Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000864.1 Hibiscus syriacus cultivar Beakdansim tig00001670_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: 191231
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3826 original size:31 final size:31
Alignment explanation
Indices: 3789--3868 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 31
3779 ATTTTTTTAA
3789 TTTGCTCACTGAACTTTACATATTGAATCAT
1 TTTGCTCACTGAACTTTACATATTGAATCAT
3820 TTTGCTCACTCTACCGTTGAACTTTACATATTGAATCAT
1 TTTG----CTC-A-C--TGAACTTTACATATTGAATCAT
3859 TTTGCTCACT
1 TTTGCTCACT
3869 CTACCGTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
31 5 0.12
33 1 0.02
34 1 0.02
35 6 0.15
36 1 0.02
37 1 0.02
39 26 0.63
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTGCTCACTGAACTTTACATATTGAATCAT
Found at i:3841 original size:39 final size:39
Alignment explanation
Indices: 3798--3876 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3788 ATTTGCTCAC
3798 TGAACTTTACATATTGAATCATTTTGCTCACTCTACCGT
1 TGAACTTTACATATTGAATCATTTTGCTCACTCTACCGT
3837 TGAACTTTACATATTGAATCATTTTGCTCACTCTACCGT
1 TGAACTTTACATATTGAATCATTTTGCTCACTCTACCGT
3876 T
1 T
3877 ATCTTTCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (39 bp):
TGAACTTTACATATTGAATCATTTTGCTCACTCTACCGT
Found at i:4577 original size:29 final size:29
Alignment explanation
Indices: 4527--4637 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 29
4517 TTCACTCCGT
* *
4527 AAAGTTCAATGAGCAAATTAGAAAAATTA
1 AAAGTACAATGAGCAAAATAGAAAAATTA
* *
4556 AAAGTACATTGAGTAAAATAGAGAGTAAATGT-
1 AAAGTACAATGAGCAAAATAGA-A--AAAT-TA
* *
4588 AAAGTTCAATGAGCAAATTAGAAAAATTA
1 AAAGTACAATGAGCAAAATAGAAAAATTA
* * *
4617 AAAGTATATTGAGTAAAATAG
1 AAAGTACAATGAGCAAAATAG
4638 GAGAGAGTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.02
29 38 0.59
30 1 0.02
31 1 0.02
32 22 0.34
33 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGTACAATGAGCAAAATAGAAAAATTA
Found at i:4595 original size:61 final size:62
Alignment explanation
Indices: 4525--4642 Score: 220
Period size: 61 Copynumber: 1.9 Consensus size: 62
4515 TATTCACTCC
4525 GTAAAGTTCAATGAGCAAATTAGAAAAATTAAAAGTACATTGAGTAAAATA-GAGAGTAAAT
1 GTAAAGTTCAATGAGCAAATTAGAAAAATTAAAAGTACATTGAGTAAAATAGGAGAGTAAAT
*
4586 GTAAAGTTCAATGAGCAAATTAGAAAAATTAAAAGTATATTGAGTAAAATAGGAGAG
1 GTAAAGTTCAATGAGCAAATTAGAAAAATTAAAAGTACATTGAGTAAAATAGGAGAG
4643 AGTAAAATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
61 50 0.91
62 5 0.09
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (62 bp):
GTAAAGTTCAATGAGCAAATTAGAAAAATTAAAAGTACATTGAGTAAAATAGGAGAGTAAAT
Found at i:4726 original size:3 final size:3
Alignment explanation
Indices: 4718--4786 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
4708 ACATTGAATG
* * * * *
4718 TAT TAT TAT TAT TAT TGT TA- TAT AAT TGT TGT TAT TAT TAT TGT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4764 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
4787 CGTGTAAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4752 original size:26 final size:26
Alignment explanation
Indices: 4718--4785 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
4708 ACATTGAATG
4718 TATTATTATTATTATTGTTATATAAT
1 TATTATTATTATTATTGTTATATAAT
* * * *
4744 TGTTGTTATTATTATTGTTTTATTAT
1 TATTATTATTATTATTGTTATATAAT
4770 TATTATTATTATTATT
1 TATTATTATTATTATT
4786 ACGTGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (26 bp):
TATTATTATTATTATTGTTATATAAT
Found at i:11247 original size:35 final size:35
Alignment explanation
Indices: 11201--11268 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
11191 GGAGGCCTTT
11201 AACTACCAACTTGTTCGACCTAAATATCGACATTC
1 AACTACCAACTTGTTCGACCTAAATATCGACATTC
11236 AACTACCAACTTGTTCGACCTAAATATCGACAT
1 AACTACCAACTTGTTCGACCTAAATATCGACAT
11269 CACAGAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (35 bp):
AACTACCAACTTGTTCGACCTAAATATCGACATTC
Found at i:12926 original size:23 final size:22
Alignment explanation
Indices: 12892--12958 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
12882 GCTCAAGTGA
12892 AAATTACATAAAAACATTACAAAC
1 AAATTA-ATAAAAACATTA-AAAC
*
12916 TAAA-TAGTAAAAACAATTAAAAC
1 -AAATTAATAAAAAC-ATTAAAAC
*
12939 AAATTAATAGAAACATTAAA
1 AAATTAATAAAAACATTAAA
12959 TAGAAATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.24
23 19 0.51
24 6 0.16
25 3 0.08
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.22
Consensus pattern (22 bp):
AAATTAATAAAAACATTAAAAC
Found at i:16598 original size:18 final size:18
Alignment explanation
Indices: 16575--16643 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
16565 AGGGATTATC
16575 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
16593 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
* *
16612 CAGTGGTCTTTCGGGATAT
1 -AGTGGTCCTTCGGGACAT
*
16631 AGTGGTCATTCGG
1 AGTGGTCCTTCGG
16644 AACAAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 26 0.62
19 4 0.10
20 12 0.29
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:16625 original size:38 final size:38
Alignment explanation
Indices: 16572--16648 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
16562 TCGAGGGATT
16572 ATCAGTGGTCCTTCGGGACATAGTGGTTC-TTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAGTGG-TCATTCGGAACA
* *
16610 ATCAGTGGTCTTTCGGGATATAGTGGTCATTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCATTCGGAACA
16648 A
1 A
16649 ATATTCAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAGTGGTCATTCGGAACA
Found at i:22823 original size:64 final size:62
Alignment explanation
Indices: 22755--22914 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 62
22745 ATTGTTCAAG
* * *
22755 GTGTATCGATGCACATG-AGGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACAAGTA-GTGCATCGATGCAC-CCCTTAAAAT-AAAACATCGAATGTCATTA
* * **
22819 GTGTATCGATGCATAAGTAGTGCATCGATGCACCCCTTAAAATACAACATCGAATGGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAAAATAAAACATCGAATGTCA-TTA
* * *
22882 -TGTACCGATGCA-TAGATTGTGCATCGATGCACC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACC
22915 AGTCAAGGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
61 2 0.02
62 40 0.48
63 12 0.14
64 28 0.34
65 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (62 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAAAATAAAACATCGAATGTCATTA
Found at i:22895 original size:62 final size:63
Alignment explanation
Indices: 22778--22914 Score: 172
Period size: 62 Copynumber: 2.2 Consensus size: 63
22768 CATGAGGTGT
* * *
22778 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTAGTGTATCGATGCATA-AGTAGTGC
1 ATCGATGCAC-CCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCGATGCATAGA-TAGTGC
* * *
22842 ATCGATGCACCCCTTAAAAT-ACAACATCGAATGGGATTTA-TGTACCGATGCATAGATTGTGC
1 ATCGATGCACCCCTTAAAATAAAAACATCGAATGGCA-TTAGTGTACCGATGCATAGATAGTGC
22904 ATCGATGCACC
1 ATCGATGCACC
22915 AGTCAAGGGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 42 0.65
63 13 0.20
64 10 0.15
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (63 bp):
ATCGATGCACCCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCGATGCATAGATAGTGC
Found at i:23510 original size:18 final size:18
Alignment explanation
Indices: 23487--23559 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
23477 AGGAATTATC
23487 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
23505 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
23524 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
23543 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
23560 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:23809 original size:2 final size:2
Alignment explanation
Indices: 23802--23828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23792 AATGCATTGT
23802 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23829 GCCTCACTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25849 original size:35 final size:36
Alignment explanation
Indices: 25771--25851 Score: 87
Period size: 40 Copynumber: 2.2 Consensus size: 36
25761 AAATCATATC
25771 TAAAATTTTATTTTATTTCATTTTAATAATCCATCGT
1 TAAAATTTTATTTTATTTCATTTTAATAATCCATC-T
* *
25808 TAAAAATTTTGATTTTGATTTTATTTTAGT-ATCC-T-T
1 T-AAAATTTT-ATTTT-ATTTCATTTTAATAATCCATCT
25844 TAAAATTT
1 TAAAATTT
25852 AACATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 7 0.18
36 2 0.05
37 1 0.03
38 9 0.23
39 9 0.23
40 11 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (36 bp):
TAAAATTTTATTTTATTTCATTTTAATAATCCATCT
Found at i:26159 original size:23 final size:24
Alignment explanation
Indices: 26115--26166 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
26105 CATTGCTCTC
* *
26115 TAATTATCTGACTGAACAAAAA-T
1 TAATTAGCTGACTCAACAAAAATT
* *
26138 TAATTAGCTGTCTCAACTAAAATT
1 TAATTAGCTGACTCAACAAAAATT
26162 TAATT
1 TAATT
26167 TCATTAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (24 bp):
TAATTAGCTGACTCAACAAAAATT
Found at i:31328 original size:3 final size:3
Alignment explanation
Indices: 31320--31352 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
31310 CTGCTTCCGG
31320 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
31353 AGTGTTTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:32600 original size:46 final size:46
Alignment explanation
Indices: 32533--32621 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
32523 TGCTTGAATC
* * * * *
32533 CTGCATTAAATGGCCTCTGAAAAGTAACTGAAATGGTTCATTATTG
1 CTGCAATAAATGACATCTGAAAAGTAACTGAAACGGTGCATTATTG
*
32579 CTGCAATAAATGACATCTGAAAAGTAGCTGAAACGGTGCATTA
1 CTGCAATAAATGACATCTGAAAAGTAACTGAAACGGTGCATTA
32622 ATTGAGCACC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (46 bp):
CTGCAATAAATGACATCTGAAAAGTAACTGAAACGGTGCATTATTG
Found at i:34341 original size:18 final size:19
Alignment explanation
Indices: 34304--34343 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
34294 TAACCTGTTA
* *
34304 TATATTTGTATAATATAAT
1 TATATTTGTAAAATAAAAT
34323 TATATTT-TAAAATAAAAT
1 TATATTTGTAAAATAAAAT
34341 TAT
1 TAT
34344 GAGAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATTTGTAAAATAAAAT
Found at i:34664 original size:60 final size:59
Alignment explanation
Indices: 34573--34698 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 59
34563 TTCAAATTGT
*
34573 TTTTATATCTATATATAATATTACATTTTATTTAAAAG-TATGGGTCTCGTGTTAGTAATG
1 TTTTATATCTATATATAATATTACATTTTATTT-AAAGTTATGGGT-TCATGTTAGTAATG
* * *
34633 TTTTATATCTATATATAATTTTATATTTTATTTAAAGTTATGTGTTCATGTTAGTAATG
1 TTTTATATCTATATATAATATTACATTTTATTTAAAGTTATGGGTTCATGTTAGTAATG
*
34692 ATTTATA
1 TTTTATA
34699 AAATTTAAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 23 0.38
60 37 0.62
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (59 bp):
TTTTATATCTATATATAATATTACATTTTATTTAAAGTTATGGGTTCATGTTAGTAATG
