Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002353.1 Hibiscus syriacus cultivar Beakdansim tig00004803_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: 124830
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2352 original size:2 final size:2
Alignment explanation
Indices: 2347--2382 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2337 TTTCACACAA
2347 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
2383 TTGTTGAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3010 original size:2 final size:2
Alignment explanation
Indices: 3003--3031 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2993 AGGAAACCCA
3003 AT 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 AT A
3032 ATGATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4333 original size:9 final size:9
Alignment explanation
Indices: 4319--4343 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4309 AAATCGGTTC
4319 ATTAACCGA
1 ATTAACCGA
4328 ATTAACCGA
1 ATTAACCGA
4337 ATTAACC
1 ATTAACC
4344 TTTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (9 bp):
ATTAACCGA
Found at i:4489 original size:20 final size:20
Alignment explanation
Indices: 4453--4492 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4443 TGTTTGAATC
*
4453 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
4473 AAATTAATT-GTAAATTATTT
1 AAATTAATTAG-AAATTATTT
4493 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:15636 original size:3 final size:3
Alignment explanation
Indices: 15628--15671 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
15618 TGTATTTTCA
15628 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15672 AACTAAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16343 original size:16 final size:16
Alignment explanation
Indices: 16344--16386 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
16334 TATTTATAAA
16344 TATAAATTCGACTAGT
1 TATAAATTCGACTAGT
* *
16360 TATAAATTCAACTATT
1 TATAAATTCGACTAGT
16376 TATAAATTCGA
1 TATAAATTCGA
16387 TTTAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (16 bp):
TATAAATTCGACTAGT
Found at i:16348 original size:22 final size:22
Alignment explanation
Indices: 16320--16366 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
16310 TAATGGTTGG
*
16320 AATATAAATTCGACTATTTATA
1 AATATAAATTCGACTAGTTATA
16342 AATATAAATTCGACTAGTTATA
1 AATATAAATTCGACTAGTTATA
16364 AAT
1 AAT
16367 TCAACTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
AATATAAATTCGACTAGTTATA
Found at i:16427 original size:11 final size:11
Alignment explanation
Indices: 16413--16508 Score: 50
Period size: 11 Copynumber: 8.2 Consensus size: 11
16403 TCTATTTAAA
*
16413 TATTTAGTCAT
1 TATTTAATCAT
* *
16424 TATTAAATAAT
1 TATTTAATCAT
16435 TATTAGTAATCAT
1 TATT--TAATCAT
*
16448 TATTAAATCAT
1 TATTTAATCAT
* *
16459 TA-TTAGTAAT
1 TATTTAATCAT
16469 TATTATAATTTCAT
1 TATT-TAA--TCAT
16483 TATTACTAATCAT
1 TATT--TAATCAT
* *
16496 TACTAAATCAT
1 TATTTAATCAT
16507 TA
1 TA
16509 ATATCAAATC
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
10 7 0.11
11 29 0.45
12 2 0.03
13 16 0.25
14 7 0.11
15 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (11 bp):
TATTTAATCAT
Found at i:16448 original size:24 final size:24
Alignment explanation
Indices: 16420--16554 Score: 118
Period size: 24 Copynumber: 5.7 Consensus size: 24
16410 AAATATTTAG
*
16420 TCATTATTAAATAATTATTAGTAA
1 TCATTATTAAATCATTATTAGTAA
16444 TCATTATTAAATCATTATTAGTAA
1 TCATTATTAAATCATTATTAGTAA
* * *
16468 TTATTA-TAATTTCATTATTACTAA
1 TCATTATTAA-ATCATTATTAGTAA
* *
16492 TCATTACTAAATCATTAATA-TCAA
1 TCATTATTAAATCATTATTAGT-AA
* * *
16516 --ATCATTAAAT-ATTAATAATAAA
1 TCATTATTAAATCATTATTAGT-AA
*
16538 TCATTACTAAATCATTA
1 TCATTATTAAATCATTA
16555 AATATCAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
21 7 0.08
22 11 0.12
23 4 0.04
24 63 0.68
25 7 0.08
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (24 bp):
TCATTATTAAATCATTATTAGTAA
