Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007572.1 Hibiscus syriacus cultivar Beakdansim tig00021572_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: 133194
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:1703 original size:23 final size:23
Alignment explanation
Indices: 1660--1709 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1650 TTGAAACTTT
*
1660 TAATAATTATATTATTTTTATTA
1 TAATAATTATATTATTATTATTA
* *
1683 TAATAA-TATATTCTTGATTATTT
1 TAATAATTATATTATT-ATTATTA
1706 TAAT
1 TAAT
1710 TACTATATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TAATAATTATATTATTATTATTA
Found at i:1907 original size:22 final size:22
Alignment explanation
Indices: 1893--1932 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1883 ATATAATATT
1893 ATATATCATATAATATTAAAGA
1 ATATATCATATAATATTAAAGA
1915 ATATATCATAT--TATTAAA
1 ATATATCATATAATATTAAA
1933 TTATGAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (22 bp):
ATATATCATATAATATTAAAGA
Found at i:4840 original size:41 final size:41
Alignment explanation
Indices: 4765--4842 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
4755 GATTATTTTA
* *
4765 ATTACTATTGAAAATAATAATATTTTTAAAATATTAAAAAC
1 ATTACTATTGAAAATAAGAATATATTTAAAATATTAAAAAC
* *
4806 ATTATTATT-AAAATAAGAATAGTATTTAATATATTAA
1 ATTACTATTGAAAATAAGAATA-TATTTAAAATATTAA
4843 GGGTTGTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.34
41 21 0.66
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (41 bp):
ATTACTATTGAAAATAAGAATATATTTAAAATATTAAAAAC
Found at i:8383 original size:2 final size:2
Alignment explanation
Indices: 8376--8419 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
8366 TTAATTCTTG
8376 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
8418 AT
1 AT
8420 TTTTTTTCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9819 original size:2 final size:2
Alignment explanation
Indices: 9812--9844 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9802 AAAATATCTT
9812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9845 TTCCAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15284 original size:12 final size:13
Alignment explanation
Indices: 15258--15292 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
15248 TAAGATTTTC
15258 TTTGAAAATCAAT
1 TTTGAAAATCAAT
15271 TTTGAAAA-CAAT
1 TTTGAAAATCAAT
15283 TTTGCAAAAT
1 TTTG-AAAAT
15293 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:20664 original size:2 final size:2
Alignment explanation
Indices: 20657--20696 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20647 TTAATTCTTG
20657 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
20697 TTTTTACGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22208 original size:20 final size:22
Alignment explanation
Indices: 22165--22209 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
22155 TTAAGACTAT
*
22165 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
22187 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
22207 TAA
1 TAA
22210 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:22442 original size:18 final size:18
Alignment explanation
Indices: 22419--22476 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
22409 AAAATAAAAG
22419 TATAATATTATATATAAT
1 TATAATATTATATATAAT
22437 TATAATATTACATAATATAA-
1 TATAATATT--AT-ATATAAT
* *
22457 TATCATATTAT-TAGAAT
1 TATAATATTATATATAAT
22474 TAT
1 TAT
22477 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 11 0.32
20 10 0.29
21 6 0.18
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATAATATTATATATAAT
Found at i:24257 original size:2 final size:2
Alignment explanation
Indices: 24248--24280 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24238 ATTATAAAAA
24248 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
24281 CCAAGAAATA
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:25315 original size:24 final size:24
Alignment explanation
Indices: 25279--25370 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
25269 CAGAGATGTT
* *
25279 AGAAATCAAAACAGAATTTAGATC
1 AGAAATCAGAACAGAATTCAGATC
* * *
25303 AGATATCAGAACAAAATCCAGATC
1 AGAAATCAGAACAGAATTCAGATC
* * *
25327 AGAAATCATAACAGGATTCATATC
1 AGAAATCAGAACAGAATTCAGATC
25351 AGAAATCAGAACAGAATTCA
1 AGAAATCAGAACAGAATTCA
25371 AAACGAAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (24 bp):
AGAAATCAGAACAGAATTCAGATC
Found at i:25365 original size:12 final size:12
Alignment explanation
Indices: 25279--25384 Score: 63
Period size: 12 Copynumber: 8.8 Consensus size: 12
25269 CAGAGATGTT
*
25279 AGAAATCAAAAC
1 AGAAATCAGAAC
* * *
25291 AGAATTTAGATC
1 AGAAATCAGAAC
*
25303 AGATATCAGAAC
1 AGAAATCAGAAC
*
25315 A-AAATCCAGATC
1 AGAAAT-CAGAAC
*
25327 AGAAATCATAAC
1 AGAAATCAGAAC
* * * *
25339 AGGATTCATATC
1 AGAAATCAGAAC
25351 AGAAATCAGAAC
1 AGAAATCAGAAC
* *
25363 AGAATTCAAAAC
1 AGAAATCAGAAC
25375 -GAAAATCAGA
1 AG-AAATCAGA
25385 TAAAACATTC
Statistics
Matches: 68, Mismatches: 23, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
