Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000282.1 Hibiscus syriacus cultivar Beakdansim tig00000521_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: 70070
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:941 original size:74 final size:75
Alignment explanation
Indices: 824--1002 Score: 209
Period size: 74 Copynumber: 2.4 Consensus size: 75
814 ATAAATAAAA
* * * ** * **
824 TCAAATATCAAGACTCAAACCACAATATTAAGT-TTGAACAATAAAATCCATAAACAAATTACAA
1 TCAAATCTCAAGACTGAAACCACAATATTAACTCTAAAATAATAAAATCCATAAACAAACCACAA
*
888 TATTAAAATG
66 CATTAAAATG
* * * *
898 TCAAATCTCAAGATTTAAA-CACAATATTAACTCTAAAATAATAAAATCCATAATCAAACCATAA
1 TCAAATCTCAAGACTGAAACCACAATATTAACTCTAAAATAATAAAATCCATAAACAAACCACAA
962 CATTAAAATG
66 CATTAAAATG
* *
972 TCAAATCTTAAGACTGAAACCATAATATTAA
1 TCAAATCTCAAGACTGAAACCACAATATTAA
1003 ATATAAAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 12 0.14
74 65 0.75
75 10 0.11
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (75 bp):
TCAAATCTCAAGACTGAAACCACAATATTAACTCTAAAATAATAAAATCCATAAACAAACCACAA
CATTAAAATG
Found at i:3867 original size:16 final size:16
Alignment explanation
Indices: 3837--3871 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3827 TAAATGTCAG
3837 GATCATCTATAACACA
1 GATCATCTATAACACA
3853 GATCAATCTAT-ACACA
1 GATC-ATCTATAACACA
3869 GAT
1 GAT
3872 TAAATTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (16 bp):
GATCATCTATAACACA
Found at i:5959 original size:22 final size:22
Alignment explanation
Indices: 5930--5979 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5920 TAACTATTGT
5930 TAAA-ACGAACTCTGCTAAAGG
1 TAAATACGAACTCTGCTAAAGG
5951 TAAATACGAACTCTGCTAAAGG
1 TAAATACGAACTCTGCTAAAGG
5973 TAAATAC
1 TAAATAC
5980 TTTTTCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (22 bp):
TAAATACGAACTCTGCTAAAGG
Found at i:19327 original size:2 final size:2
Alignment explanation
Indices: 19320--19359 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
19310 TATTTAGAAA
19320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
19360 TCAATTCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19690 original size:21 final size:21
Alignment explanation
Indices: 19649--19709 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
19639 GCCACCACTA
**
19649 CAAGGTTACATGCCGAACCTG
1 CAAGGTTACATTTCGAACCTG
*
19670 -AAGGGTTACATTTCGAGCCTG
1 CAA-GGTTACATTTCGAACCTG
* *
19691 CAAGGTTATATTTCAAACC
1 CAAGGTTACATTTCGAACC
19710 AGGCATGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (21 bp):
CAAGGTTACATTTCGAACCTG
Found at i:19736 original size:42 final size:42
Alignment explanation
Indices: 19690--19771 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
19680 TTTCGAGCCT
*
19690 GCAAGGTTATATTTCAAACCAGGCATGTTATATTCTGAGCTC
1 GCAAGGTTATATTTCAAACCAAGCATGTTATATTCTGAGCTC
** * *
19732 GCAAGGTTATATTTTGAACCAATCGTGTTATATTCTGAGC
1 GCAAGGTTATATTTCAAACCAAGCATGTTATATTCTGAGC
19772 CTAACTAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (42 bp):
GCAAGGTTATATTTCAAACCAAGCATGTTATATTCTGAGCTC
Found at i:20200 original size:13 final size:13
Alignment explanation
Indices: 20182--20207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20172 CTTTTAATTG
20182 AATGTTAAGTTTT
1 AATGTTAAGTTTT
20195 AATGTTAAGTTTT
1 AATGTTAAGTTTT
20208 TATATTTATG
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:0.15, T:0.54
Consensus pattern (13 bp):
AATGTTAAGTTTT
Found at i:20275 original size:20 final size:20
Alignment explanation
