Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000612.1 Hibiscus syriacus cultivar Beakdansim tig00001186_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: 88077
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2433 original size:12 final size:12
Alignment explanation
Indices: 2416--2458 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2406 AAAATACGGT
2416 ATGAACAATACC
1 ATGAACAATACC
*
2428 ATGAACATTA--
1 ATGAACAATACC
*
2438 ATGAATAATACC
1 ATGAACAATACC
2450 ATGAACAAT
1 ATGAACAAT
2459 GATCTGCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.32
12 17 0.68
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:3934 original size:22 final size:22
Alignment explanation
Indices: 3906--3947 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3896 GACCAATGTG
3906 TCCCAAAGGACCACTGTATATA
1 TCCCAAAGGACCACTGTATATA
3928 TCCCAAAGGACCACTGTATA
1 TCCCAAAGGACCACTGTATA
3948 ACCCTCGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (22 bp):
TCCCAAAGGACCACTGTATATA
Found at i:10768 original size:18 final size:18
Alignment explanation
Indices: 10745--10779 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10735 ACTGAATATT
*
10745 TGTCCCGAATGACCACTA
1 TGTCCCAAATGACCACTA
10763 TGTCCCAAATGACCACT
1 TGTCCCAAATGACCACT
10780 GTATAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (18 bp):
TGTCCCAAATGACCACTA
Found at i:14560 original size:23 final size:23
Alignment explanation
Indices: 14531--14657 Score: 170
Period size: 23 Copynumber: 5.6 Consensus size: 23
14521 GCACAGCAGA
*
14531 GTGCATCGATACACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
*
14554 GTGCATCGATACACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
14577 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
* *
14600 GTGCATCGATGCACCTTC-ATG-
1 GTGCATCGATGCACATTCAAGGC
* *
14621 GTGAACCGATGCACATTCAAGG-
1 GTGCATCGATGCACATTCAAGGC
14643 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
14658 TAACTAGTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.16
22 5 0.05
23 73 0.78
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:14649 original size:44 final size:46
Alignment explanation
Indices: 14537--14657 Score: 158
Period size: 44 Copynumber: 2.7 Consensus size: 46
14527 CAGAGTGCAT
* * * *
14537 CGATACACATTCAAGGCGTGCATCGATACACATTCAAGGCGTGCAT
1 CGATGCACATTCAAGGCGTGCATCGATGCACATTCAAGGCGTGAAC
* *
14583 CGATGCACATTCAAGGCGTGCATCGATGCACCTTC-ATG-GTGAAC
1 CGATGCACATTCAAGGCGTGCATCGATGCACATTCAAGGCGTGAAC
14627 CGATGCACATTCAAGG-GATGCATCGATGCAC
1 CGATGCACATTCAAGGCG-TGCATCGATGCAC
14658 TAACTAGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 1 0.01
44 33 0.49
45 2 0.03
46 32 0.47
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (46 bp):
CGATGCACATTCAAGGCGTGCATCGATGCACATTCAAGGCGTGAAC
Found at i:18489 original size:22 final size:21
Alignment explanation
Indices: 18447--18486 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18437 AAGACTATTT
18447 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
18468 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
18487 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:24315 original size:29 final size:29
Alignment explanation
Indices: 24272--24328 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
24262 AATGGGGAAG
* **
24272 TGATTGTTTTGTTACTTTTGCAATATTAA
1 TGATTGTTTTATTACTTTTAAAATATTAA
24301 TGATTGTTTTATTACTTTTAAAATATTA
1 TGATTGTTTTATTACTTTTAAAATATTA
24329 GTCAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (29 bp):
TGATTGTTTTATTACTTTTAAAATATTAA
Found at i:25457 original size:23 final size:24
Alignment explanation
Indices: 25427--25483 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
25417 TTTTAGCTTG
*
25427 TAAATGAACATGTTCACGAACGT-
1 TAAATGAACATGTTCACGAACATA
* *
25450 TAAATGAACATGTTCATGAGCATA
1 TAAATGAACATGTTCACGAACATA
25474 TAAATGAACA
1 TAAATGAACA
25484 ATAAACGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (24 bp):
TAAATGAACATGTTCACGAACATA
Found at i:27465 original size:36 final size:35
Alignment explanation
Indices: 27398--27467 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
27388 TTAAATCTAA
*
27398 ATTACTCTTTAAATAATTTTAATGATAAAACAAAAT
1 ATTACTCTTTAAATAATTTAAAT-ATAAAACAAAAT
*
27434 ATTACTCTTCTTAAATAATTTAAAT-TTAAACAAA
1 ATTACTC-T-TTAAATAATTTAAATATAAAACAAA
27468 CGCGTTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 15 0.50
37 1 0.03
38 14 0.47
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (35 bp):
ATTACTCTTTAAATAATTTAAATATAAAACAAAAT
Found at i:27925 original size:4 final size:4
Alignment explanation
Indices: 27898--27945 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