11 4 0.06
12 60 0.88
13 4 0.06
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (12 bp):
AGAAATCAGAAC
Found at i:30013 original size:24 final size:24
Alignment explanation
Indices: 29970--30016 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29960 CAGAAATTAG
29970 AACAAAATTCAAATAAAAAATCAA
1 AACAAAATTCAAATAAAAAATCAA
* **
29994 AACATAATTCAAATTGAAAATCA
1 AACAAAATTCAAATAAAAAATCA
30017 GATAAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (24 bp):
AACAAAATTCAAATAAAAAATCAA
Found at i:35645 original size:17 final size:17
Alignment explanation
Indices: 35623--35681 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
35613 AATATATTAT
35623 ATAATATTATTATTTTA
1 ATAATATTATTATTTTA
*
35640 ATAATAATTTTTAATATTTTA
1 ATAAT-A---TTATTATTTTA
*
35661 AAAATATTATTATTTTCA
1 ATAATATTATTATTTT-A
35679 ATA
1 ATA
35682 GTAATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
17 14 0.42
18 4 0.12
20 1 0.03
21 14 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATATTATTATTTTA
Found at i:35654 original size:39 final size:39
Alignment explanation
Indices: 35611--35687 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
35601 AAGACAACCC
*
35611 TTAATATATTATATAATATTATTATTTT-AATAATAATTT
1 TTAATATATTA-AAAATATTATTATTTTCAATAATAATTT
* *
35650 TTAATATTTTAAAAATATTATTATTTTCAATAGTAATT
1 TTAATATATTAAAAATATTATTATTTTCAATAATAATT
35688 AAAATAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TTAATATATTAAAAATATTATTATTTTCAATAATAATTT
Found at i:45419 original size:43 final size:43
Alignment explanation
Indices: 45358--45573 Score: 371
Period size: 43 Copynumber: 5.0 Consensus size: 43
45348 ACCGTTACAA
*
45358 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
45401 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
**
45443 CAGGTCCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
45486 CATGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
45529 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
45572 CA
1 CA
45574 AGCTCTTTTT
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 40 0.25
43 122 0.75
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.32
Consensus pattern (43 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:45505 original size:85 final size:86
Alignment explanation
Indices: 45358--45573 Score: 380
Period size: 85 Copynumber: 2.5 Consensus size: 86
45348 ACCGTTACAA
*
45358 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTATGTGCAA
45423 -GGTAAGCCTTACAGTTTCCC
66 GGGTAAGCCTTACAGTTTCCC
* *
45443 CAGGTCCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTCCCTTTGCTATGTGCAA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTATGTGCAA
45508 GGGTAAGCCTTACAGTTTCCC
66 GGGTAAGCCTTACAGTTTCCC
* *
45529 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
45574 AGCTCTTTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
85 62 0.50
86 62 0.50
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.32
Consensus pattern (86 bp):
CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTATGTGCAA
GGGTAAGCCTTACAGTTTCCC
Found at i:45588 original size:86 final size:86
Alignment explanation
Indices: 45358--45606 Score: 376
Period size: 86 Copynumber: 2.9 Consensus size: 86
45348 ACCGTTACAA
* *
45358 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTATGTGCAA
45423 -GGTAAGCCTTACAGTTTCCC
66 GGGTAAGCCTTACAGTTTCCC
* *
45443 CAGGTCCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTCCCTTTGCTATGTGCAA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTATGTGCAA
45508 GGGTAAGCCTTACAGTTTCCC
66 GGGTAAGCCTTACAGTTTCCC
* * * * *
45529 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAG-CTCTTTTTCTATGTACA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTC-CCTTTGCTATGTGCA
*
45593 AGGATAAGACCTTA
65 AGGGTAAG-CCTTA
45607 TCATTTTTGC
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
85 63 0.42
86 82 0.55
87 5 0.03
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (86 bp):
CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTATGTGCAA
GGGTAAGCCTTACAGTTTCCC
Found at i:45595 original size:43 final size:43
Alignment explanation
Indices: 45364--45606 Score: 296
Period size: 43 Copynumber: 5.7 Consensus size: 43
45354 ACAACAGGTC
* *
45364 CCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
*
45406 CCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCCCC-AGGT
1 -CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
** *
45448 CCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATG-T
1 -CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
* * *
45491 CCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTT
1 -CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
45535 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
* * * * *
45578 CTTTTTCTATGTACAAGGATAAGACCTTA
1 CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
45607 TCATTTTTGC
Statistics
Matches: 180, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
