Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000381.1 Hibiscus syriacus cultivar Beakdansim tig00000697_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: 81908
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2394 original size:2 final size:2
Alignment explanation
Indices: 2258--2374 Score: 216
Period size: 2 Copynumber: 58.0 Consensus size: 2
2248 CAGTCCTTGA
*
2258 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2301 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
2343 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
2375 TCATGGGTTA
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
2 110 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3047 original size:25 final size:25
Alignment explanation
Indices: 3019--3077 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
3009 ATTCTATCGT
3019 CAAGTTCAATAATTCCAGAGGCAAC
1 CAAGTTCAATAATTCCAGAGGCAAC
3044 CAAGTTCAATAATTCCAGAGGCAAC
1 CAAGTTCAATAATTCCAGAGGCAAC
3069 CAAGTTCAA
1 CAAGTTCAA
3078 GAGCTTCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (25 bp):
CAAGTTCAATAATTCCAGAGGCAAC
Found at i:4720 original size:22 final size:22
Alignment explanation
Indices: 4689--4743 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
4679 GCCTAAACTA
4689 TACATTTTTTGCTAAATAAGTTCC
1 TACA-TTTTTGCTAAAT-AGTTCC
* *
4713 TACTTTTTTTCTAAATAGTTCC
1 TACATTTTTGCTAAATAGTTCC
4735 TACATTTTT
1 TACATTTTT
4744 TTGATCCTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 14 0.50
23 11 0.39
24 3 0.11
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.53
Consensus pattern (22 bp):
TACATTTTTGCTAAATAGTTCC
Found at i:4744 original size:22 final size:24
Alignment explanation
Indices: 4689--4744 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
4679 GCCTAAACTA
4689 TACATTTTTTGCTAAATAAGTTCC
1 TACATTTTTTGCTAAATAAGTTCC
*
4713 TAC-TTTTTTTCTAAAT-AGTTCC
1 TACATTTTTTGCTAAATAAGTTCC
4735 TACATTTTTT
1 TACATTTTTT
4745 TGATCCTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.30
23 18 0.60
24 3 0.10
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (24 bp):
TACATTTTTTGCTAAATAAGTTCC
Found at i:17415 original size:39 final size:39
Alignment explanation
Indices: 17333--17523 Score: 105
Period size: 39 Copynumber: 4.9 Consensus size: 39
17323 GTACACCTAG
* * * * * *
17333 TAAGGGCTTACCCTATGCACAAAGAAGAGAAGCTTGTAC
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * **
17372 TAAGGTCTTATCATGTGCACAAAGCAGAGGAGCCTGTTG
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * * * *
17411 TAAGGACTTACCCTGAGCACAAAGCTGAGGAGTCTGCGA-
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTG-TAC
* * * * ** * ***
17450 TAAAGACTTGCCCTGAGCACAAAGTTGAAGAGCCTGCGG
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * * *
17489 TAAGGACTTACCCTGGGCACAAAGCCGAGAAGCCT
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCT
17524 ACGTGTTGAG
Statistics
Matches: 119, Mismatches: 31, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (39 bp):
TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
Found at i:19010 original size:23 final size:22
Alignment explanation
Indices: 18980--19023 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
18970 CAAATATATA
*
18980 TATTAAGTTCAATCATCCAAAG
1 TATTAAGTTCAAACATCCAAAG
*
19002 TATTCAAGTTTAAACATCCAAA
1 TATT-AAGTTCAAACATCCAAA
19024 AAACATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
TATTAAGTTCAAACATCCAAAG
Found at i:21089 original size:23 final size:22
Alignment explanation
Indices: 21020--21089 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
21010 GACGAGTTTG
21020 TCGATGCACATTCAAGGAATGCA
1 TCGATGCACATTCAAGG-ATGCA
* * * *
21043 TCGGTGTATC-TTCATGG-TGTA
1 TCGATGCA-CATTCAAGGATGCA
21064 TCGATGCACATTCAAGGCATGCA
1 TCGATGCACATTCAAGG-ATGCA
21087 TCG
1 TCG
21090 GTACACTGTC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
23 18 0.51
24 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
TCGATGCACATTCAAGGATGCA
Found at i:26889 original size:19 final size:19
Alignment explanation
Indices: 26865--26918 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
26855 ATAAGACTTA
26865 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
*
26884 GTGCATCAGTACACTAGGG
1 GTGCATCGGTACACTAGGG
26903 GTGCATCGGTACACTA
1 GTGCATCGGTACACTA
26919 ATTACATTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:38616 original size:23 final size:20
Alignment explanation