Found at i:16519 original size:14 final size:14
Alignment explanation
Indices: 16500--16570 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
16490 AATCATTACT
16500 AAATCATTAATATC
1 AAATCATTAATATC
16514 AAATCATTAAATAT-
1 AAATCATT-AATATC
* * *
16528 TAATAATAAATCATTAC
1 AAATCATTAAT-A-T-C
16545 TAAATCATTAAATATC
1 -AAATCATT-AATATC
16561 AAATCATTAA
1 AAATCATTAA
16571 ATATTAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
13 3 0.07
14 16 0.36
15 14 0.32
16 1 0.02
17 1 0.02
18 6 0.14
19 3 0.07
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:16531 original size:21 final size:22
Alignment explanation
Indices: 16499--16589 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 22
16489 TAATCATTAC
16499 TAAATCATTAAT-ATCAAATCAT
1 TAAATCATTAATAAT-AAATCAT
16521 TAAAT-ATTAATAATAAATCATT
1 TAAATCATTAATAATAAATCA-T
16543 ACTAAATCATTAA-ATATCAAATCAT
1 --TAAATCATTAATA-AT-AAATCAT
16568 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATCAT
16589 T
1 T
16590 CGTAGTATCA
Statistics
Matches: 61, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
21 20 0.33
22 15 0.25
23 6 0.10
24 6 0.10
25 8 0.13
26 6 0.10
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:16566 original size:15 final size:15
Alignment explanation
Indices: 16500--16574 Score: 75
Period size: 15 Copynumber: 4.9 Consensus size: 15
16490 AATCATTACT
16500 AAATCATT-AATATC
1 AAATCATTAAATATC
16514 AAATCATTAAATAT-
1 AAATCATTAAATATC
* *
16528 TAAT-AATAAATCATTAC
1 AAATCATTAAAT-A-T-C
16545 TAAATCATTAAATATC
1 -AAATCATTAAATATC
16561 AAATCATTAAATAT
1 AAATCATTAAATAT
16575 TAATAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.12
14 12 0.24
15 20 0.40
16 1 0.02
17 1 0.02
18 4 0.08
19 6 0.12
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:16574 original size:47 final size:46
Alignment explanation
Indices: 16490--16589 Score: 191
Period size: 47 Copynumber: 2.2 Consensus size: 46
16480 CATTATTACT
16490 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
16536 AATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATA
1 AATCATTACTAAATCATT-AATATCAAATCATTAAATATTAATAATA
16583 AATCATT
1 AATCATT
16590 CGTAGTATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 18 0.34
47 35 0.66
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (46 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
Found at i:17207 original size:66 final size:66
Alignment explanation
Indices: 17101--17234 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 66
17091 CACCATCCTC
* *
17101 TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
1 TACCCCTTTCATTGCCCTCAACATACCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
17166 T
66 T
* * *
17167 TACCCCTTTCATTGCCCTCAACATACCA-GAAATTTATAAAGGTTTTCAGCAATAGCCAAAATAT
1 TACCCCTTTCATTGCCCTCAACATACCATG-AATTTATAAAGGTTTTCAACAACAACCAAAATAT
17231 TT
65 TT
17233 TA
1 TA
17235 GGATTTAGGG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.02
66 61 0.98
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.34
Consensus pattern (66 bp):
TACCCCTTTCATTGCCCTCAACATACCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
T
Found at i:17434 original size:326 final size:326
Alignment explanation
Indices: 16841--17494 Score: 1290
Period size: 326 Copynumber: 2.0 Consensus size: 326
16831 CACCATCCTC
16841 TACCCCTTTCATTGCCCTCAACATACCAGAAATTTATAAAGGTTTTCAGCAATAGCCAAAATATT
1 TACCCCTTTCATTGCCCTCAACATACCAGAAATTTATAAAGGTTTTCAGCAATAGCCAAAATATT
16906 TTAGGATTTAAGGTTCACAAAATCAATATACAACAAATAATATAAGCAACTCTTGATTTTATGAA
66 TTAGGATTTAAGGTTCACAAAATCAATATACAACAAATAATATAAGCAACTCTTGATTTTATGAA
16971 TTCTAAACCCTAACCCCTAAAATATTTTGGCTATTGCTAAAAACCCTAAAGCCTAACCATTCTCC
131 TTCTAAACCCTAACCCCTAAAATATTTTGGCTATTGCTAAAAACCCTAAAGCCTAACCATTCTCC
*
17036 CTCCAATCAATTTCTTATAAAAAAACAAATCTGTAACCACCATCATGGTAGATATCACCATCCTC
196 CTCCAATCAATTTCTTATAAAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTC
17101 TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
