Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001915.1 Hibiscus syriacus cultivar Beakdansim tig00003877_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: 81206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:882 original size:22 final size:22
Alignment explanation
Indices: 857--926 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
847 AAATTAAATT
857 CAAAAGAGAATGAAACGAAGTA
1 CAAAAGAGAATGAAACGAAGTA
** * *
879 CAAAATGA-AA-GAAAATTAAATT
1 CAAAA-GAGAATG-AAACGAAGTA
901 CAAAAGAGAATGAAACGAAGTA
1 CAAAAGAGAATGAAACGAAGTA
923 CAAA
1 CAAA
927 CTGAAAGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
21 3 0.08
22 30 0.83
23 3 0.08
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.13
Consensus pattern (22 bp):
CAAAAGAGAATGAAACGAAGTA
Found at i:893 original size:44 final size:44
Alignment explanation
Indices: 845--971 Score: 211
Period size: 44 Copynumber: 2.9 Consensus size: 44
835 CGGAATGACC
845 GAAAATTAAATTCAAAAGAGAATGAAACGAAGTACAAAATGAAA
1 GAAAATTAAATTCAAAAGAGAATGAAACGAAGTACAAAATGAAA
*
889 GAAAATTAAATTCAAAAGAGAATGAAACGAAGTACAAACTGAAA
1 GAAAATTAAATTCAAAAGAGAATGAAACGAAGTACAAAATGAAA
* *
933 GAAAATTAAATTCAAAAGA-AGATGAAATGAAGTAAAAAA
1 GAAAATTAAATTCAAAAGAGA-ATGAAACGAAGTACAAAA
972 ATGCTTGCCA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
43 1 0.01
44 77 0.99
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.17
Consensus pattern (44 bp):
GAAAATTAAATTCAAAAGAGAATGAAACGAAGTACAAAATGAAA
Found at i:948 original size:22 final size:21
Alignment explanation
Indices: 881--948 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
871 ACGAAGTACA
881 AAATGAAAGAAAATTAAATTC
1 AAATGAAAGAAAATTAAATTC
* ** * *
902 AAAAGAGAATG-AAACGAAGTAC
1 AAATGA-AA-GAAAATTAAATTC
924 AAACTGAAAGAAAATTAAATTC
1 AAA-TGAAAGAAAATTAAATTC
946 AAA
1 AAA
949 AGAAGATGAA
Statistics
Matches: 33, Mismatches: 10, Indels: 7
0.66 0.20 0.14
Matches are distributed among these distances:
21 6 0.18
22 24 0.73
23 3 0.09
ACGTcount: A:0.62, C:0.07, G:0.13, T:0.18
Consensus pattern (21 bp):
AAATGAAAGAAAATTAAATTC
Found at i:7784 original size:21 final size:21
Alignment explanation
Indices: 7760--7815 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
7750 AGGGTTAGAA
* *
7760 TAAAACAAATAAAAATTAATT
1 TAAAATAAATAAAAATTAAAT
* * *
7781 TAAATTAAATAGAAGTTAAAT
1 TAAAATAAATAAAAATTAAAT
7802 TAAAATAAATAAAA
1 TAAAATAAATAAAA
7816 TAAGATTCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAATAAATAAAAATTAAAT
Found at i:9328 original size:45 final size:45
Alignment explanation
Indices: 9270--9671 Score: 590
Period size: 45 Copynumber: 8.9 Consensus size: 45
9260 ATTATTCATT
* * **
9270 ATTTCCATTTATGGCATCCTTTCATACCTTTAATGAACTATTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
9316 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
** *
9361 ATTTCATTTATGTAATCCTTTCATGCCTTTAATACACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
9406 ATTTCATTTATGTCATACTTTCATGTCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
9451 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
9496 ATTTTATTTATGGTATCCTTTCATGCCTTTAATACACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
9541 ATTTCATTTATGGCATCCTTTCATGCCTTCAATGCACTG-TATGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
9585 ATTTCATTTATGGCATCCTTTCATACCTTTAATGCATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
9630 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCGTTA
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTA
9672 CGCTTTTAGT
Statistics
Matches: 318, Mismatches: 37, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
44 39 0.12
45 275 0.86
46 4 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:9988 original size:55 final size:55
Alignment explanation
Indices: 9920--10025 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
9910 GCCAATACAG
9920 AAATTCATAAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCTCATATGA
1 AAATTCATAAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTG-TCATATGA
* *
9976 AAATTCAT-AAACTTATTATGAATTTCTTAGTTTTGTACCCAAAGTGTCAT
1 AAATTCATAAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGTCAT
10026 TTGGTAATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 4 0.08
55 36 0.75
56 8 0.17
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (55 bp):
AAATTCATAAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGTCATATGA
Found at i:11550 original size:6 final size:6
Alignment explanation
Indices: 11541--11565 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11531 ACTTGGACCT
11541 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
11566 CACAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:11690 original size:73 final size:72
Alignment explanation
Indices: 11609--11836 Score: 308
Period size: 73 Copynumber: 3.2 Consensus size: 72
11599 TTTCAAAACC
* *
11609 AAACTATATAT-TATATA-TTCGAAAAATGTTTTCCAAAC-TATATTATATAT-TTTTCAAAAAT
1 AAACTATATATATATATATTTCAAAAAATGTTTTCAAAACATATATTATATATATTTTCAAAAAT
11670 GTTTTTCA
66 G-TTTTCA
11678 AAACTATATATATATAT-TTTCAAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAA
1 AAACTATATATATATATATTTCAAAAAATGTTTTCAAAAC-ATATATTATATATATTTTC-AAAA
11742 ATGTTTTCA
64 ATGTTTTCA
* **
11751 AAACTATATAT-TACATATTTTTAAAAATGTTTTCAAAACTATATATTATATATATTTTC-AAAA
1 AAACTATATATATATATATTTCAAAAAATGTTTTCAAAAC-ATATATTATATATATTTTCAAAAA
11814 TGTTTTCA
65 TGTTTTCA
*
11822 AAAATAGTATATATA
1 AAACTA-TATATATA
11837 AATAGAACAC