Indices: 38585--38631 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
38575 ATGTTTTGAG
38585 CCTTCATGGTAGTATCGGTACTA
1 CCTTCATGGTA-T-T-GGTACTA
*
38608 CCTTGATGGTATTGGTACTA
1 CCTTCATGGTATTGGTACTA
38628 CCTT
1 CCTT
38632 TGTCTAAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 1 0.04
23 10 0.43
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CCTTCATGGTATTGGTACTA
Found at i:39304 original size:14 final size:14
Alignment explanation
Indices: 39287--39313 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39277 AAATTTTCAG
39287 CAAAAACCTTTCTC
1 CAAAAACCTTTCTC
39301 CAAAAACCTTTCT
1 CAAAAACCTTTCT
39314 GAAACTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (14 bp):
CAAAAACCTTTCTC
Found at i:44684 original size:15 final size:16
Alignment explanation
Indices: 44653--44685 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44643 TCATTAAAAA
44653 ATAATTCTTTATAATT
1 ATAATTCTTTATAATT
*
44669 ATAATT-TTTATTATT
1 ATAATTCTTTATAATT
44684 AT
1 AT
44686 GTTTTAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAATTCTTTATAATT
Found at i:52677 original size:35 final size:35
Alignment explanation
Indices: 52631--52708 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
52621 CACATTCATT
*
52631 AATTACATTCTAAACCTCAAATTCTAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
52666 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
52701 AATTACAT
1 AATTACAT
52709 GCCCAACCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
AATTACATTCTAAACCTCAAATTCCAAAATACTTC
Found at i:52722 original size:35 final size:35
Alignment explanation
Indices: 52631--52724 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
52621 CACATTCATT
* * *
52631 AATTACATTCTAAACCTCAAATTCTAAAATACTTC
1 AATTACATGCCAAACCTCAAATTCCAAAATACTTC
* *
52666 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
1 AATTACATGCCAAACCTCAAATTCCAAAATACTTC
* *
52701 AATTACATGCCCAACCCCAAATTC
1 AATTACATGCCAAACCTCAAATTC
52725 ATAATATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.30
Consensus pattern (35 bp):
AATTACATGCCAAACCTCAAATTCCAAAATACTTC
Found at i:53481 original size:143 final size:142
Alignment explanation
Indices: 53202--53483 Score: 408
Period size: 148 Copynumber: 2.0 Consensus size: 142
53192 AAACTATTTA
*
53202 AATTAGAATCAAATAATATTATATTATAAATATTTATAATTAAATTTAAACAAAAACTCAAAAAT
1 AATTAGAATCAAATAATATTATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAAAAAT
53267 TCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAATCAACTATT
66 TCAATTCAA-T--ACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAATCAACTATT
53332 TTATAAACTAAACTG
128 TTATAAACTAAACTG
* * *
53347 AATTATAATCAAATAATAATATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAAT-AT-T-ATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAAA
* * * *
53412 AATTCAATTC-A-ACTTGATTTAAATTTTATAAGCTCAAATC-GAAAAAATTTCGAGTCAATTAT
63 AATTCAATTCAATACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTT-GAATCAACTAT
53474 TTTATAAACT
127 TTTATAAACT
53484 GAATTGAGTA
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
142 9 0.07
143 47 0.38
145 16 0.13
146 2 0.02
147 2 0.02
148 49 0.39
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (142 bp):
AATTAGAATCAAATAATATTATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAAAAAT
TCAATTCAATACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTTGAATCAACTATTTTA
TAAACTAAACTG
Found at i:53703 original size:35 final size:35
Alignment explanation
Indices: 53661--53740 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
53651 GGGGTTGGGC
* *
53661 ATATAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATATAATTGAAGAATTTTGGAATTTGAGGTTTAAA
* * *
53696 ATGTAATTAAAGAATTTTGGAATTTGGGGTTTAAA
1 ATATAATTGAAGAATTTTGGAATTTGAGGTTTAAA
53731 ATATAATTGA
1 ATATAATTGA
53741 TGACTGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (35 bp):
ATATAATTGAAGAATTTTGGAATTTGAGGTTTAAA
Found at i:54440 original size:64 final size:64
Alignment explanation
Indices: 54355--54495 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 64
54345 GAATAAATTG
* * *
54355 AACATCGAATGCATTATATGCATCGATGCACATA-CCATGCATCAATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATTATATGCATCGATACACA-AGACATGCATCAATGCACTCAGGCTATTT-TG
54418 AA
64 -A
*
54420 AACATCGAATGCATT-TATGCATCGATACACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTATATGCATCGATACACAAGACATGCATCAATGCACTCAGGCTATTTTGA
54483 AACATCGAATGCA
