Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001412.1 Hibiscus syriacus cultivar Beakdansim tig00002749_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: 51695
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:11476 original size:32 final size:32
Alignment explanation
Indices: 11408--11488 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
11398 TTAAAACTCG
* *
11408 TAAAATGACCATTAAA-TTTATTGATCTATTA
1 TAAAATAATCATTAAATTTTATTGATCTATTA
* *
11439 CAAAATAATCATTAAATTTTATTGAAT-TGTTA
1 TAAAATAATCATTAAATTTTATTG-ATCTATTA
*
11471 TAAAATAATTATTAAATT
1 TAAAATAATCATTAAATT
11489 GATCTAACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.31
32 27 0.64
33 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (32 bp):
TAAAATAATCATTAAATTTTATTGATCTATTA
Found at i:11996 original size:18 final size:18
Alignment explanation
Indices: 11964--11998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11954 CGCAGGGGGG
*
11964 TTAAAAATAGTTTTTTTT
1 TTAAAAATAGATTTTTTT
*
11982 TTAAAAATTGATTTTTT
1 TTAAAAATAGATTTTTT
11999 AAAGTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TTAAAAATAGATTTTTTT
Found at i:13459 original size:118 final size:118
Alignment explanation
Indices: 13337--13558 Score: 313
Period size: 118 Copynumber: 1.9 Consensus size: 118
13327 TAACATGGCT
* *
13337 GGCTGGTGTCAACTTCTTCTAGCCCTAGCGTTAA-AAAAACAGAAGCCAAGCCATGTTTAAAAAA
1 GGCTGGTGTCAACTTCTTCTAGCCCTAGCATTAAGAAAAACAGAAGCAAAGCCATG-TTAAAAAA
* *
13401 GAACCAAACAAGAAACAGAGTTGTCCATA-CAAATTCCCAGTGCTGAAGCAACAA
65 GAAACAAACAAGAAACAGAGTT-TCCAGATCAAATTCCCAGTGCTGAAGCAACAA
* ** * * *
13455 GGCTGGTGTCATCTTCTTCTAGCTTTATCATTAAGAAAAACTGAAGCAAAGCCATGTTCAAAAAG
1 GGCTGGTGTCAACTTCTTCTAGCCCTAGCATTAAGAAAAACAGAAGCAAAGCCATGTTAAAAAAG
*
13520 AAACAAGCAAGAAACAGAGTTTCCAGATCAAATTCCCAG
66 AAACAAACAAGAAACAGAGTTTCCAGATCAAATTCCCAG
13559 CGCTCAAGTG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
117 5 0.05
118 67 0.74
119 19 0.21
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (118 bp):
GGCTGGTGTCAACTTCTTCTAGCCCTAGCATTAAGAAAAACAGAAGCAAAGCCATGTTAAAAAAG
AAACAAACAAGAAACAGAGTTTCCAGATCAAATTCCCAGTGCTGAAGCAACAA
Found at i:13607 original size:107 final size:113
Alignment explanation
Indices: 13337--13628 Score: 269
Period size: 118 Copynumber: 2.6 Consensus size: 113
13327 TAACATGGCT
* * ** ** * *
13337 GGCTGGTGTCAACTTCTTCTAGCCCTAGCGTTAA-AAAAACAGAAGCCAAGCCATGTTTAAAAAA
1 GGCTGGTGTCATCTTCTTCCAGCTTTAGCACTAAGAAAAACTGAAG-CAAGCCATG-TTCAAAAA
* *
13401 GAACCAAACAAGAAACAGAGTTGTCCATACAAATTCCCAGTGCTGAAGCAACAA
64 GAAACAAACAAGAAACAGAGTTGTCCAGACAAATTCCCAG-GC---AGCAACAA
* * *
13455 GGCTGGTGTCATCTTCTTCTAGCTTTATCATTAAGAAAAACTGAAGCAAAGCCATGTTCAAAAAG
1 GGCTGGTGTCATCTTCTTCCAGCTTTAGCACTAAGAAAAACTGAAGC-AAGCCATGTTCAAAAAG
* *
13520 AAACAAGCAAGAAACAGAGTT-TCCAGATCAAATTCCCA-GC-GC-TCAA
65 AAACAAACAAGAAACAGAGTTGTCCAGA-CAAATTCCCAGGCAGCAACAA
* * * *
13566 -G-TGGTTTCATCTTCTTCCAGCTTTAGCGCT-AG-AAAACTGAAGCCAGTCCATGTTCAAACAG
1 GGCTGGTGTCATCTTCTTCCAGCTTTAGCACTAAGAAAAACTGAAGCAAG-CCATGTTCAAAAAG
13627 AA
65 AA
13629 TCGCTAGTGC
Statistics