27888 ATCGAAGAAA
* * *
27898 AAAT AATT AAAT AAA- AAGAA AAAT AAAT AAGT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
27946 CCAAGAAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 2 0.05
4 33 0.89
5 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:27932 original size:20 final size:20
Alignment explanation
Indices: 27895--27945 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
27885 AATATCGAAG
*
27895 AAAAAATAATTAAATAAA-A
1 AAAAAATAAATAAATAAATA
*
27914 AGAAAAATAAATAAGTAAATA
1 A-AAAAATAAATAAATAAATA
*
27935 AATAAATAAAT
1 AAAAAATAAAT
27946 CCAAGAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATAAATAAATAAATA
Found at i:30471 original size:85 final size:85
Alignment explanation
Indices: 30329--30735 Score: 465
Period size: 85 Copynumber: 4.8 Consensus size: 85
30319 ATGTGCTGTC
* * * * * *
30329 GAGCTGAATGGAATCAGACTCGATAGTTTTTTGTTGACAGATAGTCCTTCTCGCCTTGAGCTATT
1 GAGCTGAATGTAATCAAACTCGA-AGGTCTTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATG
* *
30394 CTGTAAATTTGATATGGCTTT
65 CTATAAATTTGATATGTCTTT
* * * * *
30415 GAGATGAATGGAATCAAACTCGAAGGTATTTGTTGACAGATAATCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATGC
* *
30480 TATAAATTTGATAAGTCCTT
66 TATAAATTTGATATGTCTTT
* * * * *
30500 GAGCTAAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATGC
*
30565 TATAAATTTGATATGTCATT
66 TATAAATTTGATATGTCTTT
* * * *
30585 GAGCCGAATGTAATCGAACTCGAAGGTCTTTGTTGACTGAT-ATCCCTTCTCGCTTTGAGCTATG
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAAT-CCTTCTCGCCTTGAGCTATG
* * **
30649 TTGTAAATTTGATATCCCTTT
65 CTATAAATTTGATATGTCTTT
* * * * ***
30670 TAGCTGAATGTAATCAAACTCGAAGGTCTTTGCTGGCAGATAACCCTTCTCATTTTGAGCTATGC
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATGC
30735 T
66 T
30736 GCGAATAGTT
Statistics
Matches: 275, Mismatches: 44, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
84 1 0.00
85 252 0.92
86 22 0.08
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATGC
TATAAATTTGATATGTCTTT
Found at i:32097 original size:146 final size:145
Alignment explanation
Indices: 31832--32122 Score: 555
Period size: 146 Copynumber: 2.0 Consensus size: 145
31822 TCGATACCCA
31832 GGCTTGGTATCGATATCATAGCTAGGGAAATATCAGTACCATGCTTGGGGTACCGATACTACTCA
1 GGCTTGGTATCGATATCATAGCTAGGGAAATATCAGTACCATGCTTGGGGTACCGATACTACTCA
*
31897 AAGAGGAAATTGTATTTAGCATTTCGATTATCTTGAATTATTAAGGATCGAATTATGATAATTGG
66 AAGAGGAAATTGTATTTAGCATTTCGATTATCTTGAATTATTAAGGATCAAATTATGATAATTGG
31962 AATGTTGATATATAT
131 AATGTTGATATATAT
*
31977 GGCTTGGTATCGATATCATAGCTAGGGAAGTATCAGTACCATGCTTGGGGGTACCGATACTACTC
1 GGCTTGGTATCGATATCATAGCTAGGGAAATATCAGTACCATGCTT-GGGGTACCGATACTACTC
32042 AAAGAGGAAATTGTATTTAGCATTTCGATTATCTTGAATTATTAAGGATCAAATTATGATAATTG
65 AAAGAGGAAATTGTATTTAGCATTTCGATTATCTTGAATTATTAAGGATCAAATTATGATAATTG
32107 GAATGTTGATATATAT
130 GAATGTTGATATATAT
32123 ATTATATGTA
Statistics
Matches: 143, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
145 45 0.31
146 98 0.69
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (145 bp):
GGCTTGGTATCGATATCATAGCTAGGGAAATATCAGTACCATGCTTGGGGTACCGATACTACTCA
AAGAGGAAATTGTATTTAGCATTTCGATTATCTTGAATTATTAAGGATCAAATTATGATAATTGG
AATGTTGATATATAT
Found at i:35498 original size:91 final size:91
Alignment explanation
Indices: 35342--35518 Score: 248
Period size: 91 Copynumber: 1.9 Consensus size: 91
35332 AATCACCTTT
* * *
35342 ATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGACGTTTAACCAATTTCTTTAAAGGGATAACT
1 ATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGACGTTTAACCAATTACTCTAAAGGGACAACT
* *
35407 CAAGTTTTATTGTATATATATTTATA
66 CAAGCTTTATTGTATACATATTTATA
* * * * *
35433 ATCAGGCTAGCTTATTCTTATCCATAAAGCTGGCG-TGTTTAACCAATTACTCTACAGGGACAAC
1 ATCAGGCTAGCTGAATCTTATCCATAAAGCCGG-GACGTTTAACCAATTACTCTAAAGGGACAAC
35497 TCAAGCTTTATTGTATACATAT
65 TCAAGCTTTATTGTATACATAT
35519 AATATTATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
91 74 0.99
92 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (91 bp):
ATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGACGTTTAACCAATTACTCTAAAGGGACAACT
CAAGCTTTATTGTATACATATTTATA
Found at i:41157 original size:3 final size:3
Alignment explanation
Indices: 41151--41184 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
41141 AATATTAGTT
*
41151 TAA TAA TAA TAA TAA TAA TAA TAG TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41185 TACATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43036 original size:20 final size:19
Alignment explanation
Indices: 42990--43038 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
