: 13517--13556 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13507 CCGAAGTACC
*
13517 ACATATATGTTCCAAATGATT
1 ACATATATGTCCCAAATGATT
*
13538 ACATATATGTCCCGAATGA
1 ACATATATGTCCCAAATGA
13557 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
ACATATATGTCCCAAATGATT
Found at i:17076 original size:149 final size:148
Alignment explanation
Indices: 16807--17112 Score: 486
Period size: 149 Copynumber: 2.1 Consensus size: 148
16797 GAGTCGAGGG
* * * * * * *
16807 TCTACGTGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
16872 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
*
16937 ATGGCACTACGGTGCAAT
131 AAGGCACTACGGTGCAAT
* *
16955 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
17020 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
17085 TAAGGCACTACGGTGTAAT
130 TAAGGCACTACGGTGCAAT
17104 TCTACGCGG
1 TCTACGCGG
17113 CACTACGGTG
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 47 0.33
149 97 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
AAGGCACTACGGTGCAAT
Found at i:17143 original size:22 final size:23
Alignment explanation
Indices: 17088--17148 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
17078 ATTATTATAA
*
17088 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
17111 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
17133 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
17149 GATACGAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:22330 original size:149 final size:148
Alignment explanation
Indices: 22061--22366 Score: 479
Period size: 149 Copynumber: 2.1 Consensus size: 148
22051 GAGTCGAGGG
* * * * * *
22061 TCTACGCGGTCTTTCGGGACATATGTATTTTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCTTTCGGGACATATATATTTTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
22126 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
*
22191 ATGGCACTACGGTGCAAT
131 AAGGCACTACGGTGCAAT
* * *
22209 TCTACGTGGTCTTTCGGGATATATATATATTT-TGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TCTACGCGGTCTTTCGGGACATATATAT-TTTCTGTGGAACATGTATGAAGTCTT-TAAGACACA
22273 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATT
22338 ATAAGGCACTACGGTGCAAT
129 ATAAGGCACTACGGTGCAAT
22358 TCTACGCGG
1 TCTACGCGG
22367 CACTACGGTG
Statistics
Matches: 143, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
148 43 0.30
149 100 0.70
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCTTTCGGGACATATATATTTTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
AAGGCACTACGGTGCAAT
Found at i:22408 original size:22 final size:23
Alignment explanation
Indices: 22342--22402 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
22332 ATTATTATAA
22342 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
22365 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
22387 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
22403 GATACGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:24694 original size:18 final size:19
Alignment explanation
Indices: 24662--24699 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
24652 TAGATTAATA
24662 AAAAAAATATAAATAATTTT
1 AAAAAAATATAAAT-ATTTT
24682 AAAAAAA-AT-AATATTTT
1 AAAAAAATATAAATATTTT
24699 A
1 A
24700 GATTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 2 0.11
20 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAAATATAAATATTTT
Found at i:32478 original size:15 final size:16
Alignment explanation
Indices: 32448--32513 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
32438 AACAAAATGC
32448 TAAAAAATAAAAAATA
1 TAAAAAATAAAAAATA
*
32464 TAAAAAAT-AATAATA
1 TAAAAAATAAAAAATA
* *
32479 TAATGAAAGAAAGAAATAA
1 TAA-AAAATAAA-AAAT-A
32498 TAAAATAATAATAAAA
1 TAAAA-AATAA-AAAA
32514 GGTTAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 9 0.24
16 11 0.29
17 2 0.05
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
TAAAAAATAAAAAATA
Found at i:32528 original size:21 final size:20
Alignment explanation
Indices: 32499--32551 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
32489 AAGAAATAAT
* *
32499 AAAATAATAATAAAAGGTTAA
1 AAAAAAATAATAAAAAG-TAA
*
32520 AAAAAAATATTTAAAAAGTAA
1 AAAAAAATA-ATAAAAAGTAA
32541 ATAAAAAATAA
1 A-AAAAAATAA
32552 AGATAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAAAATAATAAAAAGTAA
Found at i:32528 original size:32 final size:29
Alignment explanation
Indices: 32456--32528 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 29
32446 GCTAAAAAAT
* *
32456 AAAAAATATAAAAAATAATAATATAATGA
1 AAAAAAAATAAAAAATAATAATAAAATGA
*
32485 AAGAAAGAAATAATAAAATAATAATAAAAGGTTA
1 AA-AAA-AAATAA-AAAATAATAATAAAA--TGA
32519 AAAAAAAATA
1 AAAAAAAATA
32529 TTTAAAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
29 2 0.06
30 3 0.08
31 5 0.14
32 19 0.53
33 3 0.08
34 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAAAAAATAAAAAATAATAATAAAATGA
Found at i:35107 original size:7 final size:7
Alignment explanation
Indices: 35095--35120 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35085 GAAAAGACTA
35095 CAGCTTC
1 CAGCTTC
35102 CAGCTTC
1 CAGCTTC
35109 CAGCTTC
1 CAGCTTC
35116 CAGCT
1 CAGCT
35121 GCATATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (7 bp):
CAGCTTC
Found at i:35849 original size:33 final size:33
Alignment explanation
Indices: 35806--35969 Score: 219
Period size: 33 Copynumber: 5.1 Consensus size: 33
35796 TAGAAGAACC
35806 ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
1 ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
*
35839 GCCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
1 ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
*
35872 GCCTCTTGCT-C-CTAGGAGAA-AAGTC-TCCCT
1 ACCTCTTGCTCCTCTAGGAGAATAA-TCTTCCCT
* * *
35902 ACCACTAGCTCCTCTAGGAGAATAGTCTTCCCT
1 ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
* * *
35935 ACCTCCTGCTCCTCTAGGAGAATAGTCGTCCCT
1 ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
35968 AC
1 AC
35970 GAGGAGGCGG
Statistics
Matches: 117, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.12
31 12 0.10
32 12 0.10
33 79 0.68
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (33 bp):
ACCTCTTGCTCCTCTAGGAGAATAATCTTCCCT
