Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002362.1 Hibiscus syriacus cultivar Beakdansim tig00004821_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: 121111
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:722 original size:158 final size:157
Alignment explanation
Indices: 454--770 Score: 424
Period size: 158 Copynumber: 2.0 Consensus size: 157
444 ACTCGCAACC
* * * *
454 CACCTGCAACAATCAAATTCCGAATTCATTCGAACCGAAAAAGGCTCGAAAAAGTTATGAACTTT
1 CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCGAAAAAGTTATAAACTTT
* *
519 CAAGCTTGTAGATTTACGATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAGC
66 CAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAGA
584 AATGGACA-CATGACAGTAAAGCGAATA
131 AATGGA-ATCATGACAGTAAAGCGAATA
* * *
611 CACCTGCAACAGCCAAATTCCGAATT-ATTCCAATCGAAAAAAGTTCGAAAAAAAGTTATAAACT
1 CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCG--AAAAAGTTATAAACT
* * * ** *
675 TTCAAGTTTGTAGATTTACAATTCCTTCCAAGTTTATAG-TTGTGATGATTAATTAGTTCTCAAA
64 TTCAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTT-TGATGATTAACAAGTACTCAAA
* *
739 AGAAATGGAATCATGATAGTAAAGCTAATA
128 AGAAATGGAATCATGACAGTAAAGCGAATA
769 CA
1 CA
771 GTTTTTTTTC
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
156 17 0.12
157 27 0.19
158 95 0.68
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (157 bp):
CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCGAAAAAGTTATAAACTTT
CAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAGA
AATGGAATCATGACAGTAAAGCGAATA
Found at i:3805 original size:2 final size:2
Alignment explanation
Indices: 3779--3846 Score: 106
Period size: 2 Copynumber: 35.5 Consensus size: 2
3769 AATTAATTAT
*
3779 TA TA T- TA TA TT TA TA T- TA T- 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
3818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3847 GCAAGGGTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 58 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5138 original size:10 final size:10
Alignment explanation
Indices: 5125--5183 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
5115 CGTTCGATTA
*
5125 TATGTTCGTT
1 TATGTTCATT
5135 TATGTTCATT
1 TATGTTCATT
5145 TATGTTCATT
1 TATGTTCATT
* *
5155 CATTATTCATT
1 TA-TGTTCATT
*
5166 TTTCGTTCATT
1 TAT-GTTCATT
5177 TATGTTC
1 TATGTTC
5184 GAACAGAGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 25 0.62
11 15 0.38
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.59
Consensus pattern (10 bp):
TATGTTCATT
Found at i:5462 original size:25 final size:26
Alignment explanation
Indices: 5434--5499 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
5424 GTTTTTGTGT
*
5434 TTGTGTTGTTCGTTTATTT-CGTTCG
1 TTGTGTTGTTCGTTTATTTACGTTCA
*
5459 TTGTGTT-TTGTGTTTATTTACGTTCA
1 TTGTGTTGTT-CGTTTATTTACGTTCA
*
5485 TT-T-ATGTTCGTTTAT
1 TTGTGTTGTTCGTTTAT
5500 ATTTAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 9 0.26
25 18 0.53
26 7 0.21
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (26 bp):
TTGTGTTGTTCGTTTATTTACGTTCA
Found at i:15690 original size:2 final size:2
Alignment explanation
Indices: 15683--15754 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
15673 ATGACTTCTC
15683 AT AT AT 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 AT AT AT
15725 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15755 AGCTTGTATT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16617 original size:64 final size:64
Alignment explanation
Indices: 16546--16726 Score: 190
Period size: 65 Copynumber: 2.8 Consensus size: 64
16536 TTGGACCCTT
* * *
16546 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGATGCA-T-AGCAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
16608 TG
63 TG
* * *
16610 AGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAGGCCTG
1 AGTGCATCGATGCATAGC-AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTG
* * * *
16675 AGTGCATCGATGCATGGTATGCGCATCGATGCATAAAATGCA-TCTGATGTTT
1 AGTGCATCGATGCATAGCA-GTGCATCGATGCATCAAATGCATTC-GATGTTT
16727 AATTTATTCC
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 42 0.42
65 54 0.53
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGCAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTG
Found at i:16701 original size:65 final size:65
Alignment explanation
Indices: 16568--16726 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
16558 CACTAAGAGT
* * *
16568 GCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGT
1 GCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGC
* *
16632 GCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-GGCCTGAGTGCATCGATGCATGG-TAT
1 GCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATGGCT-T
16695 GC
64 GC
16697 GCATCGATGCATAAAATGCA-TCTGATGTTT
1 GCATCGATGCATAAAATGCATTC-GATGTTT
16727 AATTTATTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 28 0.33
65 55 0.64
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGC
Found at i:19400 original size:21 final size:22
Alignment explanation
Indices: 19341--19416 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
19331 TGTCCTTGTA
19341 CATCGATGCACATTCAAGGAGTG
1 CATCGATGCACATTC-AGGAGTG
* *
19364 CATC-AGTGCACCTTCATG-GTG
1 CATCGA-TGCACATTCAGGAGTG
* * *
19385 TATCGATGCACATTCAAGAATG
1 CATCGATGCACATTCAGGAGTG
19407 CATCGATGCA
1 CATCGATGCA
19417 TTGTTAAGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 16 0.37