Statistics
Matches: 144, Mismatches: 6, Indels: 14
0.88 0.04 0.09
Matches are distributed among these distances:
69 11 0.08
70 24 0.17
71 17 0.12
72 21 0.15
73 64 0.44
74 7 0.05
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (72 bp):
AAACTATATATATATATATTTCAAAAAATGTTTTCAAAACATATATTATATATATTTTCAAAAAT
GTTTTCA
Found at i:11704 original size:36 final size:34
Alignment explanation
Indices: 11609--11836 Score: 273
Period size: 35 Copynumber: 6.4 Consensus size: 34
11599 TTTCAAAACC
* *
11609 AAACTATATAT-TATATATTCGAAAAATGTTTTCC
1 AAACTATATATATATATTTTC-AAAAATGTTTTCA
11643 AAACTATAT-TATATATTTTTCAAAAATGTTTTTCA
1 AAACTATATATATATA-TTTTCAAAAATG-TTTTCA
11678 AAACTATATATATATATTTTCAAAAAATGTTTTCA
1 AAACTATATATATATATTTTC-AAAAATGTTTTCA
11713 AAACTATATATTATATATATTTTCAAAAAATGTTTTCA
1 AAAC--TATA-TATATATATTTTC-AAAAATGTTTTCA
* *
11751 AAACTATATATTACATATTTTTAAAAATGTTTTCA
1 AAACTATATA-TATATATTTTCAAAAATGTTTTCA
11786 AAACTATATATTATATATATTTTC-AAAATGTTTTCA
1 AAAC--TATA-TATATATATTTTCAAAAATGTTTTCA
*
11822 AAAATAGTATATATA
1 AAACTA-TATATATA
11837 AATAGAACAC
Statistics
Matches: 174, Mismatches: 7, Indels: 26
0.84 0.03 0.13
Matches are distributed among these distances:
33 1 0.01
34 28 0.16
35 54 0.31
36 41 0.24
37 17 0.10
38 33 0.19
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (34 bp):
AAACTATATATATATATTTTCAAAAATGTTTTCA
Found at i:12602 original size:23 final size:23
Alignment explanation
Indices: 12574--12623 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
12564 ATTTGATGAA
*
12574 TTCTAACTATATTCCATGAATCT
1 TTCTAACTATAATCCATGAATCT
12597 TTCTAACTATAATCCATGAATCT
1 TTCTAACTATAATCCATGAATCT
12620 TTCT
1 TTCT
12624 TGAATTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (23 bp):
TTCTAACTATAATCCATGAATCT
Found at i:15542 original size:15 final size:14
Alignment explanation
Indices: 15517--15547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
15507 AATATAACTT
15517 TTTATTATTTTTAA
1 TTTATTATTTTTAA
15531 TTTATATATTTTTAA
1 TTTAT-TATTTTTAA
15546 TT
1 TT
15548 AAAATTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTATTTTTAA
Found at i:20573 original size:22 final size:22
Alignment explanation
Indices: 20537--20602 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
20527 ACTATTCACT
* *
20537 GCTACACTAATTGCTACAGTAC
1 GCTACAATAACTGCTACAGTAC
* *
20559 GCTATAATAACTGCTACAGTAA
1 GCTACAATAACTGCTACAGTAC
* *
20581 GCTACAGTAACTGCTTCAGTAC
1 GCTACAATAACTGCTACAGTAC
20603 TTCCGAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (22 bp):
GCTACAATAACTGCTACAGTAC
Found at i:21056 original size:44 final size:44
Alignment explanation
Indices: 20944--21130 Score: 252
Period size: 44 Copynumber: 4.2 Consensus size: 44
20934 TTTACCATTT
* * *
20944 TTTA-CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCA
1 TTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
* * *
20987 TTAATCCCATAAGCTCGTAAGCTTATTTTACCAATGTTCTTGCCA
1 TTTAT-CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
* *
21032 TTTATCCATAAGCTCGTAAGCTTATTTTACCATTATACTTCCCA
1 TTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
* *
21076 TTAATCCATAAGCTCGTAAGCTTATTTTACCAATATATTTGCCA
1 TTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
21120 -TTATACCATAA
1 TTTAT-CCATAA
21131 CAATGTACCA
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
43 6 0.05
44 81 0.65
45 38 0.30
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (44 bp):
TTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:21064 original size:24 final size:24
Alignment explanation
Indices: 20993--21064 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
20983 ACCATTAATC
20993 CCATAAGCTCGTAAGCTTATTTTA
1 CCATAAGCTCGTAAGCTTATTTTA
* * * *
21017 CCA-ATGTTC-T-TGC-CA-TTTA
1 CCATAAGCTCGTAAGCTTATTTTA
21036 TCCATAAGCTCGTAAGCTTATTTTA
1 -CCATAAGCTCGTAAGCTTATTTTA
21061 CCAT
1 CCAT
21065 TATACTTCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.18
22 2 0.06
23 6 0.18
24 8 0.24
25 4 0.12
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (24 bp):
CCATAAGCTCGTAAGCTTATTTTA
Found at i:21129 original size:88 final size:88
Alignment explanation
Indices: 20944--21130 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 88
20934 TTTACCATTT
20944 TTTACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTAATCCCATAAGCTCGTAAGC
1 TTTACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTAATCCCATAAGCTCGTAAGC
*
21009 TTATTTTACCAATGTTCTTGCCA
66 TTATTTTACCAATATTCTTGCCA
* ** *
21032 TTTATCCATAAGCTCGTAAGCTTATTTTACCATTATACTTCCCATTAAT-CCATAAGCTCGTAAG
1 TTTA-CCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTAATCCCATAAGCTCGTAAG
21096 CTTATTTTACCAATATAT-TTGCCA
65 CTTATTTTACCAATAT-TCTTGCCA
21120 TTATACCATAA
1 TT-TACCATAA
21131 CAATGTACCA
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
88 48 0.53
89 43 0.47
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (88 bp):
TTTACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTAATCCCATAAGCTCGTAAGC
TTATTTTACCAATATTCTTGCCA
Found at i:24496 original size:54 final size:54
Alignment explanation
Indices: 24393--24503 Score: 125
Period size: 54 Copynumber: 2.1 Consensus size: 54
24383 AGAATACATG
** * * * *
24393 TTTGTAATTTCTTATGCACATGTAGAATATAATTTTATAATGTAGAATATATTT
1 TTTGTAAAATCTTAAGCACATGTAGAATATAATTATATAATGTAAAATATATAT
* * *
24447 TTTGTAAAATCTTAAGCATATGTAGAATATAATTGATAT-TTTTAAAATATATAT
1 TTTGTAAAATCTTAAGCACATGTAGAATATAATT-ATATAATGTAAAATATATAT
24501 TTT
1 TTT