Found at i:35915 original size:63 final size:66
Alignment explanation
Indices: 35806--35969 Score: 219
Period size: 63 Copynumber: 2.5 Consensus size: 66
35796 TAGAAGAACC
* * * *
35806 ACCTCTTGCTCCTCTAGGAGAATAA-TCTTCCCTGCCTCTTGCTCCTCTAGGAGAATAATCTTCC
1 ACCTCTTGCTCCTCTAGGAGAA-AAGTCGTCCCTACCACTAGCTCCTCTAGGAGAATAATCTTCC
35870 CT
65 CT
* *
35872 GCCTCTTGCT-C-CTAGGAGAAAAGTC-TCCCTACCACTAGCTCCTCTAGGAGAATAGTCTTCCC
1 ACCTCTTGCTCCTCTAGGAGAAAAGTCGTCCCTACCACTAGCTCCTCTAGGAGAATAATCTTCCC
35934 T
66 T
* *
35935 ACCTCCTGCTCCTCTAGGAGAATAGTCGTCCCTAC
1 ACCTCTTGCTCCTCTAGGAGAAAAGTCGTCCCTAC
35970 GAGGAGGCGG
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 44 0.51
64 12 0.14
65 14 0.16
66 16 0.19
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (66 bp):
ACCTCTTGCTCCTCTAGGAGAAAAGTCGTCCCTACCACTAGCTCCTCTAGGAGAATAATCTTCCC
T
Found at i:47497 original size:23 final size:23
Alignment explanation
Indices: 47431--47490 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
47421 TCGAAATAGG
*
47431 GTATCGATACCGTATCTAGGGAA
1 GTATCGGTACCGTATCTAGGGAA
*
47454 GTATCGGTACCATATCTAGGGAA
1 GTATCGGTACCGTATCTAGGGAA
47477 GTATCGGTACCGTA
1 GTATCGGTACCGTA
47491 CATAGGGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (23 bp):
GTATCGGTACCGTATCTAGGGAA
Found at i:48324 original size:14 final size:14
Alignment explanation
Indices: 48305--48332 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48295 ATATATGTTA
48305 TATGTGGTCCTTCG
1 TATGTGGTCCTTCG
48319 TATGTGGTCCTTCG
1 TATGTGGTCCTTCG
48333 AGACATTTCT
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:0.07, C:0.21, G:0.29, T:0.43
Consensus pattern (14 bp):
TATGTGGTCCTTCG
Found at i:48664 original size:6 final size:6
Alignment explanation
Indices: 48657--49478 Score: 1484
Period size: 6 Copynumber: 138.7 Consensus size: 6
48647 AATGAGATTA
* *
48657 TATGTA TATGTG TACGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48705 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
48753 TATGTG TATGTG TATGTT TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48801 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48849 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48897 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48945 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
48993 TA--TG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49039 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49087 TATGTG TA--TG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49133 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49181 TATGTG TATGTG TATGTG TA--TG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49227 TATGTG TATGTG TA--TG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49273 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49321 TATGTG TA--TG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
49367 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * *
49415 TATGTG TATGTG TATGTG TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* *
49463 TATGTA TATGTA TATG
1 TATGTG TATGTG TATG
49479 GATATCAACC
Statistics
Matches: 800, Mismatches: 6, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
4 20 0.03
6 780 0.98
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:54471 original size:3 final size:3
Alignment explanation
Indices: 54465--54536 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
54455 TACTATTATT
54465 TAA TAA TAA TAA TAA TAA TACA TAA TAA TAA TAA T-A TCAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA
* *
54511 TAA TAT TAA TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
54537 AATGGAAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 52 0.85
4 5 0.08
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55031 original size:42 final size:41
Alignment explanation
Indices: 54955--55035 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
54945 AAGGTCTTAT
* * * *
54955 CATCTTGCTCGAAAGGCCTACAGTGACCCTAATGATTTAAG
1 CATCATGCTCGAAAGACCTACAATGACCCGAATGATTTAAG
*
54996 CATCATGCTCGAAAGACTTACTAATGACCCGAATGATTTA
1 CATCATGCTCGAAAGACCTAC-AATGACCCGAATGATTTA
55036 CTTATCAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGACCTACAATGACCCGAATGATTTAAG
Found at i:56911 original size:42 final size:42
Alignment explanation
Indices: 56835--56943 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
56825 AACTGAAGGT
* * *
56835 CTTATGGATGACCCGAAGGCTTTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGG-ATTTAAGCATCATGCTCAAAAGA
*
56878 CTTATAGATAACCCGAAGGATTTAAGCATCATGCTCAAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
*
56920 CTTACAGATGACCCGAAGGATTTA
1 CTTATAGATGACCCGAAGGATTTA
56944 CGAATCAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 43 0.72
43 17 0.28
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
Found at i:56992 original size:267 final size:265
Alignment explanation
Indices: 56423--57197 Score: 1177
Period size: 267 Copynumber: 2.9 Consensus size: 265
56413 GACACCCACC
*
56423 ACCCTCGAAAGCTTAGTTTCTTAGTTG-ACAAGGAATCCCTTTGTTAGGCTTAGC-TTCATTTAA
1 ACCCTCGAAAGCTTAGTTTCTTAGTTGTA-AAGGAACCCCTTTGTTAGGCTTAGCTTTC-TTTAA
* *
56486 CAACTCTTTTGAGATAATTATGAAACCCCTTAAAATTAGGCTTAGTTTCTAATATCTCATTTGAA
64 CAACTCTTTTGAGATAATTAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAA
* * * * * * * *
56551 AACATACTGCACTAAAGGCCTTATGGATGACCCAAAGGCTTTATCATCTTGCTTGAAAGGCTTAT
129 AGCATCCAGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGACTTAT
* * *
56616 AAATGACCCGAAGGATTTAAGCATCATGTTCGAAAGACTTACAGATGACCCGAAGGATTTACGAA
194 AGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTACGAA
56681 TCAAGAA
259 TCAAGAA
* * *
56688 ACCCTCGAAAGCTTAGTTTCTTAGTTGTTAAGGAACCCCTTTGTTAGGGTTAACTTTCTTTAACA
1 ACCCTCGAAAGCTTAGTTTCTTAGTTGTAAAGGAACCCCTTTGTTAGGCTTAGCTTTCTTTAACA
*
56753 ACTCTTTTGAGATAATTAAGAAACCCCTTAAAATTAGGCTTAGTTTATAAAATCTCATTTGAAAG
66 ACTCTTTTGAGATAATTAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAAAG
* * *
56818 CATCCAGAACTGAAGGTCTTATGGATGACCCGAAGGCTTTTAAGCATCATGCTCGAAAGACTTAT
131 CATCCAGCACTGAAGGTCTTATGGATGACCCGAAGGC-TTT-ATCATCTTGCTCGAAAGACTTAT
*
56883 AGATAACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTACGAA
194 AGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTACGAA
56948 TCAAGAA
259 TCAAGAA
* *
56955 ACCCTTGAAAGCTTAGTTTCTTAGTTGTAAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACA
1 ACCCTCGAAAGCTTAGTTTCTTAGTTGTAAAGGAACCCCTTTGTTAGGCTTAGCTTTCTTTAACA
* *
57020 ACTCTTTTGAGATAATTAGGAAACCCC-T-GAA--AGGCTTAGTTTCTAAAATCTCATTTGAAAG
66 ACTCTTTTGAGATAATTAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAAAG
* *
57081 CATCCATCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAA-AGCTTACA
131 CATCCAGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGA-CTTATA
* * *
57145 GATGACCTGAAGAATTTAAGCATCATGCTCAAAAGACTTACAGATGGCCCGAA
195 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGACCCGAA
57198 TGACTTACAA
Statistics
Matches: 466, Mismatches: 39, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
260 1 0.00
261 68 0.15
262 3 0.01
263 64 0.14
265 150 0.32
266 7 0.02
267 173 0.37
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (265 bp):
ACCCTCGAAAGCTTAGTTTCTTAGTTGTAAAGGAACCCCTTTGTTAGGCTTAGCTTTCTTTAACA
ACTCTTTTGAGATAATTAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAAAG
CATCCAGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGACTTATAG
ATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTACGAATC
AAGAA
Found at i:57904 original size:22 final size:22
Alignment explanation
Indices: 57879--57933 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
57869 AATAAAACTT
* * *
57879 TCATCTTTGAAAATATAATCTA
1 TCATCTTTGAAAAGAGAATATA
57901 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
*
57923 TCGTCTTTGAA
1 TCATCTTTGAA
57934 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:58716 original size:22 final size:22
Alignment explanation
Indices: 58681--58727 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
58671 TCTTGCTGAT
*
58681 ATGAGCCTTTAAAATGTCCAAC
1 ATGAGCCTTTAAAATGCCCAAC
*
58703 ATGAG-CTTTCAAAATGCCCCAC
1 ATGAGCCTTT-AAAATGCCCAAC
58725 ATG
1 ATG
58728 GATCTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (22 bp):
ATGAGCCTTTAAAATGCCCAAC
Found at i:58864 original size:41 final size:41
Alignment explanation
Indices: 58810--58892 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
58800 CACATGGATC
*
58810 ATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAATATTCT
1 ATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAACATTCT
* *
58851 ATTTCTGGT-TGAAATGGGCCTTCAAGATGTCCCAACATTCT
1 ATTTCT-GTCTGAAATGGGCCTTCAAAATGCCCCAACATTCT
58892 A
1 A
58893 AACTGTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.95
42 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (41 bp):
ATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAACATTCT
Found at i:60392 original size:5 final size:5
Alignment explanation
Indices: 60382--60425 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
60372 CTTGATTCAA
*
60382 TTTTC TTTTC TTCT- TTTTC TTTTC TTTTC TTTTC TTTTC ATTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTT
60426 TTCATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
4 3 0.09
5 28 0.80
6 4 0.11
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:60415 original size:29 final size:27
Alignment explanation
Indices: 60387--60455 Score: 52
Period size: 29 Copynumber: 2.4 Consensus size: 27
60377 TTCAATTTTC
60387 TTTTCTTCTTTT-TCTTTTCTTTTCTTTT
1 TTTTCTT-TTTTCTCTTTTCTTTTC-TTT
* *
60415 CTTTTCATTTTTTCATTTTTTCTCTTT-TGT
1 -TTTTC-TTTTTTC-TCTTTTCT-TTTCTTT
60445 TTTTCTTTTTT
1 TTTTCTTTTTT
60456 TCTGATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
28 6 0.18
29 14 0.41
30 4 0.12
31 7 0.21
32 3 0.09
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (27 bp):
TTTTCTTTTTTCTCTTTTCTTTTCTTT
Found at i:60416 original size:15 final size:14
Alignment explanation
Indices: 60382--60456 Score: 73
Period size: 15 Copynumber: 5.2 Consensus size: 14
60372 CTTGATTCAA
*
60382 TTTTCTTTTCTTCT
1 TTTTCTTTTCTTTT
60396 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
60410 CTTTTCTTTTCATTTT
1 -TTTTCTTTTC-TTTT
*
60426 TTCATT-TTTTCTCTT
1 TT--TTCTTTTCTTTT
*
60441 TTGT-TTTTCTTTT
1 TTTTCTTTTCTTTT
60454 TTT
1 TTT
60457 CTGATGAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
13 11 0.21
14 13 0.25
15 17 0.33
16 9 0.17
17 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Found at i:60435 original size:10 final size:9
Alignment explanation
Indices: 60382--60456 Score: 62
Period size: 10 Copynumber: 7.8 Consensus size: 9
60372 CTTGATTCAA
60382 TTTTCTTTTC
1 TTTT-TTTTC
*
60392 TTCTTTTTC
1 TTTTTTTTC
60401 TTTTCTTTTC
1 TTTT-TTTTC
60411 TTTTCTTTTC
1 TTTT-TTTTC
*
60421 -ATTTTTTC
1 TTTTTTTTC
*
60429 ATTTTTTCTC
1 -TTTTTTTTC
60439 TTTTGTTTTTC
1 -TTT-TTTTTC
60450 TTTTTTT
1 TTTTTTT
60457 CTGATGAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 5 0.09
9 14 0.26
10 30 0.56
11 5 0.09
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:62987 original size:14 final size:14
Alignment explanation
Indices: 62970--63001 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
62960 CAAACGTAAA
62970 AATGCAAAGATGTG
1 AATGCAAAGATGTG
62984 AATGCAAAGATGTG
1 AATGCAAAGATGTG
62998 AATG
1 AATG
63002 TAACATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (14 bp):
AATGCAAAGATGTG
Found at i:66365 original size:11 final size:11
Alignment explanation
Indices: 66349--66382 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
66339 TTATATGACT
66349 AAAATAAAATA
1 AAAATAAAATA
66360 AAAATAAAATA
1 AAAATAAAATA
*
66371 ATAATTAAAATA
1 A-AAATAAAATA
66383 CTAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:66898 original size:16 final size:18
Alignment explanation
Indices: 66863--66902 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
66853 TTATTCATTT
66863 TCTATTTTTGCTTCTCTC
1 TCTATTTTTGCTTCTCTC
66881 TCTATTTTTGCTTCTCTC
1 TCTATTTTTGCTTCTCTC
66899 TCTA
1 TCTA
66903 AAGAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.28, G:0.05, T:0.60
Consensus pattern (18 bp):
TCTATTTTTGCTTCTCTC
Found at i:67794 original size:3 final size:3
Alignment explanation
Indices: 67788--67878 Score: 116
Period size: 3 Copynumber: 31.0 Consensus size: 3
67778 TACTATTATT
*
