Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008802.1 Hibiscus syriacus cultivar Beakdansim tig00111952_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: 1147353
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1094502 original size:20 final size:18
Alignment explanation
Indices: 1094453--1094526 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 18
1094443 TACATACCAT
* *
1094453 ATATATATATATATATATAT
1 ATATACATATAT-TAT-TAC
* *
1094473 ATATATATATATTGTTAC
1 ATATACATATATTATTAC
*
1094491 ATTATTACATATCTTATTAC
1 A-TA-TACATATATTATTAC
1094511 ATATACATAT-TTATTA
1 ATATACATATATTATTA
1094527 TTTCTTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.13
18 10 0.21
19 6 0.13
20 25 0.53
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (18 bp):
ATATACATATATTATTAC
Found at i:1095652 original size:16 final size:17
Alignment explanation
Indices: 1095627--1095663 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1095617 TGTTAATTGT
*
1095627 TTTTTAATTTTTTTTTA
1 TTTTTAATTTTTTATTA
1095644 TTTTT-ATTTTTTATTA
1 TTTTTAATTTTTTATTA
1095660 TTTT
1 TTTT
1095664 AGTTCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTAATTTTTTATTA
Found at i:1095670 original size:61 final size:61
Alignment explanation
Indices: 1095562--1095724 Score: 168
Period size: 61 Copynumber: 2.6 Consensus size: 61
1095552 TAATTAAATA
* * * *
1095562 GTTTTTTAAAATTTTATTTTATTTTAATTCTTTT-TAATCTTATTTCTTTTCCTCCTGTTAATT
1 GTTTTTT--AATTTTATTTTATTTTTATT-TTTTATTATCTTAGTTCTTTTACTCCTGTTAATT
* * * * *
1095625 GTTTTTTAATTTTTTTTTATTTTTATTTTTTATTATTTTAGTTCTTTTACTTCTTTTATTT
1 GTTTTTTAATTTTATTTTATTTTTATTTTTTATTATCTTAGTTCTTTTACTCCTGTTAATT
* * *
1095686 GTTTTTTAAATTAATGTTATTTTTATTTATTTATT-TCTT
1 GTTTTTTAATTTTATTTTATTTTTATTT-TTTATTATCTT
1095725 TTTGTATTCT
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
60 4 0.05
61 67 0.80
62 6 0.07
63 7 0.08
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.71
Consensus pattern (61 bp):
GTTTTTTAATTTTATTTTATTTTTATTTTTTATTATCTTAGTTCTTTTACTCCTGTTAATT
Found at i:1095810 original size:14 final size:14
Alignment explanation
Indices: 1095791--1095818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1095781 TATTTAGTTC
1095791 ATTTATTTATTTTT
1 ATTTATTTATTTTT
1095805 ATTTATTTATTTTT
1 ATTTATTTATTTTT
1095819 TTTCTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTATTTATTTTT
Found at i:1095995 original size:12 final size:12
Alignment explanation
Indices: 1095966--1096000 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1095956 TGACTCCCAA
*
1095966 CATTTCATAAAGT
1 CATTTCA-AAAAT
1095979 CATTTCAAAAAT
1 CATTTCAAAAAT
1095991 CATTTCAAAA
1 CATTTCAAAA
1096001 CAACATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (12 bp):
CATTTCAAAAAT
Found at i:1096437 original size:16 final size:17
Alignment explanation
Indices: 1096405--1096438 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1096395 AACTCCTTTA
*
1096405 TACTCTCATCAATATTT
1 TACTCTCAACAATATTT
1096422 TACTCTCAAC-ATATTT
1 TACTCTCAACAATATTT
1096438 T
1 T
1096439 CTTTAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (17 bp):
TACTCTCAACAATATTT
Found at i:1097186 original size:22 final size:22
Alignment explanation
Indices: 1097175--1097289 Score: 63
Period size: 23 Copynumber: 5.5 Consensus size: 22
1097165 TAAATTATAT
1097175 TAAT-TATTATTAAAATAAGAA
1 TAATATATTATTAAAATAAGAA
*
1097196 TAATATATTATT--AATTAG-A
1 TAATATATTATTAAAATAAGAA
*
1097215 TAAT-TACTTGTTAAAAT---AA
1 TAATATA-TTATTAAAATAAGAA
**
1097234 T-A-ATATTATTAAAATATTTAA
1 TAATATATTATTAAAATA-AGAA
*
1097255 -AATTATAATATTAAAATAAGAA
1 TAA-TATATTATTAAAATAAGAA
*
1097277 TATTATATATATT
1 TAATATAT-TATT