261 TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
17166 T
326 T
17167 TACCCCTTTCATTGCCCTCAACATACCAGAAATTTATAAAGGTTTTCAGCAATAGCCAAAATATT
1 TACCCCTTTCATTGCCCTCAACATACCAGAAATTTATAAAGGTTTTCAGCAATAGCCAAAATATT
*
17232 TTAGGATTTAGGGTTCACAAAATCAATATACAACAAATAATATAAGCAACTCTTGATTTTATGAA
66 TTAGGATTTAAGGTTCACAAAATCAATATACAACAAATAATATAAGCAACTCTTGATTTTATGAA
17297 TTCTAAACCCTAACCCCTAAAATATTTTGGCTATTGCTAAAAACCCTAAAGCCTAACCATTCTCC
131 TTCTAAACCCTAACCCCTAAAATATTTTGGCTATTGCTAAAAACCCTAAAGCCTAACCATTCTCC
17362 CTCCAATCAATTTCTTATAAAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTC
196 CTCCAATCAATTTCTTATAAAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTC
17427 TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
261 TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
17492 T
326 T
17493 TA
1 TA
17495 GGGTTTAAGG
Statistics
Matches: 326, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 326 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (326 bp):
TACCCCTTTCATTGCCCTCAACATACCAGAAATTTATAAAGGTTTTCAGCAATAGCCAAAATATT
TTAGGATTTAAGGTTCACAAAATCAATATACAACAAATAATATAAGCAACTCTTGATTTTATGAA
TTCTAAACCCTAACCCCTAAAATATTTTGGCTATTGCTAAAAACCCTAAAGCCTAACCATTCTCC
CTCCAATCAATTTCTTATAAAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTC
TACCCCTTTCATTTCCCTCAACATATCATGAATTTATAAAGGTTTTCAACAACAACCAAAATATT
T
Found at i:19294 original size:22 final size:22
Alignment explanation
Indices: 19269--19310 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19259 AAACAGAGAG
*
19269 AAAAACATGTGATAATGATATA
1 AAAAACATGTGATAAAGATATA
* *
19291 AAAAATATGTTATAAAGATA
1 AAAAACATGTGATAAAGATA
19311 GAGATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAAACATGTGATAAAGATATA
Found at i:20650 original size:13 final size:13
Alignment explanation
Indices: 20632--20657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20622 TATATTTTCT
20632 GAATTTTTATTTA
1 GAATTTTTATTTA
20645 GAATTTTTATTTA
1 GAATTTTTATTTA
20658 AAAAATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
GAATTTTTATTTA
Found at i:20884 original size:22 final size:21
Alignment explanation
Indices: 20857--20908 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
20847 TTCTAATCCC
20857 CCTAAATCCATAAATCCCTAA-A
1 CCTAAATCCATAAA--CCTAATA
* *
20879 CTTAAATCCTTAAACCTAATA
1 CCTAAATCCATAAACCTAATA
20900 CCTAAATCC
1 CCTAAATCC
20909 CTAATCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 12 0.46
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (21 bp):
CCTAAATCCATAAACCTAATA
Found at i:20919 original size:21 final size:20
Alignment explanation
Indices: 20881--20923 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
20871 TCCCTAAACT
* *
20881 TAAATCCTTAAACCTAATACC
1 TAAATCCCTAAACATAAT-CC
*
20902 TAAATCCCTAATCATAATCC
1 TAAATCCCTAAACATAATCC
20922 TA
1 TA
20924 CATTTATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATCCCTAAACATAATCC
Found at i:23774 original size:6 final size:6
Alignment explanation
Indices: 23763--23789 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23753 GTACAGTTGC
23763 TTCGTT TTCGTT TTCGTT TTCGTT TTC
1 TTCGTT TTCGTT TTCGTT TTCGTT TTC
23790 TTCTTTGCTC
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:0.00, C:0.19, G:0.15, T:0.67
Consensus pattern (6 bp):
TTCGTT
Found at i:25371 original size:16 final size:16
Alignment explanation
Indices: 25337--25377 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
25327 GTTTACTTCA
*
25337 GAATGATT-AAGTACT
1 GAATGATTCAAATACT
*
25352 GAATGATTCAAATGCT
1 GAATGATTCAAATACT
25368 GAATGATTCA
1 GAATGATTCA
25378 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATACT
Found at i:27770 original size:19 final size:19
Alignment explanation
Indices: 27726--27770 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
27716 GCACATTGCT
* *
27726 TATATTTTTTATTTTTAGA
1 TATATTTTATATATTTAGA
*
27745 TAAATTTTATATATTTAGA
1 TATATTTTATATATTTAGA
*
27764 TCTATTT