24504 ATAATTAGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 44 0.94
55 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (54 bp):
TTTGTAAAATCTTAAGCACATGTAGAATATAATTATATAATGTAAAATATATAT
Found at i:29217 original size:17 final size:18
Alignment explanation
Indices: 29192--29229 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29182 CGACACTTTA
29192 ATGTATAGTAAAC-TAAT
1 ATGTATAGTAAACTTAAT
* *
29209 ATGTGTAGTAAGCTTAAT
1 ATGTATAGTAAACTTAAT
29227 ATG
1 ATG
29230 GACAATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (18 bp):
ATGTATAGTAAACTTAAT
Found at i:30476 original size:141 final size:141
Alignment explanation
Indices: 30222--30498 Score: 518
Period size: 141 Copynumber: 2.0 Consensus size: 141
30212 ATGGTAAACA
30222 TGATATTATGAATATTATTGTTAATTACATTTTGAAATTATTTGCCTCTTCTAATCCTAATCTTG
1 TGATATTATGAATATTATTGTTAATTACATTTTGAAATTATTTGCCTCTTCTAATCCTAATCTTG
30287 ATGAGTCTATTCTTAATGCCATTGAGCCTATTATTACTGGTTACATGAATAATATTATTTGTATG
66 ATGAGTCTATTCTTAATGCCATTGAGCCTATTATTACTGGTTACATGAATAATATTATTTGTATG
30352 GACTTTACTAC
131 GACTTTACTAC
* * *
30363 TGATATTATGAATATTATTGTTAATTACATTTTGAAATTATTTGTCTCTTCTAATCTTGATCTTG
1 TGATATTATGAATATTATTGTTAATTACATTTTGAAATTATTTGCCTCTTCTAATCCTAATCTTG
*
30428 ATGAGTCTATTCTTAATGCCATTGAGCCTATTATTACTGGTTACATGAATAATATTCTTTGTATG
66 ATGAGTCTATTCTTAATGCCATTGAGCCTATTATTACTGGTTACATGAATAATATTATTTGTATG
30493 GACTTT
131 GACTTT
30499 GTAGAAAAAA
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 132 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (141 bp):
TGATATTATGAATATTATTGTTAATTACATTTTGAAATTATTTGCCTCTTCTAATCCTAATCTTG
ATGAGTCTATTCTTAATGCCATTGAGCCTATTATTACTGGTTACATGAATAATATTATTTGTATG
GACTTTACTAC
Found at i:38942 original size:113 final size:113
Alignment explanation
Indices: 38756--38965 Score: 316
Period size: 113 Copynumber: 1.9 Consensus size: 113
38746 TTTATATAAA
*
38756 TAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGACAACTCCTTCC
1 TAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGACAACTCCTTCC
**
38821 TTTGATATTAATAAAAA-AAATAAATAA-TAAAAAATTATTTTAATATAG
66 TTCAATATT--TAAAAATAAATAAATAACTAAAAAATTATTTTAATATAG
* * * * *
38869 TAAGATATTTATTTATTTAAAAATATTAGAAAAGAGTTTCTAGTTGTTTTAAGACAGCTCTTTCC
1 TAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGACAACTCCTTCC
38934 TTCAATATTTAAAAATAAATAAATAACTAAAA
66 TTCAATATTTAAAAATAAATAAATAACTAAAA
38966 CATAATAATA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 6 0.07
112 10 0.11
113 71 0.82
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (113 bp):
TAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGACAACTCCTTCC
TTCAATATTTAAAAATAAATAAATAACTAAAAAATTATTTTAATATAG
Found at i:39480 original size:3 final size:3
Alignment explanation
Indices: 39474--39560 Score: 99
Period size: 3 Copynumber: 29.0 Consensus size: 3
39464 TCAATTTTTT
**
39474 TTA TTA TTA TT- TTA TT- TTA TT- TTA AAA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
39517 TTA TTA TTA TTA TTA TTA TTA TATA TATA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA
39561 AAAAAATTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 6 0.08
3 59 0.81
4 8 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41138 original size:111 final size:112
Alignment explanation
Indices: 40981--41187 Score: 312
Period size: 111 Copynumber: 1.9 Consensus size: 112
40971 TATTATTATG
**
40981 TTTTAGTTATTTATTTATTTTAAATATTGAAGGAAAGAGCTGTCTTAAAACAACTAGAAACTC-T
1 TTTTAGTTATTTATTTATTTTAAATATCAAAGGAAAGAGCTGTCTTAAAACAACTAGAAACTCTT
*
41045 TTCTAATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATT
66 TTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAATAATT
* * *
41092 TTTTA-TTATTTATTT-TTTTATTAATATCAAAGGAAGGAGCTGTCTTAAAACACCTAGAAGCTC
1 TTTTAGTTATTTATTTATTTTA--AATATCAAAGGAAAGAGCTGTCTTAAAACAACTAGAAACTC
*
41155 TTTTCTGATATTTCTAAATAAATAAATATCTTA
64 TTTTCTAATATTTCTAAATAAATAAATATCTTA
41188 TTTATATAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
109 5 0.06
110 10 0.12
111 41 0.48
112 30 0.35
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (112 bp):
TTTTAGTTATTTATTTATTTTAAATATCAAAGGAAAGAGCTGTCTTAAAACAACTAGAAACTCTT
TTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAATAATT
Found at i:43233 original size:15 final size:14
Alignment explanation
Indices: 43181--43234 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
43171 TTTACGTTTG
*
43181 TATTTACATTTACA
1 TATTTACATTTGCA
*
43195 TTTTTACATTTGCA
1 TATTTACATTTGCA
43209 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
43224 TCTTTGCATTT
1 TATTTACATTT
43235 TTTATGTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:46420 original size:6 final size:6
Alignment explanation
Indices: 46401--46450 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
46391 CTCATCCAGC
46401 AAAGAA AGAAGAA AAAGAA AAAGAA AAAG-- AAAGAA AAAGAA AAAGGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA
46449 AA
1 AA
46451 TTGAATCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.10
6 25 0.62
7 11 0.28
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:46435 original size:16 final size:16
Alignment explanation
Indices: 46405--46445 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
46395 TCCAGCAAAG
*
46405 AAAGAAGAA-AAAGAA
1 AAAGAAAAAGAAAGAA
46420 AAAGAAAAAGAAAGAA
1 AAAGAAAAAGAAAGAA
46436 AAAGAAAAAG
1 AAAGAAAAAG
46446 GAAAATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:46437 original size:22 final size:21