Found at i:36789 original size:29 final size:29
Alignment explanation
Indices: 36754--36812 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
36744 ATTTTCACAT
36754 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
36783 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
36812 A
1 A
36813 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:48305 original size:16 final size:16
Alignment explanation
Indices: 48260--48317 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
48250 GGCGAGCAAT
* *
48260 GAGCATCGAGCTTAAC
1 GAGCAACGAACTTAAC
* * *
48276 GAGTAATGAGCTTAATC
1 GAGCAACGAACTTAA-C
48293 -AGCAACGAACTTAAC
1 GAGCAACGAACTTAAC
48308 GAGCAACGAA
1 GAGCAACGAA
48318 TCAAACAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (16 bp):
GAGCAACGAACTTAAC
Found at i:59139 original size:16 final size:16
Alignment explanation
Indices: 59118--59149 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
59108 TAGTTGGTTA
59118 ACTTCAATTCATAATT
1 ACTTCAATTCATAATT
59134 ACTTCAATTCATAATT
1 ACTTCAATTCATAATT
59150 GCGCGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (16 bp):
ACTTCAATTCATAATT
Found at i:64367 original size:21 final size:21
Alignment explanation
Indices: 64341--64480 Score: 162
Period size: 21 Copynumber: 6.7 Consensus size: 21
64331 GTTTTCAGAT
*
64341 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
64362 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
64383 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
64403 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
64424 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
64445 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
64466 TCGTAATGCGAACTT
1 TCGCAATGCGAACTT
64481 GCGAACTTGG
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
20 17 0.17
21 85 0.83
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:64406 original size:41 final size:40
Alignment explanation
Indices: 64361--64477 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 40
64351 AACTTCGACT
*
64361 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAAT-TGTAA
* * *
64402 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGA-ACTTCGACTATCGCAATGCGAA-TTGTA-A
* *
64444 ATCGCAACGCGAACTTCGACTATCGTAATGCGAA
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAA
64478 CTTGCGAACT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 34 0.52
42 31 0.48
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGAACTTCGACTATCGCAATGCGAATTGTAA
Found at i:65300 original size:23 final size:21
Alignment explanation
Indices: 65274--65377 Score: 59
Period size: 21 Copynumber: 4.9 Consensus size: 21
65264 ACCAGTCGTT
65274 GCGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGAAT--ATCGCAAC
* * *
65297 GCGAACTTGGACTATCGCAAT
1 GCGAATTTGGAATATCGCAAC
* * *
65318 GCGAATATGTAA-ATCGCAAT
1 GCGAATTTGGAATATCGCAAC
* * *
65338 GCG-ATAGTCGACTATCGCAAC
1 GCGAAT-TTGGAATATCGCAAC
* * *
65359 GCGAACTTCGACTATCGCA
1 GCGAATTTGGAATATCGCA
65378 TTGCGATTTA
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
19 2 0.03
20 13 0.20
21 37 0.58
22 1 0.02
23 11 0.17
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (21 bp):
GCGAATTTGGAATATCGCAAC
Found at i:65315 original size:21 final size:20
Alignment explanation
Indices: 65289--65377 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
65279 TTTGGAATAA
*
65289 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAA-TTCGACT
* *
65310 ATCGCAATGCGAATAT-GTA-A
1 ATCGCAACGCGAAT-TCG-ACT
* *
65330 ATCGCAATGCGATAGTCGACT
1 ATCGCAACGCGA-ATTCGACT
65351 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAA-TTCGACT
65372 ATCGCA
1 ATCGCA
65378 TTGCGATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 17 0.30
21 39 0.70
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTCGACT
Found at i:65333 original size:41 final size:41
Alignment explanation
Indices: 65286--65363 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
65276 GAATTTGGAA
* * *
65286 TAAATCGCAACGCGA-ACTTGGACTATCGCAATGCGAATATG
1 TAAATCGCAACGCGATA-GTCGACTATCGCAACGCGAATATG
*
65327 TAAATCGCAATGCGATAGTCGACTATCGCAACGCGAA
1 TAAATCGCAACGCGATAGTCGACTATCGCAACGCGAA
65364 CTTCGACTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (41 bp):
TAAATCGCAACGCGATAGTCGACTATCGCAACGCGAATATG
Found at i:65422 original size:21 final size:21
Alignment explanation
Indices: 65392--65445 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
65382 GATTTACATA
*
65392 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
65413 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
65434 TTCGCGTTGCGA
1 TTCGCGTTGCGA
65446 ATCTGGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:74453 original size:60 final size:59
Alignment explanation
Indices: 74379--74538 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 59
74369 GGGTGAACTT
* *
74379 GAGATAAAATTAGAATGTTCAAAAGTTTGGGAACTAATTTAGAAAGATG-GTCATAGTTTA
1 GAGATGAAATTAGAATGTTCAAAAGTTTAGG-ACTAATTTAGAAAGA-GAGTCATAGTTTA
* *
74439 GAGATGAAATTAGAATGTTCAAAAGTTCAGGACTAATTTAGAATGAGAGTCATAGTTTA
1 GAGATGAAATTAGAATGTTCAAAAGTTTAGGACTAATTTAGAAAGAGAGTCATAGTTTA
* * ** *
74498 GGGTTGAAATT-GAAACATTCAAAAGTTTAAAGACTAATTTA
1 GAGATGAAATTAG-AATGTTCAAAAGTTT-AGGACTAATTTA
74539 AAATAAAGGT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 2 0.02
59 46 0.53