42980 ATAACCAACA
* * *
42990 AATTCGTAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
43009 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
43028 AATTTCGCAAC
1 AA-TTCGCAAC
43039 TCAGTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:43125 original size:20 final size:20
Alignment explanation
Indices: 43102--43140 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
43092 TTCGTGTTGC
43102 GATTTTCAAATTCGCAACGT
1 GATTTTCAAATTCGCAACGT
43122 GATTTTCAAATTCGCAACG
1 GATTTTCAAATTCGCAACG
43141 CGAATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (20 bp):
GATTTTCAAATTCGCAACGT
Found at i:43199 original size:20 final size:20
Alignment explanation
Indices: 43133--43191 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
43123 ATTTTCAAAT
*
43133 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATCTGTAAA
43153 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
43173 TCGCAACGTGAATCTGTAA
1 TCGCAACGCGAATCTGTAA
43192 TTTGCAACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:43217 original size:40 final size:41
Alignment explanation
Indices: 43129--43218 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
43119 CGTGATTTTC
*
43129 AAATTCGCAACGCGAATATGTAAATCGCAACGCGAATCTGT
1 AAATTCGCAACGCGAATATGTAAATCGCAACACGAATCTGT
* * * * *
43170 AAA-TCGCAACGTGAATCTGTAATTTGCAACACAGAA-GT-T
1 AAATTCGCAACGCGAATATGTAAATCGCAACAC-GAATCTGT
43209 AAATTCGCAA
1 AAATTCGCAA
43219 AGCGCGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
39 4 0.10
40 31 0.76
41 6 0.15
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (41 bp):
AAATTCGCAACGCGAATATGTAAATCGCAACACGAATCTGT
Found at i:43321 original size:27 final size:25
Alignment explanation
Indices: 43291--43349 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
43281 AACACAAATG
*
43291 TAAACAGTATAATCGCAAATCATAACC
1 TAAACA-TA-AATCACAAATCATAACC
43318 TAAACCCATAAATCACAAATCATAACC
1 TAAA--CATAAATCACAAATCATAACC
43345 TAAAC
1 TAAAC
43350 CCCTAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 1 0.03
27 24 0.83
28 2 0.07
29 2 0.07
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.20
Consensus pattern (25 bp):
TAAACATAAATCACAAATCATAACC
Found at i:43350 original size:27 final size:27
Alignment explanation
Indices: 43301--43362 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
43291 TAAACAGTAT
*
43301 AATCGCAAATCATAACCTAAACCCATA
1 AATCACAAATCATAACCTAAACCCATA
*
43328 AATCACAAATCATAACCTAAACCCCTA
1 AATCACAAATCATAACCTAAACCCATA
43355 AATCACAA
1 AATCACAA
43363 CTCAGTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.31, G:0.02, T:0.18
Consensus pattern (27 bp):
AATCACAAATCATAACCTAAACCCATA
Found at i:43433 original size:22 final size:22
Alignment explanation
Indices: 43407--43450 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43397 GACATCCGTC
*
43407 CCCATCTCTGACAAAATCTGTT
1 CCCATCTCCGACAAAATCTGTT
* *
43429 CCCATCTCCGGCGAAATCTGTT
1 CCCATCTCCGACAAAATCTGTT
43451 TATCTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.30
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCTGTT
Found at i:43890 original size:20 final size:20
Alignment explanation
Indices: 43820--43890 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
43810 TCGCAACGCA
43820 ATTTT-AGTTTCGCGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
* *
43839 ATTTTCATTTTAGCGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
*
43859 ATTTTCATTTTCGCGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
* *
43879 GTTTTAAGTTTC
1 ATTTTCAGTTTC
43891 AGAAACTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 5 0.11
20 40 0.89
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCAGTTTCGCGTTGCG
Found at i:45560 original size:21 final size:21
Alignment explanation
Indices: 45536--45585 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
45526 GTTAGGGGAG
* *
45536 TTACGTGATGAGGTCAATGCT
1 TTACGTGAGGAGGTCAATACT
**
45557 TTACGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
45578 TTACGTGA
1 TTACGTGA
45586 AGAAAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:45992 original size:21 final size:22
Alignment explanation
Indices: 45964--46069 Score: 130
Period size: 21 Copynumber: 5.0 Consensus size: 22
45954 GATTCACCTG
*
45964 TCATCGTTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCCCCTCC
**
45986 T-ATCGTTCAAGAGG-CCCTTA
1 TCATCGTTCAAGAGGCCCCTCC
*
46006 TCATCCTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
*
46028 -CATCGTTCAAGAGGCCCCT-G
1 TCATCGTTCAAGAGGCCCCTCC
*
46048 TCATCGTTCAAGAGGTCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
46070 CACATTTCGA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.06