1097290 TTAAATATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 28
0.66 0.07 0.26
Matches are distributed among these distances:
17 9 0.13
18 5 0.07
19 11 0.15
20 5 0.07
21 10 0.14
22 13 0.18
23 18 0.25
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (22 bp):
TAATATATTATTAAAATAAGAA
Found at i:1097212 original size:41 final size:41
Alignment explanation
Indices: 1097160--1097289 Score: 110
Period size: 41 Copynumber: 3.2 Consensus size: 41
1097150 AAAATAAAAT
*
1097160 TATTATAAATTATATTAATTATTATTAAAATAAGAATAATA
1 TATTATTAATTATATTAATTATTATTAAAATAAGAATAATA
* * *
1097201 TATTATTAATTAGA-TAATTACTTGTTAAAATAATAAT-AT-
1 TATTATTAATTATATTAATTA-TTATTAAAATAAGAATAATA
* *
1097240 TATTA--AAATAT-TTAAAATTATAATATTAAAATAAGAATATTA
1 TATTATTAATTATATT--AATTAT--TATTAAAATAAGAATAATA
1097282 TATATATT
1 TAT-TATT
1097290 TTAAATATTC
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
37 5 0.07
38 1 0.01
39 10 0.14
40 21 0.30
41 27 0.39
42 3 0.04
43 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (41 bp):
TATTATTAATTATATTAATTATTATTAAAATAAGAATAATA
Found at i:1097348 original size:28 final size:28
Alignment explanation
Indices: 1097275--1097348 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 28
1097265 TTAAAATAAG
* * *
1097275 AATATTATATATATT-TTAAATATTCAAT
1 AATATTA-ATTTATTATTAATTATTAAAT
*
1097303 AATATT-A-TT-TTATGAATTATTAAAT
1 AATATTAATTTATTATTAATTATTAAAT
1097328 AATATTAATTTATTATTAATT
1 AATATTAATTTATTATTAATT
1097349 TATATGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
24 2 0.05
25 17 0.46
26 2 0.05
27 2 0.05
28 14 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
AATATTAATTTATTATTAATTATTAAAT
Found at i:1098639 original size:2 final size:2
Alignment explanation
Indices: 1098634--1098828 Score: 68
Period size: 2 Copynumber: 101.5 Consensus size: 2
1098624 TTTTTTACCC
* * *
1098634 CT CT CT CT CT CT -T C- CC CT CT CT CT C- CC CT AT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * * *
1098673 CC CAT AT AT CT CT CT CT CC CT CC CT CC CT CC CT CC CT CT CT CT
1 CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * * *
1098716 CT CT C- CC CT CT CC CT CC CT C- CC CT CC CT CC CT CC CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * *
1098756 CT CT CT CT C- CC CT CT C- CC CT CT CC CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
1098796 C- CC CT CT C- CC CT CT CT C- CAT CC CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT C
1098829 AAACACACAC
Statistics
Matches: 139, Mismatches: 42, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
1 10 0.07
2 128 0.92
3 1 0.01
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.35
Consensus pattern (2 bp):
CT
Found at i:1098655 original size:10 final size:11
Alignment explanation
Indices: 1098638--1098828 Score: 83
Period size: 12 Copynumber: 16.8 Consensus size: 11
1098628 TTACCCCTCT
1098638 CTCTCTCTTCCC
1 CTCTCTC-TCCC
1098650 CTCTCTCTCCC
1 CTCTCTCTCCC
1098661 CTATCTCTCTCTCC
1 C--TCTCTCTC-CC
* * *
1098675 CATATATCT-CT
1 C-TCTCTCTCCC
*
1098686 CTCTCCCTCCC
1 CTCTCTCTCCC
* *
1098697 TCCCTCCCTCCC
1 -CTCTCTCTCCC
1098709 TCTCTCTCTCTCC
1 -CTCTCTCTC-CC
*
1098722 C-CTCTCCCTCC
1 CTCTCTCTC-CC
*
1098733 CTC-CCCT-CC
1 CTCTCTCTCCC
* *
1098742 CTCCCTCCCTCC
1 CTCTCTCTC-CC
*
1098754 CTCTCTCTCTC
1 CTCTCTCTCCC
1098765 C-C-CTCTCCC
1 CTCTCTCTCCC
*
1098774 CTCTCCCTCCC
1 CTCTCTCTCCC
*
1098785 TCTCTCTCTCTC
1 -CTCTCTCTCCC
1098797 C-C-CTCTCCC
1 CTCTCTCTCCC
1098806 CTCTCTCCATCCC
1 CTCTCT-C-TCCC
1098819 TCTCTCTCTC
1 -CTCTCTCTC
1098829 AAACACACAC
Statistics
Matches: 138, Mismatches: 23, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
9 19 0.14
10 10 0.07
11 31 0.22
12 48 0.35
