Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002734.1 Hibiscus syriacus cultivar Beakdansim tig00005638_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: 149778
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:895 original size:2 final size:2
Alignment explanation
Indices: 888--915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
878 TAAATTATTA
888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
916 CTTCACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6594 original size:6 final size:5
Alignment explanation
Indices: 6574--6610 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
6564 CTACAAATAG
6574 ATCAA ATCAA ATCAGA ATCAGA ATCAA ATCAA ATCAA
1 ATCAA ATCAA ATCA-A ATCA-A ATCAA ATCAA ATCAA
6611 TGGATGCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (5 bp):
ATCAA
Found at i:9463 original size:55 final size:55
Alignment explanation
Indices: 9377--9482 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
9367 TGAGGAGAAG
*
9377 AACAAGAACATGGGTGTTGATTTTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
1 AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
* *
9432 AACAAGAACATGTGTGTTGATTGTTGGAACTAAAAAAGGGGAAAAGAAAGG
1 AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGG
9483 GAGAAAGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.47, C:0.06, G:0.27, T:0.20
Consensus pattern (55 bp):
AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
Found at i:10150 original size:13 final size:13
Alignment explanation
Indices: 10132--10156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10122 CATTACAAAT
10132 TTAAAATATAAAA
1 TTAAAATATAAAA
10145 TTAAAATATAAA
1 TTAAAATATAAA
10157 TTTTACACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATATAAAA
Found at i:14970 original size:34 final size:34
Alignment explanation
Indices: 14888--14982 Score: 174
Period size: 33 Copynumber: 2.8 Consensus size: 34
14878 ATATGTGTTC
*
14888 AAATAGTACGAACTTAGAGTTATAAATAAAACCA
1 AAATAGTACTAACTTAGAGTTATAAATAAAACCA
14922 AAATA-TACTAACTTAGAGTTATAAATAAAACCA
1 AAATAGTACTAACTTAGAGTTATAAATAAAACCA
14955 AAATAGTACTAACTTAGAGTTATAAATA
1 AAATAGTACTAACTTAGAGTTATAAATA
14983 TGAAATACAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 32 0.54
34 27 0.46
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (34 bp):
AAATAGTACTAACTTAGAGTTATAAATAAAACCA
Found at i:15450 original size:2 final size:2
Alignment explanation
Indices: 15443--15477 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
15433 CTGGTTAGTT
15443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15478 ATCCAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15588 original size:16 final size:14
Alignment explanation
Indices: 15559--15603 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 14
15549 CAAATATGAT
15559 ATTAATTTAATTGG
1 ATTAATTTAATTGG
15573 ATTAATTTGAAATTGG
1 ATTAATTT--AATTGG
15589 ATT-A--TAATTGG
1 ATTAATTTAATTGG
15600 ATTA
1 ATTA
15604 GGTTTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.32
13 1 0.04
14 8 0.29
15 1 0.04
16 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
ATTAATTTAATTGG
Found at i:15631 original size:15 final size:15
Alignment explanation
Indices: 15613--15643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15603 AGGTTTTGTT
15613 AGTCTAGGAAATTAA
1 AGTCTAGGAAATTAA
*
15628 AGTCTAGGTAATTAA
1 AGTCTAGGAAATTAA
15643 A
1 A
15644 TTATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (15 bp):
AGTCTAGGAAATTAA
Found at i:16381 original size:35 final size:35
Alignment explanation
Indices: 16318--16405 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
16308 TTGTTTAACA
* * *
16318 CTAAAGCATGATCATTGATATTACTATTG-TTATTG
1 CTAAAG-ATGGTCATAGACATTACTATTGTTTATTG
* *
16353 TTAAAGTATGGTCATAGACATTATTATTGTTTATTG
1 CTAAAG-ATGGTCATAGACATTACTATTGTTTATTG
*
16389 CTAAAGATGGTTATAGA
1 CTAAAGATGGTCATAGA
16406 GATGTCATCC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 33 0.75
36 11 0.25
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (35 bp):
CTAAAGATGGTCATAGACATTACTATTGTTTATTG
Found at i:18112 original size:45 final size:45
Alignment explanation
Indices: 18048--18153 Score: 194
Period size: 45 Copynumber: 2.4 Consensus size: 45
18038 TTTAAGCTCG
*
18048 TGCAAAGTCAGTTTTTTATCTTTGTATATTCTTCGAAACCAAATA
1 TGCAAAGTCAGTTTTTTATCTTTGTATATTCATCGAAACCAAATA
*
18093 TGCAAAGTCAGTTTTTTATCTTTGTATATTCATCGAAACCAAGTA
1 TGCAAAGTCAGTTTTTTATCTTTGTATATTCATCGAAACCAAATA
18138 TGCAAAGTCAGTTTTT
1 TGCAAAGTCAGTTTTT
18154 AATCAAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (45 bp):
TGCAAAGTCAGTTTTTTATCTTTGTATATTCATCGAAACCAAATA
Found at i:21782 original size:21 final size:21
Alignment explanation
Indices: 21756--21800 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21746 TGATTTAAAA
21756 AAAATTGA-AAGTTTAAATACT
1 AAAATTGATAA-TTTAAATACT
*
21777 AAAATTGATAATTTAAGTACT
1 AAAATTGATAATTTAAATACT
21798 AAA
1 AAA
21801 TGCGTAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATTGATAATTTAAATACT
Found at i:29040 original size:3 final size:3
Alignment explanation
Indices: 29032--29104 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
29022 CCGATCTTAT
* * * *
29032 TTA TTA TTA TTA TTA TTA -TA ATA GTA CTA TTA TTA TATA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
29077 TATA TTA TATA TTA ATA TTA TTA -TA TTA
1 T-TA TTA T-TA TTA TTA TTA TTA TTA TTA
29105 CAAATAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
2 4 0.07
3 45 0.78
4 9 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:29082 original size:17 final size:16
Alignment explanation
Indices: 29032--29102 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
29022 CCGATCTTAT
*
29032 TTAT-TATTATTATTA
1 TTATATATTAATATTA
* *
29047 TTATAATAGTACTATTA
1 TTAT-ATATTAATATTA
29064 TTATATA-TAATTATATA
1 TTATATATTAA-TAT-TA
29081 TTATATATTAATATTA
1 TTATATATTAATATTA
29097 TTATAT
1 TTATAT
29103 TACAAATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.12
16 14 0.29
17 25 0.52
18 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
TTATATATTAATATTA
Found at i:29087 original size:15 final size:13
Alignment explanation
Indices: 29028--29104 Score: 52
Period size: 14 Copynumber: 5.8 Consensus size: 13
29018 TCGTCCGATC
* *
29028 TTATTTATTATTA
1 TTATATATTAATA
29041 TTAT-TATT-ATA
1 TTATATATTAATA
* *
29052 ATAGTACTATTATTA
1 TTA-TA-TATTAATA
29067 -TATATAATTATATA
1 TTATAT-ATTA-ATA
29081 TTATATATTAATA
1 TTATATATTAATA
29094 TTATTATATTA
1 TTA-TATATTA
29105 CAAATAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.08
12 6 0.12
13 16 0.31
14 19 0.37
15 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (13 bp):
TTATATATTAATA
Found at i:30647 original size:22 final size:21
Alignment explanation
Indices: 30622--30669 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
30612 TTATAGTAGG
*
30622 ATAATTTT-ATAATTTAATATAT
1 ATAATTTTAAT-ATTCAATAT-T
30644 ATAATTTTAATATTCAATATT
1 ATAATTTTAATATTCAATATT
30665 ATAAT
1 ATAAT
30670 AGGATTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 16 0.67
23 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATTTTAATATTCAATATT
Found at i:32915 original size:21 final size:21
Alignment explanation
Indices: 32891--32931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32881 GAATTACAAG
*
32891 AAACAT-GAAGATCGGGGCAAA
1 AAACATAG-AGATCAGGGCAAA
32912 AAACATAGAGATCAGGGCAA
1 AAACATAGAGATCAGGGCAA