1 TATATTT
27771 GCTTATTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TATATTTTATATATTTAGA
Found at i:27964 original size:27 final size:27
Alignment explanation
Indices: 27925--27977 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
27915 TAATTTTTTT
*
27925 AAATATTACTTTTATTAAAT-AATTTAA
1 AAATAATACTTTT-TTAAATAAATTTAA
* *
27952 AAATAATATTTTTTTAAGTAAATTTA
1 AAATAATACTTTTTTAAATAAATTTA
27978 CCAATGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
AAATAATACTTTTTTAAATAAATTTAA
Found at i:33363 original size:2 final size:2
Alignment explanation
Indices: 33358--33382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33348 CAACTCCATT
33358 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 T
33383 TCTGATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43861 original size:24 final size:24
Alignment explanation
Indices: 43829--43883 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
43819 GGCTTCAACT
43829 TTCCATCAAATGAGTGAAAGTGAA
1 TTCCATCAAATGAGTGAAAGTGAA
43853 TTCCATCAAATGAGTGAAAGTGAA
1 TTCCATCAAATGAGTGAAAGTGAA
*
43877 TTTCATC
1 TTCCATC
43884 CAAGAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (24 bp):
TTCCATCAAATGAGTGAAAGTGAA
Found at i:44125 original size:38 final size:38
Alignment explanation
Indices: 44060--44155 Score: 149
Period size: 38 Copynumber: 2.5 Consensus size: 38
44050 ACTTTATTTT
*
44060 GGTCGAGTCGGGTC-GGTTTTTTTAAGTGTGATATTCG
1 GGTCGAGTCGGGTCGGGTTTTTTAAAGTGTGATATTCG
*
44097 GGTCGAGTCCGGTCGGGTTTTTTAAAGTGTGATATTCG
1 GGTCGAGTCGGGTCGGGTTTTTTAAAGTGTGATATTCG
*
44135 GGTCGGGTCGGGTTCGGGTTT
1 GGTCGAGTCGGG-TCGGGTTT
44156 AGGGTGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 13 0.25
38 32 0.60
39 8 0.15
ACGTcount: A:0.11, C:0.12, G:0.39, T:0.38
Consensus pattern (38 bp):
GGTCGAGTCGGGTCGGGTTTTTTAAAGTGTGATATTCG
Found at i:44817 original size:18 final size:17
Alignment explanation
Indices: 44766--44818 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
44756 TATAGAATTG
* *
44766 GATTCCAATTTCTGACA
1 GATTACAATTTCTCACA
*
44783 GATTACAATTCCTTCACA
1 GATTACAATTTC-TCACA
*
44801 GATTTCAATTATCTCACA
1 GATTACAATT-TCTCACA
44819 AACATTCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 10 0.34
18 18 0.62
19 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (17 bp):
GATTACAATTTCTCACA
Found at i:46986 original size:27 final size:27
Alignment explanation
Indices: 46932--47004 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
46922 TTTATTTGGT
*
46932 TTGAAAATGAGTCATCTTTTTTTATTAA
1 TTGAAAATGAGTCCT-TTTTTTTATTAA
46960 TTGAAAATGAGTCCTTTTTTTTATTAA
1 TTGAAAATGAGTCCTTTTTTTTATTAA
46987 TTGAAAATGAGTCCTTTT
1 TTGAAAATGAGTCCTTTT
47005 AGTTCAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 30 0.68
28 14 0.32
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (27 bp):
TTGAAAATGAGTCCTTTTTTTTATTAA
Found at i:47014 original size:26 final size:26
Alignment explanation
Indices: 46932--47014 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
46922 TTTATTTGGT
*
46932 TTGAAAATGAGTCATCTTTT-TTTATTAA
1 TTGAAAATGAGTC--CTTTTGTTCA-TAA
* *
46960 TTGAAAATGAGTCCTTTTTTTTATTAA
1 TTGAAAATGAGTCCTTTTGTTCA-TAA
46987 TTGAAAATGAGTCCTTTTAGTTCA-AA
1 TTGAAAATGAGTCCTTTT-GTTCATAA
47013 TT
1 TT
47015 ATCGAGAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.18
27 26 0.51
28 16 0.31
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (26 bp):
TTGAAAATGAGTCCTTTTGTTCATAA
Found at i:48516 original size:19 final size:18
Alignment explanation
Indices: 48481--48524 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
48471 ACGATAAAAA
*
48481 TAATTTTATATCAATTTT
1 TAATTTTTTATCAATTTT
*
48499 TAATTTTTTTTCACATTTT
1 TAATTTTTTATCA-ATTTT
48518 T-ATTTTT
1 TAATTTTT
48525 CATAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATTTTTTATCAATTTT
Found at i:51831 original size:30 final size:30
Alignment explanation
Indices: 51795--51852 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