67788 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA CAA TAA T-A TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
67833 TAA TAA TAA TAA TAA TAA T-A TAA TAT TAG TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
67879 AATGGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
2 6 0.08
3 68 0.88
4 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67836 original size:26 final size:26
Alignment explanation
Indices: 67788--67877 Score: 130
Period size: 26 Copynumber: 3.5 Consensus size: 26
67778 TACTATTATT
67788 TAATAATAATAA-ATAATAATAATAA
1 TAATAATAATAATATAATAATAATAA
*
67813 TAATAACAATAATATAATAATAATAA
1 TAATAATAATAATATAATAATAATAA
* *
67839 TAATAATAATAATATAATATTAGTAA
1 TAATAATAATAATATAATAATAATAA
*
67865 TAATATTAA-AATA
1 TAATAATAATAATA
67878 AAATGGAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
25 15 0.25
26 44 0.75
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (26 bp):
TAATAATAATAATATAATAATAATAA
Found at i:74114 original size:24 final size:24
Alignment explanation
Indices: 74086--74131 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
74076 GTTTAAGGTA
*
74086 TATTTTATTATATTTAA-TATTTTG
1 TATTTAATT-TATTTAAGTATTTTG
74110 TATTTAATTTATTTAAGTATTT
1 TATTTAATTTATTTAAGTATTT
74132 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTAATTTATTTAAGTATTTTG
Found at i:74131 original size:17 final size:17
Alignment explanation
Indices: 74109--74146 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
74099 TTAATATTTT
*
74109 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
74126 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
74143 -TATT
1 GTATT
74147 GTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:80365 original size:50 final size:50
Alignment explanation
Indices: 80268--80365 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
80258 CGCTATATAC
* * *
80268 TGATTTGGCACCACGTGGGTATAGCGCACCCCCTGCCCCGCGATATACGG
1 TGATCTGGCACCACGTGGGTATAGCGCACCCCCTGACCAGCGATATACGG
* * * * *
80318 TGATCTGGCGCCACGTGGGTATAGCGCGCCTCCTGATCAGCGCTATAC
1 TGATCTGGCACCACGTGGGTATAGCGCACCCCCTGACCAGCGATATAC
80366 CTGGATATCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (50 bp):
TGATCTGGCACCACGTGGGTATAGCGCACCCCCTGACCAGCGATATACGG
Found at i:80529 original size:12 final size:10
Alignment explanation
Indices: 80488--80528 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
80478 TTTATCACAC
80488 CAAATTCTCT
1 CAAATTCTCT
80498 CAAATTCTCT
1 CAAATTCTCT
80508 -AAATTTCTCT
1 CAAA-TTCTCT
*
80518 CAAATACTCT
1 CAAATTCTCT
80528 C
1 C
80529 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:80845 original size:111 final size:111
Alignment explanation
Indices: 80651--80872 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
80641 TGGAAATCAT
* *
80651 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGCTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGCTTTAATTTAATTTAAATTATTAGTAA
* *
80716 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* *
80762 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGCTTTAATTTAATTTAAATTATTAGTAA
80827 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
80873 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGCTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:82754 original size:18 final size:18
Alignment explanation
Indices: 82731--82793 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
82721 ACCTGCTCAG
82731 GATGACGACGACGACGAT
1 GATGACGACGACGACGAT
* *
82749 GATGACGACGACGATGGT
1 GATGACGACGACGACGAT
* *
82767 GACGACGACGATGACGAT
1 GATGACGACGACGACGAT
82785 GATGACGAC
1 GATGACGAC
82794 AGCGAGGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.35, T:0.13
Consensus pattern (18 bp):
GATGACGACGACGACGAT
Found at i:82757 original size:12 final size:12
Alignment explanation
Indices: 82734--82793 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
82724 TGCTCAGGAT
*
82734 GACGACGACGAC
1 GACGATGACGAC
*
82746 GATGATGACGAC
1 GACGATGACGAC
**
82758 GACGATGGTGAC
1 GACGATGACGAC
* *
82770 GACGACGATGAC
1 GACGATGACGAC
*
82782 GATGATGACGAC
1 GACGATGACGAC
82794 AGCGAGGAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.35, T:0.12
Consensus pattern (12 bp):
GACGATGACGAC
Found at i:82760 original size:21 final size:21
Alignment explanation
Indices: 82752--82793 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
82742 CGACGATGAT
*
82752 GACGACGACGATGGTGACGAC
1 GACGACGACGATGATGACGAC
*
82773 GACGATGACGATGATGACGAC
1 GACGACGACGATGATGACGAC
82794 AGCGAGGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.36, T:0.12
Consensus pattern (21 bp):
GACGACGACGATGATGACGAC
Found at i:82792 original size:15 final size:15
Alignment explanation
Indices: 82731--82783 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
82721 ACCTGCTCAG
82731 GATGACGACGACGAC
1 GATGACGACGACGAC
*
82746 GATGATGACGACGAC
1 GATGACGACGACGAC
**
82761 GATGGTGACGACGAC
1 GATGACGACGACGAC
82776 GATGACGA
1 GATGACGA
82784 TGATGACGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.36, T:0.11
Consensus pattern (15 bp):
GATGACGACGACGAC
Found at i:83046 original size:35 final size:33
Alignment explanation
Indices: 83007--83091 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
82997 ATATTTTAGT
83007 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
83042 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
83077 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
83092 TAAATATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:87208 original size:2 final size:2
Alignment explanation
Indices: 87196--87231 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
87186 ATCAAAATGA
87196 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87232 GTCTACTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:88222 original size:15 final size:15
Alignment explanation
Indices: 88202--88463 Score: 331
Period size: 15 Copynumber: 17.5 Consensus size: 15
88192 TAATAAGATT
88202 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
88217 ATTTA-TTT-AAA-A
1 ATTTATTTTAAAATA
88229 A--TATTTTAAAATA
1 ATTTATTTTAAAATA
88242 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