32932 GAAGTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.49, C:0.15, G:0.27, T:0.10
Consensus pattern (21 bp):
AAACATAGAGATCAGGGCAAA
Found at i:38149 original size:119 final size:118
Alignment explanation
Indices: 38002--38494 Score: 718
Period size: 119 Copynumber: 4.1 Consensus size: 118
37992 TTTCCCACGA
* * * * *
38002 ATTTGTAAATCCT-ACGAGTCATCTGTAAAACCTCAATGTATGATATTTTCGCGTGAAAATGAGA
1 ATTTGTAAAGCCTCA-G-GTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGA
** * *
38066 AAGTTATTTTTAAAGTTTCGCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
64 AAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
38121 ATTTGCAAAGCCTCTGTGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAGCCTCAG-GTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAA
* * *
38186 AGCAATTTTTAAAGTTTCTCATTTAATGTTCTAGAAAATTGAATCCTTCGGGTG
65 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
38240 ATTTGTAAAGCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAGCCT-CAGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAA
*
38305 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATGAAATCCTCCGGGTG
65 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
*
38359 ATTTGTAAAGCCTCCAGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAGCCT-CAGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAA
* * * *
38424 AGCCATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCCGGGTC
65 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
38478 ATCTGTAAAACCTCAGG
1 ATTTGTAAAGCCTCAGG
38495 GTATGATGTT
Statistics
Matches: 344, Mismatches: 28, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
118 4 0.01
119 338 0.98
120 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (118 bp):
ATTTGTAAAGCCTCAGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAAA
GCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
Found at i:38648 original size:3 final size:3
Alignment explanation
Indices: 38640--38718 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
38630 TCGATCTTAT
*
38640 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA CTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
38685 TAA TT- TTA -TA TTA TATA TTA ATA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
38719 CAAATTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.12
3 50 0.78
4 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:38671 original size:26 final size:26
Alignment explanation
Indices: 38636--38718 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 26
38626 TCTTTCGATC
38636 TTATT-TATTATTATTATTATTATTA
1 TTATTATATTATTATTATTATTATTA
* *
38661 TTATTATATTACTATTATTATATATAA
1 TTATTATATTATTATTATTAT-TATTA
*
38688 TT-TTATATTATATATTAATATTATTA
1 TTATTATATTAT-TATTATTATTATTA
38714 -TATTA
1 TTATTA
38719 CAAATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
25 6 0.12
26 29 0.59
27 14 0.29
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTATATTATTATTATTATTATTA
Found at i:40967 original size:19 final size:19
Alignment explanation
Indices: 40943--41000 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
40933 ACATTATTTA
40943 ATTATTAAAATTATAATAT
1 ATTATTAAAATTATAATAT
* *
40962 ATTATTATAAAATAT-ATTT
1 ATTATTA-AAATTATAATAT
*
40981 ATT-TTAATAATTAAAATAT
1 ATTATTAA-AATTATAATAT
41000 A
1 A
41001 ATAAATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.03
18 7 0.23
19 17 0.55
20 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATTAAAATTATAATAT
Found at i:41001 original size:43 final size:42
Alignment explanation
Indices: 40927--41049 Score: 151
Period size: 43 Copynumber: 2.9 Consensus size: 42
40917 TTTATAATGT
* *
40927 TAAAATACATTA-TTTAATTATTAAAATTATAATATATTATTA
1 TAAAATATATTATTTTAATAATTAAAA-TATAATATATTATTA
*
40969 TAAAATATATTTATTTTAATAATTAAAATATAATAAATTATTA
1 TAAAATATA-TTATTTTAATAATTAAAATATAATATATTATTA
*
41012 T-AAATATATTATTTTAATTATTTTAAAATATTAATATA
1 TAAAATATATTATTTTAA-TA-ATTAAAATA-TAATATA
41050 ATTGGATTGA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
41 9 0.13
42 17 0.24
43 26 0.37
44 19 0.27
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
TAAAATATATTATTTTAATAATTAAAATATAATATATTATTA
Found at i:41901 original size:20 final size:20
Alignment explanation
Indices: 41876--41931 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
41866 CAAAATTAGT
*
41876 AGTATCGATACCCTTCATG-C
1 AGTATCGATACCCTT-AGGTC
*
41896 AGTATCGATACTCTTAGGTC
1 AGTATCGATACCCTTAGGTC
41916 AGTATCGATACTCCTT
1 AGTATCGATAC-CCTT
41932 TAACTATCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 26 0.84
21 3 0.10
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (20 bp):
AGTATCGATACCCTTAGGTC
Found at i:42545 original size:21 final size:20
Alignment explanation
Indices: 42501--42546 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
42491 ATTGTGGCCG
*
42501 TTTCTAGCTGTTGGGAATGA
1 TTTCTAGCCGTTGGGAATGA
* *
42521 TTTCTAGCCGTTTGGGGATGT
1 TTTCTAGCCG-TTGGGAATGA
42542 TTTCT
1 TTTCT
42547 CTGCAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.13, C:0.13, G:0.28, T:0.46
Consensus pattern (20 bp):
TTTCTAGCCGTTGGGAATGA
Found at i:58556 original size:21 final size:21
Alignment explanation
Indices: 58532--58582 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
58522 ACTTTAAAAG
58532 TTTTTAATTTCATACCTAAAC
1 TTTTTAATTTCATACCTAAAC
*
58553 TTTTTAATTTCATCCCTAAAC
1 TTTTTAATTTCATACCTAAAC
58574 TTTTTAATT
1 TTTTTAATT
58583 ACTTATATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTAATTTCATACCTAAAC
Found at i:62029 original size:22 final size:24
Alignment explanation
Indices: 62000--62045 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
61990 TATATGGTTA
62000 TAAAAATATT-TAA-ATT-GAAAT
1 TAAAAATATTATAATATTAGAAAT
62021 TAAATAATATTATAATATTAGAAAT
1 TAAA-AATATTATAATATTAGAAAT
62046 ATTTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 3 0.14
24 3 0.14
25 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAAAATATTATAATATTAGAAAT
Found at i:62162 original size:28 final size:28
Alignment explanation
Indices: 62131--62193 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
62121 AAAAATTAAG
*
62131 TCAACTTCGAGTTACAAAATATAACTCA
1 TCAACTCCGAGTTACAAAATATAACTCA
**
62159 TCAACTCCGAGTTGTAAAATATAACTCA
1 TCAACTCCGAGTTACAAAATATAACTCA
62187 TCAACTC
1 TCAACTC
62194 AAATAACTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.29
Consensus pattern (28 bp):
TCAACTCCGAGTTACAAAATATAACTCA
Found at i:62493 original size:13 final size:13
Alignment explanation
Indices: 62461--62502 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
62451 TATTTGTTGA
62461 TAATTTTAATTTT
1 TAATTTTAATTTT
*
62474 TCATTTTAA-TTT
1 TAATTTTAATTTT
62486 TAATTTTTATATTTT
1 TAA-TTTTA-ATTTT
62501 TA
1 TA
62503 TTAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.21
13 13 0.54
14 1 0.04
15 5 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:66225 original size:2 final size:2
Alignment explanation
Indices: 66218--66271 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
66208 TCTCCCCCTA
66218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66260 AT AT AT AT AT AT
1 AT AT AT AT AT AT
66272 CATCGTGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70554 original size:229 final size:229
Alignment explanation
Indices: 70135--70601 Score: 711
Period size: 229 Copynumber: 2.0 Consensus size: 229
70125 TTAACTCTTA
* *
70135 AATCAGTTTCCCTTTGTCCCTCGTACTTGAGAACCTGACTTTGATAATTTGGAGTATTGAAAAAA