13 21 0.15
14 9 0.07
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.35
Consensus pattern (11 bp):
CTCTCTCTCCC
Found at i:1098719 original size:34 final size:34
Alignment explanation
Indices: 1098681--1098828 Score: 149
Period size: 34 Copynumber: 4.1 Consensus size: 34
1098671 CTCCCATATA
1098681 TCTCTCTCTCCCTCCCTCCCTCCCTCCCTCTCTC
1 TCTCTCTCTCCCTCCCTCCCTCCCTCCCTCTCTC
*
1098715 TCTCTCCCCTCTCCCTCCCTCCCCTCCCTCCCTCCCTCCC
1 TCTCT---CTCTCCCTCCCT-CCCTCCCTCCCT--CTCTC
1098755 TCTCTCTCTCCCCTCTCC-CCTCTCCCTCCCTCTCTC
1 TCTCTCTCT-CCCTC-CCTCC-CTCCCTCCCTCTCTC
* *
1098791 TCTCTC-C-CCTCTCCCCTCTCTCCATCCCTCTCTC
1 TCTCTCTCTCC-CT-CCCTCCCTCCCTCCCTCTCTC
1098825 TCTC
1 TCTC
1098829 AAACACACAC
Statistics
Matches: 98, Mismatches: 4, Indels: 24
0.78 0.03 0.19
Matches are distributed among these distances:
33 2 0.02
34 27 0.28
35 3 0.03
36 10 0.10
37 18 0.18
38 27 0.28
39 2 0.02
40 9 0.09
ACGTcount: A:0.01, C:0.66, G:0.00, T:0.34
Consensus pattern (34 bp):
TCTCTCTCTCCCTCCCTCCCTCCCTCCCTCTCTC
Found at i:1098743 original size:46 final size:47
Alignment explanation
Indices: 1098681--1098812 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 47
1098671 CTCCCATATA
* *
1098681 TCTCTCTCTCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCCC-CTCTCC
1 TCTCCCTC-CCCTCCCTCCCTCCCTCCCTCTCTCTCTC-CCCTCTCCCC
1098729 -CTCCCTCCCCTCCCTCCCTCCCTCCCTCTCTCTCTCCCCTCTCCCC
1 TCTCCCTCCCCTCCCTCCCTCCCTCCCTCTCTCTCTCCCCTCTCCCC
* * *
1098775 TCTCCCTCCCTCTCTCTCTCTCCCCTCTCCCCTCTCTC
1 TCTCCCTCCC-CTCCCTCCCT-CCCTC-CCTCTCTCTC
1098813 CATCCCTCTC
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
45 3 0.04
46 34 0.46
47 15 0.20
48 8 0.11
49 5 0.07
50 9 0.12
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (47 bp):
TCTCCCTCCCCTCCCTCCCTCCCTCCCTCTCTCTCTCCCCTCTCCCC
Found at i:1098819 original size:76 final size:74
Alignment explanation
Indices: 1098632--1098820 Score: 215
Period size: 76 Copynumber: 2.5 Consensus size: 74
1098622 TGTTTTTTAC
* * * * ***
1098632 CCCTCTCTCTCTCTTCCCCTCTCTCT-CC-CCTATCTCTCTCTCCCATATATCTCTCTCTCCCTC
1 CCCTCTCTCTCTC-TCCCCTCTCCCTCCCTCCCATCCCTCCCTCCC-TCCCTCTCTCTCTCCCTC
1098695 CCTCCCTCCCT
64 CCTCCCTCCCT
*
1098706 CCCTCTCTCTCTCTCCCCTCTCCCTCCCTCCCCTCCCTCCCTCCCTCCCTCTCTCTCTCCCCTCT
1 CCCTCTCTCTCTCTCCCCTCTCCCTCCCTCCCATCCCTCCCTCCCTCCCTCTCTCTCT-CCCTC-
1098771 CC-CCTCTCCCT
64 CCTCC-CTCCCT
*
1098782 CCCTCTCTCTCTCTCCCCTCTCCC-CTCTCTCCATCCCTC
1 CCCTCTCTCTCTCTCCCCTCTCCCTCCCTC-CCATCCCTC
1098821 TCTCTCTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
73 11 0.11
74 25 0.25
75 23 0.23
76 40 0.40
ACGTcount: A:0.03, C:0.63, G:0.00, T:0.34
Consensus pattern (74 bp):
CCCTCTCTCTCTCTCCCCTCTCCCTCCCTCCCATCCCTCCCTCCCTCCCTCTCTCTCTCCCTCCC
TCCCTCCCT
Found at i:1098824 original size:46 final size:45
Alignment explanation
Indices: 1098689--1098813 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 45
1098679 TATCTCTCTC
*
1098689 TCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCCCCTCTCCCTCCC
1 TCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCCCCTCTCCCTCTC
1098734 TCCCCTCCCTCCCTCCCT-CC-CTCTCTCTCTCCCCTCTCCC-CTC
1 T-CCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCCCCTCTCCCTCTC
* *
1098777 TCCCTCCCTCTCTCTCTCTCCCCTCTCCCCTCTCTCC
1 TCCCTCCCTC-C-CTCCCT-CCCTCT-CTCTCTCTCC
1098814 ATCCCTCTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
42 9 0.13
43 4 0.06
44 25 0.36
45 3 0.04
46 18 0.26
47 2 0.03
48 9 0.13
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (45 bp):
TCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCCCCTCTCCCTCTC
Found at i:1099282 original size:22 final size:21
Alignment explanation
Indices: 1099233--1099352 Score: 117
