Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008710.1 Hibiscus syriacus cultivar Beakdansim tig00111759_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: 170303
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:145 original size:15 final size:15
Alignment explanation
Indices: 127--155 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
117 AGGGTTCTGT
127 AGTCCTTCGGGACGA
1 AGTCCTTCGGGACGA
142 AGTCCTTCGGGACG
1 AGTCCTTCGGGACG
156 TAGTGGTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (15 bp):
AGTCCTTCGGGACGA
Found at i:6972 original size:15 final size:15
Alignment explanation
Indices: 6954--6988 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
6944 CGAGGGTTCT
6954 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6969 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6984 GTAGT
1 GTAGT
6989 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:14629 original size:41 final size:41
Alignment explanation
Indices: 14501--14630 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 41
14491 AAACACAAAT
* * * ** *
14501 GCCATTAAATTATGAGTCTTTAGCAACATTTGTATAAAAAT
1 GCCACTAAAGTATGAGTTTTTAGTGACATTTGTATAAAAAC
* * *
14542 GCCACAAAAGTACT-AGTTTATA-TCGACATTTGTACAAAAAC
1 GCCACTAAAGTA-TGAGTTTTTAGT-GACATTTGTATAAAAAC
* * *
14583 ACCACTAAAGTATGAGTTTTTAGTGACGTTTGTATAAAAGC
1 GCCACTAAAGTATGAGTTTTTAGTGACATTTGTATAAAAAC
14624 GCCACTA
1 GCCACTA
14631 CATTACGAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
40 1 0.01
41 66 0.96
42 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (41 bp):
GCCACTAAAGTATGAGTTTTTAGTGACATTTGTATAAAAAC
Found at i:15400 original size:21 final size:21
Alignment explanation
Indices: 15374--15426 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
15364 ATTATCTAAT
**
15374 AAACTTGCCATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
15395 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
15416 AAAATTGAAAT
1 AAACTTGAAAT
15427 AAATAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.21
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:15432 original size:21 final size:21
Alignment explanation
Indices: 15387--15432 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
15377 CTTGCCATCC
* **
15387 ATAACAACAAACTTGAAATCC
1 ATAACAACAAAATTGAAATAA
*
15408 ATAACAAGAAAATTGAAATAA
1 ATAACAACAAAATTGAAATAA
15429 ATAA
1 ATAA
15433 TAATATATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.20
Consensus pattern (21 bp):
ATAACAACAAAATTGAAATAA
Found at i:16126 original size:81 final size:80
Alignment explanation
Indices: 15955--16194 Score: 229
Period size: 81 Copynumber: 3.0 Consensus size: 80
15945 TTGTAAACAC
* * *
15955 AAATGCCACTAAAATACGAGTTTATAGCGGCATTTTTACAAAAACACCACTAAAGTACGAGTCTT
1 AAATCCCACT-AAATACGAGTTTATAGCGGCGTTTGTACAAAAACACCACTAAAGTACGAGTCTT
*
16020 TAGTGACGTTTGTATA
65 TAGCGACGTTTGTATA
* * **
16036 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTA-TAAAATGCCACTAAAGTACGAGT-TT
1 AAATCCCACTAAA-TACGAGTTTATAGCGGCGTTTGTACAAAAACACCACTAAAGTACGAGTCTT
*
16099 ATAGCGGCGTTTGTATA
65 -TAGCGACGTTTGTATA
* * ** *
16116 AAATCCCCACTATAATATGAGTCTT-TAGGGGCGTTTGTTTACAAACACCA-TGAAAGT-CAGAG
1 AAAT-CCCACTA-AATACGAGT-TTATAGCGGCGTTTGTACAAAAACACCACT-AAAGTAC-GAG
* *
16178 TCTTTTGCGGCGTTTGT
61 TCTTTAGCGACGTTTGT
16195 TCAAAAAACG
Statistics
Matches: 134, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
79 2 0.01
80 41 0.31
81 58 0.43
82 31 0.23
83 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (80 bp):
AAATCCCACTAAATACGAGTTTATAGCGGCGTTTGTACAAAAACACCACTAAAGTACGAGTCTTT
AGCGACGTTTGTATA
Found at i:16149 original size:41 final size:40
Alignment explanation
Indices: 15955--16153 Score: 233
Period size: 40 Copynumber: 4.9 Consensus size: 40
15945 TTGTAAACAC
* * * *
15955 AAATGCCACTAAAATACGAGTTTATAGCGGCATTTTTACAA
1 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTA-TA
** * *
15996 AAACACCACTAAAGTACGAGTCTT-TAGTGACGTTTGTATA
1 AAATGCCACTAAAGTACGAGT-TTATAGCGGCGTTTGTATA
16036 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATA
1 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATA
16076 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATA
1 AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATA
* * *
16116 AAATCCCCACTATAA-TATGAGTCTT-TAGGGGCGTTTGT
1 AAAT-GCCACTA-AAGTACGAGT-TTATAGCGGCGTTTGT
16154 TTACAAACAC
Statistics
Matches: 138, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
39 2 0.01
40 78 0.57
41 52 0.38
42 6 0.04
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
AAATGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATA
Found at i:16288 original size:23 final size:22
Alignment explanation
Indices: 16262--16305 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
16252 TTTATGACAC
16262 GTTTATATATGCCTTTGTGGTAT
1 GTTTATATATGCCTTT-TGGTAT
* * *
16285 GTTTTTCTCTGCCTTTTGGTA
1 GTTTATATATGCCTTTTGGTA
16306 GCTTATGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTATATATGCCTTTTGGTAT
Found at i:17076 original size:247 final size:247
Alignment explanation
Indices: 16603--17338 Score: 1230
Period size: 247 Copynumber: 3.0 Consensus size: 247
16593 TAGTTTTTTT
* *
16603 ACTTTTTCCTTCTTTGGTCCTTATGTGATATAGGTGGCTAATTTTTGTCTTTATGGTAATAGAAA
1 ACTTTTTCCTTCTTTGGTCCTTATGTGATATAGATGGCTAATTTTTGTCTCTATGGTAATAGAAA
16668 AATGTCATAATTATATTTTAGGTTTACGGTTATGCTTGTAAATCTTCATTGTAATTTTGGATA-T
66 AATGTCATAATTATATTTTAGGTTTACGGTTATGCTTGTAAATCTTCATTGTAATTTTGGATATT
*
16732 ATTT-TTTTTAATAAAACTAACGACTTTCTATCAATTTTTTTGACTTTTTGAAAGTCAATAATGA
131 TTTTATTTTTAATAAAACTAACGACTTTCTATCAATTTTTTTGACTTTTTGAAAGTCAATAATGA
16796 ACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
196 ACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
*
16848 ACTTTTTCCTTCTTTGGTCCTTATTTGATATAGATGGCTAATTTTTGTCTCTATGGTAATAG-AA
1 ACTTTTTCCTTCTTTGGTCCTTATGTGATATAGATGGCTAATTTTTGTCTCTATGGTAATAGAAA
* *
16912 AATGTCATAATTATATTTTAGGTTTACGGTTTTGCTTGTAATTCTTCATTGTAATTTTGGATATT
66 AATGTCATAATTATATTTTAGGTTTACGGTTATGCTTGTAAATCTTCATTGTAATTTTGGATATT
*
16977 TTTTATTTTTAATAAAACTAATGACTTTCTATCAATTTTTTTTGACTTTTTGAAAGTCAATAATG
131 TTTTATTTTTAATAAAACTAACGACTTTCTATCAA-TTTTTTTGACTTTTTGAAAGTCAATAATG
17042 AACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
195 AACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
* *
17095 ACTTTTTTCTT-ATTGGTCCTTATGTGATATA-AGTGGCTAATTTTTGTCTCTATGGTAATAGAA
1 ACTTTTTCCTTCTTTGGTCCTTATGTGATATAGA-TGGCTAATTTTTGTCTCTATGGTAATAGAA