1 AATCAGTTTCCCTTTGTCCCTCGTACTGGAGAACCTGACTTTGATAATTTAGAGTATTG-AAAAA
70200 TCAAAGTATTTCATATCTAGTACTTTCTCGCATGACAAGAAATATATTGGCAATTCCAATTACTT
65 TCAAAGTATTTCATATCTAGTACTTTCTCGCATGACAAGAAATATATTGGCAATTCCAATTACTT
** * * *
70265 CAGTTTTATCTAAATCGTCATTTAGTATGGGGTCCGAATTTTGAACAAATTAAGAGCTAAACTCT
130 CAGTTGCATCTAAATCATCATTTAGTATGGGGACCGAATTTTCAACAAATTAAGAGCTAAACTCT
* * *
70330 CACCTAAAAATGTTGATATTTTTGTACCAACTCGC
195 CACCTAAAAATGTTGAGATTTTTGTAACAACCCGC
* * * * *
70365 AATCAGTTTGCCCTTTGTCCTTCGTGCTGGAGAATCTGACTTTGATATTTTAGAGTATTG-GAAA
1 AATCAGTTT-CCCTTTGTCCCTCGTACTGGAGAACCTGACTTTGATAATTTAGAGTATTGAAAAA
* * * * *
70429 TCAAAGTATTTCATATCTGGTACTTTCTCGTATGGCGAGAAATATATTGGCTATTCCAATTACTT
65 TCAAAGTATTTCATATCTAGTACTTTCTCGCATGACAAGAAATATATTGGCAATTCCAATTACTT
*
70494 CAGTTGCATCTAAATCATCATTTAGTATGGGGACCGAATTTTCAACAAATTAATAGCTAAACTCT
130 CAGTTGCATCTAAATCATCATTTAGTATGGGGACCGAATTTTCAACAAATTAAGAGCTAAACTCT
*
70559 CACCTAAAAATGTTGAGATTTTTGTAACAACCCGT
195 CACCTAAAAATGTTGAGATTTTTGTAACAACCCGC
70594 AATCAGTT
1 AATCAGTT
70602 GTATGGTTTT
Statistics
Matches: 214, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
229 161 0.75
230 9 0.04
231 44 0.21
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (229 bp):
AATCAGTTTCCCTTTGTCCCTCGTACTGGAGAACCTGACTTTGATAATTTAGAGTATTGAAAAAT
CAAAGTATTTCATATCTAGTACTTTCTCGCATGACAAGAAATATATTGGCAATTCCAATTACTTC
AGTTGCATCTAAATCATCATTTAGTATGGGGACCGAATTTTCAACAAATTAAGAGCTAAACTCTC
ACCTAAAAATGTTGAGATTTTTGTAACAACCCGC
Found at i:71792 original size:21 final size:21
Alignment explanation
Indices: 71739--71799 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 21
71729 TAACCTAAGA
** *
71739 ATCATAATTAATATAATAAGT
1 ATCATAATTAATATTTTAATT
*
71760 -TCAT--TTATTATTTTAATT
1 ATCATAATTAATATTTTAATT
71778 ATCATAATTAATATTTT-ATT
1 ATCATAATTAATATTTTAATT
71798 AT
1 AT
71800 AATGTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.31
19 4 0.12
20 9 0.28
21 9 0.28
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATAATTAATATTTTAATT
Found at i:78013 original size:14 final size:14
Alignment explanation
Indices: 77994--78023 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
77984 TGATATTTTG
77994 ATATGTACCTGACA
1 ATATGTACCTGACA
78008 ATATGTACCTGACA
1 ATATGTACCTGACA
78022 AT
1 AT
78024 GATATGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (14 bp):
ATATGTACCTGACA
Found at i:78030 original size:17 final size:16
Alignment explanation
Indices: 77992--78030 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
77982 TGTGATATTT
77992 TGATATGTACCTGACA
1 TGATATGTACCTGACA
78008 --ATATGTACCTGACAA
1 TGATATGTACCTGAC-A
78023 TGATATGT
1 TGATATGT
78031 CATTCTCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 13 0.65
15 1 0.05
17 6 0.30
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (16 bp):
TGATATGTACCTGACA
Found at i:85399 original size:19 final size:19
Alignment explanation
Indices: 85363--85399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
85353 ATGACCAACA
* *
85363 AAATCGCAATGCGGTCTCT
1 AAATCGCAACGCGATCTCT
85382 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
85400 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:85462 original size:21 final size:21
Alignment explanation
Indices: 85446--85497 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
85436 TTTCGACCAT
85446 CGCATTGCGATTTTCGAAATC
1 CGCATTGCGATTTTCGAAATC
* *
85467 CGCGTTGCGATTTTAGATAAT-
1 CGCATTGCGATTTTCGA-AATC
*
85488 CGCAATGCGA
1 CGCATTGCGA
85498 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
CGCATTGCGATTTTCGAAATC
Found at i:85555 original size:20 final size:20
Alignment explanation
Indices: 85527--85571 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
85517 ATAACACTTG
* *
85527 ATCGTAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
85547 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
85567 ATCGC
1 ATCGC
85572 GTTACGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:86133 original size:14 final size:14
Alignment explanation
Indices: 86114--86183 Score: 77
Period size: 14 Copynumber: 4.6 Consensus size: 14
86104 ACAAAATTCG
86114 CGTTGCGATTATCT
1 CGTTGCGATTATCT
* *
86128 CGTTGCGATAGACATTTCG
1 CGTTGCGAT-----TATCT
86147 CGTTGCGATTATCT
1 CGTTGCGATTATCT
86161 CGTTGCGATTATCT
1 CGTTGCGATTATCT
86175 CGTTGCGAT
1 CGTTGCGAT
86184 AGTCAAATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 35 0.74
19 12 0.26
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:88071 original size:31 final size:31
Alignment explanation
Indices: 88015--88076 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
88005 TTGTCTTTGT
*
88015 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
88047 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
88077 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:88220 original size:20 final size:20
Alignment explanation
Indices: 88195--88360 Score: 148
Period size: 20 Copynumber: 8.6 Consensus size: 20
88185 AGAAGAATAG
* *
88195 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
* **
88215 TCGCAACACGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
88235 TCGCAACGC-AAATTTGACTA
1 TCGCAACGCGAAA-ATGACTA
*
88255 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
* *
88269 TCGCAATGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
* *
88289 TCGCAACTCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
88309 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
88329 TCGCAACGCGAAAATGAATA
1 TCGCAACGCGAAAATGACTA
88349 TCGCAACGCGAA
1 TCGCAACGCGAA
88361 TTTAGTTTCG
Statistics
Matches: 117, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
14 8 0.07
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 2 0.02
20 102 0.87
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:88409 original size:33 final size:34
Alignment explanation
Indices: 88366--88446 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
88356 GCGAATTTAG
*
88366 TTTCGCGTTGCGATTTTCTCATTGCGATAGTC-A
1 TTTCGCGTTGCGATTATCTCATTGCGATAGTCAA
* *
88399 TTTCGTGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTATCTCATTGCGATAGTCAA
*
88433 ATTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
88447 AATCATTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.69
34 13 0.31
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (34 bp):
TTTCGCGTTGCGATTATCTCATTGCGATAGTCAA
Found at i:88443 original size:20 final size:20
Alignment explanation
Indices: 88418--88466 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
88408 GCGATTATCT
*
88418 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
**
88438 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
88458 TGTTGCGAT
1 CGTTGCGAT
88467 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:88476 original size:20 final size:20
Alignment explanation
Indices: 88453--88496 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
88443 CGATAATCAT
88453 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
88473 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
88493 TTTC
1 TTTC
88497 AGAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:89028 original size:21 final size:22
Alignment explanation
Indices: 89004--89063 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
88994 CTCCTATCGT
89004 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCGC
* *
89025 TCAAGAGTCCCCTCA-CA-CCGT
1 TCAAGAGGCCCCT-ATCATCCGC
*
89046 TCAAGAGGCCCCTGTCAT
1 TCAAGAGGCCCCTATCAT