21 61 0.87
22 5 0.07
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:46016 original size:42 final size:42
Alignment explanation
Indices: 45964--46071 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
45954 GATTCACCTG
* * *
45964 TCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCTTA
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTA
* *
46006 TCATCCTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTA
*
46048 TCATCGTTCAAGAGGTCCCTCCCA
1 TCATCGTTCAAGAGGCCCCTCCCA
46072 CATTTCGAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTA
Found at i:47434 original size:14 final size:14
Alignment explanation
Indices: 47415--47464 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
47405 GCTTATTTAA
47415 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
47429 TTGATTTGTTTAA-
1 TTGATTTGTAAAAG
47442 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
47456 TTGATTTGT
1 TTGATTTGT
47465 TTAATTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:47447 original size:13 final size:13
Alignment explanation
Indices: 47410--47473 Score: 74
Period size: 14 Copynumber: 4.8 Consensus size: 13
47400 TTTTTGCTTA
47410 TTTAATTGATTTG
1 TTTAATTGATTTG
**
47423 TAAAAGTTGATTTG
1 TTTAA-TTGATTTG
47437 TTTAATTGATTTG
1 TTTAATTGATTTG
**
47450 TAAAAGTTGATTTG
1 TTTAA-TTGATTTG
47464 TTTAATTGAT
1 TTTAATTGAT
47474 GTGTAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 19 0.46
14 22 0.54
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (13 bp):
TTTAATTGATTTG
Found at i:47448 original size:27 final size:27
Alignment explanation
Indices: 47410--47480 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
47400 TTTTTGCTTA
47410 TTTAATTGATTTGTAAAAGTTGATTTG
1 TTTAATTGATTTGTAAAAGTTGATTTG
47437 TTTAATTGATTTGTAAAAGTTGATTTG
1 TTTAATTGATTTGTAAAAGTTGATTTG
*
47464 TTTAATTGATGTGTAAA
1 TTTAATTGATTTGTAAA
47481 TAATTCTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (27 bp):
TTTAATTGATTTGTAAAAGTTGATTTG
Found at i:47509 original size:91 final size:91
Alignment explanation
Indices: 47354--47526 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 91
47344 AAATTGATGT
47354 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATTGA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATTGA
47419 TTTGTAAAAGTTGATTTGTTTAATTG
66 TTTGTAAAAGTTGATTTGTTTAATTG
* * *** *
47445 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTGA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATTGA
47510 TTTGTAAAAGTTGATTT
66 TTTGTAAAAGTTGATTT
47527 TTTGTTTTAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (91 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATTGA
TTTGTAAAAGTTGATTTGTTTAATTG
Found at i:47923 original size:18 final size:18
Alignment explanation
Indices: 47900--47935 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47890 AAGCCGGTTG
47900 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
47918 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
47936 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:50043 original size:24 final size:24
Alignment explanation
Indices: 50009--50062 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
49999 CTGAAACATC
50009 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
50033 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
50057 ATCAAA
1 ATCAAA
50063 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:50208 original size:12 final size:12
Alignment explanation
Indices: 50187--50220 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
50177 GGTTGTGGGT
*
50187 TTTGAGATTGTG
1 TTTGATATTGTG
50199 TTTGATATTGTG
1 TTTGATATTGTG
*
50211 TTTGGTATTG
1 TTTGATATTG
50221 GAAATATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:51018 original size:17 final size:19
Alignment explanation
Indices: 50990--51036 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
50980 AAAACATTTG
* *
50990 TGTTGCAAAAATAAAA-CA
1 TGTTGCGAAATTAAAATCA
51008 TGTTGCGAAATTAAAATTCA
1 TGTTGCGAAATTAAAA-TCA
51028 TGTTGCGAA
1 TGTTGCGAA
51037 TTCGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.56
20 11 0.44
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCA
Found at i:51052 original size:20 final size:20
Alignment explanation
Indices: 51029--51139 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
51019 TAAAATTCAT
51029 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
*
51049 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
51069 GTTGCGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* * *
51089 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTCGAAAATC-GA
* * *