1 AACATCGAATGCA
54496 CTAAGGGTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
63 15 0.21
64 36 0.51
65 19 0.27
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTATATGCATCGATACACAAGACATGCATCAATGCACTCAGGCTATTTTGA
Found at i:59532 original size:44 final size:44
Alignment explanation
Indices: 59482--59579 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
59472 TTTGTGCTTA
* *
59482 ATGCATCGATACA-C-TGAACAGTGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATACACCATGAA-AGTGCATCAATGCA-CCCATTGAAT
* *
59526 ATGCATCGATACACCATGAAGGTGCATCAATGCACTCATTGAAT
1 ATGCATCGATACACCATGAAAGTGCATCAATGCACCCATTGAAT
*
59570 GTGCATCGAT
1 ATGCATCGAT
59580 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 30 0.64
45 13 0.28
46 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCATCGATACACCATGAAAGTGCATCAATGCACCCATTGAAT
Found at i:59573 original size:23 final size:22
Alignment explanation
Indices: 59502--59583 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
59492 ACACTGAACA
*
59502 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA--CCATTGAAT
* * *
59526 ATGCATCGATACACCA-TGAAG
1 GTGCATCGATGCACCATTGAAT
*
59547 GTGCATCAATGCACTCATTGAAT
1 GTGCATCGATGCAC-CATTGAAT
59570 GTGCATCGATGCAC
1 GTGCATCGATGCAC
59584 AAGGCCATGC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 4 0.09
23 17 0.36
24 11 0.23
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACCATTGAAT
Found at i:62346 original size:65 final size:63
Alignment explanation
Indices: 62277--62436 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
62267 GGATAAATTG
* * * *
62277 AACATCGAATGCATTATATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGACATGCATCGATACACTAAGGCTATTT-TG
62340 AA
63 -A
62342 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATACACTAAGGCTATTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGACATGCATCGATACACTAAGGCTATTTTGA
* ** *
62406 AACATCAAATGCACTCCATGCATCGACGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
62437 TAAGGGTCCA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 28 0.34
65 51 0.61
66 4 0.05
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGACATGCATCGATACACTAAGGCTATTTTGA
Found at i:62909 original size:17 final size:17
Alignment explanation
Indices: 62889--62927 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
62879 TGCATAAATT
62889 TAAT-TTATAATAATAAA
1 TAATATTATAA-AATAAA
*
62906 TAATATTATAACATAAA
1 TAATATTATAAAATAAA
62923 TAATA
1 TAATA
62928 AAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATTATAAAATAAA
Found at i:64718 original size:25 final size:26
Alignment explanation
Indices: 64690--64740 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
64680 ATTTTATACT
*
64690 AGGA-GCAAACTTTTAAAACTTTAGA
1 AGGAGGCAAACTTATAAAACTTTAGA
*
64715 AGGAGGCAAACTTATAAAATTTTAGA
1 AGGAGGCAAACTTATAAAACTTTAGA
64741 GGGATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (26 bp):
AGGAGGCAAACTTATAAAACTTTAGA
Found at i:64971 original size:2 final size:2
Alignment explanation
Indices: 64964--64990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64954 AAGACAACTA
64964 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
64991 AAATTCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66910 original size:33 final size:34
Alignment explanation
Indices: 66839--66922 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 34
66829 CGAGGGTTTG
*
66839 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTT
*
66874 GTGTTTCAAGAGAAATAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
66907 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
66923 TGTATTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 21 0.46
35 25 0.54
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:66989 original size:36 final size:37
Alignment explanation
Indices: 66940--67009 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
66930 AAAGATTGAA
*
66940 GTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTT
66976 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAA
67010 CTTCCAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 27 0.84
37 5 0.16
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (37 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTT
Found at i:67022 original size:34 final size:35
Alignment explanation
Indices: 66949--67038 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 35
66939 AGTTTCAAGG