Indices: 20252--20290 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20242 TTTTATATTA
20252 TGTTTTTATATTAAGTTTTG
1 TGTTTTTATATTAAGTTTTG
*
20272 TGTTTTTATATTATGTTTT
1 TGTTTTTATATTAAGTTTT
20291 AAATTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (20 bp):
TGTTTTTATATTAAGTTTTG
Found at i:20290 original size:13 final size:13
Alignment explanation
Indices: 20239--20270 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20229 CTAGTTTTTT
20239 TGTTTTTATATTA
1 TGTTTTTATATTA
20252 TGTTTTTATATTA
1 TGTTTTTATATTA
*
20265 AGTTTT
1 TGTTTT
20271 GTGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (13 bp):
TGTTTTTATATTA
Found at i:20824 original size:21 final size:21
Alignment explanation
Indices: 20800--20847 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
20790 ACTAAGATTA
20800 ATGATGAAGAAACAAAGATAG
1 ATGATGAAGAAACAAAGATAG
*
20821 ATGAAGAAGAAACAAAGATAG
1 ATGATGAAGAAACAAAGATAG
20842 ATGATG
1 ATGATG
20848 GAGACCCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (21 bp):
ATGATGAAGAAACAAAGATAG
Found at i:22247 original size:170 final size:170
Alignment explanation
Indices: 21996--22331 Score: 397
Period size: 170 Copynumber: 2.0 Consensus size: 170
21986 CTTTTTGTAG
* * * * * *
21996 GGAATCTCTGCCATGTCATAGTGTGTCATTCCATCGATATGGGAGTTACTGTGGTGAATAGTTCC
1 GGAATCGCTGCCATGTCATAGTGTGTCATCCCATAGACATGAGAGTTACTGTGATGAATAGTTCC
* * * * * * * * *
22061 CTGAAGGGGGACATCATGTTTGCATATAAGTAATTGGAAAATTCAAAGA-ATCTTTGGAAAAAAA
66 CCGAAGGGGAACATCATCTATGCATATAAGTAACTAGAAAATACAAA-ATATATCTGGAAAAAAA
* ** * *
22125 -GAATGTTTTTTTTCACAAGAAGTGTTTTCACGTTTTGCAA
130 TGAAAGACTTTTTTCACAAGAAGCGTTTTCACCTTTTGCAA
* * *
22165 GGAATCGCTTCCATGTCATAGTGTGTCATCCCATTAGGCATGAGAGTTATTGTGATGAATAGTTC
1 GGAATCGCTGCCATGTCATAGTGTGTCATCCCA-TAGACATGAGAGTTACTGTGATGAATAGTTC
* * * *
22230 CCCGAAGGGTAACATCATCTATGCATATAATTTACTATAAAATACAAAATATATCTGGAAAAAAA
65 CCCGAAGGGGAACATCATCTATGCATATAAGTAACTAGAAAATACAAAATATATCTGGAAAAAAA
22295 TGAAAGACTTTTTTCACAAGAAGCGTTTTCACCTTTT
130 TGAAAGACTTTTTTCACAAGAAGCGTTTTCACCTTTT
22332 TTTCCACTAA
Statistics
Matches: 137, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
169 31 0.23
170 75 0.55
171 31 0.23
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (170 bp):
GGAATCGCTGCCATGTCATAGTGTGTCATCCCATAGACATGAGAGTTACTGTGATGAATAGTTCC
CCGAAGGGGAACATCATCTATGCATATAAGTAACTAGAAAATACAAAATATATCTGGAAAAAAAT
GAAAGACTTTTTTCACAAGAAGCGTTTTCACCTTTTGCAA
Found at i:22826 original size:102 final size:102
Alignment explanation
Indices: 22660--22874 Score: 265
Period size: 102 Copynumber: 2.1 Consensus size: 102
22650 GGAAACATAA
* * *
22660 CTTCAAGTTCAAGGGGAAGGCATTCATTTTCCAAATTCTTCGACCTCAACATTGAAACACCATCG
1 CTTCAAGTTCAAGGGGAAGACATTCATTCTACAAATTCTTCGACCTCAACATTGAAACACCATCG
** *
22725 ACACAAAAATTTGTTTCAAACGCATATGACACTATGC
66 ACACAAAAATTCATTTCAAACCCATATGACACTATGC
*
22762 CTTCAAGTTCAAGGGGAAGACATTCA-TCTACAAACTTGTTCGACCTCAACATTAGAATA-A-CA
1 CTTCAAGTTCAAGGGGAAGACATTCATTCTACAAA-TTCTTCGACCTCAACATT-GAA-ACACCA
** * **
22824 TCGACACATCAGTTCATTTTGAACCCATATGACACTATGC
63 TCGACACAAAAATTCATTTCAAACCCATATGACACTATGC
*
22864 CTTCAATTTCA
1 CTTCAAGTTCA
22875 TGAGGTAGGC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
101 6 0.06
102 86 0.89
103 4 0.04
104 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (102 bp):
CTTCAAGTTCAAGGGGAAGACATTCATTCTACAAATTCTTCGACCTCAACATTGAAACACCATCG
ACACAAAAATTCATTTCAAACCCATATGACACTATGC
Found at i:25014 original size:15 final size:15
Alignment explanation