*
17158 AAATGTCATAATTATATTTTAGGTTTACGGTTATACTTGTAAATCTTCATTGTAATTTTGGATAT
65 AAATGTCATAATTATATTTTAGGTTTACGGTTATGCTTGTAAATCTTCATTGTAATTTTGGATAT
* *
17223 TTTCTATTTTTAATAAAACTAACGACTTTCTAT-TATTTTTTTGACTTTTTGAAAG-------T-
130 TTTTTATTTTTAATAAAACTAACGACTTTCTATCAATTTTTTTGACTTTTTGAAAGTCAATAATG
* *
17279 AACACATTTAGTGAGACGGAGGGAGTAATTTGTACCCAAATTATTTCAATACA
195 AACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
17332 ACTTTTT
1 ACTTTTT
17339 TTCGTTGACA
Statistics
Matches: 468, Mismatches: 18, Indels: 18
0.93 0.04 0.04
Matches are distributed among these distances:
237 58 0.12
238 1 0.00
244 63 0.13
245 84 0.18
246 76 0.16
247 186 0.40
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (247 bp):
ACTTTTTCCTTCTTTGGTCCTTATGTGATATAGATGGCTAATTTTTGTCTCTATGGTAATAGAAA
AATGTCATAATTATATTTTAGGTTTACGGTTATGCTTGTAAATCTTCATTGTAATTTTGGATATT
TTTTATTTTTAATAAAACTAACGACTTTCTATCAATTTTTTTGACTTTTTGAAAGTCAATAATGA
ACACATTTAGTGAGATGGAAGGAGTAATTTGTACCCAAATTATTTCAATACA
Found at i:23662 original size:91 final size:90
Alignment explanation
Indices: 23556--23724 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 90
23546 AACAATGAGA
* *
23556 TACTAAAATGAAACTAAAACTAAAGTTTAGGTATACATTTGAAAAAAATTAAAAGTTTAGATATT
1 TACTAAAATGAAACTAAAACTAAACTTTAGGTATACATTTGAAAAAAA-TAAAAGTTTAGATACT
23621 AAAACGGACTAAAATAAACCGTAATT
65 AAAACGGACTAAAATAAACCGTAATT
* * *
23647 TACTAAAATGAAACTAAAATTGAACTTTAGGTATACTTTTGAAAAAAATAAAAGTTTAGATACTA
1 TACTAAAATGAAACTAAAACTAAACTTTAGGTATACATTTGAAAAAAATAAAAGTTTAGATACTA
23712 AAACGGACTAAAA
66 AAACGGACTAAAA
23725 ACGTAATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
90 29 0.40
91 44 0.60
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.28
Consensus pattern (90 bp):
TACTAAAATGAAACTAAAACTAAACTTTAGGTATACATTTGAAAAAAATAAAAGTTTAGATACTA
AAACGGACTAAAATAAACCGTAATT
Found at i:24020 original size:32 final size:32
Alignment explanation
Indices: 23978--24050 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
23968 AAAATGACAA
* * *
23978 TAAATGTTTGTT-AATTGATTATAAAATAATTAT
1 TAAAT-TTTGTTAAACT-ATTACAAAATAACTAT
*
24011 TAAATTTTGTTAAACTATTACGAAATAACTAT
1 TAAATTTTGTTAAACTATTACAAAATAACTAT
24043 TAAATTTT
1 TAAATTTT
24051 TAAACTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 27 0.77
33 8 0.23
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (32 bp):
TAAATTTTGTTAAACTATTACAAAATAACTAT
Found at i:40991 original size:2 final size:2
Alignment explanation
Indices: 40974--41025 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
40964 GTAATATAAA
* *
40974 AT AT AC AT AC 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
41016 AT AT AT AT AT
1 AT AT AT AT AT
41026 TGTTTTAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:48605 original size:21 final size:20
Alignment explanation
Indices: 48581--48640 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 20
48571 GCAAATTCGC
48581 GTTGCATTTCGCGTTGCGACA
1 GTTGCATTTCGCGTTGCGA-A
* ** *
48602 GTTGAAAATCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAA
* *
48622 TTTCCATTTCGCGTTGCGA
1 GTTGCATTTCGCGTTGCGA
48641 TAGTCCGATT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCATTTCGCGTTGCGAA
Found at i:48698 original size:30 final size:30
Alignment explanation
Indices: 48662--48745 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
48652 TCCAAATTCG
48662 TTGCGATAGTCTACAGTTGTCGTTGCGATT
1 TTGCGATAGTCTACAGTTGTCGTTGCGATT
48692 TTGCGATAGTCTACAG-T-T-GTT---A--
1 TTGCGATAGTCTACAGTTGTCGTTGCGATT
*
48714 TTGCGAAAGTCTACAGTTGTCGTTGCGATT
1 TTGCGATAGTCTACAGTTGTCGTTGCGATT
48744 TT
1 TT
48746 CCAAATTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
22 15 0.33
23 1 0.02
24 2 0.04
25 3 0.07
27 3 0.07
28 2 0.04
29 1 0.02
30 18 0.40
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.40
Consensus pattern (30 bp):
TTGCGATAGTCTACAGTTGTCGTTGCGATT
Found at i:48717 original size:22 final size:22
Alignment explanation
Indices: 48692--48742 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
48682 CGTTGCGATT
*
48692 TTGCGATAGTCTACAGTTGTTA
1 TTGCGATAGTCTACAGTTGTCA
* *
48714 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCA
48736 TTGCGAT
1 TTGCGAT
48743 TTTCCAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCA
Found at i:48880 original size:5 final size:6
Alignment explanation
Indices: 48841--48867 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
48831 GACACGTATT
48841 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
48868 GACCCGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:49512 original size:22 final size:22
Alignment explanation
Indices: 49484--49577 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
49474 AATTTGGAAA
*
49484 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTGTAGACT
*
49506 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
49528 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
49547 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
49569 ATCGCAACG
1 ATCGCAACG
49578 CGAACTGGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 13 0.22
20 2 0.03
21 2 0.03
22 41 0.71
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:49551 original size:41 final size:41
Alignment explanation
Indices: 49506--49596 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
49496 ACTATAGACT
*
49506 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAACCGAA-CTGGAAA
*
49547 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAAC-CGAACTGGAAA
49589 ATCGCAAC
1 ATCGCAAC
49597 GCGATTTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 28 0.61
42 14 0.30
43 4 0.09
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (41 bp):
ATCGCAACAACAACTGTAGACTATCGCAACCGAACTGGAAA
Found at i:49594 original size:20 final size:20
Alignment explanation
Indices: 49541--49600 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
49531 GCAACGAATT
49541 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
49561 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
49583 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
49601 TTTTCAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.13
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:49615 original size:21 final size:21
Alignment explanation
Indices: 49589--49692 Score: 109
Period size: 21 Copynumber: 4.6 Consensus size: 21
49579 GAACTGGAAA
*
49589 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