Alignment explanation
Indices: 46405--46450 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
46395 TCCAGCAAAG
46405 AAAGAAGAAAAAGAAAAAGAA
1 AAAGAAGAAAAAGAAAAAGAA
*
46426 AAAGAAAGAAAAAGAAAAAGGA
1 AAAG-AAGAAAAAGAAAAAGAA
46448 AAA
1 AAA
46451 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAAAGAAAAAGAA
Found at i:48919 original size:115 final size:115
Alignment explanation
Indices: 48717--49021 Score: 592
Period size: 115 Copynumber: 2.7 Consensus size: 115
48707 AAGTGCCATG
*
48717 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
48782 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
48832 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
48897 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
*
48947 TGTTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
49012 TGGTTTGGTA
66 TGGTTTGGTA
49022 AAATCAATCA
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 188 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
Found at i:49113 original size:83 final size:83
Alignment explanation
Indices: 48974--49279 Score: 504
Period size: 83 Copynumber: 3.6 Consensus size: 83
48964 AGGAGACTCA
48974 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATT
49039 TGGAAGAGGAATGTGCTC
66 TGGAAGAGGAATGTGCTC
49057 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATT
49122 TGGAAGAGGAATGTGCTC
66 TGGAAGAGGAATGTGCTC
*
49140 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A-AATCAAT
*
49205 TATTGAATTTGGAAGAGGAATGTGCTC
57 CATTGAATTTGGAAGAGGAATGTGCTC
*
49232 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATCTGGTTTGGTA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
49280 TGAACCACAG
Statistics
Matches: 211, Mismatches: 3, Indels: 16
0.92 0.01 0.07
Matches are distributed among these distances:
83 129 0.61
85 2 0.01
90 2 0.01
91 1 0.00
92 77 0.36
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATT
TGGAAGAGGAATGTGCTC
Found at i:49271 original size:92 final size:92
Alignment explanation
Indices: 49026--49306 Score: 463
Period size: 92 Copynumber: 3.1 Consensus size: 92
49016 TTGGTAAAAT
49026 CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
*
49091 GATCTGGTTTGG--T-----A-A-AAT
66 GATCTGGTTTGGTATGAACCACAGAAC
49109 CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
49174 GATCTGGTTTGGTATGAACCACAGAAC
66 GATCTGGTTTGGTATGAACCACAGAAC
* *
49201 CAATTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCT
1 CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
49266 GATCTGGTTTGGTATGAACCACAGAAC
66 GATCTGGTTTGGTATGAACCACAGAAC
49293 CAATCATTGGAATT
1 CAATCATT-GAATT
49307 AAAAGATGAA
Statistics
Matches: 184, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
83 77 0.42
85 1 0.01
90 1 0.01
91 1 0.01
92 99 0.54
93 5 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (92 bp):
CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
GATCTGGTTTGGTATGAACCACAGAAC
Found at i:49772 original size:95 final size:95
Alignment explanation
Indices: 49603--49802 Score: 364
Period size: 95 Copynumber: 2.1 Consensus size: 95
49593 TATTCTCCTC
* *
49603 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAAAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCAATATCTGTGAAATCATCTTG
*
49668 AAAGGTCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
49698 ATCAAAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCAATATCTGTGAAATCATCTTG
1 ATCAAAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCAATATCTGTGAAATCATCTTG
49763 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
*
49793 ATCATAATCA
1 ATCAAAATCA
49803 ACATGTTGCA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 101 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (95 bp):
ATCAAAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCAATATCTGTGAAATCATCTTG
AAAGATCACTTCATAATCAGATGAGTTGTT
Found at i:50325 original size:113 final size:113
Alignment explanation
Indices: 50116--50899 Score: 1100
Period size: 113 Copynumber: 7.0 Consensus size: 113
50106 GCAAAGATTA
* * * * *
50116 AAATCCATCATTCAATGGGTCAACATTTCCAGTTCGAGTTCGTAATGAGAAAAACTCATCTGAAG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
50181 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
*
50229 GAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
50294 AAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * *
50342 GAATTCATGATTTAATGGATCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAAATCATCTGAAG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
50407 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* *
50455 AAATCCATTATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
50520 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * *
50568 GAATTCATGATTCAATGGATCAGCATTTCCGGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
50633 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* ** * * * * *
50681 AAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTTATAATAAGAAGAACTCGTCATCTG
1 AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTG
* * *
50746 AAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * * * *****
50793 AAATCCATCA-TCTGATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATGATTC-AATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
50857 G-A--AA-AAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
50900 ATAATTCTAT
Statistics
Matches: 612, Mismatches: 52, Indels: 18
0.90 0.08 0.03
Matches are distributed among these distances:
107 3 0.00
108 3 0.00
109 40 0.07
110 1 0.00
111 1 0.00
112 73 0.12
113 473 0.77
114 1 0.00
115 5 0.01
116 12 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (113 bp):
AAATTCATGATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
Found at i:51058 original size:124 final size:120
Alignment explanation
Indices: 50818--51058 Score: 293
Period size: 124 Copynumber: 2.0 Consensus size: 120
50808 TGGATCAGCT
* * *
50818 TTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAG
1 TTTCCAAAGAAAGCTCATAATGAGAAGAACTCATCTGAAGAAAAAAAAGTTCACAATGAGAAGAA
* * * * * ** * *
50883 CTTGTTCAACCTTTTGCATAATTCTATTACCGAAAGCGATAGATTAGCATCAACC
66 CTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
* *
50938 TTTCCAGAGAAAGCTCATAATGAGAAGAACTCATCTGAAGGGGAAAGAAAAAGTTCATAATGAGA
1 TTTCCAAAGAAAGCTCATAATGAGAAGAACTCATCTGAA---GAAA-AAAAAGTTCACAATGAGA
* * *
51003 AGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCA
62 AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCA
51059 TCCCCAGCGG
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
120 37 0.37
123 4 0.04
124 59 0.59
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (120 bp):
TTTCCAAAGAAAGCTCATAATGAGAAGAACTCATCTGAAGAAAAAAAAGTTCACAATGAGAAGAA
CTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
Found at i:51240 original size:3 final size:3
Alignment explanation
Indices: 51234--51323 Score: 105
Period size: 3 Copynumber: 30.0 Consensus size: 3
51224 TCAATTTTTT
**
51234 TTA TTA TTA TT- TTA TT- TTA TT- TTA AAA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
51277 TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA
51324 AAAAAATTAC
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
2 6 0.08
3 62 0.82
4 8 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:52629 original size:12 final size:11
Alignment explanation
Indices: 52606--52649 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
52596 ATTACTTTTA
52606 TATTTCAATTAT
1 TATTT-AATTAT
52618 TACTTTAATTAT
1 TA-TTTAATTAT
*
52630 TATTTTATTAT
1 TATTTAATTAT
52641 TATCTTAAT
1 TAT-TTAAT
52650 CATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 11 0.39
12 14 0.50
13 3 0.11
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTAATTAT
Found at i:52921 original size:113 final size:113
Alignment explanation
Indices: 52760--52969 Score: 316
Period size: 113 Copynumber: 1.9 Consensus size: 113
52750 TATTATTATG
**
52760 TTTTAGTTATTTATTTATTTTTAAATATTGAAGAAAAGAGCTGTCTTAAAACAACTAGAAACTCT
1 TTTTAGTTATTTATTTATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGAAACTCT
*
52825 TTTCTAATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATT
66 TTTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAATAATT
* * * *
52873 TTTTA-TTATTTATTT-TTTTTATTAATATCAAAGGAAGGAGCTGTCTTAAAACACCTAGAAGCT
1 TTTTAGTTATTTATTTATTTTTA--AATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGAAACT
*
52936 CTTTTCTGATATTTCTAAATAAATAAATATCTTA
64 CTTTTCTAATATTTCTAAATAAATAAATATCTTA
52970 TTTATATAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 6 0.07
112 10 0.11
113 71 0.82
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (113 bp):
TTTTAGTTATTTATTTATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGAAACTCT
TTTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAATAATT
Found at i:53633 original size:41 final size:41
Alignment explanation
Indices: 53588--53709 Score: 117
Period size: 40 Copynumber: 3.0 Consensus size: 41
53578 AACTAAAATG
*
53588 CCGCAATAAAGTTGTTTATAGTGGCGTTTCTTCAACAAACA
1 CCGCAATAAAGTTGTTTATAGTGGCGTTTGTTCAACAAACA
* * *
53629 CCGCAAT--AGTTTGTTAATGTCGTGGCGTTTGTAT-AA-AAACG
1 CCGCAATAAAG-TTGTT--TATAGTGGCGTTTGT-TCAACAAACA
* * *
53670 TCGCGATAATGTTGTTTATAGTGGCGTTTGTTCAACAAAC
1 CCGCAATAAAGTTGTTTATAGTGGCGTTTGTTCAACAAAC
53710 GACGCTATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
39 3 0.05
40 20 0.31
41 20 0.31
42 19 0.30
43 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (41 bp):
CCGCAATAAAGTTGTTTATAGTGGCGTTTGTTCAACAAACA
Found at i:54658 original size:42 final size:43
Alignment explanation
Indices: 54606--54706 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
54596 TGTTACAAAT
*** *
54606 GCCGCTATATACCA-ACCTTTAGTGGCGTTTGTATACTAAAAAC
1 GCCGCTATATACCAGACCAGCAGCGGCGTTTGTATACT-AAAAC
* *
54649 GCCGC-ATATACCAGATCAGCAGCGGCGTTTGTATCCTAAAAC
1 GCCGCTATATACCAGACCAGCAGCGGCGTTTGTATACTAAAAC
54691 GCCGCTATATACCAGA
1 GCCGCTATATACCAGA
54707 TCTTTATATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 18 0.36
43 32 0.64
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
GCCGCTATATACCAGACCAGCAGCGGCGTTTGTATACTAAAAC
Found at i:54787 original size:43 final size:43
Alignment explanation
Indices: 54731--54852 Score: 190
Period size: 43 Copynumber: 2.8 Consensus size: 43
54721 TTTATCCTAA
* *
54731 AAACACCGCTAAATGTCAAAACCTATTGCGGTGTTTTTAATAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGTGTTTTTAACAC
*
54774 AAACGCCGCTAAATGTCAAAACCTATTGCGGTATTTTTAACAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGTGTTTTTAACAC
* * *
54817 AAATGCTGCTAAATGTCAAAACCTATTGCGGCGTTT
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGTGTTT
54853 ACAAACGCCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAATGTCAAAACCTATTGCGGTGTTTTTAACAC
Found at i:54892 original size:81 final size:83
Alignment explanation
Indices: 54738--54892 Score: 188
Period size: 81 Copynumber: 1.9 Consensus size: 83
54728 TAAAAACACC
* * *