42 40 0.22
43 133 0.74
44 7 0.04
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (43 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
Found at i:49841 original size:2 final size:2
Alignment explanation
Indices: 49834--49878 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
49824 AAAAATATGT
49834 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
49876 TA T
1 TA T
49879 CCAGGAAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51710 original size:65 final size:64
Alignment explanation
Indices: 51572--51724 Score: 191
Period size: 65 Copynumber: 2.4 Consensus size: 64
51562 TACACTAGGG
* * * * *
51572 GTGCATCGATACACTAATTACATTCGATGTTTCAAAGAGCCAGGAGTGCATCGATGCATGGTAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTAT
* ** *
51636 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCT-
1 GTGCATCGGTACACAAAATGCATTCGATGTTTC-AAAGAGCCAAGAGTGCATCGATGCATGG-TA
51700 T
64 T
*
51701 GTGCCTCGGTACACAAAATGCATT
1 GTGCATCGGTACACAAAATGCATT
51725 AGAAATGGGT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 29 0.38
65 47 0.61
66 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTAT
Found at i:53190 original size:538 final size:538
Alignment explanation
Indices: 52166--53243 Score: 2048
Period size: 538 Copynumber: 2.0 Consensus size: 538
52156 TAAAACGTTT
* *
52166 TTAAACAAGATTTTGGAAAACTTAGCCAATTGATTTTAAATAAATATAACTTAAGCTGCTAAGAT
1 TTAAACAAGATTTTGCAAAACTTAGCCAATTGATTTTAAATAAATATAACTTAAGCTACTAAGAT
52231 CAAAAGCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATAAAAAAATGTGCAATGG
66 CAAAAGCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATAAAAAAATGTGCAATGG
52296 TAAATTGGTCATAATGCAACTAATATGCAAATGATGCAAAACTAATAAACATTAAGCTCAAATTG
131 TAAATTGGTCATAATGCAACTAATATGCAAATGATGCAAAACTAATAAACATTAAGCTCAAATTG
* *
52361 AAAATTCAAACCAATCCAAATATATAAATATAAGTTCAAACATCCAAACATTCAAAATAAAAATA
196 AAAATTCAAACAAAGCCAAATATATAAATATAAGTTCAAACATCCAAACATTCAAAATAAAAATA
*
52426 ATCCAAAAACATCAATCCACAATCATCCAAAATATAAATCCAAAAACATTCAAAATGTTTAACAA
261 ATCCAAAAACATCAATCCACAATCATCCAAAATAAAAATCCAAAAACATTCAAAATGTTTAACAA
*
52491 TAGGTACTAAATCCATGAAAACTAAAGCAAGATAGGTCTAGTCATCCAAAGGAGGATCGGGAAGA
326 TAGGTACTAAATCCATGAAAACTAAAGCAAGATAGGTCTAGTCATCCAAAGGAGAATCGGGAAGA
52556 GGAGGATAACGTGCTCGCATCTCGAGTGTGAGCACATCTAAACGTTCGTTAATCTCCCATTGTTG
391 GGAGGATAACGTGCTCGCATCTCGAGTGTGAGCACATCTAAACGTTCGTTAATCTCCCATTGTTG
*
52621 AGCCCCCAAAGTAGTTAGATGGGAATCTATAGATGCAAACCTTAGGTCAAATGACTCCAAAAACG
456 AGCCCCCAAAGTAGTTAGATAGGAATCTATAGATGCAAACCTTAGGTCAAATGACTCCAAAAACG
52686 ATCGAAAATATGGAGGCA
521 ATCGAAAATATGGAGGCA
52704 TTAAACAAGATTTTGCAAAACTTAGCCAATTGATTTTAAATAAATATAACTTAAGCTACTAAGAT
1 TTAAACAAGATTTTGCAAAACTTAGCCAATTGATTTTAAATAAATATAACTTAAGCTACTAAGAT
*
52769 CAAAAGCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATAAACAAATGTGCAATGG
66 CAAAAGCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATAAAAAAATGTGCAATGG
*
52834 TAAATTGGTCATAATGCAACTAATATGTAAATGATGCAAAACTAATAAACATTAAGCTCAAATTG
131 TAAATTGGTCATAATGCAACTAATATGCAAATGATGCAAAACTAATAAACATTAAGCTCAAATTG
*
52899 AAAATTCAAACAAAGCCAAATATATAAATATAAGTTCAAACATCCAGACATTCAAAATAAAAATA
196 AAAATTCAAACAAAGCCAAATATATAAATATAAGTTCAAACATCCAAACATTCAAAATAAAAATA
52964 ATCCAAAAACATCAATCCACAATCATCCAAAATAAAAATCCAAAAACATTCAAAATGTTTAACAA
261 ATCCAAAAACATCAATCCACAATCATCCAAAATAAAAATCCAAAAACATTCAAAATGTTTAACAA
53029 TAGGTACTAAATCCATGAAAACTAAAGCAAGATAGGTCTAGTCATCCAAAGGAGAATCGGGAAGA
326 TAGGTACTAAATCCATGAAAACTAAAGCAAGATAGGTCTAGTCATCCAAAGGAGAATCGGGAAGA
*
53094 GGAGGATAACGTGCTCGCATCTCGAGTGTGAGCACATCTAAACGTTCGTTCATCTCCCATTGTTG
391 GGAGGATAACGTGCTCGCATCTCGAGTGTGAGCACATCTAAACGTTCGTTAATCTCCCATTGTTG
*
53159 AGCCCCCAAAGTAGTTAGATAGGACTCTATAGATGCAAACCTTAGGTCAAATGACTCCAAAAACG
456 AGCCCCCAAAGTAGTTAGATAGGAATCTATAGATGCAAACCTTAGGTCAAATGACTCCAAAAACG
53224 ATCGAAAATATGGAGGCA
521 ATCGAAAATATGGAGGCA
53242 TT
1 TT
53244 TGATCCTCTT
Statistics
Matches: 528, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
538 528 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (538 bp):
TTAAACAAGATTTTGCAAAACTTAGCCAATTGATTTTAAATAAATATAACTTAAGCTACTAAGAT
CAAAAGCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATAAAAAAATGTGCAATGG
TAAATTGGTCATAATGCAACTAATATGCAAATGATGCAAAACTAATAAACATTAAGCTCAAATTG
AAAATTCAAACAAAGCCAAATATATAAATATAAGTTCAAACATCCAAACATTCAAAATAAAAATA
ATCCAAAAACATCAATCCACAATCATCCAAAATAAAAATCCAAAAACATTCAAAATGTTTAACAA
TAGGTACTAAATCCATGAAAACTAAAGCAAGATAGGTCTAGTCATCCAAAGGAGAATCGGGAAGA
GGAGGATAACGTGCTCGCATCTCGAGTGTGAGCACATCTAAACGTTCGTTAATCTCCCATTGTTG
AGCCCCCAAAGTAGTTAGATAGGAATCTATAGATGCAAACCTTAGGTCAAATGACTCCAAAAACG
ATCGAAAATATGGAGGCA
Found at i:54954 original size:23 final size:22
Alignment explanation
Indices: 54928--54995 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
54918 AGTGCATTGA
54928 TGTACATTCAAGGAATGCATCGG
1 TGTACATTCAAGG-ATGCATCGG
* * *
54951 TGTATC-TTC-ATGATGTATCGA
1 TGTA-CATTCAAGGATGCATCGG
*
54972 TGCACATTCAAGGGATGCATCGG
1 TGTACATTCAA-GGATGCATCGG