60 39 0.45
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (59 bp):
GAGATGAAATTAGAATGTTCAAAAGTTTAGGACTAATTTAGAAAGAGAGTCATAGTTTA
Found at i:75118 original size:22 final size:22
Alignment explanation
Indices: 75086--75127 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
75076 AACCTTACAG
75086 TTAAAAACTTTGATTTTTGTCA
1 TTAAAAACTTTGATTTTTGTCA
*
75108 TTAAAACCTTTGATTTTTGT
1 TTAAAAACTTTGATTTTTGT
75128 TTCGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (22 bp):
TTAAAAACTTTGATTTTTGTCA
Found at i:79365 original size:24 final size:23
Alignment explanation
Indices: 79338--79466 Score: 89
Period size: 24 Copynumber: 5.4 Consensus size: 23
79328 GATATCAGAA
*
79338 ATCAAAACATAAATCAAGTCAAGT
1 ATCAAATCA-AAATCAAGTCAAGT
* *
79362 ATCATATCAAAATCCAGATCAAGT
1 ATCAAATCAAAATCAAG-TCAAGT
* *
79386 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAAT-CAAGTCAAGT
* * *
79410 ATCAGATCAGAATCTATGTC-AGAT
1 ATCAAATCAAAATC-AAGTCAAG-T
* * *
79434 ATCATATCAGAATCCATGTCAAGT
1 ATCAAATCAAAAT-CAAGTCAAGT
*
79458 ATCAGATCA
1 ATCAAATCA
79467 GAATTCAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.11
24 74 0.82
25 6 0.07
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.25
Consensus pattern (23 bp):
ATCAAATCAAAATCAAGTCAAGT
Found at i:79467 original size:24 final size:24
Alignment explanation
Indices: 79355--79470 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
79345 CATAAATCAA
* *
79355 GTCAAGTATCATATCAAAATCCA-
1 GTCAAGTATCAGATCAGAATCCAT
*
79378 GATCAAGTATCAGATCAGAATCCAA
1 G-TCAAGTATCAGATCAGAATCCAT
*
79403 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
79427 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
79451 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
79471 TCAAAATCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.93
25 3 0.04
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:81948 original size:18 final size:18
Alignment explanation
Indices: 81925--81966 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
81915 GGTCAATGGA
*
81925 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACAGGTCGGG
81943 TCGGGTCAACAGGTCGGG
1 TCGGGTCAACAGGTCGGG
81961 TCGGGT
1 TCGGGT
81967 TGTGACCGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (18 bp):
TCGGGTCAACAGGTCGGG
Found at i:90229 original size:61 final size:61
Alignment explanation
Indices: 90134--90256 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
90124 ATGTGTGTAG
*
90134 AAAGAGTAGTTATTATTGTTCTAAATCGTTCTTTCTCTCTATCAAAATAATAGATAATCTT
1 AAAGAGTAGTTATTATTGTTCTAAATCATTCTTTCTCTCTATCAAAATAATAGATAATCTT
90195 AAAGAGTAGTTATTATTGTTCTAAATCATTCTTTCTCTCTATCAAAATAATAGATAATCTT
1 AAAGAGTAGTTATTATTGTTCTAAATCATTCTTTCTCTCTATCAAAATAATAGATAATCTT
90256 A
1 A
90257 GTCTAGGGTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (61 bp):
AAAGAGTAGTTATTATTGTTCTAAATCATTCTTTCTCTCTATCAAAATAATAGATAATCTT
Found at i:95377 original size:18 final size:17
Alignment explanation
Indices: 95347--95420 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 17
95337 TTATCTGAAA
95347 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
*
95364 ATTTTAAATATATTTTAT
1 ATTTTAAAT-TATTATAT
* * *
95382 ATATT-ATTTATTATTT
1 ATTTTAAATTATTATAT
* *
95398 ATTTT-TATTCTTATAT
1 ATTTTAAATTATTATAT
95414 AATTTTA
1 -ATTTTA
95421 TAAATTTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
16 17 0.39
17 16 0.36
18 11 0.25
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:97320 original size:3 final size:3
Alignment explanation
Indices: 97312--97376 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
97302 TGTTGGAAGG
97312 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
97359 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
97377 GTTTAGGAGG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:97475 original size:5 final size:5
Alignment explanation
Indices: 97465--97489 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
97455 GGGTGTTTTT
97465 CTGTG CTGTG CTGTG CTGTG CTGTG
1 CTGTG CTGTG CTGTG CTGTG CTGTG
97490 AGGTGCAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
CTGTG
Found at i:98682 original size:22 final size:23
Alignment explanation
Indices: 98637--98696 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
98627 ATAGAGATGA
* *
98637 AAAATAGATATTGAATATTTATAT
1 AAAATAAATATT-AATATTAATAT
98661 AAAATAAATATT-ATATTAATAT
1 AAAATAAATATTAATATTAATAT
*
98683 ATAAT--ATATTAATA
1 AAAATAAATATTAATA
98697 ATGTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.16
21 3 0.09
22 13 0.41
24 11 0.34
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
AAAATAAATATTAATATTAATAT
Found at i:98875 original size:21 final size:21
Alignment explanation
Indices: 98826--98877 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
98816 TTAGAAAATC
* *
98826 TTTGTTTCTCATTATTTGTTT
1 TTTGTTTTTCATTATTTATTT
98847 TTTGTTTTTCATTATTTATTT
1 TTTGTTTTTCATTATTTATTT
98868 TTTGTTTTTC
1 TTTGTTTTTC
98878 TGATTGGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTGTTTTTCATTATTTATTT
Found at i:106963 original size:163 final size:163
Alignment explanation
Indices: 106784--107081 Score: 483
Period size: 163 Copynumber: 1.8 Consensus size: 163
106774 ATATATTTAA
* *
106784 TAAAATTTATTTTTTTAAAATATGATCAAAGTTTAAAATTTTTGAA-TTTTAAAAAGTCAATACG
1 TAAAATTTAATTTTTTAAAATATGATCAAAGTTTAAAAATTTT-AACTTTT-AAAAGTCAATACG