Matches: 152, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
106 2 0.01
107 26 0.17
108 2 0.01
109 24 0.16
110 1 0.01
111 3 0.02
112 2 0.01
116 2 0.01
117 5 0.03
118 67 0.44
119 18 0.12
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (113 bp):
GGCTGGTGTCATCTTCTTCCAGCTTTAGCACTAAGAAAAACTGAAGCAAGCCATGTTCAAAAAGA
AACAAACAAGAAACAGAGTTGTCCAGACAAATTCCCAGGCAGCAACAA
Found at i:16016 original size:48 final size:48
Alignment explanation
Indices: 15945--16040 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
15935 TTTTTATGTT
* *
15945 AGAATCAGAGGTATTCTAATCATTTCTGTTGGGTTTATCTGGATAATA
1 AGAATCAGAGGTATTCAAATCATTTCTGCTGGGTTTATCTGGATAATA
*
15993 AGAATCAGAGGTATTCAAATCATTTCTGCTGGGTTTATTTGGATAATA
1 AGAATCAGAGGTATTCAAATCATTTCTGCTGGGTTTATCTGGATAATA
16041 GTTTTTGTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (48 bp):
AGAATCAGAGGTATTCAAATCATTTCTGCTGGGTTTATCTGGATAATA
Found at i:16937 original size:20 final size:20
Alignment explanation
Indices: 16912--16949 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16902 TTTGATTCAC
16912 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
16932 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
16950 GGAATAGGAT
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:17177 original size:36 final size:36
Alignment explanation
Indices: 17106--17178 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
17096 GTTGGAAAAT
*
17106 ATTTATATATTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTCTTTAAAAAAATTAAAATCATAAA
* *
17142 ATTTATATAATTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTCTTTAAAAAAATT-AAAATCATAAA
17178 A
1 A
17179 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
ATTTATATATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:18789 original size:19 final size:19
Alignment explanation
Indices: 18753--18789 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18743 TGAAAATGAT
**
18753 TTGATTTTGAAAGCAAAAG
1 TTGATTTTGAAAAAAAAAG
18772 TTGATTTTGAAAAAAAAA
1 TTGATTTTGAAAAAAAAA
18790 ATAAAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (19 bp):
TTGATTTTGAAAAAAAAAG
Found at i:20611 original size:41 final size:41
Alignment explanation
Indices: 20566--20646 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
20556 AAACATAAGA
*
20566 GAAGAGCTTTTCACTATTTATTTTTATTCTCTTGTAAATAT
1 GAAGAGCTTTTCACTATTTATTTTTATTCTCTTATAAATAT
20607 GAAGAGCTTTTCACTATTTATTTTTATTCTCTTATAAATA
1 GAAGAGCTTTTCACTATTTATTTTTATTCTCTTATAAATA
20647 GTTATGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (41 bp):
GAAGAGCTTTTCACTATTTATTTTTATTCTCTTATAAATAT
Found at i:24251 original size:15 final size:15
Alignment explanation
Indices: 24231--24263 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
24221 CACTCTCAAT
24231 TATGCATGATATATA
1 TATGCATGATATATA
24246 TATGCATGATATATA
1 TATGCATGATATATA
24261 TAT
1 TAT
24264 ATATTATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (15 bp):
TATGCATGATATATA
Found at i:27583 original size:12 final size:12
Alignment explanation
Indices: 27563--27632 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
27553 GATACATGGC
*
27563 CTGAATTCTGTT