49610 ATCGCAACGCGAATTTACGCTTTTCAACT
1 ATCGCAACGCG-----A---TTTTCAACT
*
49639 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
*
49660 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTTCAACT
49681 ATCGCAACGCGA
1 ATCGCAACGCGA
49693 ATTTGCGATA
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
21 50 0.70
24 1 0.01
26 1 0.01
29 19 0.27
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:49618 original size:63 final size:62
Alignment explanation
Indices: 49465--49597 Score: 180
Period size: 63 Copynumber: 2.1 Consensus size: 62
49455 TTTTTTAACT
* **
49465 ATCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTATCGCAACAACAACTGTAGACT
1 ATCGCAACGAATTTGCAAAATCGCAACGACAACTATAGACTATCGCAACAACAACTG-AGAAA
* * *
49528 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC-GCGAACTG-GAAA
1 ATCGCAACGAATTTGCAAAATCGCAACGACAACTATAGACTATCGCAACAAC-AACTGAGAAA
49589 ATCGCAACG
1 ATCGCAACG
49598 CGATTTTCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
61 11 0.17
62 1 0.02
63 53 0.82
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (62 bp):
ATCGCAACGAATTTGCAAAATCGCAACGACAACTATAGACTATCGCAACAACAACTGAGAAA
Found at i:54233 original size:15 final size:15
Alignment explanation
Indices: 54196--54237 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
54186 AACTTTTCGG
54196 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
54211 TTAACGGTTCGGGTTTT
1 TT--CGGTTCGGGTTTT
54228 TTCGGTTCGG
1 TTCGGTTCGG
54238 TTCGGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
17 15 0.60
ACGTcount: A:0.05, C:0.14, G:0.33, T:0.48
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:54506 original size:11 final size:11
Alignment explanation
Indices: 54490--54523 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
54480 AGCCCTAGAT
54490 AAAAGGAAAGG
1 AAAAGGAAAGG
54501 AAAAGGAAAAGG
1 AAAAGG-AAAGG
*
54513 AAAAAGAAAGG
1 AAAAGGAAAGG
54524 TGAAGTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAAGGAAAGG
Found at i:55984 original size:19 final size:19
Alignment explanation
Indices: 55957--55994 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55947 CATTATATAA
55957 AATTAATAAGTT-TTAAATT
1 AATTAATAA-TTATTAAATT
*
55976 AATTTATAATTATTAAATT
1 AATTAATAATTATTAAATT
55995 TAAATAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTAATAATTATTAAATT
Found at i:57662 original size:58 final size:58
Alignment explanation
Indices: 57572--57688 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
57562 AGGAGTAATT
57572 ACAAATGAGCAAACTTTGAACATCCTCACAATAGATTGTTTGTACCAAGAACACTAGA
1 ACAAATGAGCAAACTTTGAACATCCTCACAATAGATTGTTTGTACCAAGAACACTAGA
57630 ACAAATGAGCAAACTTTGAACATCCTCACAATAGATTGTTTGTACCAAGAACACTAGA
1 ACAAATGAGCAAACTTTGAACATCCTCACAATAGATTGTTTGTACCAAGAACACTAGA
57688 A
1 A
57689 TAAAAATTAT
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:0.21, G:0.14, T:0.24
Consensus pattern (58 bp):
ACAAATGAGCAAACTTTGAACATCCTCACAATAGATTGTTTGTACCAAGAACACTAGA
Found at i:59852 original size:16 final size:17
Alignment explanation
Indices: 59833--59869 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59823 TAAAATATTA
59833 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
59849 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
59866 TTTT
1 TTTT
59870 TCATCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:61350 original size:25 final size:26
Alignment explanation
Indices: 61310--61369 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
61300 TAAATTTAAG
*
61310 AAATAT-TTTTATATTAACTT-A-TT
1 AAATATATTTAATATTAACTTAATTT
61333 AAATATATTTAATGATTAACTTAATTT
1 AAATATATTTAAT-ATTAACTTAATTT
*
61360 AAACATATTT
1 AAATATATTT
61370 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 5 0.16
25 8 0.26
26 1 0.03
27 11 0.35
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
AAATATATTTAATATTAACTTAATTT
Found at i:61397 original size:24 final size:24
Alignment explanation
Indices: 61353--61400 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61343 AATGATTAAC
*
61353 TTAATTTAAACATATTTTTTTATT
1 TTAATTTAAACATATTATTTTATT
*
61377 TTAATTTAAA-ATGTATATTTTATT
1 TTAATTTAAACATAT-TATTTTATT
61401 CTTATCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTAATTTAAACATATTATTTTATT
Found at i:61958 original size:31 final size:32
Alignment explanation
Indices: 61923--61987 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
61913 TGGTGACTAC
*
61923 ATCTTAATTAAAT-AAAAATTAAAGTGACAAT
1 ATCTTAATTAAATAAAAAATGAAAGTGACAAT
*
61954 ATCTTAATTAAATAAAAAATGAAAGTGACCAT
1 ATCTTAATTAAATAAAAAATGAAAGTGACAAT
61986 AT
1 AT
61988 ATATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (32 bp):
ATCTTAATTAAATAAAAAATGAAAGTGACAAT
Found at i:63885 original size:83 final size:83
Alignment explanation
Indices: 63767--63993 Score: 207
Period size: 83 Copynumber: 2.7 Consensus size: 83
63757 TGTAATAGAT
* *
63767 TAATATATAGTGGCG-TTTTAGCCAAAACGCCGCAATAG-ATTACA-CATATAGTGGCGTTTATT
1 TAATAAATAGTGGCGTTTTTAGACAAAACGCCGCAATAGTATTA-ATCA-ATAGTGGCGTTT-TT
* * *
63829 CCTAAAATGTCCTAATAGTGA
63 ACAAAAACGTCCTAATAGTGA
* * * *
63850 TAATAAATAGTGGCGTTTTTAGAC-AAATGCTGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 TAATAAATAGTGGCGTTTTTAGACAAAACGCCGCAATAGTATTAATCAATAGTGGCGTTTTTACA
* **
63914 AAAACGTCGTAATAGTTT
66 AAAACGTCCTAATAGTGA
* * * *
63932 TAATCAATAGTGGCGTTTTTTTTA-AC-AAACGCCACAATAGT-GTAATCAATAGTGGCATTTTT
1 TAATAAATAGTGGCG---TTTTTAGACAAAACGCCGCAATAGTATTAATCAATAGTGGCGTTTTT
63994 TTTGTATAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
82 30 0.25
83 58 0.48
84 26 0.22
85 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (83 bp):
TAATAAATAGTGGCGTTTTTAGACAAAACGCCGCAATAGTATTAATCAATAGTGGCGTTTTTACA
AAAACGTCCTAATAGTGA
Found at i:63889 original size:41 final size:41
Alignment explanation
Indices: 63773--63993 Score: 166
Period size: 41 Copynumber: 5.3 Consensus size: 41
63763 AGATTAATAT
* * *
63773 ATAGTGGCG-TTTTAGCCAAAACGCCGCAATAG-ATTACA-CA
1 ATAGTGGCGTTTTTAG-AAAAACGTCGCAATAGTGTTA-ATCA
*** * * *
63813 TATAGTGGCGTTTATTCCTAAAATGTC-CTAATAGTGATAATAA
1 -ATAGTGGCGTTT-TTAGAAAAACGTCGC-AATAGTGTTAATCA
* *
63856 ATAGTGGCGTTTTTAGACAAATG-CTGCAATAGTGTTAATCA
1 ATAGTGGCGTTTTTAGAAAAACGTC-GCAATAGTGTTAATCA
* *
63897 ATAGTGGCGTTTTTAGAAAAACGTCGTAATAGTTTTAATCA
1 ATAGTGGCGTTTTTAGAAAAACGTCGCAATAGTGTTAATCA
** * *
63938 ATAGTGGCGTTTTTTTTAACAAACGCCACAATAGTG-TAATCA
1 ATAGTGGCG-TTTTTAGAA-AAACGTCGCAATAGTGTTAATCA
*
63980 ATAGTGGCATTTTT
1 ATAGTGGCGTTTTT