54995 T
1 T
54996 ACACTGTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 3 0.09
23 16 0.47
24 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (22 bp):
TGTACATTCAAGGATGCATCGG
Found at i:59314 original size:2 final size:2
Alignment explanation
Indices: 59309--59339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59299 AAAAATCTTT
59309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59340 TTCCAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60446 original size:24 final size:24
Alignment explanation
Indices: 60408--60489 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
60398 AACAGAGATG
60408 TCAGAAATC-CAAACAGAATTCAGA
1 TCAGAAATCAC-AACAGAATTCAGA
* * * *
60432 TTAGATATCAGAACAGAATCCAGA
1 TCAGAAATCACAACAGAATTCAGA
*
60456 TCAGAAATCACAACAGAATTCAAA
1 TCAGAAATCACAACAGAATTCAGA
*
60480 TCGGAAATCA
1 TCAGAAATCA
60490 GATAAAACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (24 bp):
TCAGAAATCACAACAGAATTCAGA
Found at i:65201 original size:24 final size:24
Alignment explanation
Indices: 65121--65229 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
65111 AAACGGAGAT
* * *
65121 ATCAGAAATCAAAACAGAATTCAG
1 ATCAAAAATCAGAACAGAATTCAA
* * * *
65145 ATCAAATATCAAAACAGAATCCAG
1 ATCAAAAATCAGAACAGAATTCAA
* *
65169 ATTAGAAATCAGAACAGAATTCAA
1 ATCAAAAATCAGAACAGAATTCAA
* * *
65193 ATAAAAAATTAGAACATAATTCAA
1 ATCAAAAATCAGAACAGAATTCAA
*
65217 ATCGAAAATCAGA
1 ATCAAAAATCAGA
65230 TAAAACATTC
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (24 bp):
ATCAAAAATCAGAACAGAATTCAA
Found at i:69244 original size:31 final size:31
Alignment explanation
Indices: 69169--69244 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
69159 GAAAATTCAT
* *
69169 TATATATTATTA-AA-ATAAAAGTATAATAT
1 TATATATTATTAGAATATAAAAGAATAATAA
* *
69198 TATATATCATTAGAATATTAAAGAATAA-AA
1 TATATATTATTAGAATATAAAAGAATAATAA
69228 TATCATATTATTAGAAT
1 TAT-ATATTATTAGAAT
69245 TATGAGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 11 0.28
30 6 0.15
31 22 0.56
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (31 bp):
TATATATTATTAGAATATAAAAGAATAATAA
Found at i:69283 original size:11 final size:11
Alignment explanation
Indices: 69267--69296 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
69257 TAATTTAATA
69267 ATTAAAATTTT
1 ATTAAAATTTT
69278 ATTAAAATTTT
1 ATTAAAATTTT
*
69289 AATAAAAT
1 ATTAAAAT
69297 AGTATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTT
Found at i:69654 original size:2 final size:2
Alignment explanation
Indices: 69649--69680 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
69639 TTAATTCTTG
*
69649 AT AT AT TT 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
69681 TATTTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:74333 original size:43 final size:43
Alignment explanation
Indices: 74272--74563 Score: 406
Period size: 43 Copynumber: 6.8 Consensus size: 43
74262 CCGTTACAAT
* * *
74272 AGGTCCCTTTGTTGTGTGCAAGGGTAGGCCTTATAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
74315 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
74358 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
74401 AGGTCCCTTTGTTGTGTGCAAGGGTAAGCTTTACAGTTTCCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
74444 AGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
74487 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * * *
74530 AGG-CTCTTTTGATATGTGCAAGGATAAGACCTTA
1 AGGTC-CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
74564 TCGTTTTTGC
Statistics
Matches: 225, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
43 220 0.98
44 5 0.02
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (43 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:78862 original size:23 final size:23
Alignment explanation
Indices: 78836--78903 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
78826 GGGAAACTGT
78836 AAGGCTTACCTTTGCACACAGCA
1 AAGGCTTACCTTTGCACACAGCA
* * * * *
78859 AAGG--GACC--TGGAAACTG-T
1 AAGGCTTACCTTTGCACACAGCA
78877 AAGGCTTACCTTTGCACACAGCA
1 AAGGCTTACCTTTGCACACAGCA
78900 AAGG
1 AAGG
78904 GACCTGGGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
18 4 0.13
19 6 0.20
20 3 0.10
21 3 0.10
22 6 0.20
23 8 0.27
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (23 bp):
AAGGCTTACCTTTGCACACAGCA
Found at i:78884 original size:41 final size:42
Alignment explanation
Indices: 78787--78951 Score: 296
Period size: 42 Copynumber: 4.0 Consensus size: 42
78777 GAGCCTAGGA
*
78787 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
78829 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCT-GG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
78870 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
* *
78912 AAACTATAAGGCTTACCTTTGCAGACAGCAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
78952 ATAATACTTC
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
41 41 0.34
42 78 0.66
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