1 CTGATTTCTGTT
27575 CTGATTTCT-TAT
1 CTGATTTCTGT-T
27587 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
27599 ATGATATCTGTT
1 CTGATTTCTGTT
*
27611 CTGAATTCTGTT
1 CTGATTTCTGTT
*
27623 TTGATTTCTG
1 CTGATTTCTG
27633 ATATCTTCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.07
12 40 0.87
13 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:27594 original size:24 final size:24
Alignment explanation
Indices: 27563--27632 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
27553 GATACATGGC
*
27563 CTGAATTCTGTTCTGATTTCT-TAT
1 CTGAATTCTGTTATGATTTCTGT-T
* *
27587 CTGGATTCTGTTATGATATCTGTT
1 CTGAATTCTGTTATGATTTCTGTT
*
27611 CTGAATTCTGTTTTGATTTCTG
1 CTGAATTCTGTTATGATTTCTG
27633 ATATCTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 38 0.97
25 1 0.03
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGTT
Found at i:32183 original size:24 final size:25
Alignment explanation
Indices: 32152--32209 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
32142 TAATTATTTT
*
32152 TATT-TGATTTC-CGACTTGAATTC
1 TATTCTGATTTCACGACCTGAATTC
* *
32175 TATTCTGA-TACATGACCTGAATTC
1 TATTCTGATTTCACGACCTGAATTC
*
32199 TGTTCTGATTT
1 TATTCTGATTT
32210 TTGATCTGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 6 0.22
24 20 0.74
25 1 0.04
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (25 bp):
TATTCTGATTTCACGACCTGAATTC
Found at i:32206 original size:12 final size:12
Alignment explanation
Indices: 32191--32248 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
32181 GATACATGAC
32191 CTGAATTCTGTT
1 CTGAATTCTGTT
* * *
32203 CTGATTTTTGAT
1 CTGAATTCTGTT
*
32215 CTGGATTCTGTT
1 CTGAATTCTGTT
32227 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
32239 TTGATTTCTG
1 CTGAATTCTG
32249 ATATCTCCGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:33367 original size:31 final size:30
Alignment explanation
Indices: 33298--33368 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
33288 ATAAAAATAA
33298 AAATTTA-ATGTATACAATTAAACTAAGATT
1 AAATTTATATGTATACAATTAAACTAA-ATT
* * *
33328 AAAGTTATATGTATATAATTACACTAAATT
1 AAATTTATATGTATACAATTAAACTAAATT
33358 AAACTTTATAT
1 AAA-TTTATAT
33369 AACGTATTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTTATATGTATACAATTAAACTAAATT
Found at i:34135 original size:23 final size:23
Alignment explanation
Indices: 34081--34140 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
34071 TTATAAATTA
34081 TATTAAT-TATTATTAAACTAATAT
1 TATTAATATATT-TTAAAC-AATAT
34105 TATT-ATATATTTTAAA-AATAT
1 TATTAATATATTTTAAACAATAT
34126 TAGTTAATATATTTT
1 TA-TTAATATATTTT
34141 TAATATCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
21 7 0.21
22 2 0.06
23 16 0.48
24 8 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTAATATATTTTAAACAATAT
Found at i:34145 original size:21 final size:20
Alignment explanation
Indices: 34099--34146 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
34089 ATTATTAAAC
34099 TAATATTATTATATATTTTAA
1 TAATATTATTATATATTTT-A
*
34120 AAATATTAGTTAATATATTTT-
1 TAATATTA-TT-ATATATTTTA
34141 TAATAT
1 TAATAT