Indices: 24994--25055 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
24984 TGGACCATAA
*
24994 TTATGTAATTGTATT
1 TTATGTTATTGTATT
* *
25009 TTATGTTATTGAAAT
1 TTATGTTATTGTATT
*
25024 TTATGTTATTTTAGTT
1 TTATGTTATTGTA-TT
25040 TCTA-G-TATTGTATT
1 T-TATGTTATTGTATT
25054 TT
1 TT
25056 TTGTCTTCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 29 0.76
16 3 0.08
17 2 0.05
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (15 bp):
TTATGTTATTGTATT
Found at i:25331 original size:20 final size:20
Alignment explanation
Indices: 25283--25333 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
25273 AAATTTAAAC
*
25283 TTTAGGGTTTACTATTTTGG
1 TTTAGGGTTTAATATTTTGG
* *
25303 GTTAAGGTTTAAT-TTTTAGG
1 TTTAGGGTTTAATATTTT-GG
25323 TTTAGGGTTTA
1 TTTAGGGTTTA
25334 TAATTTTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (20 bp):
TTTAGGGTTTAATATTTTGG
Found at i:27276 original size:75 final size:75
Alignment explanation
Indices: 27146--27354 Score: 244
Period size: 74 Copynumber: 2.8 Consensus size: 75
27136 CAAAGCCAAA
* * * **
27146 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
27211 TT-TGGCTCCGAG
64 TTCT-GCTCCGAG
* *
27223 ATTTCCAGAATGCTTGGAGGGAACCGATTCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
27287 CTGTTCCGAG
66 CTGCTCCGAG
* * * *
27297 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCTCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCC-CCCCT
27355 TGTACAACGG
Statistics
Matches: 114, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
74 55 0.48
75 29 0.25
76 5 0.04
77 25 0.22
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
CTGCTCCGAG
Found at i:35845 original size:75 final size:75
Alignment explanation
Indices: 35688--35896 Score: 260
Period size: 75 Copynumber: 2.8 Consensus size: 75
35678 CAAAGCCAAA
* * * * **
35688 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACTGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
35753 TTGGCTCCGAG
65 TTGGCTCCGAG
*
35764 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
35829 CT-GTTCCGAG
66 -TGGCTCCGAG
* * * *
35839 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCTCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCC-CCCCT
35897 TGTACAACGG
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
75 79 0.68
76 38 0.32
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:40380 original size:16 final size:16
Alignment explanation
Indices: 40359--40389 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40349 ATTCTTTATT
*
40359 AAATAAATATTTAATA
1 AAATAAATACTTAATA
40375 AAATAAATACTTAAT
1 AAATAAATACTTAAT
40390 CACCAAGAAT
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:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAAATACTTAATA
Found at i:43220 original size:23 final size:23
Alignment explanation
Indices: 43168--43213 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
43158 AAATACCTTA
*
43168 ATGAACATTTAAACGAACATGTTC
1 ATGAACA-TTAAACGAACACGTTC
*
43192 ATGAACATTAAACGAGCACGTT
1 ATGAACATTAAACGAACACGTT
43214 TGTGAACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (23 bp):
ATGAACATTAAACGAACACGTTC
Found at i:45193 original size:20 final size:20
Alignment explanation
Indices: 45170--45209 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
45160 TGATTCAATT
45170 CGAACCAAACTGAGTCAACC
1 CGAACCAAACTGAGTCAACC
***
45190 CGAACCTGCCTGAGTCAACC
1 CGAACCAAACTGAGTCAACC
45210 TGGACTGGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.38, G:0.17, T:0.12