51110 GTTACGAATTTGTAAATC-A
1 GTTGCGAATTCGAAAATCGA
51129 CGTTGCGAATT
1 -GTTGCGAATT
51140 TGGAAATCAC
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.01
20 59 0.77
21 17 0.22
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:51140 original size:20 final size:19
Alignment explanation
Indices: 51029--51162 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 19
51019 TAAAATTCAT
*
51029 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTG-AAATCGA
* *
51049 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTTG-AAATCGA
*
51069 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATT-TGAAATCGA
*
51089 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAA-TC-GA
*
51110 GTTACGAATTTGTAAATC-A
1 GTTGCGAATTTG-AAATCGA
51129 CGTTGCGAATTTGGAAATC-A
1 -GTTGCGAATTT-GAAATCGA
*
51149 CATTGCGAATTTGA
1 -GTTGCGAATTTGA
51163 CTTCTGTGTT
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.06
20 74 0.75
21 16 0.16
22 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (19 bp):
GTTGCGAATTTGAAATCGA
Found at i:51193 original size:20 final size:20
Alignment explanation
Indices: 51170--51216 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
51160 TGACTTCTGT
51170 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
51190 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
51210 GTTGCGA
1 GTTGCGA
51217 ATTTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:51385 original size:20 final size:20
Alignment explanation
Indices: 51362--51572 Score: 110
Period size: 20 Copynumber: 10.5 Consensus size: 20
51352 AAATCGCAAC
*
51362 GCGAATTTGTAAATCACGTT
1 GCGAATTTGAAAATCACGTT
* *
51382 GCGAAATT-AAAATTCATGTT
1 GCGAATTTGAAAA-TCACGTT
*
51402 GCGAATTCGAAAATCGA-GTT
1 GCGAATTTGAAAATC-ACGTT
* *
51422 GTGAATTCGAAAATCGA-GTT
1 GCGAATTTGAAAATC-ACGTT
* *
51442 GTGAATTCGAAAATCGA-GTT
1 GCGAATTTGAAAATC-ACGTT
*
51462 GCGAA-TTCAGAAATCGA-GTT
1 GCGAATTTGA-AAATC-ACGTT
* *
51482 GCGAATTTGAAATTCAGTGTT
1 GCGAATTTGAAAATCA-CGTT
* * * ***
51503 ACGAATTTGTAAATCGCAAC
1 GCGAATTTGAAAATCACGTT
* * *
51523 GCGAATTTGTAAAGCGCGTT
1 GCGAATTTGAAAATCACGTT
* * *
51543 ACGAATTTGGAAATCGCGTT
1 GCGAATTTGAAAATCACGTT
51563 GCGAATTTGA
1 GCGAATTTGA
51573 CTTCTCTGTT
Statistics
Matches: 155, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
19 6 0.04
20 126 0.81
21 23 0.15
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (20 bp):
GCGAATTTGAAAATCACGTT
Found at i:51428 original size:60 final size:58
Alignment explanation
Indices: 51362--51494 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 58
51352 AAATCGCAAC
51362 GCGAATTTGTAAATC-ACGTTGCGAAATT-AAAATTC-ATGTTGCGAATTC-GAAAATCGAGTT
1 GCGAATTTG-AAATCGA-GTTGCG-AATTCAAAA-TCGA-GTTGCGAATTCAG-AAATCGAGTT
* * *
51422 GTGAATTCGAAAATCGAGTTGTGAATTCGAAAATCGAGTTGCGAATTCAGAAATCGAGTT
1 GCGAATTTG-AAATCGAGTTGCGAATTC-AAAATCGAGTTGCGAATTCAGAAATCGAGTT
51482 GCGAATTTGAAAT
1 GCGAATTTGAAAT
51495 TCAGTGTTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
59 8 0.13
60 47 0.76
61 7 0.11
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (58 bp):
GCGAATTTGAAATCGAGTTGCGAATTCAAAATCGAGTTGCGAATTCAGAAATCGAGTT
Found at i:51448 original size:40 final size:40
Alignment explanation
Indices: 51399--51493 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
51389 TAAAATTCAT
*
51399 GTTGCGAATTCGAAAATCGAGTTGTGAATTC-GAAAATCGA
1 GTTGCGAATTCGAAAATCGAGTTGCGAATTCAG-AAATCGA
*
51439 GTTGTGAATTCGAAAATCGAGTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCGAAAATCGAGTTGCGAATTCAGAAATCGA
*
51479 GTTGCGAATTTGAAA
1 GTTGCGAATTCGAAA
51494 TTCAGTGTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 49 0.98
41 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (40 bp):
GTTGCGAATTCGAAAATCGAGTTGCGAATTCAGAAATCGA
Found at i:51644 original size:60 final size:61
Alignment explanation
Indices: 51537--51652 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 61
51527 ATTTGTAAAG
* * * *
51537 CGCGTTACGAATTTGGAAATCGCGTTGCGAATTTGACTTCTCTGTTGCG-ATTTATAGATT
1 CGCGTTACGAATTTAGAAATCGAGTTGCGAATTGGACTTCGCTGTTGCGAATTTATAGATT
* *
51597 CGCGTTGCGAATTTAGAAA-CTGAGTTGCGAAATTGGAGTTCGC-GTTGCGAATTTAT
1 CGCGTTACGAATTTAGAAATC-GAGTTGCG-AATTGGACTTCGCTGTTGCGAATTTAT
51653 TGGTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
59 1 0.02
60 30 0.64
61 16 0.34
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (61 bp):
CGCGTTACGAATTTAGAAATCGAGTTGCGAATTGGACTTCGCTGTTGCGAATTTATAGATT
Found at i:53097 original size:50 final size:51
Alignment explanation
Indices: 53016--53116 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 51
53006 ATCTAAAGTA
*
53016 TACGAAGAGTTTGACTTGCCCTTAGGCTCATCCCTGCACAATACCTACTTG