63994 TTTGTATAAA
Statistics
Matches: 145, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
40 1 0.01
41 78 0.54
42 49 0.34
43 17 0.12
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (41 bp):
ATAGTGGCGTTTTTAGAAAAACGTCGCAATAGTGTTAATCA
Found at i:63996 original size:42 final size:40
Alignment explanation
Indices: 63882--63996 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 40
63872 ACAAATGCTG
* ** * *
63882 CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGTCG
1 CAATAGTG-TAATCAATAGTGGCTTTTTTTTAAAAACGCCA
* *
63923 TAATAGTTTTAATCAATAGTGGCGTTTTTTTTAACAAACGCCA
1 CAATAG-TGTAATCAATAGTGGC-TTTTTTTTAA-AAACGCCA
63966 CAATAGTGTAATCAATAGTGGCATTTTTTTT
1 CAATAGTGTAATCAATAGTGGC-TTTTTTTT
63997 GTATAAACGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 19 0.31
42 31 0.51
43 11 0.18
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
CAATAGTGTAATCAATAGTGGCTTTTTTTTAAAAACGCCA
Found at i:65680 original size:83 final size:82
Alignment explanation
Indices: 65482--65696 Score: 202
Period size: 82 Copynumber: 2.6 Consensus size: 82
65472 GCAATTTTCA
* * *
65482 AAAAATGCCGCAATAGTTTTGTCCTTTAGTGGCATTTTTG-TAATAAATGCTACTAAAAACTTGT
1 AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGAT-ATAAACGCTACTAAAAACTTGT
*
65546 ACTTTAGTGGCGTTTTTT
65 ACGTTAGTGGCGTTTTTT
* * ** ** ** * ** *
65564 TAAAACACCGCAATAGTCATGTAATTTTTTGGCGTTTTTGATGTAAACG-TAGC-AATTGAGTTG
1 AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGCTA-CTAA-AAACTTG
* *
65627 TTCGTTATTGGCGTTTTTT
64 TACGTTAGTGGCGTTTTTT
*
65646 AATAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTAATATAAACGC
1 AA-AAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGC
65697 CGTCATTGTC
Statistics
Matches: 100, Mismatches: 28, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
81 4 0.04
82 57 0.57
83 39 0.39
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (82 bp):
AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGCTACTAAAAACTTGTA
CGTTAGTGGCGTTTTTT
Found at i:67143 original size:83 final size:82
Alignment explanation
Indices: 66946--67160 Score: 211
Period size: 82 Copynumber: 2.6 Consensus size: 82
66936 GCAATTTTCA
* * *
66946 AAAAATGCCGCAATAGTTTTGTCCTTTAGTGGCATTTTTG-TAATAAATGCTACTAAAAACTTGT
1 AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGAT-ATAAACGCTACTAAAAACTTGT
*
67010 ACTTTAGTGGCGTTTTTT
65 ACGTTAGTGGCGTTTTTT
* * ** ** * * ** *
67028 TAAAACACCGCAATAGTCATGTAATTTTGTGGCGTTTTTGATGTAAACG-TAGC-AATTGAGTTG
1 AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGCTA-CTAA-AAACTTG
* *
67091 TTCGTTATTGGCGTTTTTT
64 TACGTTAGTGGCGTTTTTT
*
67110 AATAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTAATATAAACGC
1 AA-AAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGC
67161 CGTCATTGTC
Statistics
Matches: 102, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
81 4 0.04
82 58 0.57
83 40 0.39
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (82 bp):
AAAAACGCCGCAATAGTTTTGTCCTTTAGTGGCGTTTTTGATATAAACGCTACTAAAAACTTGTA
CGTTAGTGGCGTTTTTT
Found at i:74253 original size:21 final size:21
Alignment explanation
Indices: 74185--74253 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
74175 AGCGAAAAAT
*
74185 GAAGCAAGGGAAGCAGAGAGA
1 GAAGCAACGGAAGCAGAGAGA
* **
74206 GTAA-CAACAGAAGCAGCCAGA
1 G-AAGCAACGGAAGCAGAGAGA
* *
74227 GCAGCAACGGAAGCAGAGAAA
1 GAAGCAACGGAAGCAGAGAGA
74248 GAAGCA
1 GAAGCA
74254 GCGGCAACAC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.48, C:0.17, G:0.33, T:0.01
Consensus pattern (21 bp):
GAAGCAACGGAAGCAGAGAGA
Found at i:74919 original size:42 final size:42
Alignment explanation
Indices: 74734--75026 Score: 261
Period size: 43 Copynumber: 6.9 Consensus size: 42
74724 TTTGTGAGAA
* * * * * * * *
74734 AAACGCCACAAAACATCAAAACCTACTACGGCGTTTGTTGA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAC
* * * * * * *
74775 AAATGCCGCAAAAAATCAACACCTACTGCGGCGTTTGTGAGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTA-AC
* * *
74818 AAACGCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTAAA
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTT-TTTAAC
74861 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAC
* * *
74903 AAACGCCTCTAAATATCAACACCTATTGCGGCATTTTTCTGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT-TAAC
* *
74946 AAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTCACAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTA-AC
* * * *
74989 AATA--CTGATAAATATCAATACCTATTGCAGCGTTTTTT
1 AA-ACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTT
75027 GTTTAAAAAC
Statistics
Matches: 213, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
41 33 0.15
42 70 0.33
43 107 0.50
44 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAC
Found at i:74950 original size:85 final size:86
Alignment explanation
Indices: 74705--74983 Score: 298
Period size: 85 Copynumber: 3.3 Consensus size: 86
74695 ACCGTAAAAC
* * * * * * * *
74705 ATCAATACATATTGCGGC-TTTTGTGAGAAAAACGCCACAAAACATCAAAACCTACTACGGCGTT
1 ATCAACACCTATTGCGGCGTTTT-TGAGAAAAACGCCGCTAAACATCATAACCTATTGCGGCATT
* * * *
74769 TGT-T-GAAAATGCCGCAAAAA
65 TGTCTAAAAAACGCCGCTAAAT
* * *
74789 ATCAACACCTACTGCGGCGTTTGTGAGAAAAACGCCGCTAAACATCATAACCTATTGCGGCGTTT
1 ATCAACACCTATTGCGGCGTTTTTGAGAAAAACGCCGCTAAACATCATAACCTATTGCGGCATTT
74854 GTCTAAAAAACGCCGCTAAAT
66 GTCTAAAAAACGCCGCTAAAT
* * * *
74875 ATCAACACCTATTGCGGCGTTTTTTA-ACAAACGCCTCTAAATATCA-ACACCTATTGCGGCATT
1 ATCAACACCTATTGCGGCGTTTTTGAGAAAAACGCCGCTAAACATCATA-ACCTATTGCGGCATT
* * *
74938 TTTCTGACAAACGCCGCTAAAT
65 TGTCTAAAAAACGCCGCTAAAT
*
74960 ATCAACACCTATTACGGCGTTTTT
1 ATCAACACCTATTGCGGCGTTTTT
74984 CACACAATAC
Statistics
Matches: 167, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
84 55 0.33
85 77 0.46
86 35 0.21
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (86 bp):
ATCAACACCTATTGCGGCGTTTTTGAGAAAAACGCCGCTAAACATCATAACCTATTGCGGCATTT
GTCTAAAAAACGCCGCTAAAT
Found at i:74984 original size:43 final size:43
Alignment explanation
Indices: 74705--74981 Score: 276
Period size: 43 Copynumber: 6.5 Consensus size: 43
74695 ACCGTAAAAC
* * * ** * * *
74705 ATCAATACATATTGCGGCTTTTGTGAGAAAAACGCCACAAAAC
1 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
* * * * * *
74748 ATCAAAACCTACTACGGCGTTTGT-TG-AAAATGCCGCAAAAA
1 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
* ** *
74789 ATCAACACCTACTGCGGCGTTTGTGAGAAAAACGCCGCTAAAC