Consensus pattern (20 bp):
CGAACCAAACTGAGTCAACC
Found at i:45472 original size:12 final size:13
Alignment explanation
Indices: 45455--45488 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
45445 TGCATATGTA
45455 ATTTAAGT-ATTT
1 ATTTAAGTGATTT
45467 ATTTAAGTGATTT
1 ATTTAAGTGATTT
*
45480 AATTAAGTG
1 ATTTAAGTG
45489 CATCTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (13 bp):
ATTTAAGTGATTT
Found at i:48790 original size:3 final size:3
Alignment explanation
Indices: 48784--48834 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
48774 TTTTTTTTAA
* *
48784 TAT TAT TAT TA- AAA TAT TAT TAT TAT T-T TATT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
48827 TAT TAT TA
1 TAT TAT TA
48835 AATAATTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 5 0.12
3 33 0.80
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:48801 original size:14 final size:14
Alignment explanation
Indices: 48782--48808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48772 TGTTTTTTTT
48782 AATATTATTATTAA
1 AATATTATTATTAA
48796 AATATTATTATTA
1 AATATTATTATTA
48809 TTTTATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:48815 original size:14 final size:14
Alignment explanation
Indices: 48784--48834 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
48774 TTTTTTTTAA
***
48784 TATTATTATTAAAA
1 TATTATTATTATTT
48798 TATTATTATTATTT
1 TATTATTATTATTT
48812 TATTTATT-TTATTAT
1 TA-TTATTATTATT-T
48827 TATTATTA
1 TATTATTA
48835 AATAATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 23 0.74
15 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:50191 original size:28 final size:32
Alignment explanation
Indices: 50160--50221 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
50150 TTGTTTAGTC
50160 ATAT-TTTAATT-TTA-TATGATTATT-TTTA
1 ATATATTTAATTGTTATTATGATTATTATTTA
*
50188 ATATATTTAATTGTTATTATTATTATTATTTA
1 ATATATTTAATTGTTATTATGATTATTATTTA
50220 AT
1 AT
50222 CATGTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 7 0.24
30 3 0.10
31 9 0.31
32 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (32 bp):
ATATATTTAATTGTTATTATGATTATTATTTA
Found at i:50459 original size:125 final size:127
Alignment explanation
Indices: 50317--50550 Score: 287
Period size: 129 Copynumber: 1.9 Consensus size: 127
50307 CATTGTAATC
* * *
50317 ATATTTTAATATATA-TT-TA-TTAATATTAAGAAAAGA-CAGTCTTAAAGCAACTGGATGTTCA
1 ATATTTTAATATATATTTATATTTAATATTAAGAAAAGAGCAGTCTTAAAGCAACTAGAAG-CCA
** * * *
50378 TTTTCTTATATTTTTAAATAAATAAATATTTTACTTTATATATATTTTAATTATTTTTAGATAA
65 TTTAATGATATTTCTAAATAAATAAATATCTTA-TTTATATATATTTTAATTATTTTTAGATAA
* * * * * *
50442 ATATTTTAATATTTATTTATATTTTTATGTTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCC
1 ATATTTTAATATATATTTATA-TTTAATATTAAGAAAAGAGCAGTCTTAAAGCAACTAGAAGCCA
50507 TTTAATGATATTTCTAAATAAATAAATATCTTATTTATATATAT
65 TTTAATGATATTTCTAAATAAATAAATATCTTATTTATATATAT
50551 AAATTAATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
125 14 0.16
126 2 0.02
127 2 0.02
128 11 0.12
129 44 0.49
130 17 0.19
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (127 bp):
ATATTTTAATATATATTTATATTTAATATTAAGAAAAGAGCAGTCTTAAAGCAACTAGAAGCCAT
TTAATGATATTTCTAAATAAATAAATATCTTATTTATATATATTTTAATTATTTTTAGATAA
Found at i:61262 original size:19 final size:19
Alignment explanation
Indices: 61240--61284 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
61230 AGACTACTGA
61240 AACTTACAAAGATTGGCAC
1 AACTTACAAAGATTGGCAC
61259 AACTTACAAAGATTGGCAC