89064 TGTTGAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCGC
Found at i:90535 original size:36 final size:30
Alignment explanation
Indices: 90455--90520 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
90445 ATAAAAGTTG
90455 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
90485 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
90515 ATTTGT
1 ATTTGT
90521 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:90645 original size:20 final size:20
Alignment explanation
Indices: 90617--90859 Score: 201
Period size: 20 Copynumber: 12.8 Consensus size: 20
90607 CGATTTTCTT
90617 GTTGCGATAGTCAAATTC-C
1 GTTGCGATAGTCAAATTCGC
* *
90636 TGTTGTGATAATCAAATTCGC
1 -GTTGCGATAGTCAAATTCGC
* *
90657 GTTGCGATAGT-TATTTCGC
1 GTTGCGATAGTCAAATTCGC
90676 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
90696 GTTGCGATAGTTAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
90716 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
**
90736 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
* *
90756 ATTGCGAT--T---A-TCCC
1 GTTGCGATAGTCAAATTCGC
** *
90770 GTTGCGATAGTCATTTTCCC
1 GTTGCGATAGTCAAATTCGC
*
90790 ATTGCGAT--T---A-TC-C
1 GTTGCGATAGTCAAATTCGC
* *
90803 TGTTGCGATATTCAAATTCAC
1 -GTTGCGATAGTCAAATTCGC
*
90824 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCAAATTCGC
90844 GTTGCGATAGTCAAAT
1 GTTGCGATAGTCAAAT
90860 GAATGTGTAA
Statistics
Matches: 183, Mismatches: 24, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.01
14 19 0.10
16 2 0.01
18 2 0.01
19 18 0.10
20 139 0.76
21 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:90691 original size:59 final size:60
Alignment explanation
Indices: 90617--90859 Score: 246
Period size: 54 Copynumber: 4.3 Consensus size: 60
90607 CGATTTTCTT
* *
90617 GTTGCGATAGTCAAATTC-CTGTTGTGATAATCAAATTCGCGTTGCGATAGTTA-TTTCGC
1 GTTGCGATAGTCAAATTCGC-GTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGC
* *
90676 GTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGC
** * * *
90736 GTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCCCGTTGCGATAGTCATTTTCCC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGC
* * * *
90790 ATTGCGAT--T---A-TC-CTGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCAAATTCGC-GTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGC
90844 GTTGCGATAGTCAAAT
1 GTTGCGATAGTCAAAT
90860 GAATGTGTAA
Statistics
Matches: 153, Mismatches: 16, Indels: 29
0.77 0.08 0.15
Matches are distributed among these distances:
47 1 0.01
48 9 0.06
50 1 0.01
52 1 0.01
53 1 0.01
54 57 0.37
55 1 0.01
56 1 0.01
58 1 0.01
59 48 0.31
60 32 0.21
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (60 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGC
Found at i:90778 original size:34 final size:34
Alignment explanation
Indices: 90735--90812 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
90725 GTCATTTTCG
*
90735 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCCCATTGCGATTATCC
90769 CGTTGCGATAGTCATTTTCCCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCCCATTGCGATTATCC
*
90803 TGTTGCGATA
1 CGTTGCGATA
90813 TTCAAATTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCCCATTGCGATTATCC
Found at i:90829 original size:34 final size:34
Alignment explanation
Indices: 90735--90831 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 34
90725 GTCATTTTCG
** *
90735 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCACATTGCGATTATCC
** *
90769 CGTTGCGATAGTCATTTTCCCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCACATTGCGATTATCC
* * *
90803 TGTTGCGATATTCAAATTCACGTTGCGAT
1 CGTTGCGATAGTCAAATTCACATTGCGAT
90832 AGTCATATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCACATTGCGATTATCC
Found at i:94227 original size:20 final size:20
Alignment explanation
Indices: 94199--94338 Score: 115
Period size: 20 Copynumber: 6.9 Consensus size: 20
94189 AATTCAGTGA
*
94199 TGCGTTAGTCAGAATC-CAGT
1 TGCGATAGTCAGAATCGCA-T
*
94219 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCAT
**
94239 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCAT
*
94260 TGCGATAGTCAGAATCTCAT
1 TGCGATAGTCAGAATCGCAT
* *
94280 TGCGATAGTCAGAATTGCGT
1 TGCGATAGTCAGAATCGCAT
**
94300 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCAT
* *
94321 TGCAATAGTCCGAATCGC
1 TGCGATAGTCAGAATCGC
94339 GTTACGATCA
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
19 4 0.04
20 59 0.63
21 27 0.29
22 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCAT
Found at i:94270 original size:61 final size:61
Alignment explanation
Indices: 94199--94336 Score: 224
Period size: 61 Copynumber: 2.3 Consensus size: 61
94189 AATTCAGTGA
*
94199 TGCGTTAGTCAGAATC-CAGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCAT
1 TGCGATAGTCAGAATCTCA-TTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCAT
*
94260 TGCGATAGTCAGAATCTCATTGCGATAGTCAGAATTGCGTTGCGATCACGTATTATCGCAT
1 TGCGATAGTCAGAATCTCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCAT
* *
94321 TGCAATAGTCCGAATC
1 TGCGATAGTCAGAATC
94337 GCGTTACGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 70 0.97
62 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (61 bp):
TGCGATAGTCAGAATCTCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCAT
Found at i:94322 original size:41 final size:41
Alignment explanation
Indices: 94277--94367 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
94267 GTCAGAATCT
* * *
94277 CATTGCGATAGTCAGAATTGCGTTGCGATCACGTATTATCG
1 CATTGCGATAGTCAGAATCGCGTTACGATCAAGTATTATCG
* * *
94318 CATTGCAATAGTCCGAATCGCGTTACGATCAAGTGTTATCG
1 CATTGCGATAGTCAGAATCGCGTTACGATCAAGTATTATCG
*
94359 CGTTGCGAT
1 CATTGCGAT
94368 TTACATATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (41 bp):
CATTGCGATAGTCAGAATCGCGTTACGATCAAGTATTATCG
Found at i:94458 original size:20 final size:21
Alignment explanation
Indices: 94435--94488 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
94425 GCGATGGTCA
94435 AAATCGCGTTGCGAAT-ATGG
1 AAATCGCGTTGCGAATAATGG
* **
94455 AAATTGAATTGCG-ATAATGG
1 AAATCGCGTTGCGAATAATGG
*
94475 AGATCGCGTTGCGA
1 AAATCGCGTTGCGA
94489 TTTAGAGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (21 bp):
AAATCGCGTTGCGAATAATGG
Found at i:95723 original size:17 final size:17
Alignment explanation
Indices: 95701--95739 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
95691 TAGTGGTTCG
95701 ACTTCTCAACCAAGTCT
1 ACTTCTCAACCAAGTCT
95718 ACTTCTCAACCAAGTCT
1 ACTTCTCAACCAAGTCT
95735 ACTTC
1 ACTTC
95740 CACTACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (17 bp):
ACTTCTCAACCAAGTCT
Found at i:96175 original size:21 final size:21
Alignment explanation
Indices: 96143--96182 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
96133 AACTGCCCAA
*
96143 TACAGAGGGTATTGGTACTCC
1 TACAGAGGGTATCGGTACTCC
96164 TACAG-GGAGTATCGGTACT
1 TACAGAGG-GTATCGGTACT
96183 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TACAGAGGGTATCGGTACTCC
Found at i:96764 original size:11 final size:10
Alignment explanation
Indices: 96738--96769 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
96728 CTGGTTCACT
96738 GGTTCAACCG
1 GGTTCAACCG
96748 GGTTCAACCG
1 GGTTCAACCG
96758 CGGTTCAACCG
1 -GGTTCAACCG
96769 G
1 G
96770 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:100334 original size:32 final size:32
Alignment explanation
Indices: 100291--100365 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
100281 ATTCGGTGAG