* *
106848 AGACATTTTTAATAGGACA-AACTAATGCAATCTTCTTAACATTTTCGATTGAATATTCTAAAAT
64 AGACATTTTTAATAGGACAGAACTAATACAATCTTCTTAACATCTTCGATTGAATATTCTAAAAT
*
106912 GTTATGATTCTTATCGCAATTTCATTTGGATTTTT
129 ATTATGATTCTTATCGCAATTTCATTTGGATTTTT
106947 TAAAATTTAATTTTTTAAAATATGATCAAAGTTTAAAAATTTTAACTTTTAAAAGTCAATACGAG
1 TAAAATTTAATTTTTTAAAATATGATCAAAGTTTAAAAATTTTAACTTTTAAAAGTCAATACGAG
* * * *
107012 ACATTTTTAATAGGATAGAAGTAGTACAATCTTTTTAACATCTTCGATTGAATATTCTAAAATAT
66 ACATTTTTAATAGGACAGAACTAATACAATCTTCTTAACATCTTCGATTGAATATTCTAAAATAT
107077 TATGA
131 TATGA
107082 AGAATGTAAC
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
162 33 0.27
163 91 0.73
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (163 bp):
TAAAATTTAATTTTTTAAAATATGATCAAAGTTTAAAAATTTTAACTTTTAAAAGTCAATACGAG
ACATTTTTAATAGGACAGAACTAATACAATCTTCTTAACATCTTCGATTGAATATTCTAAAATAT
TATGATTCTTATCGCAATTTCATTTGGATTTTT
Found at i:107741 original size:29 final size:29
Alignment explanation
Indices: 107696--107781 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
107686 AGTGTTGGCC
*
107696 GTAGGTCGCCATTCACTCCGGGCGACCTT
1 GTAGGTCGCCATACACTCCGGGCGACCTT
*
107725 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATACACTCCGGGCGACCTT
*
107754 GTAGGTCACCATACACTCCGGGCGACCT
1 GTAGGTCGCCATACACTCCGGGCGACCT
107782 ACCCTTGCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATACACTCCGGGCGACCTT
Found at i:107907 original size:33 final size:33
Alignment explanation
Indices: 107870--107954 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
107860 GCGACCTACC
* *
107870 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCACATAG
107903 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
* * *
107936 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
107955 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.09, C:0.39, G:0.26, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
Found at i:107926 original size:10 final size:10
Alignment explanation
Indices: 107882--107994 Score: 55
Period size: 10 Copynumber: 10.3 Consensus size: 10
107872 CGCTCGGCTT
*
107882 CCCTCGGATT
1 CCCTCGGATG
*
107892 CCCTCGCATAG
1 CCCTCGGAT-G
*
107903 CTCGCTCGGTTG
1 C-C-CTCGGATG
107915 CCCTCGGATG
1 CCCTCGGATG
**
107925 CCCTCACATAG
1 CCCTCGGAT-G
*
107936 CTCGTTCGGATGG
1 C-C-CTCGGAT-G
107949 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
107962 GCCTCGGATG
1 CCCTCGGATG
*
107972 CTCTCGGATG
1 CCCTCGGATG
*
107982 GCCTCGGATG
1 CCCTCGGATG
107992 CCC
1 CCC
107995 AGCGTGTTGG
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
10 47 0.62
11 4 0.05
12 6 0.08
13 13 0.17
14 6 0.08
ACGTcount: A:0.11, C:0.36, G:0.29, T:0.24
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:107958 original size:14 final size:14
Alignment explanation
Indices: 107936--107968 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
107926 CCTCACATAG
*
107936 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
107950 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
107964 CTCGG
1 CTCGG
107969 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:107980 original size:20 final size:20
Alignment explanation
Indices: 107955--107992 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
107945 ATGGCCTCGG
107955 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
107975 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
107993 CCAGCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:108068 original size:29 final size:29
Alignment explanation
Indices: 108031--108088 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
108021 GCAATCTCTT
*
108031 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
108060 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
108089 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:116623 original size:31 final size:31
Alignment explanation
Indices: 116560--116636 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
116550 TTACTTTTTA
* * *
116560 TTTCATTTTAGTACCTAAAATTTACTTTTTG
1 TTTCATTTTAGTACCCAAAATTAACTTCTTG
***
116591 TTTCATTTTAGTACCCATTGTTAACTTCTTG
1 TTTCATTTTAGTACCCAAAATTAACTTCTTG
*
116622 TTTCATTCTAGTACC
1 TTTCATTTTAGTACC
116637 TAAATTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.52
Consensus pattern (31 bp):
TTTCATTTTAGTACCCAAAATTAACTTCTTG
Found at i:120536 original size:2 final size:2
Alignment explanation
Indices: 120529--120563 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
120519 TTGCACATTA
120529 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
120564 TTCTGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:120802 original size:23 final size:25
Alignment explanation
Indices: 120762--120807 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
120752 TATTTATTAG
* *
120762 AAAATAATTAATATAA-TTATTTTT
1 AAAATAATTAAAACAATTTATTTTT
120786 AAAAT-ATTAAAACAATTTATTT
1 AAAATAATTAAAACAATTTATTT
120808 AATATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATAATTAAAACAATTTATTTTT
Found at i:121017 original size:28 final size:26
Alignment explanation
Indices: 120986--121049 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
120976 TTAATAATTA
*
120986 ATATTTT-TTAAAATGATATTAAAATAGT
1 ATATTTTATT-AAAT-ATA-TAAAATAAT
121014 ATATTATTATTAAATATATAAAATAAT
1 ATATT-TTATTAAATATATAAAATAAT
121041 ATTATTTTA
1 A-TATTTTA
121050 AGTATTTCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 12 0.38