22 15 0.35
23 12 0.28
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAGGAGTG
Found at i:25353 original size:65 final size:65
Alignment explanation
Indices: 25233--25391 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
25223 TGCACTAAGA
* * *
25233 GTGCA-CGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGTATCGATGCATGGCT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGG-TA
25295 T
65 T
* *
25296 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-GGCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATGGTA
25360 T
65 T
*
25361 GTGCATCAATGCATAAAATGCA-TCTGATGTT
1 GTGCATCGATGCATAAAATGCATTC-GATGTT
25392 CAATTTATTC
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 5 0.06
64 24 0.28
65 53 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGTAT
Found at i:36417 original size:16 final size:17
Alignment explanation
Indices: 36396--36447 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
36386 TTTTTAATTT
36396 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
36412 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
36427 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
36444 AATT
1 AATT
36448 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:43737 original size:3 final size:3
Alignment explanation
Indices: 43731--43790 Score: 66
Period size: 3 Copynumber: 18.0 Consensus size: 3
43721 AACCCCCAGG
43731 TCT TCT TCT TCT TCT TCT TCTT TCTT TCTT TCT TCTT TCT TCT TCCT
1 TCT TCT TCT TCT TCT TCT TC-T TC-T TC-T TCT TC-T TCT TCT T-CT
43778 TCCT TCT TCT TCT
1 T-CT TCT TCT TCT
43791 GAACTTTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
3 33 0.61
4 21 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:43854 original size:21 final size:22
Alignment explanation
Indices: 43795--43859 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 22
43785 TCTTCTGAAC
*
43795 TTTTAAAATTATATTTGTATAAT
1 TTTTAAAATTATATATGTAT-AT
*
43818 TTTGTATAATGTTATATATGTAT-T
1 TTT-TA-AA-ATTATATATGTATAT
43842 TTTTAAAATTATATATGT
1 TTTTAAAATTATATATGT
43860 CCAAGCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 10 0.28
22 2 0.06
23 5 0.14
24 6 0.17
25 2 0.06
26 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TTTTAAAATTATATATGTATAT
Found at i:44971 original size:2 final size:2
Alignment explanation
Indices: 44964--44993 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
44954 GATAAAAATG
44964 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44994 AATAAATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47296 original size:17 final size:17
Alignment explanation
Indices: 47276--47320 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
47266 TAAAATATAA
47276 AAATATTCAAAAATT-TT
1 AAATA-TCAAAAATTATT
*
47293 AAATATCTAAAATTATT
1 AAATATCAAAAATTATT
47310 AAA-AT-AAAAAT
1 AAATATCAAAAAT
47321 ACTATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 10 0.40
17 10 0.40
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATCAAAAATTATT
Found at i:47338 original size:44 final size:44
Alignment explanation
Indices: 47256--47339 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
47246 TTAAAAATAA
47256 TAAAATAATATAAAATATAAAAATATTCAAAAATTTTAAATATC
1 TAAAATAATATAAAATATAAAAATATTCAAAAATTTTAAATATC
*
47300 TAAAATTAT-TAAAATA-AAAATACTATT-AAAAACTTTTAAA
1 TAAAATAATATAAAATATAAAA-A-TATTCAAAAA-TTTTAAA
47340 AAAATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 4 0.11
43 13 0.36
44 19 0.53
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (44 bp):
TAAAATAATATAAAATATAAAAATATTCAAAAATTTTAAATATC
Found at i:52044 original size:50 final size:50
Alignment explanation
Indices: 51986--52086 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
51976 CCTCGCGTCC
51986 TCCAATCTGGTGAAGCGAACAAAGCCAAACCTACTTCCTCCCTTGCTTCT
1 TCCAATCTGGTGAAGCGAACAAAGCCAAACCTACTTCCTCCCTTGCTTCT
52036 TCCAATCTGGTGAAGCGAACAAAGCCAAACCTACTTCCTCCCTTGCTTCT
1 TCCAATCTGGTGAAGCGAACAAAGCCAAACCTACTTCCTCCCTTGCTTCT
52086 T
1 T
52087 TTGTTAGGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.27
Consensus pattern (50 bp):
TCCAATCTGGTGAAGCGAACAAAGCCAAACCTACTTCCTCCCTTGCTTCT
Found at i:52405 original size:44 final size:44
Alignment explanation
Indices: 52339--52439 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
52329 GGGAAGATCG
* * * * *
52339 ATGAGTGTAAGTGTGGATATCCAA-TTTTGAAATGGATTGAAGCT
1 ATGAGAGTGAGTGTGGACATCCAACTTTT-AAATGAATTGAAGCA
* * *
52383 ATGAGCGTGAGTGTGTACATCCAACTTTTACATGAATTGAAGCA
1 ATGAGAGTGAGTGTGGACATCCAACTTTTAAATGAATTGAAGCA
*
52427 ACGAGAGTGAGTG
1 ATGAGAGTGAGTG
52440 CAGATACCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 43 0.91
45 4 0.09
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (44 bp):
ATGAGAGTGAGTGTGGACATCCAACTTTTAAATGAATTGAAGCA
Found at i:56251 original size:20 final size:20
Alignment explanation
Indices: 56226--56264 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56216 TAAAATATAA
56226 ATAGATATTTATA-AGAAAAT
1 ATAGATATTT-TAGAGAAAAT
*
56246 ATAGATCTTTTAGAGAAAA
1 ATAGATATTTTAGAGAAAA
56265 AAAAGACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (20 bp):
ATAGATATTTTAGAGAAAAT
Found at i:57274 original size:20 final size:20
Alignment explanation
Indices: 57238--57283 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
57228 TGATTGTTCT
57238 TAAA-ATATTATAATTTTTA
1 TAAATATATTATAATTTTTA