88257 ATTTATTATAAAACA
1 ATTTATTTTAAAATA
*
88272 ATTTATTTTAAAACA
1 ATTTATTTTAAAATA
*
88287 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
88302 A-TTATTTTAAAACA
1 ATTTATTTTAAAATA
*
88316 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
88331 ATTTATTTTAAAACA
1 ATTTATTTTAAAATA
*
88346 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
88361 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
88376 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
88391 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
88406 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
88425 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
88443 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
88457 ATTTATT
1 ATTTATT
88464 AGTATGGATT
Statistics
Matches: 217, Mismatches: 16, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 5 0.02
13 5 0.02
14 29 0.13
15 152 0.70
16 4 0.02
17 2 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 4 0.02
22 7 0.03
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:88434 original size:22 final size:22
Alignment explanation
Indices: 88406--88508 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
88396 TTTTAAAATA
*
88406 ATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** *
88428 ATTTATTTTAAAATAATTTATTTA
1 ATTTATTTTAAAAT-ATGGA-TTG
** * * *
88452 AAATAATTTATTAGTATGGATTG
1 ATTTATTTTA-AAATATGGATTG
88475 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
88497 ATTTATTTTAAA
1 ATTTATTTTAAA
88509 TAATTTATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:88498 original size:69 final size:66
Alignment explanation
Indices: 88361--88517 Score: 226
Period size: 69 Copynumber: 2.3 Consensus size: 66
88351 TTATAAAATA
88361 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTA-TTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
88426 TG
65 TG
** * * *
88428 ATTTATTTTAAAATAATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
1 ATTTATTTTAAAATAATTTATTTAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATGG
88493 ATTG
63 ATTG
88497 ATTTATTTT-AAATAATTTATT
1 ATTTATTTTAAAATAATTTATT
88518 AGTATAGATT
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
66 16 0.20
67 20 0.24
68 13 0.16
69 33 0.40
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (66 bp):
ATTTATTTTAAAATAATTTATTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATT
G
Found at i:88514 original size:54 final size:53
Alignment explanation
Indices: 88443--88556 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 53
88433 TTTTAAAATA
* *
88443 ATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTGATTTA-TTTAAAATATAGATTG
*
88497 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAAATATAGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTGATTTATTTAAAATATAGATTG
*
88550 CTTTATT
1 ATTTATT
88557 ATTAGTTGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
53 21 0.38
54 35 0.62
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.52
Consensus pattern (53 bp):
ATTTATTTAAAATAATTTATTAGTATAGATTGATTTATTTAAAATATAGATTG
Found at i:88579 original size:76 final size:76
Alignment explanation
Indices: 88491--88632 Score: 243
Period size: 76 Copynumber: 1.9 Consensus size: 76
88481 TTTAAAATAT
*
88491 GGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTA-TTTAAAATATAGATTGCTTT
1 GGATTGATTTATTTTAAATAATTT-TTAGTATGA-ATTGATTTATTTTAAAATATAGATTGATTT
88554 ATTATTAGTTGTA
64 ATTATTAGTTGTA
88567 GGATTGATTTATTTTAAATAATTTTTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTAT
1 GGATTGATTTATTTTAAATAATTTTTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTAT
88632 T
66 T
88633 TTAATAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
75 16 0.25
76 47 0.75
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (76 bp):
GGATTGATTTATTTTAAATAATTTTTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTAT
TATTAGTTGTA
Found at i:88604 original size:31 final size:29
Alignment explanation
Indices: 88568--88858 Score: 140
Period size: 32 Copynumber: 10.6 Consensus size: 29
88558 TTAGTTGTAG
88568 GATTGATTTATTTTAAATAATTTTTAGTAT
1 GATTGATTTATTTT-AATAATTTTTAGTAT
88598 GAATTGATTTATTTTAA-AA----TA-TA-
1 G-ATTGATTTATTTTAATAATTTTTAGTAT
88621 GATTGATTTATTTTAATAATTTATTAGTAT
1 GATTGATTTATTTTAATAATTT-TTAGTAT
88651 GGATTGATTTATTTT-A-AA-----A-TA-
1 -GATTGATTTATTTTAATAATTTTTAGTAT
* *
88672 GATTAATTTATTTTAAATAA-TATTAGTAT
1 GATTGATTTATTTT-AATAATTTTTAGTAT
*
88701 GGATTGATTTATTTTAA-AA----CAG---
1 -GATTGATTTATTTTAATAATTTTTAGTAT
* * * *
88723 GATTGATTTATTATT-GT-AGTTGTATGGAT
1 GATTGATTTATT-TTAATAATTTTTA-GTAT
*
88752 GATT-A--T-TTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAATAATTT-TTAGTAT
*
88778 GGATTGATTTAATTTAAATAATTTATTAGTAT
1 -GATTGATTT-ATTTTAATAATTT-TTAGTAT
88810 GGATTGATTTATTTTAAATAATTTATTAGTAT
1 -GATTGATTTATTTT-AATAATTT-TTAGTAT
88842 GGATTGATTTATTTTAA
1 -GATTGATTTATTTTAA
88859 AATATGGATT
Statistics
Matches: 210, Mismatches: 11, Indels: 79
0.70 0.04 0.26
Matches are distributed among these distances:
20 13 0.06
21 13 0.06
22 20 0.10
23 6 0.03
24 3 0.01
25 8 0.04
26 8 0.04
27 7 0.03
28 8 0.04
29 12 0.06
30 18 0.09
31 33 0.16
32 61 0.29
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (29 bp):
GATTGATTTATTTTAATAATTTTTAGTAT
Found at i:88632 original size:53 final size:52
Alignment explanation
Indices: 88568--88734 Score: 243
Period size: 53 Copynumber: 3.2 Consensus size: 52
88558 TTAGTTGTAG
*
88568 GATTGATTTATTTTAAATAATTTTTAGTATGAATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTTTAGTATGGATTGATTTATTTTAAAA-ATA
88621 GATTGATTTATTTT-AATAATTTATTAGTATGGATTGATTTATTTT-AAAATA
1 GATTGATTTATTTTAAATAATTT-TTAGTATGGATTGATTTATTTTAAAAATA
* * *
88672 GATTAATTTATTTTAAATAA-TATTAGTATGGATTGATTTATTTTAAAACA-G
1 GATTGATTTATTTTAAATAATTTTTAGTATGGATTGATTTATTTTAAAA-ATA
88723 GATTGATTTATT
1 GATTGATTTATT
88735 ATTGTAGTTG
Statistics
Matches: 105, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
50 22 0.21
51 31 0.30
52 17 0.16
53 35 0.33
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (52 bp):
GATTGATTTATTTTAAATAATTTTTAGTATGGATTGATTTATTTTAAAAATA
Found at i:88655 original size:27 final size:27