1 TACGAAGAGTTTGACTTGCCCTTAGGCTCATCCCTACACAATACCTACTTG
*
53067 TACG-AGAGTTTGACTTGCCCTTAGGTTCATCCCTACACAATACCTACTTG
1 TACGAAGAGTTTGACTTGCCCTTAGGCTCATCCCTACACAATACCTACTTG
53117 AAAAATATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 44 0.92
51 4 0.08
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (51 bp):
TACGAAGAGTTTGACTTGCCCTTAGGCTCATCCCTACACAATACCTACTTG
Found at i:54661 original size:27 final size:27
Alignment explanation
Indices: 54631--54686 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
54621 ATTTTTAGTT
*
54631 TATGTCTAATATGATTAAAAGTCTATG
1 TATGTCTAATATGATTAAAAATCTATG
*
54658 TATGTCTAATATGATTAAAAATCTCTG
1 TATGTCTAATATGATTAAAAATCTATG
54685 TA
1 TA
54687 ATAAATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (27 bp):
TATGTCTAATATGATTAAAAATCTATG
Found at i:56791 original size:23 final size:23
Alignment explanation
Indices: 56765--56811 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
56755 ATTGCCCTCT
56765 TCAAGTGGGAATTAGAGCTTGTG
1 TCAAGTGGGAATTAGAGCTTGTG
56788 TCAAGTGGGAATTAGAGCTTGTG
1 TCAAGTGGGAATTAGAGCTTGTG
56811 T
1 T
56812 GTCAGCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.32
Consensus pattern (23 bp):
TCAAGTGGGAATTAGAGCTTGTG
Found at i:59389 original size:39 final size:39
Alignment explanation
Indices: 59335--59413 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
59325 TTCTCTTTTC
59335 ACGCTCATATCATGCTATATATATAATCCTATATATCCA
1 ACGCTCATATCATGCTATATATATAATCCTATATATCCA
59374 ACGCTCATATCATGCTATATATATAATCCTATATATCCA
1 ACGCTCATATCATGCTATATATATAATCCTATATATCCA
59413 A
1 A
59414 TTACACAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (39 bp):
ACGCTCATATCATGCTATATATATAATCCTATATATCCA
Found at i:59986 original size:17 final size:16
Alignment explanation
Indices: 59964--59997 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59954 CATAATTGAC
59964 ATGTTCTATTTTATTAT
1 ATGTTC-ATTTTATTAT
*
59981 ATGTTCGTTTTATTAT
1 ATGTTCATTTTATTAT
59997 A
1 A
59998 AATTTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (16 bp):
ATGTTCATTTTATTAT
Found at i:60674 original size:22 final size:22
Alignment explanation
Indices: 60646--60693 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
60636 ATAAAGAATA
60646 TAACTTGGCCTAACAATTTTAT
1 TAACTTGGCCTAACAATTTTAT
**
60668 TAACTTGGCCTAATGATTTTAT
1 TAACTTGGCCTAACAATTTTAT
60690 TAAC
1 TAAC
60694 AAGGAATGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (22 bp):
TAACTTGGCCTAACAATTTTAT
Found at i:65234 original size:29 final size:30
Alignment explanation
Indices: 65181--65237 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
65171 TCGAACTTTG
* **
65181 TTCGGTTCAGTTAATTATTTTTGAAAAAAT
1 TTCGGTTCAGTTAATGATTAATGAAAAAAT
65211 TTCGGTTC-GTTAATGATTAATGAAAAA
1 TTCGGTTCAGTTAATGATTAATGAAAAA
65238 TTTTTGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (30 bp):
TTCGGTTCAGTTAATGATTAATGAAAAAAT
Found at i:66384 original size:9 final size:9
Alignment explanation
Indices: 66372--66430 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
66362 AAAAACAACA
*
66372 AAATAGAAT
1 AAATAAAAT
66381 AAATAAAAT
1 AAATAAAAT
66390 AAAATAAAATT
1 -AAATAAAA-T
* *
66401 TAA-AAAGT
1 AAATAAAAT
66409 -AATAAAAT
1 AAATAAAAT
*
66417 AAATGAAAT
1 AAATAAAAT
66426 AAATA
1 AAATA
66431 TATATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 22 0.55
10 10 0.25
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:66441 original size:36 final size:36
Alignment explanation
Indices: 66373--66442 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
66363 AAAACAACAA
* *
66373 AATAGAATAAATAAAATAAAATAAAATTTAAAAAGT
1 AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
* *
66409 AATAAAATAAATGAAAT-AAATATATATATAAAAA
1 AATAAAATAAATAAAATAAAATA-AAATATAAAAA
66443 CCATAATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (36 bp):
AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
Found at i:67499 original size:20 final size:21
Alignment explanation
Indices: 67457--67503 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
67447 TCCTACAAAA
67457 AATAA-AATAAAGAAATTATT
1 AATAATAATAAAGAAATTATT
*
67477 AATAATAATAAATAAATTA-T
1 AATAATAATAAAGAAATTATT
67497 AATAATA
1 AATAATA
67504 GAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAATAAAGAAATTATT
Found at i:67873 original size:84 final size:84
Alignment explanation
Indices: 67785--67962 Score: 259
Period size: 84 Copynumber: 2.1 Consensus size: 84
67775 TTGAGCTATA
* *
67785 CTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAAC
1 CTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAAC
* *
67849 CCTTCTAGATTCAAGTTGTG