57257 TAAATATATT-TAATTTTT-
1 TAAATATATTATAATTTTTA
*
57275 TAAAAATAT
1 TAAATATAT
57284 CGTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATATTATAATTTTTA
Found at i:57289 original size:20 final size:19
Alignment explanation
Indices: 57239--57283 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
57229 GATTGTTCTT
57239 AAAATATTATAATTTTTATA
1 AAAATATT-TAATTTTTATA
*
57259 AATATATTTAATTTTT-TA
1 AAAATATTTAATTTTTATA
57277 AAAATAT
1 AAAATAT
57284 CGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATATTTAATTTTTATA
Found at i:68222 original size:18 final size:18
Alignment explanation
Indices: 68201--68247 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
68191 GAGAATATAT
*
68201 AAAAAATTAAAAGTGTTA
1 AAAAAATTAAAAGTGTGA
*
68219 AAAAAA-T-AATGTGTGA
1 AAAAAATTAAAAGTGTGA
68235 AAAAAACTTAAAA
1 AAAAAA-TTAAAA
68248 AATTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 13 0.57
17 1 0.04
18 7 0.30
19 2 0.09
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAAATTAAAAGTGTGA
Found at i:69044 original size:13 final size:13
Alignment explanation
Indices: 69026--69052 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
69016 TCCTCATTAC
69026 TTGCATATTTTAT
1 TTGCATATTTTAT
69039 TTGCATATTTTAT
1 TTGCATATTTTAT
69052 T
1 T
69053 AATTTGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTGCATATTTTAT
Found at i:72205 original size:20 final size:21
Alignment explanation
Indices: 72180--72231 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
72170 TTTTCCCAAT
*
72180 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
72200 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
72221 TCGCAATGCGA
1 TCGCAATGCGA
72232 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:72245 original size:20 final size:20
Alignment explanation
Indices: 72220--72333 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
72210 AATTGGGAAA
*
72220 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
72240 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
72260 ATCACAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
72281 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
72301 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
72321 TTCGCAACGCGAT
1 ATCGCAACGCGAT
72334 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:72333 original size:61 final size:61
Alignment explanation
Indices: 72217--72333 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
72207 GCGAATTGGG
* * * * *
72217 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCACAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * * *
72278 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGAT
72334 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:72889 original size:19 final size:19
Alignment explanation
Indices: 72851--72917 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
72841 TTCGAGAATG
72851 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
72871 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
72890 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
72909 AAAATCGCA
1 AAAATCGCA
72918 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:72935 original size:19 final size:19
Alignment explanation
Indices: 72913--73057 Score: 130
Period size: 19 Copynumber: 8.1 Consensus size: 19
72903 GAAACCAAAA
*
72913 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
72932 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
72946 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
72965 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
72984 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
72998 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
73017 TCGCGTTGTGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
73036 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
73056 TC
1 TC
73058 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 6 0.06
19 55 0.54
20 16 0.16
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:72997 original size:52 final size:52
Alignment explanation
Indices: 72913--73049 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 52
72903 GAAACCAAAA
* * **
72913 TCGCATTGCGATTTTCATTTCGCGTTGTGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
72965 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
* * *
73017 TCGCGTTGTGATTCTCATTATCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATT
73050 TTCATTTCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 65 0.84
53 12 0.16
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:73016 original size:33 final size:33
Alignment explanation
Indices: 72968--73032 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
72958 TTTCATTTCG
**
72968 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
73001 CGTTGCGATAGTCATTTCGCGTTGTGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
73033 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:74603 original size:63 final size:63
Alignment explanation
Indices: 74504--74634 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
74494 GTTACGTGAT
*
74504 GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
*
74567 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCTTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
74630 GAGGT
1 GAGGT
74635 GTCTACTTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.25