Alignment explanation
Indices: 88572--88660 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
88562 TTGTAGGATT
88572 GATTTATTTTAAATAATTT-TTAGTATG
1 GATTTATTTT-AATAATTTATTAGTATG
*
88599 AATTGATTTATTTTAA-AA--TA-TAG-ATT
1 ----GATTTATTTTAATAATTTATTAGTATG
88625 GATTTATTTTAATAATTTATTAGTATG
1 GATTTATTTTAATAATTTATTAGTATG
*
88652 GATTGATTT
1 GATTTATTT
88661 ATTTTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 12 0.24
23 2 0.04
25 2 0.04
26 5 0.10
27 14 0.29
29 2 0.04
30 2 0.04
31 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (27 bp):
GATTTATTTTAATAATTTATTAGTATG
Found at i:88797 original size:32 final size:32
Alignment explanation
Indices: 88744--88859 Score: 209
Period size: 32 Copynumber: 3.7 Consensus size: 32
88734 TATTGTAGTT
88744 GTATGGA-TGA-TTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
88774 GTATGGATTGATTTAATTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
88806 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
88838 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
88860 ATATGGATTG
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
30 7 0.09
31 3 0.04
32 72 0.88
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:88864 original size:22 final size:22
Alignment explanation
Indices: 88839--88881 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
88829 AATTTATTAG
88839 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
88861 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
88882 TCTCAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:94765 original size:17 final size:17
Alignment explanation
Indices: 94739--94776 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
94729 AATTAAATAC
*
94739 AATA-TTAAATAATTTA
1 AATACTTAAATAAATTA
94755 AATACTTAAATAAATTA
1 AATACTTAAATAAATTA
94772 AATAC
1 AATAC
94777 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATACTTAAATAAATTA
Found at i:94781 original size:24 final size:24
Alignment explanation
Indices: 94754--94799 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
94744 TAAATAATTT
*
94754 AAATACTTAAATA-AATTAAATACA
1 AAATA-TTAAATATAATAAAATACA
94778 AAATATTAAATATAATAAAATA
1 AAATATTAAATATAATAAAATA
94800 TACCTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATATTAAATATAATAAAATACA
Found at i:99921 original size:29 final size:29
Alignment explanation
Indices: 99880--99960 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
99870 TTTTATATGT
99880 TCATGT-ACTCATGTCATTTCTCTTGTGA
1 TCATGTAACTCATGTCATTTCTCTTGTGA
99908 TCATGTAACTCATGTCATTTCTCTTGTGA
1 TCATGTAACTCATGTCATTTCTCTTGTGA
*
99937 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAACTCATGTCAT-TTCTC
99961 ATATCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 6 0.12
29 39 0.78
30 5 0.10
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (29 bp):
TCATGTAACTCATGTCATTTCTCTTGTGA
Found at i:100493 original size:64 final size:64
Alignment explanation
Indices: 100341--100497 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
100331 TAATGAAGGT
** * * *
100341 ATGCATCGATGCACTATTTGTGCATCGGTGCATAAAATGCATTCAATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCAATGTTTTATTATTAAAGAG
* * * * * *
100405 ATGCATCGATTCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATCTTTTTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCAAT-GTTTTATTATTAAAG
100466 AG
63 AG
100468 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
100498 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 3 0.04
64 60 0.81
65 11 0.15
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCAATGTTTTATTATTAAAGAG
Found at i:111138 original size:20 final size:20
Alignment explanation
Indices: 111113--111150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
111103 TTTTGGTGCA
111113 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
*
111133 GAGGGAATCGATTCCCCC
1 GAGGGAATCGATACCCCC
111151 TTTGAAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:115556 original size:15 final size:15
Alignment explanation
Indices: 115532--115565 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
115522 CCGTAGGATC
115532 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
115547 ACTACGTCCCGAATG
1 ACTACATCCCGAAGG
115562 ACTA
1 ACTA
115566 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:115696 original size:29 final size:29
Alignment explanation
Indices: 115650--115730 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
115640 TTTTATATGT
*
115650 TCATGTA-CTCATGCCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
115678 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
115707 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
115731 ATATCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:116182 original size:64 final size:63
Alignment explanation
Indices: 116109--116265 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
116099 TAATGAAGGT
* * **
116109 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGTATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
116172 G
63 G
* * * *
116173 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
116236 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
116266 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:117249 original size:75 final size:75
Alignment explanation
Indices: 117126--117276 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
117116 ATGAGTTGGG
117126 GTTCGCGTATGAAGAGATCCTATGTCGTGATGACATCATTAATAAAGACATTAGATTAAAGTTGA
1 GTTCGCGTATGAAGAGATCCTATGTCGTGATGACATCATTAATAAAGACATTAGATTAAAGTTGA
*
117191 ATGTATTCGA
66 ATGCATTCGA
117201 GTTCGCGTATGAAGAGATCCTATGTCGTGATGACATCATTAATAAAGACATTAGATTAAAGTTGA
1 GTTCGCGTATGAAGAGATCCTATGTCGTGATGACATCATTAATAAAGACATTAGATTAAAGTTGA
117266 ATGCATTCGA
66 ATGCATTCGA
117276 G
1 G
117277 AATCAGCTAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (75 bp):
GTTCGCGTATGAAGAGATCCTATGTCGTGATGACATCATTAATAAAGACATTAGATTAAAGTTGA
ATGCATTCGA
Found at i:118534 original size:43 final size:43
Alignment explanation
Indices: 118466--118563 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
118456 TAATCAATCG
*
118466 CCCAAAAATTATGACTTAGCATCCTTAAGAGGAAGGAGTAAGA