Period size: 22 Copynumber: 5.7 Consensus size: 21
1099223 AGGGTGTCAA
1099233 AGTGCATCCATGCACC--CCT
1 AGTGCATCCATGCACCTGCCT
1099252 GCAGTGCATCCATGCACCTGCACT
1 --AGTGCATCCATGCACCTGC-CT
*
1099276 AGTGCATCGATGCACCATG-C-
1 AGTGCATCCATGCACC-TGCCT
*
1099296 AGTGCATCCATGCACTTGCACT
1 AGTGCATCCATGCACCTGC-CT
*
1099318 AGTGCATCGATGCACCATG-C-
1 AGTGCATCCATGCACC-TGCCT
1099338 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1099353 TCCATTTCGA
Statistics
Matches: 85, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
19 2 0.02
20 28 0.33
21 19 0.22
22 29 0.34
23 5 0.06
24 2 0.02
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGCCT
Found at i:1099353 original size:42 final size:42
Alignment explanation
Indices: 1099233--1099353 Score: 206
Period size: 42 Copynumber: 2.9 Consensus size: 42
1099223 AGGGTGTCAA
* * *
1099233 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCGATGCA-CCATGCAGTGCATCCATGCACTTGCACT
1099276 AGTGCATCGATGCACCATGCAGTGCATCCATGCACTTGCACT
1 AGTGCATCGATGCACCATGCAGTGCATCCATGCACTTGCACT
1099318 AGTGCATCGATGCACCATGCAGTGCATCCATGCACT
1 AGTGCATCGATGCACCATGCAGTGCATCCATGCACT
1099354 CCATTTCGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 62 0.83
43 13 0.17
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCACCATGCAGTGCATCCATGCACTTGCACT
Found at i:1099397 original size:20 final size:20
Alignment explanation
Indices: 1099372--1099464 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 20
1099362 AATGCACTTA
* * *
1099372 GTGCATCAATGCATCCTGAT
1 GTGCATCGATGCATCATGTT
*
1099392 GTGCATCGATGCATCATTTT
1 GTGCATCGATGCATCATGTT
*
1099412 GTGCATCGATACATCATGTT
1 GTGCATCGATGCATCATGTT
* *
1099432 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCATGTT
*
1099452 GTGCATCCATGCA
1 GTGCATCGATGCA
1099465 CGAAGGCTGC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCATGTT
Found at i:1100348 original size:57 final size:57
Alignment explanation
Indices: 1100260--1100370 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
1100250 TCGTGAGACA
* *
1100260 ACAATCTCTGAACGCAAACTACATATCTATCAAAGATAAAGATTAAATTAGATTGGC
1 ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATTGGC
* * *
1100317 ACAATCTTTGAACGCAAACCACATATCTATCAAAGGTAAAGACTATATTAGATT
1 ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATT
1100371 ATCCAATCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (57 bp):
ACAATCTCTGAACGCAAACCACATATCTATCAAAGATAAAGACTAAATTAGATTGGC
Found at i:1101806 original size:12 final size:13
Alignment explanation
Indices: 1101789--1101818 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1101779 ACAAAAAAAT
1101789 AAAAAAA-GGCAA
1 AAAAAAAGGGCAA
1101801 AAAAAAAGGGCAA
1 AAAAAAAGGGCAA
1101814 AAAAA
1 AAAAA
1101819 CAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGGCAA
Found at i:1111150 original size:36 final size:36
Alignment explanation
Indices: 1111102--1111173 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1111092 GCTTTTAAAG
1111102 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
*
1111138 AAAGGGTTTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
1111174 TTTTATTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32
Consensus pattern (36 bp):
AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
Found at i:1111760 original size:20 final size:20
Alignment explanation
Indices: 1111735--1111784 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1111725 ATAAATAAAA
*
1111735 TATTTTATTGAAGAAGATAT
1 TATTTTATTGAAAAAGATAT
1111755 TATTTTATTGAAAAAGATAT
1 TATTTTATTGAAAAAGATAT
1111775 TATTTATATT
1 TATTT-TATT
1111785 TTTTAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TATTTTATTGAAAAAGATAT