51785 TACATTCTGT
51795 ACTTTATCATAGGAAAAATATGTTAAATGC
1 ACTTTATCATAGGAAAAATATGTTAAATGC
51825 ACTTTATCATAGGAAAAATATGTTAAAT
1 ACTTTATCATAGGAAAAATATGTTAAAT
51853 TCAAGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (30 bp):
ACTTTATCATAGGAAAAATATGTTAAATGC
Found at i:63999 original size:2 final size:2
Alignment explanation
Indices: 63987--64017 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
63977 ATATTTTATT
*
63987 TA TA AA 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 TA TA T
64018 TTTCTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:64575 original size:24 final size:28
Alignment explanation
Indices: 64508--64565 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
64498 TAAACCCTTC
* *
64508 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATACTTATTA
64536 TTTTCATAATATTTATATATA-TTATT-
1 TTTTCATAATATTTATATATACTTATTA
64562 TTTT
1 TTTT
64566 ATATCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 19 0.68
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTCATAATATTTATATATACTTATTA
Found at i:68696 original size:17 final size:17
Alignment explanation
Indices: 68653--68697 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
68643 TCGTCCATCA
68653 AAAAAAG-AAATAAAGG
1 AAAAAAGTAAATAAAGG
68669 AAAAAAGTAAATAAAGG
1 AAAAAAGTAAATAAAGG
*
68686 AAAAAATTAAAT
1 AAAAAAGTAAAT
68698 CAAGATGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (17 bp):
AAAAAAGTAAATAAAGG
Found at i:74090 original size:113 final size:113
Alignment explanation
Indices: 73892--74468 Score: 689
Period size: 113 Copynumber: 4.9 Consensus size: 113
73882 TAGCAAATAT
73892 TCGAATTCATCACTTA-ATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTG
1 TCGAATTCATCAC-TAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTG
* * *
73956 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
74005 TCGAATTCATCACTCGATGGATCAACATTCCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
74070 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-ATTTGTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT-TGC
*
74118 TCG-ATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGATAAAGTTCATAATGAGAA
1 TCGAATTC-ATCAC---------TAGAT--GGATCAACATTTCCAGATAAAGTTCATAATGAGAA
* *
74182 GAACTCATCAGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
74242 TCGAATTCATCACTCGATGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAA
1 TCGAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
74307 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** *
74354 TTGATACTATCAATGAATGAGATAGATCAGCATCAACATTTCCAGA-AGTGTTCATAACGAGAAG
1 TCGA-A-T-TC-ATCACT-AGAT-G----G-ATCAACATTTCCAGATAAAGTTCATAATGAGAAG
*
74418 AACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAATAACTTGTTCAAC
55 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
74469 ATTTCCTTAA
Statistics
Matches: 405, Mismatches: 31, Indels: 47
0.84 0.06 0.10
Matches are distributed among these distances:
112 55 0.14
113 154 0.38
114 1 0.00
115 6 0.01
116 4 0.01
117 3 0.01
118 1 0.00
122 63 0.16
123 17 0.04
124 94 0.23
125 7 0.02
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (113 bp):
TCGAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:74168 original size:124 final size:123
Alignment explanation
Indices: 74025--74472 Score: 595
Period size: 124 Copynumber: 3.7 Consensus size: 123
74015 CACTCGATGG
*
74025 ATCAACATTCCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
74090 AATGAGAAGAACTTGTTCAA-ATTTGTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACATTT-TGCTCGATTCTATCACAGAA-GAGATAGATCAGC
* *
74149 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
74214 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCAC--------TCGAT--GC
66 AATGAGAAGAACTTGTTCAACATTTTGCTCG-ATTCTATCACAGAAGAGATAGATCAGC
* * * *
74262 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAG-AGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