1 CCCAGAAATTATGACTTAGCATCCTTAAGAGGAAGGAGTAAGA
*
118509 CCCAGAGATTATGACTTAGCATCCTTAAGAGGAAGGAGTAAGA
1 CCCAGAAATTATGACTTAGCATCCTTAAGAGGAAGGAGTAAGA
118552 CCCAGAAATTAT
1 CCCAGAAATTAT
118564 TTACGCGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (43 bp):
CCCAGAAATTATGACTTAGCATCCTTAAGAGGAAGGAGTAAGA
Found at i:124779 original size:21 final size:21
Alignment explanation
Indices: 124753--124797 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
124743 AAACTACATA
* *
124753 TTTAGTACCTAAACTATTAGT
1 TTTAGTACCAAAACTATTAAT
*
124774 TTTAGTACCAAAACTTTTAAT
1 TTTAGTACCAAAACTATTAAT
124795 TTT
1 TTT
124798 TTTTCAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAGTACCAAAACTATTAAT
Found at i:125163 original size:16 final size:16
Alignment explanation
Indices: 125144--125180 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
125134 TCATAGATAT
125144 ATTTATAAATATATTC
1 ATTTATAAATATATTC
125160 ATTTATAAATATATTC
1 ATTTATAAATATATTC
125176 ATTTA
1 ATTTA
125181 ATGTTCGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTATAAATATATTC
Found at i:131173 original size:3 final size:3
Alignment explanation
Indices: 131165--131205 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
131155 GATCAGAAAA
*
131165 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
131206 CAATTACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:143498 original size:60 final size:60
Alignment explanation
Indices: 143419--143561 Score: 236
Period size: 58 Copynumber: 2.4 Consensus size: 60
143409 TCGAATGACA
* * *
143419 ATTTTTTAACTTTTAATAGTCGAGAAACTCAACAAAATAACTTCATATAGTTGAGAGATT
1 ATTTTATAATTTTTAATAGTCGAGAAACTCAACAAAACAACTTCATATAGTTGAGAGATT
*
143479 ATTTTATAATTTTTAATAGTCG-G-AACTCAACAAAACAACTTCATATAGTTGAGGGATT
1 ATTTTATAATTTTTAATAGTCGAGAAACTCAACAAAACAACTTCATATAGTTGAGAGATT
143537 ATTTTATAATTTTTAATAGTCGAGA
1 ATTTTATAATTTTTAATAGTCGAGA
143562 CTCAATAAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
58 55 0.71
59 2 0.03
60 20 0.26
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (60 bp):
ATTTTATAATTTTTAATAGTCGAGAAACTCAACAAAACAACTTCATATAGTTGAGAGATT
Found at i:152521 original size:20 final size:20
Alignment explanation
Indices: 152498--152548 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
152488 TAAGGAATGT
152498 ACCGATGCACTAAAGAGTGC
1 ACCGATGCACTAAAGAGTGC
152518 ACCGATGCACTAAAGAGTGC
1 ACCGATGCACTAAAGAGTGC
152538 ACCGATGCACT
1 ACCGATGCACT
152549 TCAAAGGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
ACCGATGCACTAAAGAGTGC
Found at i:153279 original size:22 final size:22
Alignment explanation
Indices: 153256--153336 Score: 135
Period size: 22 Copynumber: 3.7 Consensus size: 22
153246 GGATATATAG
* *
153256 TGGTCATTCGGGACATATACAG
1 TGGTCCTTCGGGACATATACAA
153278 TGGTCCTTCGGGACATATACAA
1 TGGTCCTTCGGGACATATACAA
153300 TGGTCCTTCGGGACATATACAA
1 TGGTCCTTCGGGACATATACAA
*
153322 TGGTCTTTCGGGACA
1 TGGTCCTTCGGGACA
153337 AATTTCATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (22 bp):
TGGTCCTTCGGGACATATACAA
Found at i:157813 original size:40 final size:42
Alignment explanation
Indices: 157729--157814 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 42
157719 ATAACTAATG
*
157729 AATAAAATAATAACAAACTAAACATGTCTTAACTCTAATTCTT
1 AATAAAATAATAACAAAC-AAACATGTCTTAACTCTAATCCTT
*
157772 AATAAAATAATAACTAAA-AATA-ATGTTTTAACTC-AA-CCTT
1 AATAAAATAATAAC-AAACAA-ACATGTCTTAACTCTAATCCTT
157812 AAT
1 AAT
157815 TCCTAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
40 6 0.15
41 2 0.05
42 13 0.33
43 15 0.38
44 3 0.08
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (42 bp):
AATAAAATAATAACAAACAAACATGTCTTAACTCTAATCCTT
Found at i:158621 original size:32 final size:32
Alignment explanation
Indices: 158579--158642 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
158569 GTTGTCCTTC
*
158579 GGTAATCGAAAACACAACCAGGGTAATCTCAA
1 GGTAACCGAAAACACAACCAGGGTAATCTCAA
**
158611 GGTAACCGAAAACACAGTCAGGGTAATCTCAA
1 GGTAACCGAAAACACAACCAGGGTAATCTCAA
158643 CCCACTCGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (32 bp):
GGTAACCGAAAACACAACCAGGGTAATCTCAA
Found at i:168878 original size:2 final size:2
Alignment explanation
Indices: 168871--168897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
168861 ATTTACTTTT
168871 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
168898 TACATTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:169807 original size:21 final size:20
Alignment explanation
Indices: 169760--169815 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
169750 CGATGCTGAA
*
169760 GAGAAGATAGAGAGGCGGAG
1 GAGAAGAAAGAGAGGCGGAG
* * *
169780 GATGAAGAGAGAGAGAGTGGTG
1 GA-GAAGAAAGAGAG-GCGGAG
169802 GAGAAGAAAGAGAG
1 GAGAAGAAAGAGAG
169816 CTTTGTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 22 0.73
22 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.48, T:0.07
Consensus pattern (20 bp):
GAGAAGAAAGAGAGGCGGAG
Found at i:170745 original size:29 final size:30
Alignment explanation
Indices: 170503--170743 Score: 216
Period size: 30 Copynumber: 8.3 Consensus size: 30
170493 TTGATTTATG
170503 TTTTAGTCCCTTAAG--T-T-TTTTTGCTA
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
* ** *
170529 TTTTAGTCCTTTGAA-TGACTA-TTTTACTA
1 TTTTAGTCCCTT-AAGTTTCTATTTTTGCTA
170558 TTTTAGTCCCTTAAGTTTCTATTTTTG-TGA
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCT-A
* * * * *
170588 ATTTAGTCTCTTAAATGTCTATTTTTTCTA
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
* * * *
170618 TTTTAGTCCTTTAAATTTCTATGTATGCTA
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
* * *
170648 TTTTAATCCCTTATGTTT-TAGTTTTGCT-
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
170676 TTTTAGTCCCTTCAA-TTTCTA-TTTTGCTA
1 TTTTAGTCCCTT-AAGTTTCTATTTTTGCTA
*
170705 TTTTAGTCCCTTAAGTTTCTTTTTTTGCTA
1 TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
*
170735 TTTTGGTCC
1 TTTTAGTCC
170744 TTTTAAATAG
Statistics
Matches: 171, Mismatches: 30, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
26 11 0.06
27 2 0.01
28 25 0.15
29 51 0.30
30 81 0.47
31 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.56
Consensus pattern (30 bp):