* *
100291 CTTAACAAGCAACAAGACGAGCAACAAATTTT
1 CTTAACGAGCAACAAGACGAACAACAAATTTT
** *
100323 CTTAACGAGCAACAAGTTGAACAATAAATTTT
1 CTTAACGAGCAACAAGACGAACAACAAATTTT
100355 CTTAACGAGCA
1 CTTAACGAGCA
100366 CGAGTCGAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (32 bp):
CTTAACGAGCAACAAGACGAACAACAAATTTT
Found at i:106144 original size:30 final size:30
Alignment explanation
Indices: 106081--106137 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
106071 AAAATCGGTA
*
106081 GAACCGGCTGAAAACCAGTAAAACCGGGGT
1 GAACCGGCTGAAAACCAGCAAAACCGGGGT
*
106111 GAACTGGCTGAAAACCAGCAAAACCGG
1 GAACCGGCTGAAAACCAGCAAAACCGG
106138 TTTGAACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.09
Consensus pattern (30 bp):
GAACCGGCTGAAAACCAGCAAAACCGGGGT
Found at i:106708 original size:24 final size:24
Alignment explanation
Indices: 106676--106726 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
106666 ATGTTTTACC
*
106676 TTAAATATTATGTTGT-AGTTGATT
1 TTAAATATTATGTT-TCACTTGATT
* *
106700 TTAATTATTTTGTTTCACTTGATT
1 TTAAATATTATGTTTCACTTGATT
106724 TTA
1 TTA
106727 TGGTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.59
Consensus pattern (24 bp):
TTAAATATTATGTTTCACTTGATT
Found at i:108406 original size:13 final size:13
Alignment explanation
Indices: 108385--108444 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
108375 ATTTTGTTAG
108385 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
108398 TATTGTA-TTATT
1 TATTTTATTTAAT
108410 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
108422 TATTTTATTTAAT
1 TATTTTATTTAAT
108435 TATTTTATTT
1 TATTTTATTT
108445 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:108410 original size:21 final size:20
Alignment explanation
Indices: 108385--108449 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
108375 ATTTTGTTAG
108385 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
108406 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
108422 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
108443 TTTTTTA
1 TATTTTA
108450 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:108420 original size:29 final size:29
Alignment explanation
Indices: 108387--108449 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
108377 TTTGTTAGTA
108387 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
108416 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
108445 TTTTA
1 TTTTA
108450 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:108431 original size:16 final size:16
Alignment explanation
Indices: 108389--108431 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
108379 TGTTAGTATT
* *
108389 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
108405 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
108421 TTATTTTATTT
1 TTATTTAATTT
108432 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:108737 original size:28 final size:27
Alignment explanation
Indices: 108698--108760 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
108688 TATAACTACA
*
108698 AAAAAATAAAATAATTAAATTAAATAAT
1 AAAAAATAAAATAA-TAAAATAAATAAT
* *
108726 AAAAAATTAAATAATAAAATAATTAAT
1 AAAAAATAAAATAATAAAATAAATAAT
*
108753 ACAAAATA
1 AAAAAATA
108761 TGATTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAAATAAAATAATAAAATAAATAAT
Found at i:108753 original size:15 final size:15
Alignment explanation
Indices: 108714--108751 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
108704 TAAAATAATT
108714 AAATTAAATAATAAA
1 AAATTAAATAATAAA
108729 AAATTAAATAATAAA
1 AAATTAAATAATAAA
108744 ATAATTAA
1 A-AATTAA
108752 TACAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:109359 original size:21 final size:20
Alignment explanation
Indices: 109273--109430 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
109263 AAATGACCAA
**
109273 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
109292 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
109312 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
109332 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
109353 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
109374 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
109394 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
109415 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
109431 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:109440 original size:20 final size:20
Alignment explanation
Indices: 109395--109446 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
109385 TGCGATTTTC
*
109395 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGAACAT
*
109415 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAACAT
109434 CATAAATCGCAAC
1 CA-AAATCGCAAC
109447 ACGTATCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (20 bp):
CAAAATCGCAACGCGAACAT
Found at i:109446 original size:40 final size:40
Alignment explanation
Indices: 109397--109706 Score: 361
Period size: 40 Copynumber: 7.8 Consensus size: 40
109387 CGATTTTCCA
* * * *
109397 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATC-CGT
* * * * *
109437 AAATCGCAACACGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* * * * * *
109477 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* * * *
109517 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
109557 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
109597 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
109637 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
109677 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCTGTAAATCGCAAC
109707 ACTGAAATTT
Statistics
Matches: 248, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 247 1.00
41 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
Found at i:109459 original size:20 final size:20
Alignment explanation
Indices: 109436--109708 Score: 201
Period size: 20 Copynumber: 13.7 Consensus size: 20
109426 CGCGAACACA
109436 TAAATCGCAACACGTATCCG
1 TAAATCGCAACACGTATCCG
**
109456 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACACGTATCCG
* *
109476 TATATCGCAACGCGTATCCG
1 TAAATCGCAACACGTATCCG
**
109496 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACACGTATCCG
* *
109516 TATATCGCAACGCGTATCCG
1 TAAATCGCAACACGTATCCG
109536 TAAATCGC-A-ACGATAATCCG
1 TAAATCGCAACACG-T-ATCCG
* *
109556 TAAATCGCAACGA-GAATCTG
1 TAAATCGCAAC-ACGTATCCG
109576 TAAATCGC-A-ACGATAATCCG
1 TAAATCGCAACACG-T-ATCCG
* *
109596 TAAATCGCAACGA-GAATCTG
1 TAAATCGCAAC-ACGTATCCG
109616 TAAATCGC-A-ACGATAATCCG
1 TAAATCGCAACACG-T-ATCCG
* *
109636 TAAATCGCAACGA-GAATCTG
1 TAAATCGCAAC-ACGTATCCG
109656 TAAATCGC-A-ACGATAATCCG
1 TAAATCGCAACACG-T-ATCCG
* *
109676 TAAATCGCAACGA-GAATCTG
1 TAAATCGCAAC-ACGTATCCG
*
109696 TAAATCACAACAC
1 TAAATCGCAACAC
109709 TGAAATTTTG
Statistics
Matches: 204, Mismatches: 25, Indels: 48
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.01
18 5 0.02
19 6 0.03
20 178 0.87
21 4 0.02
22 4 0.02
23 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACACGTATCCG
Found at i:109483 original size:60 final size:60
Alignment explanation
Indices: 109397--109686 Score: 302
Period size: 60 Copynumber: 4.8 Consensus size: 60
109387 CGATTTTCCA
* ** * * *
109397 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAACACGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATC-CGTAAATCGCAACACGTATCCGT
* * * * **
109457 AAATCGCAACGTGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACACGTATCCGT
* * * * * *
109517 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGA-GAATCTGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAAC-ACGTATCCGT
*
109577 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGC-A-ACGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACACG-T-ATCCGT
* * *
109637 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAATCGCAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAAC
109687 GAGAATCTGT
Statistics
Matches: 190, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 1 0.01
60 185 0.97
61 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACACGTATCCGT
Found at i:109687 original size:60 final size:60
Alignment explanation
Indices: 109451--109706 Score: 320
Period size: 60 Copynumber: 4.3 Consensus size: 60
109441 CGCAACACGT
* * * *
109451 ATCCGTAAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCGTAAATCGCAATGCG-T-
1 ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAA--CGATA
* * * *
109511 ATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGATA
* * * *
109571 ATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGATA
* *
109631 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGATA
* *
109691 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
109707 ACTGAAATTT
Statistics
Matches: 172, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
58 2 0.01
59 1 0.01
60 169 0.98
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (60 bp):
ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGATA
Found at i:110428 original size:24 final size:24
Alignment explanation
Indices: 110389--110435 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
110379 AAATTTGGTC
110389 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
110413 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
110436 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:112914 original size:33 final size:34
Alignment explanation
Indices: 112863--113027 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
112853 CGGAAATTAC
* *
112863 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
112896 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
112930 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
112968 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
113001 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
113028 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:112946 original size:19 final size:19
Alignment explanation
Indices: 112877--113065 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
112867 GCAACGAGAG
112877 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
112896 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
112910 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
112930 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
112949 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
112968 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
112982 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
113001 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113020 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
113034 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
113053 AATCGCATTGCGA
1 AATCGCAATGCGA
113066 TTCTCCCGTT
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 84 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:113004 original size:52 final size:52
Alignment explanation
Indices: 112863--113065 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
112853 CGGAAATTAC
*
112863 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
112910 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
112968 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
113020 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
113066 TTCTCCCGTT
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 85 0.61
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:113114 original size:19 final size:19
Alignment explanation
Indices: 113074--113171 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
113064 GATTCTCCCG
113074 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
113094 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
113113 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
113127 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
113146 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
113165 TTGCGAT
1 TTGCGAT
113172 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:113168 original size:52 final size:53
Alignment explanation
Indices: 113055--113171 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
113045 GAAATTAAAA
113055 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
113108 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
113160 TCGCATTGCGAT
1 TCGCATTGCGAT
113172 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:113297 original size:14 final size:14
Alignment explanation
Indices: 113278--113314 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
113268 CATCAATTAC
*
113278 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
113292 ACAAATCATCTTTT
1 ACAAATCAACTTTT
113306 ACAAATCAA
1 ACAAATCAA
113315 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:115190 original size:20 final size:20
Alignment explanation
Indices: 115165--115230 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
115155 TAGTTTACTT
* *
115165 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
115185 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
115204 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
115223 TCGCAACG
1 TCGCAACG
115231 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:115248 original size:33 final size:33
Alignment explanation
Indices: 115202--115294 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
115192 GCGAAACCAA
*
115202 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
115235 AATCGCATTGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
115268 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
115295 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:115259 original size:19 final size:19
Alignment explanation
Indices: 115244--115299 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
115234 GAATCGCATT
115244 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
115262 -CGAAA-G--AATCGCAAC
1 GCGAAATGAAAATCGCAAC
*
115277 GCGAAATGAAAATCGCAAT
1 GCGAAATGAAAATCGCAAC
115296 GCGA
1 GCGA
115300 TTTTGGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 8 0.25
16 6 0.19
17 6 0.19
19 12 0.38
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:115273 original size:14 final size:14
Alignment explanation
Indices: 115221--115277 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
115211 GCGAAATGAA
*
115221 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
115235 AATCGCATTGCGAAATG
1 AATCGCA--ACGAAA-G
115252 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
115268 AATCGCAACG
1 AATCGCAACG
115278 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:115317 original size:19 final size:19
Alignment explanation
Indices: 115295--115423 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
115285 AAAATCGCAA
115295 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
115314 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
115328 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