Found at i:78926 original size:83 final size:83
Alignment explanation
Indices: 78787--78951 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 83
78777 GAGCCTAGGA
*
78787 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
78852 CACAGCAAAGGGACCTGG
66 CACAGCAAAGGGACCTGG
*
78870 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
*
78935 GACAGCAAAGGGACCTG
66 CACAGCAAAGGGACCTG
78952 ATAATACTTC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (83 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
CACAGCAAAGGGACCTGG
Found at i:79832 original size:29 final size:29
Alignment explanation
Indices: 79785--79973 Score: 166
Period size: 29 Copynumber: 6.6 Consensus size: 29
79775 ATCAACCATT
* * * *
79785 TTACGAAAATAGCATCATTTTGAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
79814 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* ** * *
79843 TTACTAAAATATCACTTTTTTAAAAAAAA
1 TTACCAAAATATCACCATTTTCAAAATAA
** * ** *
79872 TTAAGAAATTATCATTATTTT-AAAAAAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* *
79900 TTACGAAAATAGCACCCA-TTTCAAAATAA
1 TTACCAAAATATCA-CCATTTTCAAAATAA
* * *
79929 TTACCAGAATACCACCATTTTCTAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
*
79958 TTACCAAAATACCACC
1 TTACCAAAATATCACC
79974 CGGTCAACGG
Statistics
Matches: 132, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
28 24 0.18
29 108 0.82
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (29 bp):
TTACCAAAATATCACCATTTTCAAAATAA
Found at i:79880 original size:28 final size:28
Alignment explanation
Indices: 79852--79907 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
79842 ATTACTAAAA
79852 TATCACTT-TTTTAAAAAAAATTAAGAAAT
1 TATCA-TTATTTT-AAAAAAATTAAGAAAT
*
79881 TATCATTATTTTAAAAAAATTACGAAA
1 TATCATTATTTTAAAAAAATTAAGAAA
79908 ATAGCACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.38
Consensus pattern (28 bp):
TATCATTATTTTAAAAAAATTAAGAAAT
Found at i:80828 original size:385 final size:385
Alignment explanation
Indices: 80118--80887 Score: 1531
Period size: 385 Copynumber: 2.0 Consensus size: 385
80108 GGCTCGTGGG
80118 ACCTCCTTCGGTGTCCTATAATTCACAAAAAAATTTCCAGAAATTATTTTAAGTGATTTCGAGGT
1 ACCTCCTTCGGTGTCCTATAATTCACAAAAAAATTTCCAGAAATTATTTTAAGTGATTTCGAGGT
80183 ACTTACAAAGCTCGGTTCAAATTTTTGAATGGTGGAGAGCTCGATTTCAACAAATCGGAAACTTT
66 ACTTACAAAGCTCGGTTCAAATTTTTGAATGGTGGAGAGCTCGATTTCAACAAATCGGAAACTTT
80248 GACCGTCTCACCTCCTCACGCGCCGCCATCGACGGAGACCAAGGATGACACCGGCAGACTCGAAA
131 GACCGTCTCACCTCCTCACGCGCCGCCATCGACGGAGACCAAGGATGACACCGGCAGACTCGAAA
80313 CGACACAAGGAACACGATGGTGCGGGAGGTGTCGTAAATGGAGCAACGATCGGTGATGAATTTAA
196 CGACACAAGGAACACGATGGTGCGGGAGGTGTCGTAAATGGAGCAACGATCGGTGATGAATTTAA
*
80378 GATTTTCTCGGCGATTGAGCTAAAAAAAACGTCGAGACTTTGACTTGAAATTCACGGCGTTTGGC
261 GATTTTCTCGGCGATGGAGCTAAAAAAAACGTCGAGACTTTGACTTGAAATTCACGGCGTTTGGC
80443 AATGTTTCACTTCAATTAATTTAAGGGATTTGTTCCTCACTCGATGGCGAACATGATGGT
326 AATGTTTCACTTCAATTAATTTAAGGGATTTGTTCCTCACTCGATGGCGAACATGATGGT
80503 ACCTCCTTCGGTGTCCTATAATTCACAAAAAAATTTCCAGAAATTATTTTAAGTGATTTCGAGGT
1 ACCTCCTTCGGTGTCCTATAATTCACAAAAAAATTTCCAGAAATTATTTTAAGTGATTTCGAGGT
80568 ACTTACAAAGCTCGGTTCAAATTTTTGAATGGTGGAGAGCTCGATTTCAACAAATCGGAAACTTT
66 ACTTACAAAGCTCGGTTCAAATTTTTGAATGGTGGAGAGCTCGATTTCAACAAATCGGAAACTTT
80633 GACCGTCTCACCTCCTCACGCGCCGCCATCGACGGAGACCAAGGATGACACCGGCAGACTCGAAA
131 GACCGTCTCACCTCCTCACGCGCCGCCATCGACGGAGACCAAGGATGACACCGGCAGACTCGAAA
80698 CGACACAAGGAACACGATGGTGCGGGAGGTGTCGTAAATGGAGCAACGATCGGTGATGAATTTAA
196 CGACACAAGGAACACGATGGTGCGGGAGGTGTCGTAAATGGAGCAACGATCGGTGATGAATTTAA
80763 GATTTTCTCGGCGATGGAGCTAAAAAAAACGTCGAGACTTTGACTTGAAATTCACGGCGTTTGGC
261 GATTTTCTCGGCGATGGAGCTAAAAAAAACGTCGAGACTTTGACTTGAAATTCACGGCGTTTGGC
80828 AATGTTTCACTTCAATTAATTTAAGGGATTTGTTCCTCACTCGATGGCGAACATGATGGT
326 AATGTTTCACTTCAATTAATTTAAGGGATTTGTTCCTCACTCGATGGCGAACATGATGGT
80888 GGTTTCAAAA
Statistics
Matches: 384, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
385 384 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (385 bp):
ACCTCCTTCGGTGTCCTATAATTCACAAAAAAATTTCCAGAAATTATTTTAAGTGATTTCGAGGT
ACTTACAAAGCTCGGTTCAAATTTTTGAATGGTGGAGAGCTCGATTTCAACAAATCGGAAACTTT
GACCGTCTCACCTCCTCACGCGCCGCCATCGACGGAGACCAAGGATGACACCGGCAGACTCGAAA
CGACACAAGGAACACGATGGTGCGGGAGGTGTCGTAAATGGAGCAACGATCGGTGATGAATTTAA
GATTTTCTCGGCGATGGAGCTAAAAAAAACGTCGAGACTTTGACTTGAAATTCACGGCGTTTGGC
AATGTTTCACTTCAATTAATTTAAGGGATTTGTTCCTCACTCGATGGCGAACATGATGGT
Found at i:85460 original size:83 final size:83
Alignment explanation
Indices: 85367--85524 Score: 280
Period size: 83 Copynumber: 1.9 Consensus size: 83
85357 GAGCCTAGGA
*
85367 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
85432 CACAGCAAAGGGACCTGG
66 CACAGCAAAGGGACCTGG
** *
85450 AAACTGTAAGGCTTACCTTTTCACACAACAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTTCA
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
85515 CACAGCAAAG
66 CACAGCAAAG