28 12 0.38
29 6 0.19
30 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
ATATTTTATTAAATATATAAAATAAT
Found at i:121027 original size:30 final size:25
Alignment explanation
Indices: 120984--121050 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
120974 TTTTAATAAT
120984 TAATATT-TTTTAAAATGATATTAAAA
1 TAATATTATTTTAAAAT-ATA-TAAAA
121010 TAGTATATTATTATT-AAATATATAAAA
1 TA--ATATTATT-TTAAAATATATAAAA
121037 TAATATTATTTTAA
1 TAATATTATTTTAA
121051 GTATTTCTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
24 2 0.06
25 9 0.25
26 2 0.06
27 7 0.19
28 8 0.22
29 6 0.17
30 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TAATATTATTTTAAAATATATAAAA
Found at i:121043 original size:19 final size:19
Alignment explanation
Indices: 120994--121044 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
120984 TAATATTTTT
*
120994 TAAAATGATATTAAAATAG
1 TAAAATAATATTAAAATAG
* * *
121013 TATATTATTATTAAATATA-
1 TAAAATAATATTAAA-ATAG
121032 TAAAATAATATTA
1 TAAAATAATATTA
121045 TTTTAAGTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAAATAATATTAAAATAG
Found at i:121709 original size:45 final size:45
Alignment explanation
Indices: 121654--121772 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
121644 CGATAAAACA
**
121654 CTACCTAAAACATTATTTTTCTACCGAAAATGTTAAAATTGAGTG
1 CTACCTAAAACATTATTTTTCTACCGAAAATGTTAAAATTGAACG
* * *
121699 CTATCTAAAACATTATTTTTCTATCGAAAATGTTAATATTGAACG
1 CTACCTAAAACATTATTTTTCTACCGAAAATGTTAAAATTGAACG
* *
121744 TTACCTAAAATATTATTTTTTTCTACCGA
1 CTACCTAAAACATTA--TTTTTCTACCGA
121773 TTTTTAAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 52 0.83
47 11 0.17
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (45 bp):
CTACCTAAAACATTATTTTTCTACCGAAAATGTTAAAATTGAACG
Found at i:122418 original size:15 final size:16
Alignment explanation
Indices: 122398--122438 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
122388 ATCGTTACCA
*
122398 AAAATCCCTAAATCT-
1 AAAATCCCTAAATATC
122413 AAAATCCC-AAATATC
1 AAAATCCCTAAATATC
*
122428 CAAATCCCTAA
1 AAAATCCCTAA
122439 TTCTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 5 0.23
15 15 0.68
16 2 0.09
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATCCCTAAATATC
Found at i:126743 original size:30 final size:30
Alignment explanation
Indices: 126707--126766 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
126697 ATATGCGTTT
*
126707 TCGATTGTGCTGTGATTATCGCGATTTCGG
1 TCGATTGTGCTGTGACTATCGCGATTTCGG
126737 TCGATTGTGCTGTGACTATCGCGATTTCGG
1 TCGATTGTGCTGTGACTATCGCGATTTCGG
126767 GCTGCAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.13, C:0.18, G:0.30, T:0.38
Consensus pattern (30 bp):
TCGATTGTGCTGTGACTATCGCGATTTCGG
Found at i:130556 original size:68 final size:68
Alignment explanation
Indices: 130446--130581 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
130436 CAGAAATATT
* ** * *
130446 TTTACAATTATTATATGTATATTAATAATACAAAAATTTTATATAAATAGACTCGAATAAAATCT
1 TTTACAATGATTATATGTATATTAATAATACAAAAAAATTATACAAATAGACTCGAAGAAAATCT
130511 TAA
66 TAA
130514 TTTACAATGATTATATGTATATTAATAATACAAAAAAATTATACAAATAGACTCGAAGAAAATCT
1 TTTACAATGATTATATGTATATTAATAATACAAAAAAATTATACAAATAGACTCGAAGAAAATCT
130579 TAA
66 TAA
130582 GATAAATACA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (68 bp):
TTTACAATGATTATATGTATATTAATAATACAAAAAAATTATACAAATAGACTCGAAGAAAATCT
TAA
Found at i:131869 original size:21 final size:21
Alignment explanation
Indices: 131824--131869 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
131814 TTTATGTGTG
* *
131824 TTTTTTTAATTATATTTTTTA
1 TTTTTTTAATTATATTATATA
131845 TTTTTTTAATTATA-TATATA
1 TTTTTTTAATTATATTATATA
131865 TTTTT
1 TTTTT
131870 CAAAATTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTAATTATATTATATA
Found at i:133641 original size:257 final size:240
Alignment explanation
Indices: 133105--133698 Score: 662
Period size: 257 Copynumber: 2.4 Consensus size: 240
133095 CTCCATCCGA
*
133105 GACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAAACCGACCCGAAATAAT
1 GACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATAAATTAGAAAACCGACCCGAAATAAT
* **
133170 AAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAAATATATATAGAGAGGGGT
66 AAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATATAGAGAGGAAT
* *
133235 ATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTTTTTGGGTCGAGTCTGGTATT
131 ATTATTATAATTATTCCTAAATATATAAGATAAAATTATATATTTTTCGGGTC-AG--TGGTATT
133300 TTCACCCTAAACCCGAACCTGACCCAAATATCACACTTAAAAAAAATC
193 TTCACCCTAAACCCGAACCTGACCCAAATATCACACTTAAAAAAAATC
* * *
133348 GACCTGACCAAAATAAAGTTCACACGACCTGACCCGAATATATAAATTATAAATCTGACCCGACC
1 GACCCGACCAAAATAAAGTT-TCAC--CC-GACCCGAATATATAAATTAGAAA----A-CCGA--
* *
133413 CGATCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAAT-T
55 C---CCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATAT
* *
133477 ATATATAGAGGAATATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGG
117 ATATAGAGAGGAATATTATTATAATTATTCCTAAATATATAAGATAAAATTATATAT-TTTTCGG
* *
133542 GTC-G-GGTATTTTTCACCTTAAACTCGAA-CTCGACCCGACCCGAATATCACACTTAAAAAACC
181 GTCAGTGGTA-TTTTCACCCTAAACCCGAACCT-GACCC-A----AATATCACACTTAAAAAA--
*
133604 GACTC
237 -AATC
* * * *
133609 GACCCGATCAAAATAAAATTTCACCCGACCCGATCCGAATATATGAATTAGAAATCCGACCC--A
1 GACCCGACCAAAATAAAGTTTCACCCGA--C---CCGAATATATAAATTAGAAAACCGACCCGAA