54738 GCTAAATGTCAAAACCTATTGCGGTGTTTTTAATACAAACGCCGCTAAATGTCAAAACCTATTGC
1 GCTAAATGTCAAAACCTATTGCGGCG--TTT-ATACAAACGCCGCTAAATATCAAAACATATTGC
*
54803 GGTATTTTTAACACAAATGCT
63 GGCATTTTTAACACAAATGCT
* ***
54824 GCTAAATGTCAAAACCTATTGCGGCG-TT-TACAAACGCCGCTATATATCGTTACATATTGCGGC
1 GCTAAATGTCAAAACCTATTGCGGCGTTTATACAAACGCCGCTAAATATCAAAACATATTGCGGC
*
54887 GTTTTT
66 ATTTTT
54893 GGTTCACAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
81 33 0.55
83 2 0.03
86 25 0.42
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (83 bp):
GCTAAATGTCAAAACCTATTGCGGCGTTTATACAAACGCCGCTAAATATCAAAACATATTGCGGC
ATTTTTAACACAAATGCT
Found at i:56533 original size:22 final size:22
Alignment explanation
Indices: 56498--56551 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
56488 AATAAAAACT
* *
56498 AATTCAAAAA-TTGAT-TTAAA
1 AATTAAAAAATTTGATGATAAA
*
56518 AATATAAAAAATTTGATGATACA
1 AAT-TAAAAAATTTGATGATAAA
56541 AATTAAAAAAT
1 AATTAAAAAAT
56552 ATGAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 6 0.21
22 13 0.46
23 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AATTAAAAAATTTGATGATAAA
Found at i:56698 original size:16 final size:16
Alignment explanation
Indices: 56674--56715 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
56664 ATGCTGCTTT
* *
56674 TAATGATTTATAAATA
1 TAATTATTTATAAAAA
56690 TAATTATTTATAAAAA
1 TAATTATTTATAAAAA
56706 TAA-TATTTAT
1 TAATTATTTAT
56716 TTTCGCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTATTTATAAAAA
Found at i:57529 original size:2 final size:2
Alignment explanation
Indices: 57522--57547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57512 CTTTATTAGG
57522 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
57548 TATGAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63576 original size:29 final size:29
Alignment explanation
Indices: 63543--63605 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
63533 CTCTTATTAT
* *
63543 TTTTTGT-ATTTGCATTTTTGCCCTTTTAA
1 TTTTTGTAATTTACATGTTT-CCCTTTTAA
* *
63572 TTTTTGTAATTTATATGTTTCCCTTTTAT
1 TTTTTGTAATTTACATGTTTCCCTTTTAA
63601 TTTTT
1 TTTTT
63606 TATGTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.14, C:0.11, G:0.08, T:0.67
Consensus pattern (29 bp):
TTTTTGTAATTTACATGTTTCCCTTTTAA
Found at i:64190 original size:7 final size:7
Alignment explanation
Indices: 64175--64399 Score: 99
Period size: 7 Copynumber: 31.0 Consensus size: 7
64165 TTTCGTCCAG
*
64175 TATAGTA
1 TATATTA
64182 TATATTA
1 TATATTA
*
64189 TATAGTA
1 TATATTA
*
64196 T-TAGTA
1 TATATTA
64202 TAT-TATA
1 TATAT-TA
**
64209 TATAGCA
1 TATATTA
64216 TATA-TA
1 TATATTA
*
64222 CATATTA
1 TATATTA
**
64229 TATGGTA
1 TATATTA
*
64236 TA-AGTA
1 TATATTA
*
64242 CAT-TGTA
1 TATAT-TA
64249 TATTATATA
1 TA-TAT-TA
64258 TAATATTA
1 TA-TATTA
64266 TATATTA
1 TATATTA
*
64273 TTTA-TA
1 TATATTA
64279 GTATAATTA
1 -TAT-ATTA
64288 TATATTA
1 TATATTA
*
64295 TGTATTA
1 TATATTA
*
64302 TATATAA
1 TATATTA
64309 TATA-TA
1 TATATTA
64315 TTATATTA
1 -TATATTA
64323 TTATATTA
1 -TATATTA
64331 TATTATTATA
1 TA-TA-T-TA
64341 TTATATTA
1 -TATATTA
*
64349 TATGTTA
1 TATATTA
64356 TAGTA-TA
1 TA-TATTA
*
64363 TATATCA
1 TATATTA
64370 TATATTA
1 TATATTA
64377 TTATATTTAA
1 -TATA-TT-A
64387 TATATTA
1 TATATTA
64394 T-TATTA
1 TATATTA
64400 CAAATATTAT
Statistics
Matches: 170, Mismatches: 26, Indels: 45
0.71 0.11 0.19
Matches are distributed among these distances:
6 24 0.14
7 91 0.54
8 30 0.18
9 18 0.11
10 5 0.03
11 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (7 bp):
TATATTA
Found at i:64192 original size:2 final size:2
Alignment explanation
Indices: 64175--64391 Score: 83
Period size: 2 Copynumber: 117.5 Consensus size: 2
64165 TTTCGTCCAG
*
64175 TA TA GTA TA TA T- TA TA TA GTA T- TA GTA TA T- TA TA TA TA GCA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
64216 TA TA TA CA TA T- TA TA TGG TA TA -A GTA CA T- TG TA TA T- TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA
*
64256 TA TA -A TA T- TA TA TA T- TA TT TA TA GTA TA -A T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
64293 TA TG TA T- TA TA TA TA -A TA TA TA T- TA TA T- TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
64329 TA TA T- TA T- TA TA T- TA TA T- TA TA TG T- TA TA GTA 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
*
64367 TCA TA TA T- TA T- TA TA TT TA -A TA TA T
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA T
64392 TATTATTACA
Statistics
Matches: 163, Mismatches: 16, Indels: 72
0.65 0.06 0.29
Matches are distributed among these distances:
1 27 0.17
2 121 0.74
3 15 0.09
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64205 original size:18 final size:18
Alignment explanation
Indices: 64173--64367 Score: 111
Period size: 18 Copynumber: 10.6 Consensus size: 18
64163 ATTTTCGTCC
64173 AGTATAGTATATATTATAT
1 AGTATA-TATATATTATAT
64192 AGTAT-TAGTATATTATATAT
1 AGTATATA-TATA-T-TATAT
*
64212 AGCATATATACATATTATAT
1 AG--TATATATATATTATAT
* * *
64232 GGTATA-AGTACATTGTAT
1 AGTATATA-TATATTATAT
*
64250 ATTATATATAATATTATAT
1 AGTATATAT-ATATTATAT
* * *
64269 ATTATTTATAGTATAAT-T
1 AGTATATATA-TATTATAT
*
64287 A-TATATTATGTATTATAT
1 AGTATA-TATATATTATAT
64305 A-TA-ATATATATTATATT
1 AGTATATATATATTATA-T
*
64322 ATTATAT-TATATTATTAT
1 AGTATATATATATTA-TAT
*
64340 ATTATAT-TATATGT-TAT
1 AGTATATATATAT-TATAT
64357 AGTATATATAT
1 AGTATATATAT
64368 CATATATTAT
Statistics
Matches: 142, Mismatches: 16, Indels: 37
0.73 0.08 0.19