85525 AGACTTGATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (83 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
CACAGCAAAGGGACCTGG
Found at i:85464 original size:41 final size:42
Alignment explanation
Indices: 85367--85524 Score: 273
Period size: 42 Copynumber: 3.8 Consensus size: 42
85357 GAGCCTAGGA
*
85367 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
85409 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCT-GG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
* *
85450 AAACTGTAAGGCTTACCTTTTCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
*
85492 AAACTGTAAGGCTTACCTTTTCACACAGCAAAG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAG
85525 AGACTTGATA
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 39 0.35
42 72 0.65
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
Found at i:86365 original size:29 final size:29
Alignment explanation
Indices: 86328--86514 Score: 175
Period size: 29 Copynumber: 6.6 Consensus size: 29
86318 ATCAACCATT
* *
86328 TTACTAAAATAGCATCATTTTCAAAATAA
1 TTACTAAAATATCACCATTTTCAAAATAA
*
86357 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACTAAAATATCACCATTTTCAAAATAA
* ** * *
86386 TTACTAAAATATAACTTTTTTTAAAAAAAA
1 TTACTAAAATATCAC-CATTTTCAAAATAA
* * *
86416 TTA-TGAAAT-T-ATCATTTT-AAAAAAA
1 TTACTAAAATATCACCATTTTCAAAATAA
* * *
86441 TTACAAAAATATCACCCTTTTAAAAATAA
1 TTACTAAAATATCACCATTTTCAAAATAA
* *
86470 TTACTATAATACCACCATTTTCAAAATAA
1 TTACTAAAATATCACCATTTTCAAAATAA
* *
86499 TTACCAAAATACCACC
1 TTACTAAAATATCACC
86515 CGATGAACGG
Statistics
Matches: 128, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
25 10 0.08
26 8 0.06
27 2 0.02
28 7 0.05
29 88 0.69
30 13 0.10
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (29 bp):
TTACTAAAATATCACCATTTTCAAAATAA
Found at i:86541 original size:13 final size:13
Alignment explanation
Indices: 86523--86560 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
86513 CCCGATGAAC
86523 GGTCAACGGGTCG
1 GGTCAACGGGTCG
86536 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
86549 AGTCAATGGGTC
1 GGTCAACGGGTC
86561 TAGTCGTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:86565 original size:13 final size:13
Alignment explanation
Indices: 86524--86565 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
86514 CCGATGAACG
*
86524 GTCAACGGGTCGG
1 GTCAACGGGTCGA
86537 GTCAACGGGTCGA
1 GTCAACGGGTCGA
* *
86550 GTCAATGGGTCTA
1 GTCAACGGGTCGA
86563 GTC
1 GTC
86566 GTAACCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:89464 original size:17 final size:17
Alignment explanation
Indices: 89421--89465 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
89411 TATATATATA
*
89421 TATAAATATTATTTTTT
1 TATAAATAATATTTTTT
89438 T-TGAAA-AATATTTTTT
1 TAT-AAATAATATTTTTT
89454 TATAAATAATAT
1 TATAAATAATAT
89466 AAAATTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATAAATAATATTTTTT
Found at i:92183 original size:8 final size:8
Alignment explanation
Indices: 92172--92222 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
92162 AAAATAAAAG
92172 TATAATAT
1 TATAATAT
92180 TATATATCAT
1 TATA-AT-AT
92190 TATAATAT
1 TATAATAT
* *
92198 TA-AAGAA
1 TATAATAT
92205 TATAATAT
1 TATAATAT
*
92213 CATAATAT
1 TATAATAT
92221 TA
1 TA
92223 GAATTATGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
7 5 0.15
8 19 0.56
9 4 0.12
10 6 0.18
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (8 bp):
TATAATAT
Found at i:92642 original size:2 final size:2
Alignment explanation
Indices: 92635--92680 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
92625 TTAATTCTTG
92635 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
92677 AT AT
1 AT AT
92681 TTTTTTTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96318 original size:20 final size:20
Alignment explanation
Indices: 96293--96330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
96283 CAATTTATTC
96293 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
96313 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
96331 TCCTTTGAAA
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:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:104661 original size:10 final size:10
Alignment explanation
Indices: 104646--104680 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
104636 CTCTTGATTC
104646 TTGTTTCTTG
1 TTGTTTCTTG
*
104656 TTGTTTCTTA
1 TTGTTTCTTG
104666 TTGTTTCTTG
1 TTGTTTCTTG
104676 TTGTT
1 TTGTT
104681 GATCAATGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.03, C:0.09, G:0.17, T:0.71
Consensus pattern (10 bp):
TTGTTTCTTG
Found at i:104970 original size:19 final size:19
Alignment explanation
Indices: 104946--104994 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
104936 AGCCTGAGTA
104946 CATCGATGCATGTCTTGTG
1 CATCGATGCATGTCTTGTG
104965 CATCGATGCATGTCTTGTG
1 CATCGATGCATGTCTTGTG
104984 CATCGATGCAT
1 CATCGATGCAT
104995 CAAATGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (19 bp):
CATCGATGCATGTCTTGTG
Found at i:105115 original size:65 final size:64