TTTTAGTCCCTTAAGTTTCTATTTTTGCTA
Found at i:173128 original size:36 final size:36
Alignment explanation
Indices: 173036--173479 Score: 236
Period size: 36 Copynumber: 12.3 Consensus size: 36
173026 TAATATACAT
* * *
173036 AATATATA-ATA-ATAATTTTGAGAACATTTTTCG-AA
1 AATATATATATATATAGTTTT-AAAAAATTTTT-GAAA
*
173071 AATATATATAATATATAGTTTTAAAAAATTTTTTAAA
1 AATATATAT-ATATATAGTTTTAAAAAATTTTTGAAA
*
173108 AATATATATATATATGGTTTTAAAAACATTTTTGAAA
1 AATATATATATATATAGTTTTAAAAA-ATTTTTGAAA
* **
173145 TATATATAT-TATATAGTTTTGAAAGCATTTTTTTG-AA
1 AATATATATATATATAGTTTT-AAA--AAATTTTTGAAA
*
173182 AACATA-ATA-ATATAGTTTTAAAAAATATTTTTGAAA
1 AATATATATATATATAGTTTT-AAAAA-ATTTTTGAAA
* * * *
173218 AATA-ATATGTA-AT--TTTGAAAACACTTTTGAAA
1 AATATATATATATATAGTTTTAAAAAATTTTTGAAA
* * *
173250 TCATATATA-ATATATAATTTAAAAAAAACATTTTTGAAA
1 -AATATATATATATATAGTTT--TAAAAA-ATTTTTGAAA
* * * *
173289 ACATATATATATGTAT--TTTGAAAACACTTTTGAAA
1 A-ATATATATATATATAGTTTTAAAAAATTTTTGAAA
**
173324 ACA-A-ATAT-TATACCGTTTTGAAAAACATTTTTGAAA
1 A-ATATATATATATATAGTTTT-AAAAA-ATTTTTGAAA
*
173360 ACATATA-A-ATATA-A-TTTTAAAATATTTTTG-AA
1 A-ATATATATATATATAGTTTTAAAAAATTTTTGAAA
*
173392 AACATATATA-ATATAGTTTTTAAAAATGTATTTTT-AAA
1 AATATATATATATATAG-TTTTAAAAA---ATTTTTGAAA
* ***
173430 AACATATA-ATATATAGTTTTTTTAAATATTTTGAAA
1 AATATATATATATATAGTTTTAAAAAAT-TTTTGAAA
173466 ACATATAGTATATA
1 A-ATATA-TATATA
173480 GTTTTTAAAA
Statistics
Matches: 321, Mismatches: 43, Indels: 86
0.71 0.10 0.19
Matches are distributed among these distances:
31 4 0.01
32 19 0.06
33 22 0.07
34 19 0.06
35 47 0.15
36 73 0.23
37 67 0.21
38 45 0.14
39 20 0.06
40 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
AATATATATATATATAGTTTTAAAAAATTTTTGAAA
Found at i:173479 original size:35 final size:35
Alignment explanation
Indices: 173076--173502 Score: 320
Period size: 35 Copynumber: 12.0 Consensus size: 35
173066 TCGAAAATAT
* * *
173076 ATATAATATATAGTTTTAAAAAAT-TTTTTAAAAAT
1 ATAT-ATATATAGTTTTTAAAAATATTTTTGAAAAC
* * *
173111 ATATATATATATGGTTTTAAAAACATTTTTGAAATAT
1 ATATATATATA-GTTTTTAAAAATATTTTTGAAA-AC
* * *
173148 ATATATTATATAGTTTTGAAAGCATTTTTTTGAAAAC
1 ATATA-TATATAGTTTTTAAA-AATATTTTTGAAAAC
*
173185 ATA-ATAATATAGTTTTAAAAAATATTTTTGAAAA-
1 ATATAT-ATATAGTTTTTAAAAATATTTTTGAAAAC
* * * * * *
173219 ATA-ATATGTA-ATTTTGAAAACACTTTTGAAATC
1 ATATATATATAGTTTTTAAAAATATTTTTGAAAAC
* *
173252 ATATATAATATA-TAATTTAAAAAAAACATTTTTGAAAAC
1 ATATAT-ATATAGT--TTT--TAAAAATATTTTTGAAAAC
* * *
173291 ATATATATAT-GTATTTTGAAAACACTTTTGAAAAC
1 ATATATATATAGT-TTTTAAAAATATTTTTGAAAAC
* * *
173326 AAATAT-TATACCGTTTTGAAAAACATTTTTGAAAAC
1 ATATATATATA--GTTTTTAAAAATATTTTTGAAAAC
* *
173362 ATATAAATATA-ATTTT-AAAATATTTTTGAAAAC
1 ATATATATATAGTTTTTAAAAATATTTTTGAAAAC
*
173395 ATATATAATATAGTTTTTAAAAATGTATTTTTAAAAAC
1 ATATAT-ATATAGTTTTTAAAAA--TATTTTTGAAAAC
**
173433 ATATAATATATAGTTTTTTTAAATA-TTTTGAAAAC
1 ATAT-ATATATAGTTTTTAAAAATATTTTTGAAAAC
*
173468 ATATAGTATATAGTTTTT-AAAATGGTTTTTGAAAA
1 ATATA-TATATAGTTTTTAAAAAT-ATTTTTGAAAA
173503 TACATAAATT
Statistics
Matches: 319, Mismatches: 46, Indels: 53
0.76 0.11 0.13
Matches are distributed among these distances:
32 16 0.05
33 28 0.09
34 30 0.09
35 80 0.25
36 60 0.19
37 31 0.10
38 51 0.16
39 23 0.07
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATATATAGTTTTTAAAAATATTTTTGAAAAC
Found at i:173508 original size:73 final size:70
Alignment explanation
Indices: 173062--173508 Score: 286
Period size: 73 Copynumber: 6.2 Consensus size: 70
173052 TTTGAGAACA
* * * * *
173062 TTTTTCGAAAATATATATAATATATAGTTTTAAAAAATTTTTTAAAA-ATATATATATATATGGT
1 TTTTT-GAAAA-ACATATAA-ATATAATTTTAAAATATTTTTGAAAACATATATA-ATATA-GTT
**
173126 TTTAAAAACA
61 TTTAAAAATG
* * * * *
173136 TTTTTGAAATATATATATTATATAGTTTTGAAAGCATTTTTTTGAAAACATA-ATAATATAGTTT
1 TTTTTGAAAAACATATA-AATATAATTTT-AAA--ATATTTTTGAAAACATATATAATATAGTTT
* *
173200 TAAAAAATA
62 TTAAAAATG
* * * * *
173209 TTTTTG-AAAA-ATA-ATATGTAATTTTGAAAACACTTTTGAAATCATATATAATATA-TAATTT
1 TTTTTGAAAAACATATAAATATAATTTT-AAAATATTTTTGAAAACATATATAATATAGT--TTT
* **
173270 AAAAAAAACA
63 --TAAAAATG
* * * * * * ** *
173280 TTTTTG-AAAACATATATATATGTATTTTGAAAACACTTTTGAAAACAAATATTATACCGTTTTG
1 TTTTTGAAAAACATATAAATAT-AATTTT-AAAATATTTTTGAAAACATATATAATATAGTTTTT
**
173344 AAAAACA
64 AAAAATG
173351 TTTTTG-AAAACATATAAATATAATTTTAAAATATTTTTGAAAACATATATAATATAGTTTTTAA
1 TTTTTGAAAAACATATAAATATAATTTTAAAATATTTTTGAAAACATATATAATATAGTTTTTAA
173415 AAATG
66 AAATG
* * *
173420 TATTTTTAAAAACATATAATATATAGTTTTTTTAAATA-TTTTGAAAACATATAGT-ATATAGTT
1 T-TTTTGAAAAACATATAA-ATATA--ATTTTAAAATATTTTTGAAAACATATA-TAATATAGTT
173483 TTT-AAAATGG
61 TTTAAAAAT-G
173493 TTTTTGAAAATACATA
1 TTTTTGAAAA-ACATA
173509 AATTAATATA
Statistics
Matches: 312, Mismatches: 39, Indels: 45
0.79 0.10 0.11
Matches are distributed among these distances:
67 14 0.04
68 8 0.03
69 50 0.16
70 10 0.03
71 58 0.19
72 41 0.13
73 64 0.21
74 50 0.16
75 14 0.04
76 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (70 bp):
TTTTTGAAAAACATATAAATATAATTTTAAAATATTTTTGAAAACATATATAATATAGTTTTTAA
AAATG
Found at i:173536 original size:11 final size:11
Alignment explanation
Indices: 173520--173592 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
173510 ATTAATATAC
173520 ATATTATTTAT
1 ATATTATTTAT
173531 ATATTATTTAT
1 ATATTATTTAT
*
173542 ATATTATATAT
1 ATATTATTTAT
*
173553 ATTTTA-TTAT
1 ATATTATTTAT
*
173563 ATATT-TAT-T
1 ATATTATTTAT
173572 ATATTATGTTAT
1 ATATTAT-TTAT
173584 -TAATTATTT
1 AT-ATTATTT
173593 TTCATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 6 0.12
10 9 0.18
11 30 0.59
12 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (11 bp):
ATATTATTTAT
Found at i:173583 original size:21 final size:20
Alignment explanation
Indices: 173524--173583 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
173514 ATATACATAT
173524 TATTTA-TATATTATTTATA
1 TATTTATTATATTATTTATA
*
173543 TA-TTATATATATTTTATTATA
1 TATTTAT-TATATTAT-TTATA
173564 TATTTATTATATTATGTTAT
1 TATTTATTATATTAT-TTAT
173584 TAATTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 7 0.21
21 18 0.53
22 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTATTATATTATTTATA
Done.