1 AACTTACAAAGATTGGCAC
*
61278 AAGTTAC
1 AACTTAC
61285 CTTTTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (19 bp):
AACTTACAAAGATTGGCAC
Found at i:61793 original size:15 final size:15
Alignment explanation
Indices: 61755--61801 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
61745 ATATTATGCT
61755 TGAAGAAGAAAAAAAA
1 TGAA-AAGAAAAAAAA
*
61771 -GATGAAGAAAAAAAA
1 TGA-AAAGAAAAAAAA
61786 TGAAAAGAAAAGAAAA
1 TGAAAAGAAAA-AAAA
61802 AAATGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
TGAAAAGAAAAAAAA
Found at i:63519 original size:105 final size:108
Alignment explanation
Indices: 63352--63781 Score: 591
Period size: 113 Copynumber: 3.9 Consensus size: 108
63342 TTAGCAAAGA
63352 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
63417 AAGAAGGAAGAAGAAGTTCATAATG-AG-A-TTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATGAAGAATTTTAACCTTTTG
63457 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
*
63522 AAGAAGGAAGAAGAAGTTCATAACGAGAAGAACTTGTTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAA--TGAAGAA--T-TTTAACCTTTTG
* *
63570 TTTTAATTCATCACTCGATGGATTAACTTTTACAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
*
63635 AAGATGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAAT--GAAGAA--T-TTTAACCTTTTG
* * * * * * *
63683 CTTT-AATTCATCACCCGATGGATCAGCATTTCCAGAAGAAGTTCATAATAAGAAGAATTCATCT
1 -TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCT
* *
63747 GAAGAATG-AGAAGAAATTCATAATAAGAAGAATTT
65 GAAGAAGGAAGAAGAAGTTCATAAT--GAAGAATTT
63782 GTTCAATTTT
Statistics
Matches: 297, Mismatches: 17, Indels: 18
0.89 0.05 0.05
Matches are distributed among these distances:
105 88 0.30
107 1 0.00
108 2 0.01
109 3 0.01
110 1 0.00
112 22 0.07
113 177 0.60
114 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (108 bp):
TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAAGAATTTTAACCTTTTG
Found at i:65333 original size:28 final size:29
Alignment explanation
Indices: 65302--65360 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
65292 TTGTTTAGTC
65302 ATAT-TTTAATT-TTATATGATTATT-TTTA
1 ATATATTTAATTATTAT-T-ATTATTATTTA
65330 ATATATTTAATTATTATTATTATTATTTA
1 ATATATTTAATTATTATTATTATTATTTA
65359 AT
1 AT
65361 CATGTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 10 0.36
29 14 0.50
30 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
ATATATTTAATTATTATTATTATTATTTA
Found at i:67019 original size:22 final size:22
Alignment explanation
Indices: 66968--67029 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
66958 CCGTTAACCA
66968 GACTCGTTGACTTTGACC--TTT
1 GACT-GTTGACTTTGACCAATTT
**
66989 GACCATTGACTTTGACCAATTT
1 GACTGTTGACTTTGACCAATTT
67011 GACTGTTGACTTTGACCAA
1 GACTGTTGACTTTGACCAA
67030 AAGTCAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.34
21 3 0.09
22 20 0.57
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (22 bp):
GACTGTTGACTTTGACCAATTT
Found at i:67808 original size:36 final size:36
Alignment explanation
Indices: 67764--67872 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
67754 ATGAAGTTTT
* ** *
67764 TATAGGTTCAGCTTCGATCAAACTGGTAATTCCTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
67800 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
* *
67836 TATAGTTTCAACACCGATCAAGCTGGTAATTCTTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
67872 T
1 T
67873 GGACCTAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (36 bp):
TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
Done.