* * *
66949 GAAACTGTCTCAAGAGAGA-AAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAAA--TCTTCCAAAA
66985 GAAACTGTCTCAAGAGAGACAAAAA-CTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAAATCTTCCAAAA
* *
67019 GAAATTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
67039 GAGATTTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 24 0.50
36 19 0.40
37 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAAATCTTCCAAAA
Found at i:67105 original size:30 final size:30
Alignment explanation
Indices: 67064--67121 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
67054 TAAAACATAC
*
67064 TCAAAGATTATGTTTCAA-AGGAAACTGTTT
1 TCAAAGATTATGCTTCAAGA-GAAACTGTTT
*
67094 TCAAAGTTTATGCTTCAAGAGAAACTGT
1 TCAAAGATTATGCTTCAAGAGAAACTGT
67122 CTCAAGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (30 bp):
TCAAAGATTATGCTTCAAGAGAAACTGTTT
Found at i:67154 original size:36 final size:36
Alignment explanation
Indices: 67107--67189 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
67097 AAGTTTATGC
* * * **
67107 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
* *
67143 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
67179 TTCAAGGGAAA
1 TTCAAGGGAAA
67190 TGTTTTCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:67278 original size:102 final size:101
Alignment explanation
Indices: 67076--67458 Score: 444
Period size: 102 Copynumber: 3.8 Consensus size: 101
67066 AAAGATTATG
* * * *
67076 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
67141 GTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * *
67178 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTT
1 TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTT
* *
67243 GTTTCAAGGGAACCTATCTCAAGAGAGACTAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * * *
67280 TCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTTAAAAGAGACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTT
* ** * * * * **
67345 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTG
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
**** *
67382 TTTCAAGGGAAAAAAATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTC
1 TTTCAAGGGAAATGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
67446 ATTTCAAGGGAAA
65 GTTTCAAGGGAAA
67459 TGTTTTCAAT
Statistics
Matches: 240, Mismatches: 39, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
101 56 0.23
102 181 0.75
103 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:67411 original size:167 final size:164
Alignment explanation
Indices: 67238--67743 Score: 723
Period size: 167 Copynumber: 3.1 Consensus size: 164
67228 GGGAGAAAAA
* * * *
67238 ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACTAAATTCATCTCAAGGGAAATGTTTTCAATG
1 ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
67303 TTTATGTTTCAAGAGAAACTATCTTAAAAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAG
66 TTTATGTTTCAAGAGAAACT-TC-T-AAAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAG
*
67368 GGAGACGAAATTTGTTTCAAGGGAAAAAAATTCAAAG
128 GGAGACGAAATTTGTTTCAAGGGAAAAAGATTCAAAG
67405 ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
1 ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
67470 TTTATGTTTC-A-AG----------AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
66 TTTATGTTTCAAGAGAAACTTCTAAAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
*
67523 GACGAAATTTGTTTCAAGGGAAACAGATTCAAAG
131 GACGAAATTTGTTTCAAGGGAAAAAGATTCAAAG
*
67557 ATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
1 ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
* * *
67622 TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAACAGAAAATGTCTCAAG
66 TTTATGTTTCAAGAGAAACT-TCT-AA-AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAG
* * * *
67687 GGAGACGAAATTAGTTTCAA-TGAAAACAGATTTAAAT
128 GGAGACGAAATTTGTTTCAAGGGAAAA-AGATTCAAAG
*
67724 ATTTTGTTTTAAGAGAAACT
1 ATTTTGTTTCAAGAGAAACT
67744 TGGAAACTGT
Statistics
Matches: 306, Mismatches: 17, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
152 146 0.48
153 1 0.00
154 2 0.01
165 2 0.01
166 5 0.02
167 150 0.49
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (164 bp):
ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG
TTTATGTTTCAAGAGAAACTTCTAAAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
GACGAAATTTGTTTCAAGGGAAAAAGATTCAAAG
Found at i:67467 original size:65 final size:65
Alignment explanation