Alignment explanation
Indices: 104962--105124 Score: 168
Period size: 65 Copynumber: 2.5 Consensus size: 64
104952 TGCATGTCTT
* * *
104962 GTGCATCGATGCAT-GTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAACCTT
1 GTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAAACATT
105026 A
64 A
* * * ** **
105027 ATGCATTGATGCGTGGTATGTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCATTA
1 GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTC-ATAAAAACATTA
* *
105091 GTGCATCGATGCATGGAATGGTGCATCGGTGCAT
1 GTGCATCGATGCATGGTAT-GTGCATCGATGCAT
105125 TCCTTTGAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 3 0.04
64 22 0.28
65 53 0.66
66 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAAACATTA
Found at i:107209 original size:37 final size:37
Alignment explanation
Indices: 107133--107209 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
107123 AAATTAATTA
**
107133 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
107170 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
107207 TAT
1 TAT
107210 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:109723 original size:406 final size:406
Alignment explanation
Indices: 108971--109786 Score: 1312
Period size: 406 Copynumber: 2.0 Consensus size: 406
108961 TACAAGTCCA
*
108971 TCTTGTTCTGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAGCTCCACTTGAAAAAATAACA
1 TCTTGTTCTGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGAAAAAATAACA
*
109036 AGAATCGCTATAGTAGCAAAAACGTTTAGATTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
66 AGAATCGCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
* * * * * *
109101 ATGACTTTGGTCGGCATAAGACTTTACTCCTATTGCAACAGTTGTTTTACAACAAATATGGTCAT
131 ATGACTTTGGTCAGCAGAAGACCTTACTCCTATTGCAACAATTCTTTGACAACAAATATGGTCAT
109166 TTATAGAGTATCTTAATGGTTGTGGAATGAATCTAAGGTTTTAAGAAAAATTAATAACATTTTCA
196 TTATAGAGTATCTTAATGGTTGTGGAATGAATCTAAGGTTTTAAGAAAAATTAATAACATTTTCA
*
109231 CTTTAATTATCAGTTTCACATCAATAAAACATTCAAGTAATGTTTTTAATTACCATTTAATTCAA
261 CTATAATTATCAGTTTCACATCAATAAAACATTCAAGTAATGTTTTTAATTACCATTTAATTCAA
* * * *
109296 TATACTGTAACAAATTTCATATAGTTTGAATAAACTTCAATAGATTATTTAATGATAGTAATGAT
326 TATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATGAT
*
109361 ATTTCTTTGTTTTTTG
391 ATTTCTTTGTTTCTTG
* **
109377 TCTTGTTCTGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCGCTTGCGAAAATAACA
1 TCTTGTTCTGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGAAAAAATAACA
* *
109442 AGAATCAG-TATAGTAGCATAAAGGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTT
66 AGAATC-GCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTT
* * * * * * * **
109506 TATGATTTTGGTCAGTAGAAGACCTTACTGCTGTTTCAACAATTCTTTGATAGCATTTATGGTCA
130 TATGACTTTGGTCAGCAGAAGACCTTACTCCTATTGCAACAATTCTTTGACAACAAATATGGTCA
*
109571 TTTATAGAGTATCTTAATGGTTGT-GACATGAATCTAAGGTTTTAAGAGAAATTAATAACATTTT
195 TTTATAGAGTATCTTAATGGTTGTGGA-ATGAATCTAAGGTTTTAAGAAAAATTAATAACATTTT
* * *
109635 CACTATAATTATCAGTTTCACATCAATAATACTTTCATGTAATGTTTTTAATTACCATTTAATTC
259 CACTATAATTATCAGTTTCACATCAATAAAACATTCAAGTAATGTTTTTAATTACCATTTAATTC
109700 AATATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATG
324 AATATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATG
109765 ATATTTCTTTGTTTCTTG
389 ATATTTCTTTGTTTCTTG
109783 TCTT
1 TCTT
109787 TAGTTTAATA
Statistics
Matches: 376, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
405 2 0.01
406 373 0.99
407 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (406 bp):
TCTTGTTCTGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGAAAAAATAACA
AGAATCGCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
ATGACTTTGGTCAGCAGAAGACCTTACTCCTATTGCAACAATTCTTTGACAACAAATATGGTCAT
TTATAGAGTATCTTAATGGTTGTGGAATGAATCTAAGGTTTTAAGAAAAATTAATAACATTTTCA
CTATAATTATCAGTTTCACATCAATAAAACATTCAAGTAATGTTTTTAATTACCATTTAATTCAA
TATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATGAT
ATTTCTTTGTTTCTTG
Found at i:112624 original size:166 final size:165
Alignment explanation
Indices: 112335--112679 Score: 595
Period size: 166 Copynumber: 2.1 Consensus size: 165
112325 ATGGTCATTT
* *
112335 ATAGAGTATCTTAATGGTTGTGACATGAATCTAAGGTTTTAATATAAATTAATAAATTTTCACTT
1 ATAGAGTATCTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAAATTTTCACTT
* *
112400 TATTTTCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATATA
66 AATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATATA
112465 CGGTAA-AAATTTCATATAATTTGAATAAACTTCA
131 CGGTAACAAATTTCATATAATTTGAATAAACTTCA
112499 ATAGAGTATCTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAACATTTTCACT
1 ATAGAGTATCTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAA-ATTTTCACT
*
112564 TAAATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTTAATTACCATTTAATTCAATA
65 T-AATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATA
* *
112629 TACGGTAACAAATTTCTTATAGTTTGAATAAACTTCA
129 TACGGTAACAAATTTCATATAATTTGAATAAACTTCA
112666 ATAGAGTAT-TTAAT