1 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
*
74832 ATCATA-ACCTATTGCGGCGTTTGTCTAAAAAACGCCGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
* *
74875 ATCAACACCTATTGCGGCGTTT-T-TTAACAAACGCCTCTAAAT
1 ATCAACACCTATTGCGGCGTTTGTCTGAA-AAACGCCGCTAAAT
* * *
74917 ATCAACACCTATTGCGGCATTTTTCTGACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
*
74960 ATCAACACCTATTACGGCGTTT
1 ATCAACACCTATTGCGGCGTTT
74982 TTCACACAAT
Statistics
Matches: 199, Mismatches: 28, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
41 37 0.19
42 38 0.19
43 121 0.61
44 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCCGCTAAAT
Found at i:75001 original size:85 final size:83
Alignment explanation
Indices: 74838--75025 Score: 243
Period size: 85 Copynumber: 2.2 Consensus size: 83
74828 AAACATCATA
* * *
74838 ACCTATTGCGGCGTTTGTCTAAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAC
1 ACCTATTGCGGCGTTTTTCTAAAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTCAAC
*
74903 AAACGCCTCTAAATATCAAC
66 AAACG-C-ATAAATATCAAC
* * *
74923 ACCTATTGCGGCATTTTTCTGACAAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTCACA
1 ACCTATTGCGGCGTTTTTCTAAAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTCA-A
*
74988 CAATACTG-ATAAATATCAAT
65 CAA-AC-GCATAAATATCAAC
*
75008 ACCTATTGCAGCGTTTTT
1 ACCTATTGCGGCGTTTTT
75026 TGTTTAAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
85 83 0.92
86 4 0.04
87 2 0.02
88 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (83 bp):
ACCTATTGCGGCGTTTTTCTAAAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTCAAC
AAACGCATAAATATCAAC
Found at i:76094 original size:17 final size:17
Alignment explanation
Indices: 76072--76107 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
76062 AATTAAGAGT
76072 TAATTTAATAAATGAAC
1 TAATTTAATAAATGAAC
* *
76089 TAATTTAATTATTGAAC
1 TAATTTAATAAATGAAC
76106 TA
1 TA
76108 CTTCCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TAATTTAATAAATGAAC
Found at i:82432 original size:17 final size:17
Alignment explanation
Indices: 82410--82443 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
82400 TAAGAGTTAA
82410 TTTAATAAACGAACTAG
1 TTTAATAAACGAACTAG
* *
82427 TTTAATTAATGAACTAG
1 TTTAATAAACGAACTAG
82444 ATGATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTAATAAACGAACTAG
Found at i:84561 original size:19 final size:19
Alignment explanation
Indices: 84537--84586 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
84527 GAATGCAATT
84537 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
84556 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
84575 AGTGCATCGATG
1 AGTGCATCGATG
84587 TACCTGCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:85408 original size:30 final size:30
Alignment explanation
Indices: 85372--85461 Score: 162
Period size: 30 Copynumber: 3.0 Consensus size: 30
85362 TATGGACAAT
85372 TTATCGAGGATCTTTATGACCTCTGGATAG
1 TTATCGAGGATCTTTATGACCTCTGGATAG
*
85402 TTATCGAGGATCTTTATGACCTCTGAATAG
1 TTATCGAGGATCTTTATGACCTCTGGATAG
*
85432 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTATCGAGGATCTTTATGACCTCTGGATAG
85462 GTCCTTTGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (30 bp):
TTATCGAGGATCTTTATGACCTCTGGATAG
Found at i:85962 original size:18 final size:18
Alignment explanation
Indices: 85939--85975 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
85929 ATGTCTTTTG
85939 TCGTGTATAGTGTTGGCA
1 TCGTGTATAGTGTTGGCA
85957 TCGTGTATAGTGTTGGCA
1 TCGTGTATAGTGTTGGCA
85975 T
1 T
85976 GTAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (18 bp):
TCGTGTATAGTGTTGGCA
Found at i:88016 original size:21 final size:21
Alignment explanation
Indices: 87975--88016 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
87965 TTTATTATAA
* *
87975 TTATATTTTTATTTGTATTTT
1 TTATATTTTTAGTTATATTTT
*
87996 TTATATTTTT-GTTATAGTTT
1 TTATATTTTTAGTTATATTTT
88016 T
1 T
88017 AATTGATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (21 bp):
TTATATTTTTAGTTATATTTT
Found at i:88208 original size:20 final size:21
Alignment explanation
Indices: 88175--88217 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
88165 GGCTTTTTAT
88175 TCTTTTTTCATTCCTTTATTC
1 TCTTTTTTCATTCCTTTATTC
88196 TCTTTTTTC-TTCCTTTATTC
1 TCTTTTTTCATTCCTTTATTC
88216 TC
1 TC
88218 ATCATCACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTTTTTCATTCCTTTATTC
Found at i:93074 original size:24 final size:24
Alignment explanation
Indices: 93047--93100 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
93037 ATATATATAT
* *
93047 AATATAGTTTTTGAAAATATTTAA
1 AATATAATTTTTGAAAACATTTAA
*
93071 AATATAATTTTTGAAAACATTTTA
1 AATATAATTTTTGAAAACATTTAA
93095 AATATA
1 AATATA
93101 TATATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
AATATAATTTTTGAAAACATTTAA
Found at i:93112 original size:37 final size:37
Alignment explanation
Indices: 93055--93257 Score: 247
Period size: 37 Copynumber: 5.5 Consensus size: 37
93045 ATAATATAGT
*
93055 TTTTGAAAATAT-T-TAAAATATA-ATTTTTGAAAACA
1 TTTT-AAAATATATATATAATATATATTTTTGAAAACA
* *
93090 TTTTAAATATATATATATAATATATAATTTTAAAAACA
1 TTTTAAA-ATATATATATAATATATATTTTTGAAAACA
* *
93128 TTTTGAAA-ATATATGTAATATATAGTTTTTGAAAACA
1 TTTTAAAATATATATATAATATATA-TTTTTGAAAACA
93165 TTTTAAAA-ATATATATAATATATAGTTTTTGAAAACA
1 TTTTAAAATATATATATAATATATA-TTTTTGAAAACA
* *
93202 TTTTAAAA-ATATATATAATATATAGTTTTGAAAGCA
1 TTTTAAAATATATATATAATATATATTTTTGAAAACA
93238 TTTTGAAAATATATAGTATA
1 TTTT-AAAATATATA-TATA
93258 TAGTTTTAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
34 3 0.02
35 8 0.05
36 30 0.20
37 82 0.55
38 22 0.15
39 4 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTTAAAATATATATATAATATATATTTTTGAAAACA
Found at i:93148 original size:73 final size:75
Alignment explanation
Indices: 93055--93259 Score: 274
Period size: 73 Copynumber: 2.7 Consensus size: 75
93045 ATAATATAGT
* *
93055 TTTTGAAAATATTTAAAATATA-ATTTTTGAAAACATTTTAAATATATATATATAATATATA-AT
1 TTTTGAAAATATATATAATATATATTTTTGAAAACATTTTAAATATATATATATAATATATAGAT
93118 TTTAAAAACA
66 TTTAAAAACA
* *
93128 TTTTGAAAATATATGTAATATATAGTTTTTGAAAACATTTTAAA-A-ATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATA-TTTTTGAAAACATTTTAAATATATATATATAATATATAGA
*
93191 TTTTGAAAACA
65 TTTTAAAAACA
* * *
93202 TTTTAAAAATATATATAATATATAGTTTTGAAAGCATTTTGAAAATATATAGTATATA
1 TTTTGAAAATATATATAATATATATTTTTGAAAACATTTT--AAATATATA-TATATA
93260 GTTTTAAAAA
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