34147 CTTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.52
22 2 0.09
23 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATATTATTATATATTTTA
Found at i:34281 original size:40 final size:42
Alignment explanation
Indices: 34232--34311 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
34222 TTTCTATGAA
*
34232 ATTAATAAATAAT-ATAAAT-T-TTATTAATAATTTAGTATAT
1 ATTAATAAATAATAATAAATATCTTA-TAATAATTGAGTATAT
*
34272 ATTATTAAATAATAATAAATATCTTATAATAATTGAGTAT
1 ATTAATAAATAATAATAAATATCTTATAATAATTGAGTAT
34312 TTGATTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 12 0.34
41 6 0.17
42 14 0.40
43 3 0.09
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (42 bp):
ATTAATAAATAATAATAAATATCTTATAATAATTGAGTATAT
Found at i:34293 original size:22 final size:21
Alignment explanation
Indices: 34232--34298 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
34222 TTTCTATGAA
*
34232 ATTAATAAATAATATAAAT-T
1 ATTATTAAATAATATAAATAT
* *
34252 -TTATT-AATAATTTAGTATAT
1 ATTATTAAATAATATA-AATAT
34272 ATTATTAAATAATAATAAATAT
1 ATTATTAAATAAT-ATAAATAT
*
34294 CTTAT
1 ATTAT
34299 AATAATTGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 8 0.22
19 6 0.17
20 1 0.03
21 5 0.14
22 14 0.39
23 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
ATTATTAAATAATATAAATAT
Found at i:35164 original size:88 final size:87
Alignment explanation
Indices: 35015--35180 Score: 273
Period size: 88 Copynumber: 1.9 Consensus size: 87
35005 AATTTGAATA
35015 TATATTAATAACAAAATATATATTTTAAATTAATAAAAGAATAAATATATTTTAAGTTAAAATAA
1 TATATTAATAACAAAATATATATTTTAAATTAATAAAAGAATAAATATATTTTAAGTTAAAATAA
*
35080 ATATAAAATATATTTAATAAGT
66 AAATAAAATATATTTAATAAGT
*
35102 TATATTAATAAGAAAATATAT-TTTCT-AATTAATAAAAGAATAAAAATATATTTTAAGTTAAAA
1 TATATTAATAACAAAATATATATTT-TAAATTAATAAAAGAAT--AAATATATTTTAAGTTAAAA
35165 TAAAAATAAAATATAT
63 TAAAAATAAAATATAT
35181 ATTTTTAAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
86 18 0.24
87 21 0.28
88 35 0.47
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (87 bp):
TATATTAATAACAAAATATATATTTTAAATTAATAAAAGAATAAATATATTTTAAGTTAAAATAA
AAATAAAATATATTTAATAAGT
Found at i:35181 original size:30 final size:30
Alignment explanation
Indices: 35027--35222 Score: 149
Period size: 29 Copynumber: 6.5 Consensus size: 30
35017 TATTAATAAC
*
35027 AAAATATATATTTTAAATT--AATAAAAGA-
1 AAAATATATATTTTAAGTTAAAATAAAA-AT
* *
35055 ATAA-ATATATTTTAAGTTAAAATAAATAT
1 AAAATATATATTTTAAGTTAAAATAAAAAT
* * * * *
35084 AAAATATAT-TTAATAAGTTATATTAATAAG
1 AAAATATATATT-TTAAGTTAAAATAAAAAT
*
35114 AAAATATAT-TTTCTAA-TTAATAA-AAGAAT
1 AAAATATATATTT-TAAGTTAA-AATAAAAAT
35143 AAAA-ATATATTTTAAGTTAAAATAAAAAT
1 AAAATATATATTTTAAGTTAAAATAAAAAT
*
35172 AAAATATATATTTTTAAAGTTGGAACATAAAAGAAT
1 AAAATATATA-TTTT-AAGTT--AAAAT-AAA-AAT
35208 AAAATATATATTTTA
1 AAAATATATATTTTA
35223 TTTTTTTATT
Statistics
Matches: 134, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
27 13 0.10
28 13 0.10
29 38 0.28
30 36 0.27
31 4 0.03
32 5 0.04
34 5 0.04
35 7 0.05
36 13 0.10
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATATATATTTTAAGTTAAAATAAAAAT
Found at i:35211 original size:36 final size:33