133672 A-AATAAAAAAAATATTTTTATTCAATA
61 ATAATAAAAAAAATATTTTTATTCAATA
133699 TATGAATAAG
Statistics
Matches: 297, Mismatches: 24, Indels: 54
0.79 0.06 0.14
Matches are distributed among these distances:
243 19 0.06
244 3 0.01
246 2 0.01
247 21 0.07
249 25 0.08
250 2 0.01
251 1 0.00
252 12 0.04
253 22 0.07
254 2 0.01
255 2 0.01
256 53 0.18
257 71 0.24
258 20 0.07
259 1 0.00
260 3 0.01
261 20 0.07
262 18 0.06
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (240 bp):
GACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATAAATTAGAAAACCGACCCGAAATAAT
AAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATATAGAGAGGAAT
ATTATTATAATTATTCCTAAATATATAAGATAAAATTATATATTTTTCGGGTCAGTGGTATTTTC
ACCCTAAACCCGAACCTGACCCAAATATCACACTTAAAAAAAATC
Found at i:139642 original size:17 final size:17
Alignment explanation
Indices: 139622--139657 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
139612 AATATTTATA
*
139622 TATTATATTAATTTAAT
1 TATTATATTAATTCAAT
*
139639 TATTATTTTAATTCAAT
1 TATTATATTAATTCAAT
139656 TA
1 TA
139658 ATTAAATTTA
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATTAATTCAAT
Found at i:140143 original size:120 final size:120
Alignment explanation
Indices: 140016--140241 Score: 393
Period size: 120 Copynumber: 1.9 Consensus size: 120
140006 ATAAGTTTAA
140016 TATTTTTTACAATTATTTTTAAATAATAATATATAAATTACATTAAAAAT-AAAATT-TCATTAA
1 TATTTTTTACAATTATTTTTAAATAATAATATATAAATTACATTAAAAATAAAAATTAT-ATTAA
140079 AATTATTCAGAGAATCCAAATCACAAAATAAAAATAAATTTAATATTTTATTTAAAT
65 AATTATTCAGAGAATCCAAATCACAAAATAAAAAT-AATTTAATATTTTATTTAAAT
*
140136 TATTTTTTACAATTATTTTTAAATAATAATATATAAATTATATTAAAAATAAAAATTATATTAAA
1 TATTTTTTACAATTATTTTTAAATAATAATATATAAATTACATTAAAAATAAAAATTATATTAAA
* *
140201 ATTATTTAGGGAATCCAAATCACAAAATAAAAATAATTTAA
66 ATTATTCAGAGAATCCAAATCACAAAATAAAAATAATTTAA
140242 CTTAAAAATA
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
120 56 0.55
121 44 0.44
122 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (120 bp):
TATTTTTTACAATTATTTTTAAATAATAATATATAAATTACATTAAAAATAAAAATTATATTAAA
ATTATTCAGAGAATCCAAATCACAAAATAAAAATAATTTAATATTTTATTTAAAT
Found at i:140264 original size:21 final size:22
Alignment explanation
Indices: 140224--140264 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
140214 TCCAAATCAC
*
140224 AAAATAAAAATAATTTAACTTA
1 AAAATAAAAATAATTAAACTTA
140246 AAAATAAAAAT-ATTAAACT
1 AAAATAAAAATAATTAAACT
140265 CATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAAAATAATTAAACTTA
Found at i:141428 original size:31 final size:33
Alignment explanation
Indices: 141393--141456 Score: 78
Period size: 36 Copynumber: 1.9 Consensus size: 33
141383 GAAAATTTTA
141393 AGCTC-GC-GAGTTTTCGAGTCGAGTCGAGTCG
1 AGCTCAGCAGAGTTTTCGAGTCGAGTCGAGTCG
*
141424 AGCTCAATTTCAGAGTTTTCGAGTCGAGTCGAG
1 AGCTC-A--GCAGAGTTTTCGAGTCGAGTCGAG
141457 CTCAGCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.19
35 1 0.04
36 21 0.78
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (33 bp):
AGCTCAGCAGAGTTTTCGAGTCGAGTCGAGTCG
Found at i:147426 original size:18 final size:18
Alignment explanation
Indices: 147403--147439 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
147393 GTAGGTTGAG
147403 CACGAAATCCTCCATATT
1 CACGAAATCCTCCATATT
147421 CACGAAATCCTCCATATT
1 CACGAAATCCTCCATATT
147439 C
1 C
147440 CTTTTTATCT
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:0.32, C:0.35, G:0.05, T:0.27
Consensus pattern (18 bp):
CACGAAATCCTCCATATT
Found at i:164373 original size:173 final size:172
Alignment explanation
Indices: 164079--164435 Score: 678
Period size: 173 Copynumber: 2.1 Consensus size: 172
164069 ATTACAAGTG
*
164079 GGTACCTAAACTATCAATTTTGATTTGTTATAGTATTTAAACTTTCACATTTTTCAAAACCATAC
1 GGTA-CTAAACTATCAATTTTGATTTGTTATAGTATTTAAACTTTCACATTTTCCAAAACCATAC
164144 CTAAAGTTTAGTTTTTGTTTCATTTTAGTATCCCGTTCAAAATTTAATGTTAAGTTTTGAAAAAA
65 CTAAAGTTTAGTTTTTGTTTCATTTTAGTATCCCGTTCAAAATTTAATGTTAAGTTTTGAAAAAA
164209 ATTTAAAAGTTTAGGTACTAAAATGGACCAAAACTAATAGTTTA
130 A-TTAAAAGTTTAGGTACTAAAATGGACCAAAACTAATAGTTTA
164253 GGTACTAAACTATCAATTTTGATTTGTTATAGTATTTAAACTTTCACATTTTCCAAAACCATACC
1 GGTACTAAACTATCAATTTTGATTTGTTATAGTATTTAAACTTTCACATTTTCCAAAACCATACC
164318 TAAAGTTTAGTTTTTGTTTCATTTTAGTATCCCGTTCAAAATTTAATGTTAAGTTTTGAAAAAAA
66 TAAAGTTTAGTTTTTGTTTCATTTTAGTATCCCGTTCAAAATTTAATGTTAAGTTTTGAAAAAAA
*
164383 TTAAAATTTTAGGTACTAAAATGGACCAAAACTAATAGTTTA
131 TTAAAAGTTTAGGTACTAAAATGGACCAAAACTAATAGTTTA
164425 GGTACTAAACT
1 GGTACTAAACT
164436 CATTAAGTTT
Statistics
Matches: 181, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
172 52 0.29
173 125 0.69
174 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (172 bp):
GGTACTAAACTATCAATTTTGATTTGTTATAGTATTTAAACTTTCACATTTTCCAAAACCATACC
TAAAGTTTAGTTTTTGTTTCATTTTAGTATCCCGTTCAAAATTTAATGTTAAGTTTTGAAAAAAA
TTAAAAGTTTAGGTACTAAAATGGACCAAAACTAATAGTTTA
Found at i:187436 original size:2 final size:2
Alignment explanation
Indices: 187429--187615 Score: 126
Period size: 2 Copynumber: 99.0 Consensus size: 2
187419 CACAAATGAG
* * *
187429 GA GA GA GA GA GA GA GA G- GG GA GA GA GA GA GA G- GG GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
187469 GG GA G- GG GA G- GA G- GA GA GG GA GA GA GG GA GA GG GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