73 49 0.43
74 34 0.30
75 22 0.19
76 1 0.01
77 3 0.03
78 6 0.05
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (75 bp):
TTTTGAAAATATATATAATATATATTTTTGAAAACATTTTAAATATATATATATAATATATAGAT
TTTAAAAACA
Found at i:93332 original size:2 final size:2
Alignment explanation
Indices: 93320--93348 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
93310 GTTTTGAAAC
93320 AT AT A- 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
93349 TTATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106397 original size:64 final size:64
Alignment explanation
Indices: 106344--106506 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
106334 CGGTGCACCA
*
106344 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
106408 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
106473 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
106507 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:106478 original size:19 final size:19
Alignment explanation
Indices: 106454--106504 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
106444 GAAAATATTC
106454 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
106473 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
106492 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
106505 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:106546 original size:65 final size:65
Alignment explanation
Indices: 106348--106555 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
106338 GCACCAAGTG
* * ** *
106348 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
106411 G-
64 GA
* * *
106412 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
106475 A
65 A
* *
106476 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
106538 CTGA
62 CTGA
106542 TGCATCGGTGCATG
1 TGCATCGGTGCATG
106556 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:112234 original size:22 final size:21
Alignment explanation
Indices: 112192--112231 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
112182 GAGTTTGTTT
*
112192 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
112213 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
112232 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:114228 original size:64 final size:64
Alignment explanation
Indices: 114175--114337 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
114165 CGGTGCACCA
*
114175 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
114239 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCACCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
114304 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
114338 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 39 0.46
65 45 0.54
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:114309 original size:19 final size:19
Alignment explanation
Indices: 114285--114323 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
114275 GAAAATATTC
114285 AGAGTGCACCGATGCATGG
1 AGAGTGCACCGATGCATGG
* *
114304 AGAGTGCATCGGTGCATGG
1 AGAGTGCACCGATGCATGG
114323 A
1 A
114324 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (19 bp):
AGAGTGCACCGATGCATGG
Found at i:114377 original size:65 final size:65
Alignment explanation
Indices: 114179--114386 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
114169 GCACCAAGTG
* * ** *
114179 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
114242 G-
64 GA
* * * *
114243 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCACCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
114306 A
65 A
* *
114307 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
114369 CTGA
62 CTGA
114373 TGCATCGGTGCATG
1 TGCATCGGTGCATG
114387 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 50 0.41
65 59 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:122934 original size:30 final size:30
Alignment explanation
Indices: 122876--122956 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
122866 AAAAGAATTG
* *
122876 AATAC-TTTAGGTACTTATTTTGATCAAAA
1 AATACTTTTAGGTACTTATTTCGACCAAAA
* *
122905 AATACTTTTAAGTACCTATTTCGACCAAAA
1 AATACTTTTAGGTACTTATTTCGACCAAAA
*
122935 AGATAATTTTAGGTACTTATTT
1 A-ATACTTTTAGGTACTTATTT
122957 TAATTAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.12
30 21 0.49
31 17 0.40
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (30 bp):
AATACTTTTAGGTACTTATTTCGACCAAAA
Found at i:122966 original size:31 final size:30
Alignment explanation
Indices: 122881--122967 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 30
122871 AATTGAATAC
*
122881 TTTAGGTACTTATTTTGATCAAAAAATACT
1 TTTAGGTACTTATTTTGATCAAAAAATAAT
* * * *
122911 TTTAAGTACCTATTTCGACCAAAAAGATAAT
1 TTTAGGTACTTATTTTGATCAAAAA-ATAAT
* *
122942 TTTAGGTACTTATTTTAATTAAAAAA
1 TTTAGGTACTTATTTTGATCAAAAAA
122968 ATACTTTAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (30 bp):
TTTAGGTACTTATTTTGATCAAAAAATAAT
Found at i:124330 original size:48 final size:48
Alignment explanation
Indices: 124275--124372 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
124265 ATGAGGCAAA
124275 TATAACCAATGAAAAATTCATCCAACTATGACCATAGCTCCAAATGGT
1 TATAACCAATGAAAAATTCATCCAACTATGACCATAGCTCCAAATGGT
124323 TATAACCAATGAAAAATTCATCCAACTATGACCATAGCTCCAAATGGT
1 TATAACCAATGAAAAATTCATCCAACTATGACCATAGCTCCAAATGGT
124371 TA
1 TA
124373 ACACAACCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (48 bp):
TATAACCAATGAAAAATTCATCCAACTATGACCATAGCTCCAAATGGT
Found at i:124846 original size:9 final size:9
Alignment explanation
Indices: 124815--124923 Score: 61
Period size: 9 Copynumber: 12.3 Consensus size: 9
124805 ATGTTAGAAG
124815 GAAAA-AAA
1 GAAAATAAA
*
124823 TGAAAATGAA
1 -GAAAATAAA
*
124833 TAAAATAAA
1 GAAAATAAA
124842 GAAAATAAA
1 GAAAATAAA
*
124851 GTAAAGTAAA
1 G-AAAATAAA
124861 -AGAAAT-AA
1 GA-AAATAAA
*
124869 -AAAGTAAA
1 GAAAATAAA
*
124877 -TAAA-AAA
1 GAAAATAAA
*
124884 GTAAATAAA
1 GAAAATAAA
*
124893 -ATAGATAAA
1 GA-AAATAAA
124902 GTAAAATAAA
1 G-AAAATAAA
124912 GAAAATAAA
1 GAAAATAAA
124921 GAA
1 GAA
124924 TTCAAAAAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
7 6 0.08
8 12 0.15
9 44 0.56
10 16 0.20
11 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (9 bp):
GAAAATAAA
Found at i:124864 original size:20 final size:20
Alignment explanation
Indices: 124835--124980 Score: 67
Period size: 20 Copynumber: 7.2 Consensus size: 20
124825 AAAATGAATA
*
124835 AAAT-AAAGAAA-ATAAAGT
1 AAATAAAAGAAATAAAAAGT