65 CCTTCTAGACTCAAGTTATG
* * *
67869 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
1 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACC
*
67934 CTTCTCGACTCAAGTTATG
66 CTTCTAGACTCAAGTTATG
*
67953 TTGCAAATGA
1 CTGCAAATGA
67963 ACACGATATC
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
83 2 0.02
84 82 0.98
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (84 bp):
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACC
CTTCTAGACTCAAGTTATG
Found at i:68390 original size:105 final size:104
Alignment explanation
Indices: 67981--68728 Score: 1291
Period size: 105 Copynumber: 7.1 Consensus size: 104
67971 TCCTTTGCTA
*
67981 TGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATT-GGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
68046 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCTG
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
68087 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTG-GAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
68152 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
68193 TGAAGTTGAAATTGGCTCTGAAATTGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 TGAAGTTGAAATTGGCTCTGAAATTGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
68258 GTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCGTTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
68297 TGAAGTTGAAATTGGCTCTGAAATTGGTAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
1 TGAAGTTGAAATTGGCTCTGAAATTGG-AAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
68362 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
68402 TGAAGTTGAAATTGGCTCTAAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
1 TGAAGTTGAAATTGGCTCTGAAATTG-GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
*
68467 AGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
68507 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
1 TGAAGTTGAAATTGGCTCTGAAATT-GGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
*
68572 AGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
68612 TGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
1 TGAAGTTGAAATTGGCTCTGAAATTG-GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
* *
68677 AGTTGAACTTGCGTTGTCTAGAGT-CAAGATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
68716 AGAAGTTGAAATT
1 TGAAGTTGAAATT
68729 TACTCTCGAG
Statistics
Matches: 616, Mismatches: 20, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
104 126 0.20
105 364 0.59
106 126 0.20
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (104 bp):
TGAAGTTGAAATTGGCTCTGAAATTGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
Found at i:72427 original size:9 final size:9
Alignment explanation
Indices: 72415--72473 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
72405 AAAAACAACA
*
72415 AAATAGAAT
1 AAATAAAAT
72424 AAATAAAAT
1 AAATAAAAT
72433 AAAATAAAATT
1 -AAATAAAA-T
* *
72444 TAA-AAAGT
1 AAATAAAAT
72452 -AATAAAAT
1 AAATAAAAT
*
72460 AAATGAAAT
1 AAATAAAAT
72469 AAATA
1 AAATA
72474 TATATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 22 0.55
10 10 0.25
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:72484 original size:36 final size:36
Alignment explanation
Indices: 72416--72485 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
72406 AAAACAACAA
* *
72416 AATAGAATAAATAAAATAAAATAAAATTTAAAAAGT
1 AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
* *
72452 AATAAAATAAATGAAAT-AAATATATATATAAAAA
1 AATAAAATAAATAAAATAAAATA-AAATATAAAAA
72486 CCATAATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (36 bp):
AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
Found at i:73543 original size:20 final size:21
Alignment explanation
Indices: 73501--73547 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
73491 TCCTACAAAA
73501 AATAA-AATAAAGAAATTATT
1 AATAATAATAAAGAAATTATT
*
73521 AATAATAATAAATAAATTA-T
1 AATAATAATAAAGAAATTATT
73541 AATAATA
1 AATAATA
73548 GAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAATAAAGAAATTATT
Found at i:75776 original size:2 final size:2
Alignment explanation
Indices: 75769--75794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
75759 AGAATTTTAA
75769 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
75795 TTGATAACTA
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:82579 original size:182 final size:182
Alignment explanation
Indices: 82139--82612 Score: 646
Period size: 182 Copynumber: 2.6 Consensus size: 182
82129 GATCCAAATT
* * * * * * * **
82139 AAAAATGTATCGATCCACAAAGATATAACAGGTAAAACTATGACAAAATCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