74326 AATGAGAAGAACTTGTTCAACCTTTTGCTTGATACTATCA-ATGAATGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACATTTTGCTCGATTCTATCACA-GAA-GAGATAGATCAGC
** *
74385 ATCAACATTTCCAGA-AGTGTTCATAACGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
74448 AATGAGAATAACTTGTTCAACATTT
66 AATGAGAAGAACTTGTTCAACATTT
74473 CCTTAATTCA
Statistics
Matches: 286, Mismatches: 22, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
111 3 0.01
112 50 0.17
113 44 0.15
115 4 0.01
121 4 0.01
122 62 0.22
123 19 0.07
124 93 0.33
125 7 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACATTTTGCTCGATTCTATCACAGAAGAGATAGATCAGC
Found at i:74343 original size:20 final size:20
Alignment explanation
Indices: 74281--74344 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
74271 TCCAGAGAAA
74281 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
74301 -ATC-TAAAGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACTT
74320 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
74340 GTTCA
1 GTTCA
74345 ACCTTTTGCT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 13 0.42
21 5 0.16
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:76509 original size:18 final size:18
Alignment explanation
Indices: 76486--76523 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
76476 ATTAGTCATA
76486 TAAATA-TATATATTTATT
1 TAAATATTA-ATATTTATT
76504 TAAATATTAATATTTATT
1 TAAATATTAATATTTATT
76522 TA
1 TA
76524 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATATTAATATTTATT
Found at i:76521 original size:22 final size:23
Alignment explanation
Indices: 76491--76536 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
76481 TCATATAAAT
76491 ATATATATTTA-TTTAAATATTA
1 ATATATATTTATTTTAAATATTA
* *
76513 ATATTTATTTATTTTTAATATTA
1 ATATATATTTATTTTAAATATTA
76536 A
1 A
76537 GAAATGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATATATTTATTTTAAATATTA
Found at i:76763 original size:2 final size:2
Alignment explanation
Indices: 76751--76789 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
76741 ATATCTTATT
*
76751 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76790 TTTCTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:76807 original size:148 final size:145
Alignment explanation
Indices: 76507--76810 Score: 397
Period size: 148 Copynumber: 2.1 Consensus size: 145
76497 ATTTATTTAA
*
76507 ATATTAATATTTATTTATTTTTAATATTAAGAAATGGGTTGTCTTAAAGCATCTAGAAGCTCTTT
1 ATATTAATATTTATTTATTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTTT
* *
76572 TTTGATATTCTTAAATAAATAAATATTCTATTTTTATAAATTATATATATTAATTTATTTTAATT
66 TTTGATATTCTTAAATAAATAAATATTCTATATTTATAAATTATATATATTAATTTATATTAATT
76637 ATTTTTAGAAAAATATT
131 ATTTTT--AAAAATATT
*
76654 TTATTAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAG-T-TT
1 ATATTAATATTTATTTA-TTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTT
*
76717 TTTCTGATATT-TCTAAGTAAATAAATA-TCT-TATTTATAAATATATATATATATATATATATA
65 TTT-TGATATTCT-TAAATAAATAAATATTCTATATTTATAAAT-TATATATAT-TA-AT-T-TA
*
76779 TATTAATATATTTTCT-TAAA-ATT
123 TATTAAT-TATTTT-TAAAAATATT
76802 ATATTAATA
1 ATATTAATA
76811 AATAACAGAA
Statistics
Matches: 140, Mismatches: 7, Indels: 19
0.84 0.04 0.11
Matches are distributed among these distances:
145 10 0.07
146 18 0.13
147 39 0.28
148 54 0.39
149 4 0.03
150 8 0.06
151 6 0.04
152 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (145 bp):
ATATTAATATTTATTTATTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTTT
TTTGATATTCTTAAATAAATAAATATTCTATATTTATAAATTATATATATTAATTTATATTAATT
ATTTTTAAAAATATT
Found at i:88925 original size:22 final size:22
Alignment explanation
Indices: 88893--88965 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
88883 TATTTGAACT
88893 TTTAAAAACTATGTATCTTAAG
1 TTTAAAAACTATGTATCTTAAG
* *
88915 TTTAAATACTA--AAT-TTAA-
1 TTTAAAAACTATGTATCTTAAG
**
88933 -AAAAAAACTATGTATCTTAAG
1 TTTAAAAACTATGTATCTTAAG
88954 TTTAAAAACTAT
1 TTTAAAAACTAT