124853 AAAGTAAAAGAAATAAAAAGT
1 AAA-TAAAAGAAATAAAAAGT
124874 AAATAAAAAAGTAAAT-AAAA-T
1 AAAT--AAAAG-AAATAAAAAGT
* * *
124895 AGAT-AAAGTAAA-ATAAAGA
1 AAATAAAAG-AAATAAAAAGT
*
124914 AAAT-AAAGAATTCAAAAAGT
1 AAATAAAAGAAAT-AAAAAGT
* *
124934 AAAAATAAAG-AAGAAAAA-T
1 AAATA-AAAGAAATAAAAAGT
*
124953 AAATAAATAAGATAAAAAAAAGT
1 AAAT-AA-AAGA-AATAAAAAGT
124976 AAATA
1 AAATA
124981 CAATAATGAC
Statistics
Matches: 98, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
18 16 0.16
19 13 0.13
20 25 0.26
21 14 0.14
22 21 0.21
23 9 0.09
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (20 bp):
AAATAAAAGAAATAAAAAGT
Found at i:124882 original size:60 final size:60
Alignment explanation
Indices: 124837--124978 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
124827 AATGAATAAA
* *
124837 ATAAAG-AAAATAAAGTAAAGTAAAAGAAAT-AAAAAGTAAATAAAAAAGTAAATAAAATAG
1 ATAAAGTAAAATAAAG-AAAAT-AAAGAAATCAAAAAGTAAATAAAAAAGAAAATAAAATAG
* * * *
124897 ATAAAGTAAAATAAAGAAAATAAAGAATTCAAAAAGTAAA-AATAAAGAAGA-AAAATAA
1 ATAAAGTAAAATAAAGAAAATAAAGAAATCAAAAAGTAAATAAAAAAGAAAATAAAATAG
* *
124955 ATAAA-TAAGATAAAAAAAAGTAAA
1 ATAAAGTAAAATAAAGAAAA-TAAA
124979 TACAATAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
57 12 0.17
58 15 0.21
59 15 0.21
60 20 0.28
61 9 0.13
ACGTcount: A:0.73, C:0.01, G:0.11, T:0.16
Consensus pattern (60 bp):
ATAAAGTAAAATAAAGAAAATAAAGAAATCAAAAAGTAAATAAAAAAGAAAATAAAATAG
Found at i:124884 original size:12 final size:12
Alignment explanation
Indices: 124858--124907 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
124848 AAAGTAAAGT
124858 AAAAG-AAAT-A
1 AAAAGTAAATAA
124868 AAAAGTAAATAA
1 AAAAGTAAATAA
124880 AAAAGTAAATAA
1 AAAAGTAAATAA
*
124892 AATAGATAAAGTAA
1 AAAAG-TAAA-TAA
124906 AA
1 AA
124908 TAAAGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 17 0.49
13 4 0.11
14 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAAAGTAAATAA
Found at i:124939 original size:31 final size:30
Alignment explanation
Indices: 124843--124980 Score: 90
Period size: 31 Copynumber: 4.5 Consensus size: 30
124833 TAAAATAAAG
* *
124843 AAAATAAAGTAAAGTAAAAGAAATAAAAAGTA
1 AAAATAAAG-AAAAT-AAAGAATTAAAAAGTA
* *
124875 AATAAAAAAGTAAAT-AA-AA-TAGATAAAGT-
1 AA-AATAAAGAAAATAAAGAATTA-A-AAAGTA
124904 AAAATAAAGAAAATAAAGAATTCAAAAAGTA
1 AAAATAAAGAAAATAAAGAATT-AAAAAGTA
* *
124935 AAAATAAAGAAGAA-AAATAAATAAATAAGATA
1 AAAATAAAGAA-AATAAAGAATTAAA-AAG-TA
*
124967 AAAA-AAAGTAAATA
1 AAAATAAAGAAAATA
124981 CAATAATGAC
Statistics
Matches: 86, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
28 12 0.14
29 7 0.08
30 19 0.22
31 28 0.33
32 14 0.16
33 6 0.07
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (30 bp):
AAAATAAAGAAAATAAAGAATTAAAAAGTA
Found at i:124958 original size:17 final size:18
Alignment explanation
Indices: 124844--124969 Score: 54
Period size: 19 Copynumber: 6.9 Consensus size: 18
124834 AAAATAAAGA
*
124844 AAATAAAGTAA-AGTAAAAG
1 AAATAAAG-AAGA-TAAAAT
124863 AAATAAA-AAG-T-AAAT
1 AAATAAAGAAGATAAAAT
124878 AAA-AAAGTAA-ATAAAAT
1 AAATAAAG-AAGATAAAAT
* *
124895 AGATAAAGTAAAATAAAGA-
1 AAATAAAG-AAGATAAA-AT
*
124914 AAATAAAGAA-TTCAAAAAGT
1 AAATAAAGAAGAT--AAAA-T
124934 AAAAATAAAGAAGA-AAAAT
1 --AAATAAAGAAGATAAAAT
*
124953 AAATAAATAAGATAAAA
1 AAATAAAGAAGATAAAA
124970 AAAAGTAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 33
0.69 0.05 0.27
Matches are distributed among these distances:
14 3 0.04
15 6 0.07
16 4 0.05
17 20 0.24
18 14 0.16
19 23 0.27
20 5 0.06
22 10 0.12
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (18 bp):
AAATAAAGAAGATAAAAT
Found at i:125038 original size:21 final size:20
Alignment explanation
Indices: 125013--125071 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
125003 TAAATTCGGG
125013 ATAAAAATAAATAAAAAAAA
1 ATAAAAATAAATAAAAAAAA
*
125033 ATTAAAATTAAA-AATTAAAAAA
1 A-TAAAAATAAATAA--AAAAAA
125055 ATAAGAAAGTAAATAAA
1 ATAA-AAA-TAAATAAA
125072 TAAATGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
20 3 0.10
21 12 0.39
22 10 0.32
23 4 0.13
24 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (20 bp):
ATAAAAATAAATAAAAAAAA
Found at i:125320 original size:3 final size:3
Alignment explanation
Indices: 125307--125348 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
125297 AATATAATTA
125307 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
125349 GGGTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:126186 original size:9 final size:9
Alignment explanation
Indices: 126165--126321 Score: 89
Period size: 9 Copynumber: 17.8 Consensus size: 9
126155 AGTTAGAAGG
126165 AAAA-AAAT
1 AAAATAAAT
*
126173 GAAAATGAAT
1 -AAAATAAAT
*
126183 AAAATAAAG
1 AAAATAAAT
126192 AAAATAAAT
1 AAAATAAAT
*
126201 -AAACAAAT
1 AAAATAAAT
126209 -AAATAAAGT
1 AAAATAAA-T
*
126218 AAAAGAAAT
1 AAAATAAAT
*
126227 AAAA-AAGT
1 AAAATAAAT
126235 -AAATAAAGT
1 AAAATAAA-T
126244 -AAATAAA-
1 AAAATAAAT
*
126251 ATAGATAAAGT
1 A-AAATAAA-T
*
126262 AAAATAAAG
1 AAAATAAAT
*
126271 AAAATAAAG
1 AAAATAAAT
126280 AAGAA-AAAT
1 AA-AATAAAT
126289 -AAATAAAT
1 AAAATAAAT
* *
126297 AAGATAAAG
1 AAAATAAAT
*
126306 AAAGTAAAT
1 AAAATAAAT
*
126315 ACAATAA
1 AAAATAA
126322 TGACAACATA
Statistics
Matches: 116, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.04
8 23 0.20
9 70 0.60
10 17 0.15
11 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:126202 original size:4 final size:4
Alignment explanation
Indices: 126193--126321 Score: 80
Period size: 4 Copynumber: 29.5 Consensus size: 4
126183 AAAATAAAGA
* *
126193 AAAT AAAT AAAC AAAT AAAT AAAGT AAAAG AAAT AAA- AAAGT AAAT AAAGT
1 AAAT AAAT AAAT AAAT AAAT AAA-T -AAAT AAAT AAAT AAA-T AAAT AAA-T
* * * *
126244 AAAT AAAAT AGAT AAAGT AAAAT AAAGA AAAT AAAG AAGAA AAAT AAAT
1 AAAT -AAAT AAAT AAA-T -AAAT AAA-T AAAT AAAT AA-AT AAAT AAAT
*
126293 AAAT AAGAT AAAG AAAGT AAAT ACAAT AA
1 AAAT AA-AT AAAT AAA-T AAAT A-AAT AA
126322 TGACAACATA
Statistics
Matches: 99, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
3 3 0.03
4 59 0.60
5 31 0.31
6 6 0.06
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:126314 original size:26 final size:27
Alignment explanation
Indices: 126184--126315 Score: 113
Period size: 26 Copynumber: 5.2 Consensus size: 27
126174 AAAATGAATA
* *
126184 AAATAAAGAAAAT-AAATAAACAAA-T
1 AAATAAAGTAAATAAAATAAAGAAAGT
126209 AAATAAAGTAAA-AGAAATAAA-AAAGT
1 AAATAAAGTAAATA-AAATAAAGAAAGT
* *
126235 AAATAAAGTAAATAAAATAGATAAAGT