115347 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
115361 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
115380 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
115399 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
115419 TGCGA
1 TGCGA
115424 AAGTAACTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:115337 original size:33 final size:33
Alignment explanation
Indices: 115295--115386 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
115285 AAAATCGCAA
115295 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
115328 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
115361 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
115387 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:115606 original size:93 final size:93
Alignment explanation
Indices: 115470--115938 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
115460 ATGGATTGCA
115470 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115534 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115562 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115627 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115655 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115720 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115748 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115813 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115841 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
115906 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115934 TTACT
1 TTACT
115939 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 371 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:117663 original size:14 final size:14
Alignment explanation
Indices: 117641--117738 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 14
117631 TGGTTGAAAT
117641 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
117655 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
*
117673 TGAAAATCGCAACTA
1 -GAAAATCGCAACGA
*
117688 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
117706 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
117721 GAGAATCGCAACGC
1 GAAAATCGCAACGA
117735 GAAA
1 GAAA
117739 TGAAAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
14 35 0.54
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.31
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:117676 original size:33 final size:33
Alignment explanation
Indices: 117636--117750 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
117626 TCTTTTGGTT
117636 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
117669 GAAATGAAAATCGCAACTAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
117702 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
117735 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
117751 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:117682 original size:19 final size:19
Alignment explanation
Indices: 117658--117755 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
117648 GCAACGAGAG
117658 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
117677 AATCGCAA--C--TA-GAT
1 AATCGCAACGCGAAATGAA
117691 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
117710 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
117724 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
117743 AATCGCAATGCGA
1 AATCGCAACGCGA
117756 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:117784 original size:19 final size:19
Alignment explanation
Indices: 117751--117869 Score: 95
Period size: 21 Copynumber: 6.3 Consensus size: 19
117741 AAAATCGCAA
** *
117751 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCTCGT
*
117770 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCTCGT
117789 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCTCGT
117803 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCTCGT
***
117824 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCTCGT
117844 TGCGATTTTCATTTATCTCGT
1 TGCGATTTTCA-TT-TCTCGT
117865 TGCGA
1 TGCGA
117870 CTCTTCTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 22 0.27
20 17 0.21
21 27 0.33
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCTCGT
Found at i:117850 original size:41 final size:41
Alignment explanation
Indices: 117793--117870 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
117783 TCGCGTTGCG
*
117793 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
117834 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
117871 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:117855 original size:20 final size:21
Alignment explanation
Indices: 117794--117869 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
117784 CGCGTTGCGA
117794 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
117815 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
117835 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
117856 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
117870 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:117991 original size:33 final size:33
Alignment explanation
Indices: 117949--118019 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
117939 AATACTAACT
*
117949 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
117982 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
118015 TGAAA
1 TGAAA
118020 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:118253 original size:22 final size:22
Alignment explanation
Indices: 118201--118255 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
118191 TGGTTGTGAG
**
118201 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
118223 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
118245 GGATTTCTTCG
1 GGATTTCTTCG
118256 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:118431 original size:20 final size:20
Alignment explanation
Indices: 118402--118555 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
118392 CTTTAAATAT
*
118402 CGCGTAGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
118422 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
118444 -TCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
118463 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
118483 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
118503 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
118523 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
118543 CGCGTTGCGATTT
1 CGCGTTGCGATTT
118556 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:118529 original size:40 final size:40
Alignment explanation
Indices: 118401--118555 Score: 168
Period size: 40 Copynumber: 3.9 Consensus size: 40
118391 GCTTTAAATA
* *
118401 TCGCGTAGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * * *
118442 TATCGTTGCGATTTATGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
118482 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
118522 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
118556 TGGAAAATCG
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
40 65 0.70
41 28 0.30
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:118572 original size:21 final size:21
Alignment explanation
Indices: 118542--118624 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
118532 ATTTTCATAT
*
118542 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
118563 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