Found at i:1112462 original size:21 final size:21
Alignment explanation
Indices: 1112438--1112508 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1112428 TACCCTTAAC
* * *
1112438 TTTAATCCTTAAATTATAAAT
1 TTTAAACCCTAAACTATAAAT
1112459 TTTAAACCCTAAACTAT-AAT
1 TTTAAACCCTAAACTATAAAT
* *
1112479 TTCTAAACCCTAAACCATAATT
1 TT-TAAACCCTAAACTATAAAT
1112501 TTTAAACC
1 TTTAAACC
1112509 ATGAACTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 5 0.12
21 34 0.79
22 4 0.09
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAACCCTAAACTATAAAT
Found at i:1113194 original size:64 final size:62
Alignment explanation
Indices: 1113115--1113236 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 62
1113105 GGTATTTATC
* *
1113115 ATCTATTTAACTTTGAATATTAAAATATAA-TTATATACTTTTGAATATTTCAAATTAAAATAAT
1 ATCTATTTAACTTTGAATAGTAAAAGA-AATTTATAT-CTTTTGAATATTT-AAATTAAAATAAT
* *
1113179 ATCTATTTAAGTTTGAATAGTAAAAGAAGTTTATATCTTTTGAATATTTAAATTAAAA
1 ATCTATTTAACTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTAAATTAAAA
1113237 GATATTATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
62 9 0.17
63 14 0.26
64 30 0.57
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (62 bp):
ATCTATTTAACTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTAAATTAAAATAAT
Found at i:1113284 original size:33 final size:33
Alignment explanation
Indices: 1113211--1113307 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
1113201 AAAGAAGTTT
*
1113211 ATATCTTTTGAATATTTAAATTAAAAGATATTA
1 ATATCTTTTGAATATTTAAATTAAAAGATATCA
* * * *
1113244 TTGTCTTTTTAA-ATTTAAATATTAAAGATATCA
1 ATATCTTTTGAATATTTAAAT-TAAAAGATATCA
* **
1113277 ATATC-TTTAAATATATCGAATTAAAAGATAT
1 ATATCTTTTGAATAT-TTAAATTAAAAGATAT
1113308 TGTCTTTAGA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
32 13 0.26
33 33 0.66
34 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
ATATCTTTTGAATATTTAAATTAAAAGATATCA
Found at i:1115279 original size:57 final size:56
Alignment explanation
Indices: 1115144--1115283 Score: 176
Period size: 57 Copynumber: 2.5 Consensus size: 56
1115134 TCATTTGTAG
* ** ** *
1115144 AAGAAATAAATTGTTAAATTT-TTTC-ACAGAATCTTGTATGATTCTATTTTGCAA
1 AAGAAATAAATCGTTAAATTTATTTCTTGAGAATCAAGTATGATTCTATTTTGAAA
* * *
1115198 AAGAATTAAATCATTGAATTTATTTCTTGAGAATCAAGTATGATTCTATTTTGTAAA
1 AAGAAATAAATCGTTAAATTTATTTCTTGAGAATCAAGTATGATTCTATTTTG-AAA
1115255 AAGAAATAAATCGTTAAATTTATTTCTTG
1 AAGAAATAAATCGTTAAATTTATTTCTTG
1115284 GAAGTATCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 17 0.24
55 4 0.06
56 22 0.31
57 28 0.39
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (56 bp):
AAGAAATAAATCGTTAAATTTATTTCTTGAGAATCAAGTATGATTCTATTTTGAAA
Found at i:1120137 original size:192 final size:193
Alignment explanation
Indices: 1119809--1120177 Score: 571
Period size: 192 Copynumber: 1.9 Consensus size: 193
1119799 CATTTTTCGA
* * * * *
1119809 AAAACATATGAAAACATCCTGCTCGAAGGTCTTATGTATGGCCCGAAGGACTTATCCTCTTGCTC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* *
1119874 GAAAGACTCATAGATGACCTGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCTCGAA
* *
1119939 GGACTTACCAATTTTAGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGAAAGTCTTTATG
131 GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATG
* *
1120002 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATG-GTGCCCCAAAGGACTTATCATCTTTATC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* * *
1120066 GAAAGGCTTATAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGC-CTGA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCTC-GA
* *
1120130 AGGACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAA
130 AGGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAA
1120178 TTTTTCTTAC
Statistics
Matches: 159, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
191 1 0.01
192 123 0.77
193 35 0.22
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (193 bp):
AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCTCGAA
GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATG
Found at i:1120628 original size:258 final size:252
Alignment explanation
Indices: 1120002--1120634 Score: 727
Period size: 255 Copynumber: 2.5 Consensus size: 252
1119992 AGTCTTTATG
* * * *
1120002 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGGTGCCCCAAAGGACTTATCATCTTTATCG
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGATGACCCGAAGGACTTATCATCTTTCTCG
* * * **
1120067 AAAGGCTTATAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGAAG
66 AAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGACGGCCCAAAG
1120132 GACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAATTTTTCTTACTTTTCAAAA
131 GACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAATTTTTCTTACTTTTCAAAA
* * *
1120197 ATTTCAATTTTTAGAAAAAATTTAAATGAGAAACATTGGAAATTATTTTCTTATTTTTCGA
196 ATTTCAATTTTCAG----AATTTAAATGAGAAACATTGAAAATTATTTTCTTATTTTTCAA
** * * **
1120258 AAATGATAT--CAACATCTTGCCCGAAGGTCTTATGGATGACATGAAGGACTTATCATCTTTCTC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTAT-GATGACCCGAAGGACTTATCATCTTTCTC
* * * * * * *
1120321 GAAAGACTTACAAATTACCTAAAGGATTTAATCATCACGCTCGAAAGACTTACTGACGGCCCAAA
65 GAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGACGGCCCAAA
* * * * *
1120386 TGTCTTGTCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATTGTTTTCTTATTTTTC
130 GGACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGG-AA-T-TTTTCTTACTTTTC
* * * *
1120451 AAAAATTTTAATTTTCAG-ATTTAAATGAGAAAC-TTTAAAATTTGTTTTCTCATTTTTTTTTCA
192 AAAAATTTCAATTTTCAGAATTTAAATGAGAAACATTGAAAA-TT-ATTT-TC--TTATTTTTCA
1120514 A
252 A
* * * * * * * *
1120515 AAAACATGTGAAAACATCCTACTCGAAGGTCTTATGAATGGCCCGAATGAC-TATTATCCTGCTC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATG-ATGACCCGAAGGACTTATCATCTTTCTC
1120579 GAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
65 GAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
1120635 TGTCTCGAAG
Statistics
Matches: 310, Mismatches: 55, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
252 5 0.02
253 17 0.05
254 25 0.08
255 119 0.38
256 9 0.03
257 16 0.05
258 89 0.29
259 30 0.10
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (252 bp):
AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGATGACCCGAAGGACTTATCATCTTTCTCG
AAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGACGGCCCAAAG
GACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAATTTTTCTTACTTTTCAAAA
ATTTCAATTTTCAGAATTTAAATGAGAAACATTGAAAATTATTTTCTTATTTTTCAA
Found at i:1120783 original size:177 final size:176
Alignment explanation
Indices: 1120514--1120862 Score: 504
Period size: 177 Copynumber: 2.0 Consensus size: 176
1120504 TTTTTTTTCA
* * * * * * *
1120514 AAAAACATGTGAAAACATCCTACTCGAAGGTCTTATGAATGGCCCGAATGACTATTATCCTGCTC
1 AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGACTATCATCCTGCTC
* * *
1120579 GAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTC-AAAAGACTTACTGATGTCTCGA
66 AAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAA-ACTTACTGATGGCCCGA
1120643 AGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
130 AGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
* * *
1120690 AAAAACATATAAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
1 AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGAC-TATCATCCTGCT
*
1120755 CAAAAGGCTTATAGATGA-CTCGAAGGATTTAATCATCATGCTCGAATAACTTACTGATGGCCCG