Alignment explanation
Indices: 35027--35221 Score: 135
Period size: 30 Copynumber: 6.4 Consensus size: 33
35017 TATTAATAAC
*
35027 AAAATATATA-TTTTAAATT--AATAAAAGAAT
1 AAAATATATATTTTTAAGTTAAAATAAAAGAAT
*
35057 --AA-ATATA-TTTTAAGTTAAAAT-AAA-TAT
1 AAAATATATATTTTTAAGTTAAAATAAAAGAAT
** * *
35084 AAAATATAT-TTAATAAGTTATATTAATAAG---
1 AAAATATATATTTTTAAGTTAAAATAA-AAGAAT
*
35114 AAAATATAT-TTTCTAA-TT--AATAAAAGAAT
1 AAAATATATATTTTTAAGTTAAAATAAAAGAAT
35143 AAAA-ATATA-TTTTAAGTTAAAAT-AAA-AAT
1 AAAATATATATTTTTAAGTTAAAATAAAAGAAT
*
35172 AAAATATATATTTTTAAAGTTGGAACATAAAAGAAT
1 AAAATATATATTTTT-AAGTT--AAAATAAAAGAAT
35208 AAAATATATATTTT
1 AAAATATATATTTT
35222 ATTTTTTTAT
Statistics
Matches: 131, Mismatches: 11, Indels: 40
0.72 0.06 0.22
Matches are distributed among these distances:
26 3 0.02
27 19 0.15
28 14 0.11
29 20 0.15
30 36 0.27
31 8 0.06
32 7 0.05
34 4 0.03
35 3 0.02
36 17 0.13
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (33 bp):
AAAATATATATTTTTAAGTTAAAATAAAAGAAT
Found at i:35274 original size:28 final size:30
Alignment explanation
Indices: 35213--35285 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
35203 AGAATAAAAT
35213 ATATATTTTATTTTTTTATTGAAATTATTAA
1 ATATATTTTATTTTTTTATTGAAATTA-TAA
*
35244 ATATATTTTATTTTTATT-TT-AACTTA-AA
1 ATATATTTTATTTTT-TTATTGAAATTATAA
35272 ATATATTTTATTTT
1 ATATATTTTATTTT
35286 AAATAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 16 0.40
30 5 0.12
31 17 0.43
32 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
ATATATTTTATTTTTTTATTGAAATTATAA
Found at i:35398 original size:23 final size:19
Alignment explanation
Indices: 35361--35422 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
35351 TAATAAAAGA
*
35361 ATAAAATAT-TTTTTAAGT
1 ATAAAATATACTTTTAAGT
*
35379 ATAAATATACTACTACTTTAA-A
1 ATAAA-ATA-TACT--TTTAAGT
35401 ATAAAATATACTTTTAAGT
1 ATAAAATATACTTTTAAGT
35420 ATA
1 ATA
35423 TTATTTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 5 0.14
21 4 0.11
22 5 0.14
23 5 0.14
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (19 bp):
ATAAAATATACTTTTAAGT
Found at i:43084 original size:67 final size:67
Alignment explanation
Indices: 42971--43097 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
42961 AATTATACAT
*
42971 ACCTTATAAGACACTGTATTATCTCTATCTTTTGCGAAATGACTATCAAAAGAGTGCACCATAGC
1 ACCTTATAAGACACTGTATTATCTCTATCTTGTGCGAAATGACTATCAAAAGAGTGCACCATAGC
43036 GG
66 GG
* *
43038 ACCTTATAAGACACTGTATTATCTCTATCTTGTGTGAAATGGCTATCAAAAGAGTGCACC
1 ACCTTATAAGACACTGTATTATCTCTATCTTGTGCGAAATGACTATCAAAAGAGTGCACC
43098 GCATGGACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (67 bp):
ACCTTATAAGACACTGTATTATCTCTATCTTGTGCGAAATGACTATCAAAAGAGTGCACCATAGC
GG
Found at i:50570 original size:24 final size:26
Alignment explanation
Indices: 50541--50588 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
50531 ATTAACATCT
*
50541 TTAAAAAT-AATTAATTT-TGATTAC
1 TTAAAAATAAATAAATTTATGATTAC
50565 TTAAAAATAAATAAATTTATGATT
1 TTAAAAATAAATAAATTTATGATT
50589 TATACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAAAAATAAATAAATTTATGATTAC
Done.