88966 ATCTTTGATT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
17 7 0.18
19 6 0.16
20 6 0.16
22 19 0.50
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (22 bp):
TTTAAAAACTATGTATCTTAAG
Found at i:96087 original size:23 final size:23
Alignment explanation
Indices: 96061--96129 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
96051 CACCACAGCT
*
96061 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
96084 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
96107 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
96130 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:97966 original size:21 final size:21
Alignment explanation
Indices: 97942--97986 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
97932 TTTTGTTCGT
* *
97942 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
97963 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
97984 TTG
1 TTG
97987 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:101942 original size:56 final size:56
Alignment explanation
Indices: 101882--101994 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
101872 ACATAATTTT
101882 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
101938 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
101994 A
1 A
101995 GGGTAAAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (56 bp):
AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
Found at i:105151 original size:3 final size:3
Alignment explanation
Indices: 105135--105178 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
105125 ATACCAAAAA
*
105135 TAT TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
105179 AACAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:106651 original size:23 final size:23
Alignment explanation
Indices: 106618--106685 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
106608 ATTATTATAT
* *
106618 GGCACTACGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
**
106641 GGCACTTCGGTGCAATTCTACTT
1 GGCACTTCGGTGCAATTCTACGC
* *
106664 GGCACTTTGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
106686 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:107211 original size:2 final size:2
Alignment explanation
Indices: 107129--107196 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
107119 TGTATAAACT
*
107129 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
107171 TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
107197 GTATTTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:109806 original size:25 final size:23
Alignment explanation
Indices: 109778--109837 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
109768 AAATCACTAA
109778 TTTTTTAAAATAAAAGTCATAACTG
1 TTTTTTAAAATAAAA--CATAACTG
* * *
109803 TTTTTTTAAATAATACATAATTG
1 TTTTTTAAAATAAAACATAACTG
*
109826 TTTTTCAAAATA
1 TTTTTTAAAATA
109838 GTTATGACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 17 0.57
25 13 0.43
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAATAAAACATAACTG
Found at i:123342 original size:31 final size:31
Alignment explanation
Indices: 123319--123397 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
123309 CATAGATTCT
* *
123319 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
123350 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
123381 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
123398 CCTCGACCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:124012 original size:35 final size:37
Alignment explanation
Indices: 123955--124023 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
123945 TCATTTAGGG
123955 GGAATCGATACTCCCCCA-GGGGGAATATGTTCCTGA
1 GGAATCGATACTCCCCCAGGGGGGAATATGTTCCTGA
*
123991 GGAATCGATAC-CCCCCAGGGGGGAATCTGTTCC
1 GGAATCGATACTCCCCCAGGGGGGAATATGTTCC
124024 CCCTGCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.23, C:0.28, G:0.29, T:0.20
Consensus pattern (37 bp):
GGAATCGATACTCCCCCAGGGGGGAATATGTTCCTGA
Done.