82204 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTATC-AGTACTTTAATATAAGGATCGATACTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGA-TACTTTAATATAAGGATCGACACTT
* *
82268 CGTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * * * * *
82321 AAAAATATATCAATCAACAACGATATAATATGTAAAAATATGATAAAACTGGTATCCAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
82386 AAACTGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
82450 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
82502 AAAAATGTATCGATCAAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
82567 AAAACCGGTAAAATGATACTGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
82613 CGTAAGTACG
Statistics
Matches: 253, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
181 80 0.32
182 172 0.68
183 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:82581 original size:17 final size:19
Alignment explanation
Indices: 82542--82584 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
82532 ATGTAAAAAT
82542 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
82562 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
82579 ATGATA
1 ATGATA
82585 CTGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:87757 original size:181 final size:181
Alignment explanation
Indices: 87438--88056 Score: 1057
Period size: 180 Copynumber: 3.4 Consensus size: 181
87428 TTTTACATTT
* *
87438 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
87503 AACAATATAACAG-GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
66 AACAATATAAC-GTGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
87567 CCGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACATTTTTGAAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACA-TTTTGGAA
87620 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
87684 AACAATATAACGTATAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACGTGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
87749 CAGTTATGTTGAAAGTGTCGGTAATTTATTATAAGTATCGAC-TTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACATTTTGGAA
* *
87799 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATAATTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* *
87863 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGAGAAAACAGGTAAAGCGCTA
65 TAACAATATAACGTGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
87928 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGGCACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACA-TTTTGGAA
87981 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
88046 AACAATATAAC
66 AACAATATAAC
88057 AGGTAATAGA
Statistics
Matches: 412, Mismatches: 19, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
178 4 0.01
179 15 0.04
180 150 0.36
181 149 0.36
182 90 0.22
183 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (181 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACGTGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACATTTTGGAA
Found at i:87916 original size:180 final size:180
Alignment explanation
Indices: 87438--88077 Score: 1069
Period size: 181 Copynumber: 3.6 Consensus size: 180
87428 TTTTACATTT
* *
87438 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
87503 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
87568 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACATTTTTGAAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAC--TTTTGGAA
87620 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
87684 AACAATATAAC-GTATAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGCGCTA
66 AACAATATAACAG-GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
87748 CCAGTTATGTTGAAAGTGTCGGTAATTTATTATAAGTATCGACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
* *
87799 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATAATTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* *
87863 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGAGAAAACAGGTAAAGCGCTA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
87928 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGGCACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATC-G-ACTTTTGGAA
87981 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
88046 AACAATATAACAGGT---AATA-GACAAAACCGGTC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTC
Statistics
Matches: 432, Mismatches: 19, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
178 17 0.04
179 19 0.04
180 147 0.34
181 150 0.35
182 95 0.22
183 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (180 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
Done.