65 CAAAAGGCTTATAGATGACCT-GAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGGCCCG
* **
1120819 AAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTT
129 AAGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTT
1120863 CTTAACTTAT
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
176 46 0.30
177 104 0.68
178 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (176 bp):
AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGACTATCATCCTGCTC
AAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGGCCCGAA
GGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
Found at i:1128668 original size:126 final size:126
Alignment explanation
Indices: 1128431--1128675 Score: 295
Period size: 126 Copynumber: 1.9 Consensus size: 126
1128421 GGATTTTAAG
* *
1128431 AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGTCTTAAAGCAGTCA
1 AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGTCA
* *
1128496 TTTATTACTCCAATCGAATGAAGAGATATCACTATGTCGTCTTAAATTCAATATTGATTCA
66 TTTATTACTCCAATCGAATGAAGAGATATCACTATGTCATCCTAAATTCAATATTGATTCA
**
1128557 AGAGAAAATGAT-ATAACTAATTATTTCCAATCGAGAATAAATGACCTC-TCAT-ACCT-AAGCA
1 AGAGAAAATGATAAT-A-TAATTATTTCCAAT-GAGAATAAACAACCTCAT-ATGACCTAAAGCA
* * * * *
1128618 TTCATTTATTACTCCAATTGAAATGAA-A-ATAATTACTTTTTCATCCTAAATTCAATAT
62 GTCATTTATTACTCCAATCG-AATGAAGAGAT-ATCACTATGTCATCCTAAATTCAATAT
1128676 AATTCGAGTG
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
125 4 0.04
126 59 0.58
127 23 0.23
128 16 0.16
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (126 bp):
AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGTCA
TTTATTACTCCAATCGAATGAAGAGATATCACTATGTCATCCTAAATTCAATATTGATTCA
Found at i:1130476 original size:15 final size:16
Alignment explanation
Indices: 1130456--1130485 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1130446 TGACGGCTGG
1130456 AAACCCTAGG-GTTTT
1 AAACCCTAGGTGTTTT
1130471 AAACCCTAGGTGTTT
1 AAACCCTAGGTGTTT
1130486 AGTTTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (16 bp):
AAACCCTAGGTGTTTT
Found at i:1130620 original size:6 final size:6
Alignment explanation
Indices: 1130609--1130656 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
1130599 AAGGCTTGTA
* * *
1130609 AAAAAT AAAAAT AAAAAT -AAAA- AAAAAC AAAAAT AATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1130655 AA
1 AA
1130657 TTAATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:1130640 original size:16 final size:17
Alignment explanation
Indices: 1130610--1130650 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1130600 AGGCTTGTAA
*
1130610 AAAATAAAAATAAAAAT
1 AAAATAAAAACAAAAAT
1130627 AAAA-AAAAACAAAAAT
1 AAAATAAAAACAAAAAT
1130643 AATAATAA
1 AA-AATAA
1130651 TAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 13 0.62
17 6 0.29
18 2 0.10
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAACAAAAAT
Found at i:1130640 original size:22 final size:22
Alignment explanation
Indices: 1130608--1130650 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1130598 AAAGGCTTGT
*
1130608 AAAAAATAAAAATAAAAATAAA
1 AAAAAACAAAAATAAAAATAAA
*
1130630 AAAAAACAAAAATAATAATAA
1 AAAAAACAAAAATAAAAATAA
1130651 TAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAAACAAAAATAAAAATAAA
Found at i:1133404 original size:10 final size:11
Alignment explanation
Indices: 1133358--1133416 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
1133348 GAATGTTATG
1133358 ATAC-ATGTAT
1 ATACAATGTAT
*
1133368 ATATAATGTAT
1 ATACAATGTAT
*
1133379 ATTACAATATATT
1 A-TACAATGTA-T
1133392 ATACAA-GTAT
1 ATACAATGTAT
*
1133402 ATACATATATAT
1 ATACA-ATGTAT
1133414 ATA
1 ATA