1 ATAGAGTATCTTAAT
112680 TATAGTAACG
Statistics
Matches: 171, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
164 53 0.31
165 10 0.06
166 73 0.43
167 35 0.20
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (165 bp):
ATAGAGTATCTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAAATTTTCACTT
AATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATATA
CGGTAACAAATTTCATATAATTTGAATAAACTTCA
Found at i:113026 original size:2 final size:2
Alignment explanation
Indices: 113019--113050 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
113009 TTGGCTTACG
113019 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
113051 TTGAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114101 original size:6 final size:7
Alignment explanation
Indices: 114092--114150 Score: 56
Period size: 6 Copynumber: 8.9 Consensus size: 7
114082 AAATTAAATT
114092 TATTA-A
1 TATTATA
114098 TATTATA
1 TATTATA
114105 TA-TATA
1 TATTATA
114111 TA-TATA
1 TATTATA
114117 TA-TATA
1 TATTATA
114123 TATATATA
1 TAT-TATA
114131 TATATATA
1 TAT-TATA
*
114139 TATAATA
1 TATTATA
114146 -ATTAT
1 TATTAT
114151 TTTAGTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
6 27 0.56
7 6 0.12
8 15 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TATTATA
Found at i:114108 original size:2 final size:2
Alignment explanation
Indices: 114097--114142 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
114087 AAATTTATTA
114097 AT AT -T 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
114138 AT AT A
1 AT AT A
114143 ATAATTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116012 original size:24 final size:24
Alignment explanation
Indices: 115971--116052 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
115961 AACAGAGATG
* * *
115971 TCAGAAACCAAAATAAAATTCAGA
1 TCAGAAATCAGAACAAAATTCAGA
* * *
115995 TCAGATATCAGAACAAAATCCGGA
1 TCAGAAATCAGAACAAAATTCAGA
116019 TCAGAAATCAGAACAGAAA-TCAGA
1 TCAGAAATCAGAACA-AAATTCAGA
*
116043 ACAGAAATCA
1 TCAGAAATCA
116053 AATCGGAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 44 0.94
25 3 0.06
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAGA
Found at i:116037 original size:12 final size:12
Alignment explanation
Indices: 115990--116066 Score: 77
Period size: 12 Copynumber: 6.4 Consensus size: 12
115980 AAAATAAAAT
* *
115990 TCAGATCAGATA
1 TCAGAACAGAAA
116002 TCAGAACA-AAA
1 TCAGAACAGAAA
* *
116013 TCCGGATCAGAAA
1 T-CAGAACAGAAA
116026 TCAGAACAGAAA
1 TCAGAACAGAAA
116038 TCAGAACAGAAA
1 TCAGAACAGAAA
*
116050 TCA-AATCGGAAA
1 TCAGAA-CAGAAA
116062 TCAGA
1 TCAGA
116067 TAAAACATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
11 5 0.09
12 44 0.81
13 5 0.09
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (12 bp):
TCAGAACAGAAA
Found at i:116062 original size:36 final size:36
Alignment explanation
Indices: 115990--116066 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
115980 AAAATAAAAT
* * **
115990 TCAGATCAGATATCAGAACAAAATCCGGATCAGAAA
1 TCAGAACAGAAATCAGAACAAAATCCAAATCAGAAA
*
116026 TCAGAACAGAAATCAGAACAGAAAT-CAAATCGGAAA
1 TCAGAACAGAAATCAGAACA-AAATCCAAATCAGAAA
116062 TCAGA
1 TCAGA
116067 TAAAACATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (36 bp):
TCAGAACAGAAATCAGAACAAAATCCAAATCAGAAA
Found at i:120325 original size:18 final size:18
Alignment explanation
Indices: 120282--120318 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
120272 TTGTGTTATA
*
120282 AATATTAAATTATTTAAT
1 AATATTAAATTATGTAAT
120300 AATATTAAATTTATGTAAT
1 AATATTAAA-TTATGTAAT
120319 TTATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATATTAAATTATGTAAT
Found at i:123363 original size:39 final size:39
Alignment explanation
Indices: 123267--123385 Score: 98
Period size: 40 Copynumber: 2.9 Consensus size: 39
123257 AAATTATATT
* ** *
123267 ACTTTTTTATTAAAATAATAATAATATATTATTGATATTTTTA
1 ACTTTATTATTAAAATAATAAT-ATAT-TTA-AAATA-TTATA
*
123310 A--TTACTATTGAAAATAATAATATATTTAAAATATTATA
1 ACTTTATTATT-AAAATAATAATATATTTAAAATATTATA
* * *
123348 ACTTTATTATTAAAATAAGAATATTATATAATATATTA
1 ACTTTATTATTAAAATAATAATA-TATTTAAAATATTA
123386 AAGGTTGTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
38 5 0.08
39 14 0.22
40 22 0.35
41 10 0.16
42 11 0.17
43 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (39 bp):
ACTTTATTATTAAAATAATAATATATTTAAAATATTATA
Found at i:126396 original size:3 final size:3
Alignment explanation
Indices: 126388--126414 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
126378 ATATTAATTT
126388 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
126415 TATTCTTGAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:126706 original size:12 final size:12
Alignment explanation
Indices: 126689--126721 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
126679 TATAATTTAA
*
126689 TAATTAAAATTT
1 TAATTAAAATGT
126701 TAATTAAAATGT
1 TAATTAAAATGT
126713 TAA-TAAAAT
1 TAATTAAAAT
126722 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Done.