Matches are distributed among these distances:
16 10 0.07
17 23 0.16
18 55 0.39
19 32 0.23
20 13 0.09
21 1 0.01
22 6 0.04
23 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
AGTATATATATATTATAT
Found at i:64228 original size:40 final size:37
Alignment explanation
Indices: 64183--64394 Score: 120
Period size: 38 Copynumber: 5.7 Consensus size: 37
64173 AGTATAGTAT
64183 ATATTATATAGTATTAGTATATTATATATAGCATATATA
1 ATATTATATAGTATTAGTATATTATATAT--CATATATA
* * * * *
64222 CATATTATATGGTATAAGTACATTGTATATTATATATA
1 -ATATTATATAGTATTAGTATATTATATATCATATATA
* * *
64260 ATATTATATATTATT--TATAGTATA-ATTATATATTA
1 ATATTATATAGTATTAGTATATTATATATCATATA-TA
* * *
64295 TGTATTATATA-TAATA-TATATTATATTATTATATTATA
1 -ATATTATATAGTATTAGTATATTATA-TATCATA-TATA
* *
64333 TTATTATATTA-TATTA-TATGTTATAGTAT-ATATATCA
1 ATATTATA-TAGTATTAGTATATTATA-TATCATATAT-A
*
64370 TATATTAT-TA-TATTTAATATATTAT
1 -ATATTATATAGTA-TTAGTATATTAT
64395 TATTACAAAT
Statistics
Matches: 141, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
34 8 0.06
35 11 0.08
36 24 0.17
37 26 0.18
38 45 0.32
39 2 0.01
40 25 0.18
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (37 bp):
ATATTATATAGTATTAGTATATTATATATCATATATA
Found at i:64292 original size:36 final size:38
Alignment explanation
Indices: 64252--64383 Score: 127
Period size: 36 Copynumber: 3.6 Consensus size: 38
64242 CATTGTATAT
64252 TATATATA-ATATTA-TATATTATTTATAGTATAATTA
1 TATATATATATATTATTATATTATTTATAGTATAATTA
* * * *
64288 TATAT-TATGTATTA-TATATAATATATATTAT-ATTA
1 TATATATATATATTATTATATTATTTATAGTATAATTA
*
64323 T-TATAT-TATATTATTATATTATATTATATGT-TATAGTA
1 TATATATATATATTATTATATTAT-TTATA-GTATA-ATTA
64361 TATATATCATATATTATTATATT
1 TATATAT-ATATATTATTATATT
64384 TAATATATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
34 9 0.12
35 15 0.19
36 29 0.38
37 1 0.01
38 4 0.05
39 5 0.06
41 14 0.18
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (38 bp):
TATATATATATATTATTATATTATTTATAGTATAATTA
Found at i:64319 original size:5 final size:5
Alignment explanation
Indices: 64247--64399 Score: 80
Period size: 5 Copynumber: 31.4 Consensus size: 5
64237 AAGTACATTG
* *
64247 TATAT TATA- TATAA TAT-T ATATAT TAT-T TATAG TATAAT TATA- TAT-T
1 TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TAT-AT TATAT TATAT
*
64294 ATGTAT TATA- TATAAT ATATAT TATA- T-TAT TATAT TATA- T-TAT
1 -TATAT TATAT TAT-AT -TATAT TATAT TATAT TATAT TATAT TATAT
* *
64337 TATAT TATAT TATATGT TATAG TATA- TATAT CATA- TATTAT TATAT
1 TATAT TATAT TATA--T TATAT TATAT TATAT TATAT TA-TAT TATAT
*
64383 T-TAA TATAT TATTAT TA
1 TATAT TATAT TA-TAT TA
64400 CAAATATTAT
Statistics
Matches: 116, Mismatches: 10, Indels: 43
0.69 0.06 0.25
Matches are distributed among these distances:
3 4 0.03
4 26 0.22
5 63 0.54
6 15 0.13
7 8 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:64319 original size:41 final size:41
Alignment explanation
Indices: 64247--64397 Score: 154
Period size: 38 Copynumber: 3.7 Consensus size: 41
64237 AAGTACATTG
*
64247 TATATTATATATAATATTATATATTATTTATAGTATAATTATATA
1 TATATTAT-TAT-ATATAATATATTA-TTATAGTAT-ATTATATA
64292 T-TATGTATTATATATAATATA-TATTATA-T-TATTATAT-
1 TATAT-TATTATATATAATATATTATTATAGTATATTATATA
* *
64329 TATATTATTATATTATATTATA-TGTTATAGTATA-TATATCA
1 TATATTATTATA-TATAATATATTATTATAGTATATTATAT-A
*
64370 TATATTATTATATTTAATATATTATTAT
1 TATATTATTATATATAATATATTATTAT
64398 TACAAATATT
Statistics
Matches: 92, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
37 8 0.09
38 24 0.26
39 7 0.08
40 10 0.11
41 22 0.24
42 2 0.02
43 9 0.10
44 6 0.07
45 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (41 bp):
TATATTATTATATATAATATATTATTATAGTATATTATATA
Found at i:69090 original size:21 final size:21
Alignment explanation
Indices: 69061--69103 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
69051 AAAAAGGGAA
69061 CAAGAACTGGACACACCTCAT
1 CAAGAACTGGACACACCTCAT
* *
69082 CAAGCACTGGACACATCTCAT
1 CAAGAACTGGACACACCTCAT
69103 C
1 C
69104 CTTACAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.14, T:0.16
Consensus pattern (21 bp):
CAAGAACTGGACACACCTCAT
Found at i:69421 original size:24 final size:24
Alignment explanation
Indices: 69394--69443 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
69384 TCAAGAAGAC
*
69394 TCATATGCTGCAAAAGCACAAGCT
1 TCATATGCGGCAAAAGCACAAGCT
* *
69418 TCATTTGCGGTAAAAGCACAAGCT
1 TCATATGCGGCAAAAGCACAAGCT
69442 TC
1 TC
69444 CTTAACCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (24 bp):
TCATATGCGGCAAAAGCACAAGCT
Found at i:76910 original size:24 final size:24
Alignment explanation
Indices: 76865--76911 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
76855 AATCAAGAAC
*
76865 CAAGAATCAGAAAATCAGGATTGG
1 CAAGAATCAGAAAACCAGGATTGG
*
76889 CAAGAATCA-AGAAACCATGATTG
1 CAAGAATCAGA-AAACCAGGATTG
76912 ATAGAAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (24 bp):
CAAGAATCAGAAAACCAGGATTGG
Found at i:77779 original size:2 final size:2
Alignment explanation
Indices: 77767--78017 Score: 87
Period size: 2 Copynumber: 130.5 Consensus size: 2
77757 TCTAGGATAG
* *
77767 TA TA TA T- TA TA TA -A TA TA TA TA CA TA T- TA TA TGG TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* *
77806 GTA CA TA GTA TA TA TA T- TA TA T- TA TA TA T- TA TT TA TA GTA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
77846 -A T- TA CA TA GTA TG TA TT TA TT TA GTA TA T- TA TA TA TA GTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * *
77886 TA T- TC TA TA TA TC TA T- TA TA TA T- TA TA GTA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
77926 T- TA T- TA TA TA T- TA TGG TA T- TA TA TA -A TA TA -A TA TT TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
77963 TA T- TA TG T- TA TA TG TA T- TA TA GTA TA TA TA TT TA TA TA GCA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
78004 TA TA TA TCA TA TA T
1 TA TA TA T-A TA TA T
78018 TATTCTTATA
Statistics
Matches: 183, Mismatches: 32, Indels: 68
0.65 0.11 0.24
Matches are distributed among these distances:
1 22 0.12
2 141 0.77
3 20 0.11
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77779 original size:7 final size:7
Alignment explanation
Indices: 77767--78020 Score: 122
Period size: 7 Copynumber: 36.4 Consensus size: 7
77757 TCTAGGATAG
77767 TATATAT
1 TATATAT
*
77774 TATATAA
1 TATATAT
77781 TATATA-
1 TATATAT
*
77787 TACATAT
1 TATATAT
**
77794 TATATGG
1 TATATAT
*
77801 TATA-AG
1 TATATAT
* *
77807 TACATAG
1 TATATAT
77814 TATATA-
1 TATATAT
77820 TATTATAT
1 TA-TATAT
77828 TATATAT
1 TATATAT
*
77835 TATTTA-
1 TATATAT
77841 TAGTA-AT
1 TA-TATAT
* *
77848 TACATAG
1 TATATAT
*
77855 TATGTAT
1 TATATAT
77862 T-TAT-T
1 TATATAT
77867 TAGTATAT
1 TA-TATAT
77875 TATATA-
1 TATATAT
77881 TAGTATAT
1 TA-TATAT
*
77889 TCTATA-
1 TATATAT
*
77895 TATCTAT
1 TATATAT
77902 TATATAT
1 TATATAT
77909 TATAGTA-
1 TATA-TAT
77916 TATATAT
1 TATATAT
77923 T-TATTAT
1 TATA-TAT
77930 TATATAT
1 TATATAT
*
77937 TATGGTAT
1 TAT-ATAT
*
77945 TATATAA
1 TATATAT
77952 TATAATAT
1 TAT-ATAT
77960 T-TATAT
1 TATATAT
*
77966 TATGT-T
1 TATATAT
*
77972 ATATGTAT
1 -TATATAT
77980 TATAGTA-
1 TATA-TAT
77987 TATATATT
1 TATATA-T
*
77995 TATATAGCA
1 TATATA--T
78004 TATATAT
1 TATATAT
*
78011 CATATAT
1 TATATAT
78018 TAT
1 TAT
78021 TCTTATAAAT
Statistics
Matches: 190, Mismatches: 31, Indels: 52
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.01
6 35 0.18
7 118 0.62
8 29 0.15
9 6 0.03
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:77849 original size:25 final size:24
Alignment explanation
Indices: 77821--77964 Score: 63
Period size: 23 Copynumber: 5.9 Consensus size: 24
77811 TAGTATATAT
77821 ATTATATTATATATTATTTATAGTA
1 ATTATATTATATA-TATTTATAGTA
* *
77846 ATTACA-TAGTATGTATTTATTTAGTA
1 ATTATATTA-TATATATTTA--TAGTA
77872 TATTATA-TATAGTATATTCTATA-T-
1 -ATTATATTATA-TATATT-TATAGTA
* *
77896 A-TCTATTATATATTATAGTATA-TA
1 ATTATATTATATA-TAT-TTATAGTA
*
77920 TATT-TATTAT-TATATATTATGGT-
1 -ATTATATTATATATAT-TTATAGTA
*
77943 ATTATATAATATAATATTTATA
1 ATTATATTATAT-ATATTTATA
77965 TTATGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 33
0.68 0.07 0.24
Matches are distributed among these distances:
22 8 0.09
23 25 0.27
24 16 0.17
25 20 0.22
26 10 0.11
27 12 0.13
28 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
ATTATATTATATATATTTATAGTA
Found at i:77912 original size:18 final size:18
Alignment explanation
Indices: 77767--78020 Score: 112
Period size: 20 Copynumber: 13.6 Consensus size: 18
77757 TCTAGGATAG
77767 TATATATTATATAATATAT
1 TATATATTATAT-ATATAT
* * *
77786 ATACATATTATATGGTATAAG
1 -TATATATTATAT-ATAT-AT
*
77807 TACATAGTATATATATTATAT
1 TATATA-T-TATATA-TATAT
*
77828 TATATATTATTTATAGTAAT
1 TATATATTATATATA-T-AT
* * * *
77848 TACATAGTATGTATTTATT
1 TATATATTATATATATA-T
77867 TAGTATATTATATATAGTA-
1 TA-TATATTATATATA-TAT
* *
77886 TAT-T-CTATATATCTAT
1 TATATATTATATATATAT
77902 TATATATTATAGTATATA-
1 TATATATTATA-TATATAT
*
77920 TATTTATTAT-TATATAT
1 TATATATTATATATATAT
*
77937 TATGGTATTATATA-ATAT
1 TAT-ATATTATATATATAT
* *
77955 AATAT-TTATAT-TATGT
1 TATATATTATATATATAT
77971 TATATGTATTATAGTATATA-
1 TATA--TATTATA-TATATAT
* *
77991 TATTTATATAGCATATATAT
1 TATATAT-TA-TATATATAT
*
78011 CATATATTAT
1 TATATATTAT
78021 TCTTATAAAT
Statistics
Matches: 177, Mismatches: 32, Indels: 52
0.68 0.12 0.20
Matches are distributed among these distances:
15 2 0.01
16 28 0.16
17 6 0.03
18 33 0.19
19 34 0.19
20 53 0.30
21 13 0.07
22 8 0.05
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
TATATATTATATATATAT
Found at i:77947 original size:43 final size:42
Alignment explanation
Indices: 77818--77994 Score: 80
Period size: 43 Copynumber: 4.1 Consensus size: 42
77808 ACATAGTATA
* * * *
77818 TATATTATATTATATATTATTTATAGTAATTACATAGTAT-GTAT
1 TATATTATAGTATATA-TATTTAT-GT-ATTATATATTATAATAT
* * * * *
77862 T-TATT-TAGTATATTATATATAGTATATTCTATATATCTATTA-
1 TATATTATAGTATA-TATATTTA-TGTATTATATAT-TATAATAT
**
77904 TATATTATAGTATATATATTTAT-TATTATATATTATGGTAT
1 TATATTATAGTATATATATTTATGTATTATATATTATAATAT
* * * *
77945 TATATAATA-TAATATTTATATTATGT-TATATGTATTATAGTAT
1 TATATTATAGT-ATATATAT-TTATGTAT-TATATATTATAATAT
77988 ATATATT
1 -TATATT
77995 TATATAGCAT
Statistics
Matches: 103, Mismatches: 18, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
40 5 0.05
41 30 0.29
42 21 0.20
43 34 0.33
44 13 0.13
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (42 bp):
TATATTATAGTATATATATTTATGTATTATATATTATAATAT
Found at i:79359 original size:15 final size:14
Alignment explanation
Indices: 79339--79385 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
79329 TCCTAGATTC
79339 TTAATTCTTTTCAAT
1 TTAATTCTTTT-AAT
79354 TTAATTCTTTTAAT
1 TTAATTCTTTTAAT
79368 TTGAATTTTCTTTTAAT
1 TT-AA--TTCTTTTAAT
79385 T
1 T
79386 CTTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.17
15 13 0.45
17 11 0.38
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (14 bp):
TTAATTCTTTTAAT
Done.