118584 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
118605 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
118625 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:118615 original size:42 final size:43
Alignment explanation
Indices: 118522--118620 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
118512 ATTTATGTGT
* *
118522 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
118563 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
118605 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
118621 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:122723 original size:22 final size:21
Alignment explanation
Indices: 122698--122738 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
122688 GTTTATGTTG
*
122698 AGTAAATTTATAGAATTTTAAT
1 AGTAAA-TTATAAAATTTTAAT
*
122720 AGTAGATTATAAAATTTTA
1 AGTAAATTATAAAATTTTA
122739 TGAGATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
AGTAAATTATAAAATTTTAAT
Found at i:123838 original size:15 final size:15
Alignment explanation
Indices: 123818--123869 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
123808 ATATTTAGCT
*
123818 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
123833 GGGCGGGCGGATACG
1 GGGCGGGCGGATGCG
123848 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
123863 GGGCGGG
1 GGGCGGG
123870 TAATGTCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:124743 original size:25 final size:25
Alignment explanation
Indices: 124713--124769 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
124703 AATAATCACT
124713 CGAAC-AAAAAGAATACTACTTTT-TA
1 CGAACAAAAAAG-ATACTA-TTTTGTA
124738 CGAACAAAAAAGATACTATTTTGTA
1 CGAACAAAAAAGATACTATTTTGTA
*
124763 TGAACAA
1 CGAACAA
124770 CCATCGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 19 0.66
26 6 0.21
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (25 bp):
CGAACAAAAAAGATACTATTTTGTA
Found at i:134804 original size:20 final size:20
Alignment explanation
Indices: 134779--134817 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
134769 ATTAGCCAAA
134779 ATCACAAAGACACTATAGAT
1 ATCACAAAGACACTATAGAT
134799 ATCACAAAGACACTATAGA
1 ATCACAAAGACACTATAGA
134818 CACCATCACT
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:0.51, C:0.21, G:0.10, T:0.18
Consensus pattern (20 bp):
ATCACAAAGACACTATAGAT
Found at i:138466 original size:36 final size:36
Alignment explanation
Indices: 138419--138491 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
138409 TAAGTTTACA
138419 AGTACGGGGGGACTCCCAAAGTATTCAAAATAATAC
1 AGTACGGGGGGACTCCCAAAGTATTCAAAATAATAC
138455 AGTACGGGGGGACTCCCAAAGTATTCAAAATAATAC
1 AGTACGGGGGGACTCCCAAAGTATTCAAAATAATAC
138491 A
1 A
138492 ATACTGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (36 bp):
AGTACGGGGGGACTCCCAAAGTATTCAAAATAATAC
Found at i:140248 original size:76 final size:75
Alignment explanation
Indices: 140149--140415 Score: 290
Period size: 74 Copynumber: 3.6 Consensus size: 75
140139 AAGTGAGTTA
* * *
140149 TCTCATTTGACTTAAACCCGCGAAGAGGAGTCATCCAAAAAAATCAAGACTAGCTTAGA-CATGC
1 TCTCATTTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCA--C
140213 GAAGGGAAGTCG
64 GAAGGGAAGTCG
* * *** * * *
140225 TCTCAATTAACTTAAACTTGCGAAGGGGAGTCATCCAAAAAAATCGAGATTGGCTTAAACCACGA
1 TCTCATTTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGA
* *
140290 ATGAAAGTCG
66 AGGGAAGTCG
* * *
140300 TCTCATTTGACTTAAACCCACGAAGATGAGCCATCC-AAAAAATAAAGACTGGCTTAAACCACGA
1 TCTCATTTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGA
*
140364 AGAGG-GGTCG
66 AG-GGAAGTCG
* * *
140374 TTTCACTTGACTTAAACTCACGAAG-GAGAGTCATCCAAAAAA
1 TCTCATTTGACTTAAACCCACGAAGAG-GAGTCATCCAAAAAA
140416 CATGACTTAA
Statistics
Matches: 157, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
74 60 0.38
75 45 0.29
76 50 0.32
77 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (75 bp):
TCTCATTTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGA
AGGGAAGTCG
Found at i:140384 original size:74 final size:75
Alignment explanation
Indices: 140080--140415 Score: 274
Period size: 75 Copynumber: 4.5 Consensus size: 75
140070 TTCATCTTAT
* * * * * * **
140080 TTGACTTAAACCCGCAAAGGGGGAGTCATCC-AAAAACTTAAGACTAG-TTAAAACTGCGAA-AG
1 TTGACTTAAACCCACGAA-GAGGAGTCATCCAAAAAAATCAAGACTGGCTT-AAACCACGAAGAG
** *
140142 TGAGTTATCTCAT
64 -GAGTCGTCTCAA
* * *
140155 TTGACTTAAACCCGCGAAGAGGAGTCATCCAAAAAAATCAAGACTAGCTTAGA-CATGCGAAG-G
1 TTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCA--CGAAGAG
140218 GAAGTCGTCTCAA
64 G-AGTCGTCTCAA
* *** * * * *
140231 TTAACTTAAACTTGCGAAGGGGAGTCATCCAAAAAAATCGAGATTGGCTTAAACCACGAATGA-A
1 TTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGAA-GAGG
*
140295 AGTCGTCTCAT
65 AGTCGTCTCAA
* * * *
140306 TTGACTTAAACCCACGAAGATGAGCCATCC-AAAAAATAAAGACTGGCTTAAACCACGAAGAGGG
1 TTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGAAGAGGA
* *
140370 GTCGTTTCAC
66 GTCGTCTCAA
*
140380 TTGACTTAAACTCACGAAG-GAGAGTCATCCAAAAAA
1 TTGACTTAAACCCACGAAGAG-GAGTCATCCAAAAAA
140416 CATGACTTAA
Statistics
Matches: 212, Mismatches: 37, Indels: 24
0.78 0.14 0.09
Matches are distributed among these distances:
73 2 0.01
74 71 0.33
75 76 0.36
76 61 0.29
77 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (75 bp):
TTGACTTAAACCCACGAAGAGGAGTCATCCAAAAAAATCAAGACTGGCTTAAACCACGAAGAGGA
GTCGTCTCAA
Found at i:140520 original size:81 final size:81
Alignment explanation
Indices: 140374--140525 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
140364 AGAGGGGTCG
* * * *
140374 TTTCACTTGACTTAAACTCACGAAGGAGAGTCATCCAAAAAACATGACTTAAACCCATAAGGGGA
1 TTTCACATGACTTAAACTCACGAAGGAGAGTCATACAAAAAACATAACTTAAACCCAGAAGGGGA
140439 GTCACCCAAAGAATCA
66 GTCACCCAAAGAATCA
* * **
140455 TTTCACATGACTTAAACTCGCGAAAGG-GAGTCATACGAAGCACATAACTT-AACCCACGGAA-G
1 TTTCACATGACTTAAACTCACG-AAGGAGAGTCATACAAAAAACATAACTTAAACCCA--GAAGG
140517 GGAGTCACC
63 GGAGTCACC
140526 TACAACTCGA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
80 6 0.10
81 48 0.80
82 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (81 bp):
TTTCACATGACTTAAACTCACGAAGGAGAGTCATACAAAAAACATAACTTAAACCCAGAAGGGGA
GTCACCCAAAGAATCA
Found at i:141230 original size:12 final size:12
Alignment explanation
Indices: 141213--141246 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
141203 TTTCAAAATT
141213 TTAATTATTTTA
1 TTAATTATTTTA
141225 TTAATTATTTTA
1 TTAATTATTTTA
141237 TTAATTATTT
1 TTAATTATTT
141247 GTGAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATTATTTTA
Found at i:143313 original size:58 final size:58
Alignment explanation
Indices: 143223--143339 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
143213 AACCCATTCC
143223 ATCATAGCCCTAGTAGAGAATTGGACAAAAAAAAGTAGAATCCTCGTAACTAGGTTTA
1 ATCATAGCCCTAGTAGAGAATTGGACAAAAAAAAGTAGAATCCTCGTAACTAGGTTTA
143281 ATCATAGCCCTAGTAGAGAATTGGACAAAAAAAAGTAGAATCCTCGTAACTAGGTTTA
1 ATCATAGCCCTAGTAGAGAATTGGACAAAAAAAAGTAGAATCCTCGTAACTAGGTTTA
143339 A
1 A
143340 AATCGCGGTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (58 bp):
ATCATAGCCCTAGTAGAGAATTGGACAAAAAAAAGTAGAATCCTCGTAACTAGGTTTA
Found at i:149142 original size:15 final size:15
Alignment explanation
Indices: 149122--149151 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
149112 CTTTCTCATA
149122 GTTGTTGTTGTAATT
1 GTTGTTGTTGTAATT
149137 GTTGTTGTTGTAATT
1 GTTGTTGTTGTAATT
149152 CCACCTCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (15 bp):
GTTGTTGTTGTAATT
Done.