1133417 TATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 9 0.23
11 10 0.26
12 18 0.46
13 2 0.05
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (11 bp):
ATACAATGTAT
Found at i:1133594 original size:98 final size:97
Alignment explanation
Indices: 1133430--1133624 Score: 275
Period size: 98 Copynumber: 2.0 Consensus size: 97
1133420 ATATATATTG
* * * *
1133430 TAATTATGTATGATCAATAATGTATGTTTTATAGGTGTATATAAGCCTATTTATGCATGTATGTA
1 TAATTATGTATGATC-A-AATGTATGTTTTATAGATATATATAAGCATATATATGCATGTATGTA
1133495 CATATGTATGATGTATGCATGATGCATGTATATA
64 CATATGTATGATGTATGCATGATGCATGTATATA
* *
1133529 TAATTATGTATGATC-AATGTATGTTTTATATGTATATATATAAGTATATATATGCATTTATGTA
1 TAATTATGTATGATCAAATGTATGTTTTATA-G-ATATATATAAGCATATATATGCATGTATGTA
* *
1133593 CATATGTATTATGTATGTATGATGCATGTATA
64 CATATGTATGATGTATGCATGATGCATGTATA
1133625 CACATATATT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
96 15 0.17
97 1 0.01
98 55 0.64
99 15 0.17
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (97 bp):
TAATTATGTATGATCAAATGTATGTTTTATAGATATATATAAGCATATATATGCATGTATGTACA
TATGTATGATGTATGCATGATGCATGTATATA
Found at i:1133700 original size:2 final size:2
Alignment explanation
Indices: 1133693--1133799 Score: 80
Period size: 2 Copynumber: 54.0 Consensus size: 2
1133683 AAATTAATGT
* *
1133693 TA TA TA TA TA TA TA TA TA -A GT- TA TA CA CA TA TA TA -A GTA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
1133734 TA TG TA TGA TG TA TGA TG TA TG TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1133778 TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1133800 CATTATACGC
Statistics
Matches: 84, Mismatches: 12, Indels: 18
0.74 0.11 0.16
Matches are distributed among these distances:
1 5 0.06
2 74 0.88
3 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1133724 original size:21 final size:21
Alignment explanation
Indices: 1133678--1133727 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1133668 ATGATATATG
* *
1133678 CATATAAATTAATGTTATATA
1 CATATATATTAATGTTATACA
*
1133699 TATATATATATAA-GTTATACA
1 CATATATAT-TAATGTTATACA
1133720 CATATATA
1 CATATATA
1133728 AGTATATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
CATATATATTAATGTTATACA
Found at i:1136799 original size:20 final size:21
Alignment explanation
Indices: 1136753--1136802 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1136743 AGTCCAATCG
1136753 TTTGTAACTCATGCAATTACA
1 TTTGTAACTCATGCAATTACA
* *
1136774 TTTGTAACTCTTGCATTTAC-
1 TTTGTAACTCATGCAATTACA
1136794 TTTGTAACT
1 TTTGTAACT
1136803 GGCAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTGTAACTCATGCAATTACA
Found at i:1142593 original size:18 final size:18
Alignment explanation
Indices: 1142564--1142620 Score: 96
Period size: 18 Copynumber: 3.1 Consensus size: 18
1142554 GTTAATGAAT
1142564 TTTAAGATTTTATATTCGA
1 TTTAA-ATTTTATATTCGA
1142583 TTTAAATTTTATATTCGA
1 TTTAAATTTTATATTCGA
*
1142601 TTTAAATATTATATTCGA
1 TTTAAATTTTATATTCGA
1142619 TT
1 TT
1142621 CAATTATTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 32 0.86
19 5 0.14
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (18 bp):
TTTAAATTTTATATTCGA
Found at i:1142628 original size:18 final size:18
Alignment explanation
Indices: 1142573--1142628 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1142563 TTTTAAGATT
1142573 TTATATTCGATTTAAATT-
1 TTATATTCGA-TTAAATTA
1142591 TTATATTCGATTTAAA-TA
1 TTATATTCGA-TTAAATTA
*
1142609 TTATATTCGATTCAATTA
1 TTATATTCGATTAAATTA
1142627 TT
1 TT
1142629 CGAATATCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
17 5 0.14
18 30 0.86
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (18 bp):
TTATATTCGATTAAATTA
Done.