1 AAATAAAGTAAATAAAATAAAGAAAGT
* *
126262 --A-AAA-TAAAGAAAATAAAG-AAGAA
1 AAATAAAGTAAATAAAATAAAGAAAG-T
*
126285 AAATAAA-TAAATAAGATAAAGAAAGT
1 AAATAAAGTAAATAAAATAAAGAAAGT
126311 AAATA
1 AAATA
126316 CAATAATGAC
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.03
23 11 0.12
24 3 0.03
25 16 0.18
26 46 0.52
27 9 0.10
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.17
Consensus pattern (27 bp):
AAATAAAGTAAATAAAATAAAGAAAGT
Found at i:139810 original size:3 final size:3
Alignment explanation
Indices: 139790--139847 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
139780 GGGCCCGCAA
* *
139790 AAT AAT ATAT AA- ATT AAT AAT AAT AAT AGT AAT AAT AAT -AT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
139834 AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
139848 TTTTTGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
2 7 0.15
3 36 0.78
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:139834 original size:8 final size:8
Alignment explanation
Indices: 139790--139842 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
139780 GGGCCCGCAA
139790 AATAATAT
1 AATAATAT
139798 -ATAA-ATT
1 AATAATA-T
139805 AATAATAAT
1 AATAAT-AT
*
139814 AATAGTAAT
1 AATAAT-AT
139823 AATAATAT
1 AATAATAT
139831 AATAATAT
1 AATAATAT
139839 AATA
1 AATA
139843 TAATATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.03
7 5 0.13
8 18 0.46
9 14 0.36
10 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
AATAATAT
Found at i:144968 original size:17 final size:18
Alignment explanation
Indices: 144930--144970 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
144920 TATGAACATC
*
144930 AAATAAATTAATCAAAAA
1 AAATAAAATAATCAAAAA
*
144948 AAATAAAATAA-CAATAA
1 AAATAAAATAATCAAAAA
144965 AAATAA
1 AAATAA
144971 TTTCTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAAATAATCAAAAA
Found at i:146568 original size:25 final size:25
Alignment explanation
Indices: 146534--146608 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
146524 GAGTAGGGGA
* *
146534 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
146559 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
146584 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
146609 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:146719 original size:3 final size:3
Alignment explanation
Indices: 146713--146759 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
146703 AAAAAAAATG
146713 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
146757 TAA
1 TAA
146760 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:146758 original size:13 final size:14
Alignment explanation
Indices: 146713--146767 Score: 69
Period size: 13 Copynumber: 4.0 Consensus size: 14
146703 AAAAAAAATG
146713 TAATAATAATAATAA
1 TAATAATAA-AATAA
*
146728 TAATAAT-AATTAA
1 TAATAATAAAATAA
146741 TAATAATAAAATAA
1 TAATAATAAAATAA
*
146755 -AATAAAAAAATAA
1 TAATAATAAAATAA
146768 ATATAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 23 0.64
14 6 0.17
15 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:146768 original size:13 final size:13
Alignment explanation
Indices: 146742--146775 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
146732 AATAATTAAT
*
146742 AATAATAAAATAA
1 AATAAAAAAATAA
146755 AATAAAAAAATAA
1 AATAAAAAAATAA
146768 ATATAAAA
1 A-ATAAAA
146776 GACCCGGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:159937 original size:17 final size:17
Alignment explanation
Indices: 159915--159954 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
159905 ATAGAACATC
*
159915 AAATAAATTAATCAA-AA
1 AAATAAAATAA-CAATAA
159932 AAATAAAATAACAATAA
1 AAATAAAATAACAATAA
159949 AAATAA
1 AAATAA
159955 TTTCTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAAAATAACAATAA
Found at i:161539 original size:25 final size:25
Alignment explanation
Indices: 161505--161579 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
161495 GAGTAGGGGA
* *
161505 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
161530 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
161555 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
161580 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:161611 original size:22 final size:22
Alignment explanation
Indices: 161586--161656 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
161576 TGATGGGTTG
161586 TTGGGCTCCGGGATTGGGCCAA
1 TTGGGCTCCGGGATTGGGCCAA
*
161608 TTGGGCTTCGGG-TT--G----
1 TTGGGCTCCGGGATTGGGCCAA
161623 TTGGGCTCCGGGATTGGGCCAA
1 TTGGGCTCCGGGATTGGGCCAA
*
161645 TTGGGCTTCGGG
1 TTGGGCTCCGGG
161657 TTGTTGGGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
18 1 0.03
19 1 0.03
21 2 0.05
22 22 0.56
ACGTcount: A:0.08, C:0.20, G:0.44, T:0.28
Consensus pattern (22 bp):
TTGGGCTCCGGGATTGGGCCAA
Found at i:161630 original size:37 final size:37
Alignment explanation
Indices: 161580--161679 Score: 200
Period size: 37 Copynumber: 2.7 Consensus size: 37
161570 CTAATCTGAT
161580 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
161617 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
161654 GGGTTGTTGGGCTCCGGGATTGGGCC
1 GGGTTGTTGGGCTCCGGGATTGGGCC
161680 TTTGTAATCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.07, C:0.19, G:0.45, T:0.29
Consensus pattern (37 bp):
GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
Found at i:161726 original size:3 final size:3
Alignment explanation
Indices: 161720--161762 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
161710 CAAAAAAATG
161720 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
161763 AAAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:161766 original size:12 final size:14
Alignment explanation
Indices: 161724--161770 Score: 69
Period size: 15 Copynumber: 3.4 Consensus size: 14
161714 AAAATGTAAT
161724 AATAATAATAATAA
1 AATAATAATAATAA
161738 TAATAATAATAATAA
1 -AATAATAATAATAA
*
161753 AATAA-AATAAAAA
1 AATAATAATAATAA
161766 AATAA
1 AATAA
161771 ATATAAAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
14 5 0.16
15 14 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:161857 original size:22 final size:20
Alignment explanation
Indices: 161814--161853 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
161804 CCATTAATTA
161814 AATATTTTATTAAAAATATT
1 AATATTTTATTAAAAATATT
161834 AATATTTT-TTATAAAATATT
1 AATATTTTATTA-AAAATATT
161854 TTAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTTATTAAAAATATT
Done.