Indices: 67361--67485 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 65
67351 AAAGAAAATG
* * **
67361 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAAAAAATTCAAAGATTT-TGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAAAATTCAAAG-TTTATGTTTCAAGAGAAACT
67425 A
65 A
**** *
67426 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAAAATTCAAAGTTTATGTTTCAAGAGA
67486 GACAAAACTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 3 0.06
65 47 0.94
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAAAATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:67537 original size:152 final size:152
Alignment explanation
Indices: 67331--67637 Score: 587
Period size: 152 Copynumber: 2.0 Consensus size: 152
67321 CTATCTTAAA
67331 AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAAAA
1 AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAAAA
*
67396 AATTCAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG
66 AATTCAAAGATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG
67461 TTTTCAATGTTTATGTTTCAAG
131 TTTTCAATGTTTATGTTTCAAG
*
67483 AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACA
1 AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAAAA
*
67548 GATTCAAAGATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG
66 AATTCAAAGATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG
67613 TTTTCAATGTTTATGTTTCAAG
131 TTTTCAATGTTTATGTTTCAAG
67635 AGA
1 AGA
67638 AACTGTCTCA
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (152 bp):
AGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAAAA
AATTCAAAGATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG
TTTTCAATGTTTATGTTTCAAG
Found at i:67582 original size:65 final size:65
Alignment explanation
Indices: 67513--67663 Score: 189
Period size: 65 Copynumber: 2.3 Consensus size: 65
67503 AAAGAAAATG
* *
67513 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATTT-TATTTCAAGAGAAAC
1 TCTCAAGGGAGACAAAATTTATTTCAAGGGAAA-AGTATTCAAAG-TTTATATTTCAAGAGAAAC
67576 TA
64 TA
* * * * * * *
67578 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTG
1 TCTCAAGGGAGACAAAATTTATTTCAAGGGAAAAGTATTCAAAGTTTATATTTCAAGAGAAACTA
67643 TCTCAAGGGAGACAAAATTTA
1 TCTCAAGGGAGACAAAATTTA
67664 GTTCCAACAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 4 0.05
65 69 0.95
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (65 bp):
TCTCAAGGGAGACAAAATTTATTTCAAGGGAAAAGTATTCAAAGTTTATATTTCAAGAGAAACTA
Found at i:68083 original size:106 final size:106
Alignment explanation
Indices: 67891--68213 Score: 457
Period size: 106 Copynumber: 3.0 Consensus size: 106
67881 TGTATTGTTC
* * * * * **
67891 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
67956 GCCAGCCGGCCCTTTGTTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
67997 CGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
68062 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
68103 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGATA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
68168 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTTTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
68209 CGAGT
1 CGAGT
68214 GGCACAATAT
Statistics
Matches: 192, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 192 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:68844 original size:32 final size:32
Alignment explanation
Indices: 68808--68902 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
68798 ATTCCCAAAG
* *
68808 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
68840 ATGCCCCAACATTTGATGTTAAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
*
68872 ATGCCACAACATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
68903 GATGCCCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 51 0.93
33 4 0.07
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:68908 original size:32 final size:32
Alignment explanation
Indices: 68803--68909 Score: 126
Period size: 32 Copynumber: 3.3 Consensus size: 32
68793 TTTGAATTCC
* * *
68803 CAAAGATGCCCCAATATTCGATGTTGAATC-T
1 CAAAAATGCCCCAACATTTGATGTTGAATCTT
* *
68834 CAAAAAATGCCCCAACATTTGATGTTAAATCTA
1 C-AAAAATGCCCCAACATTTGATGTTGAATCTT
* *
68867 AAAAAATGCCACAACATTTGATGTTGAATCTT
1 CAAAAATGCCCCAACATTTGATGTTGAATCTT
*
68899 CAAAGATGCCC
1 CAAAAATGCCC
68910 TCATTGTTCC
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 61 0.98
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (32 bp):