187507 GA GA -A G- GA GA GA GA GG GA GG GA GA GG GA GA GA GG GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
187547 GA GA GA GG GA GA GA GG GA GG GA GA GA GG GA GA G- GA GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
187587 GA GA GA GA GA G- GG GG GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
187616 TTCAATAATT
Statistics
Matches: 144, Mismatches: 30, Indels: 22
0.73 0.15 0.11
Matches are distributed among these distances:
1 11 0.08
2 133 0.92
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (2 bp):
GA
Found at i:189001 original size:29 final size:28
Alignment explanation
Indices: 188959--189014 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
188949 AGTGTTGGTC
188959 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCC-GGCGACCTT
188988 GTAGGTCGCCATGCACTCCGGCGACCT
1 GTAGGTCGCCATGCACTCCGGCGACCT
189015 ACCCTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.31
29 17 0.65
30 1 0.04
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (28 bp):
GTAGGTCGCCATGCACTCCGGCGACCTT
Found at i:189211 original size:33 final size:33
Alignment explanation
Indices: 189161--189279 Score: 199
Period size: 33 Copynumber: 3.7 Consensus size: 33
189151 CCGGGCGACC
189161 TTCCCTGCGCATA-CTCGCTCGGCTGCCCTCGGA
1 TTCCCT-CGCATAGCTCGCTCGGCTGCCCTCGGA
189194 TTCCCTCGCATAGCTCGCTCGGCTGCCCTCGGA
1 TTCCCTCGCATAGCTCGCTCGGCTGCCCTCGGA
*
189227 TTCCCTCGCATAGCTCGCTCGGATGCCCTCGGA
1 TTCCCTCGCATAGCTCGCTCGGCTGCCCTCGGA
189260 TTCCCTCG-ATAGCTCG-TCGG
1 TTCCCTCGCATAGCTCGCTCGG
189280 ATGGCCTCAG
Statistics
Matches: 84, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
31 4 0.05
32 14 0.17
33 66 0.79
ACGTcount: A:0.10, C:0.40, G:0.24, T:0.25
Consensus pattern (33 bp):
TTCCCTCGCATAGCTCGCTCGGCTGCCCTCGGA
Found at i:189300 original size:41 final size:40
Alignment explanation
Indices: 189248--189327 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
189238 AGCTCGCTCG
* *
189248 GATGCCCTCGGATTCCCTC-GATAGCTCGTCGGATGGCCTCA
1 GATGCCCTCGGATGCCCTCAGAT-GCTC-TCGGATAGCCTCA
* *
189289 GATGCTCTCGGATGGCCTCAGATGCTCTCGGATAGCCTC
1 GATGCCCTCGGATGCCCTCAGATGCTCTCGGATAGCCTC
189328 GTCGGATGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 11 0.32
41 20 0.59
42 3 0.09
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGCCCTCGGATGCCCTCAGATGCTCTCGGATAGCCTCA
Found at i:189301 original size:20 final size:20
Alignment explanation
Indices: 189248--189327 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
189238 AGCTCGCTCG
* **
189248 GATGCCCTCGGATTCCCTC-
1 GATGCTCTCGGATGGCCTCA
189267 GATAGCTCGTCGGATGGCCTCA
1 GAT-GCTC-TCGGATGGCCTCA
189289 GATGCTCTCGGATGGCCTCA
1 GATGCTCTCGGATGGCCTCA
*
189309 GATGCTCTCGGATAGCCTC
1 GATGCTCTCGGATGGCCTC
189328 GTCGGATGGC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.06
20 34 0.63
21 14 0.26
22 3 0.06
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.25
Consensus pattern (20 bp):
GATGCTCTCGGATGGCCTCA
Found at i:189302 original size:10 final size:11
Alignment explanation
Indices: 189271--189347 Score: 65
Period size: 10 Copynumber: 7.2 Consensus size: 11
189261 TCCCTCGATA
189271 GCTCGTCGGATG
1 GCTC-TCGGATG
*
189283 GC-CTCAGAT-
1 GCTCTCGGATG
189292 GCTCTCGGATG
1 GCTCTCGGATG
*
189303 GC-CTCAGAT-
1 GCTCTCGGATG
189312 GCTCTCGGATAG
1 GCTCTCGGAT-G
*
189324 CCTCGTCGGATG
1 GCTC-TCGGATG
189336 GC-CTCGGATG
1 GCTCTCGGATG
189346 GC
1 GC
189348 CAGCGTGTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 4 0.08
10 32 0.60
11 4 0.08
12 7 0.13
13 6 0.11
ACGTcount: A:0.13, C:0.30, G:0.34, T:0.23
Consensus pattern (11 bp):
GCTCTCGGATG
Found at i:189332 original size:53 final size:51
Alignment explanation
Indices: 189244--189345 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 51
189234 GCATAGCTCG
* *
189244 CTCGGATGCCCTCGGATTCCCTCGATAGCTCGTCGGATGGCCTCAGATGCT
1 CTCGGATGCCCTCAGATGCCCTCGATAGCTCGTCGGATGGCCTCAGATGCT
* * *
189295 CTCGGATGGCCTCAGATGCTCTCGGATAGCCTCGTCGGATGGCCTCGGATG
1 CTCGGATGCCCTCAGATGCCCTC-GATAG-CTCGTCGGATGGCCTCAGATG
189346 GCCAGCGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 19 0.43
52 5 0.11
53 20 0.45
ACGTcount: A:0.14, C:0.31, G:0.30, T:0.25
Consensus pattern (51 bp):
CTCGGATGCCCTCAGATGCCCTCGATAGCTCGTCGGATGGCCTCAGATGCT
Found at i:189348 original size:10 final size:10
Alignment explanation
Indices: 189244--189348 Score: 63
Period size: 10 Copynumber: 10.1 Consensus size: 10
189234 GCATAGCTCG
*
189244 CTCGGATGCC
1 CTCGGATGGC
**
189254 CTCGGATTCC
1 CTCGGATGGC
*
189264 CTC-GATAGC
1 CTCGGATGGC
189273 TCGTCGGATGGC
1 -C-TCGGATGGC
*
189285 CTCAGAT-GC
1 CTCGGATGGC
189294 TCTCGGATGGC
1 -CTCGGATGGC
*
189305 CTCAGAT-GC
1 CTCGGATGGC
*
189314 TCTCGGATAGCC
1 -CTCGGAT-GGC
189326 TCGTCGGATGGC
1 -C-TCGGATGGC
189338 CTCGGATGGC
1 CTCGGATGGC
189348 C
1 C
189349 AGCGTGTTGG
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
9 8 0.11
10 46 0.61
11 6 0.08
12 10 0.13
13 6 0.08
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.24
Consensus pattern (10 bp):
CTCGGATGGC
Found at i:189421 original size:16 final size:16
Alignment explanation
Indices: 189397--189427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
189387 AGCTCGTCGG
189397 GAAGACATGGCGACCC
1 GAAGACATGGCGACCC
*
189413 GAAGGCATGGCGACC
1 GAAGACATGGCGACC
189428 TACGGCCAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.35, T:0.06
Consensus pattern (16 bp):
GAAGACATGGCGACCC
Done.