CAAAAATGCCCCAACATTTGATGTTGAATCTT
Found at i:72085 original size:69 final size:69
Alignment explanation
Indices: 71969--72106 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
71959 TGTCTCTCTC
**
71969 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
72034 TCAT
66 TCAT
72038 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
72103 TCAT
66 TCAT
72107 AGTTTGAATC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:72210 original size:13 final size:12
Alignment explanation
Indices: 72189--72234 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 12
72179 TGTTCCTTTG
72189 TTTTTTTTTCTC
1 TTTTTTTTTCTC
72201 TTTTTATTTTCTC
1 TTTTT-TTTTCTC
72214 TTTGCTTTTTCTCTC
1 TTT--TTTTT-TCTC
72229 TTTTTT
1 TTTTTT
72235 CTTTTTGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.17
13 13 0.43
14 3 0.10
15 9 0.30
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:72971 original size:23 final size:22
Alignment explanation
Indices: 72945--73008 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
72935 CAGCTCATAT
72945 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
72968 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
72991 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
73009 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:73195 original size:103 final size:103
Alignment explanation
Indices: 73024--73238 Score: 412
Period size: 103 Copynumber: 2.1 Consensus size: 103
73014 TAATGTCCAT
*
73024 AAGGACTACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
73089 GACCTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
73127 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
73192 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
73230 AAGGACCAC
1 AAGGACCAC
73239 GTAGACCCTT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:73743 original size:20 final size:20
Alignment explanation
Indices: 73718--73775 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
73708 TTTTTTTATA
*
73718 TGGGGGAATCGGTTCCCCCC
1 TGGGGGTATCGGTTCCCCCC
73738 TGGGGGTATCGGTTCCCCCC
1 TGGGGGTATCGGTTCCCCCC
*
73758 TGGGGGTATCGATTCCCC
1 TGGGGGTATCGGTTCCCC
73776 TCTAGCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.09, C:0.33, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGTATCGGTTCCCCCC
Found at i:73826 original size:21 final size:21
Alignment explanation
Indices: 73802--73844 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73792 TTCATATTCG
* *
73802 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
73823 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
73844 T
1 T
73845 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:79915 original size:23 final size:22
Alignment explanation
Indices: 79889--79952 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
79879 CAGCTCATAT
79889 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
*
79912 AATTGCA-CTGGAGTGCCGCGTAG
1 AATTGCACCT--AGTGCCACGTAG
79935 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
79953 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 1 0.03
25 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:80150 original size:100 final size:102
Alignment explanation
Indices: 79968--80179 Score: 392
Period size: 100 Copynumber: 2.1 Consensus size: 102
79958 TAATGTCCAT
79968 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACA-ATACCAAGGATCAAGTATGTGTCTCACCA
*
80033 GACCTCACACATGTTCC-AAGAATACATATATGTCCCG
65 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
80070 AAGGACCACATATCATTCCTTAAGAATCATATAC-ATACCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATACAATACCAAGGATCAAGTATGTGTCTCACCAG
80134 ACCTCACACATATTCCAAAGAATACATATATGTCCCG
66 ACCTCACACATATTCCAAAGAATACATATATGTCCCG
80171 AAGGACCAC
1 AAGGACCAC
80180 GTAGACCCTC
Statistics
Matches: 108, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
100 45 0.42
101 29 0.27
102 34 0.31
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACAATACCAAGGATCAAGTATGTGTCTCACCAG
ACCTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:80692 original size:19 final size:20
Alignment explanation
Indices: 80655--80692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80645 TTTTTTTATA
*
80655 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
80675 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
80693 TCTAACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Done.