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:75278 original size:41 final size:42
Alignment explanation
Indices: 75201--75371 Score: 184
Period size: 41 Copynumber: 4.1 Consensus size: 42
75191 CGACTCGCTG
* *
75201 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * * * *
75243 TCATTCCTCGAGAGTCCCCTCCCA-CGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * *
75284 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * * * * *
75326 TCAT-TCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
75367 TCATC
1 TCATC
75372 GTTGAAGAGG
Statistics
Matches: 103, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
41 66 0.64
42 37 0.36
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
Found at i:75374 original size:21 final size:21
Alignment explanation
Indices: 75267--75381 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
75257 TCCCCTCCCA
75267 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
75288 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * * *
75309 CATTGAAGAGGCCCCTATCAT
1 CGTTCAAGAGGCCACTGTCAT
* * * ** *
75330 --TCTCGAGAGTCCCCTCCCAC
1 CGT-TCAAGAGGCCACTGTCAT
75350 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
75371 CGTTGAAGAGG
1 CGTTCAAGAGG
75382 TCCCTCCCAC
Statistics
Matches: 66, Mismatches: 23, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
19 1 0.02
20 13 0.20
21 50 0.76
22 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:75380 original size:83 final size:83
Alignment explanation
Indices: 75198--75371 Score: 323
Period size: 83 Copynumber: 2.1 Consensus size: 83
75188 GCCCGACTCG
*
75198 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
75263 CCCACGTTCAAGAGGCCA
66 CCCACGTTCAAGAGGCCA
75281 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
75345 CCCACCGTTCAAGAGGCCA
66 CCCA-CGTTCAAGAGGCCA
75364 CTGTCATC
1 CTGTCATC
75372 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 18 0.20
83 71 0.80
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACGTTCAAGAGGCCA
Found at i:75400 original size:21 final size:20
Alignment explanation
Indices: 75341--75401 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
75331 CTCGAGAGTC
75341 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
75361 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
75382 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
75402 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:75401 original size:83 final size:83
Alignment explanation
Indices: 75198--75401 Score: 286
Period size: 83 Copynumber: 2.5 Consensus size: 83
75188 GCCCGACTCG
* * * *
75198 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
75263 CCCACGTTCAAGAGGCCA
66 CCCACGTTCAAGAGGCCA
* * *
75281 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
75345 CCCACCGTTCAAGAGGCCA
66 CCCA-CGTTCAAGAGGCCA
** *
75364 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
75402 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
82 18 0.16
83 90 0.80
84 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACGTTCAAGAGGCCA
Found at i:76756 original size:14 final size:14
Alignment explanation
Indices: 76737--76772 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
76727 GATTGTTAAT
76737 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
76751 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
76765 TGATTTGT
1 TGATTTGT
76773 TTAATGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:76918 original size:14 final size:14
Alignment explanation
Indices: 76896--76952 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
76886 GCGAAATGAA
*
76896 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
76910 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
76929 AATCGCAACGAGAG
1 AATCGCAACGAGAG
76943 AATCGCAACG
1 AATCGCAACG
76953 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:76923 original size:33 final size:33
Alignment explanation
Indices: 76878--76958 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
76868 AAAAAGTACT
*
76878 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
*
76911 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
76944 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
76959 TAAATTCGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGAGAGA
Found at i:76934 original size:19 final size:19
Alignment explanation
Indices: 76878--76938 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
76868 AAAAAGTACT
*
76878 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
76897 ATCACAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
76911 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
76930 ATCGCAACG
1 ATCGCAACG
76939 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:76985 original size:19 final size:19
Alignment explanation
Indices: 76963--77092 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
76953 CGAAATTAAA
*
76963 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
76982 TTCGCATTGCGA--TTCCC
1 TTCGCATTGCGATTTTCAT
76999 TT-G--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
77015 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
77029 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
77048 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
77064 CTCG--TTGCGATTTTCA-
1 TTCGCATTGCGATTTTCAT
77080 TTCGCATTGCGAT
1 TTCGCATTGCGAT
77093 AGTAATTCCG
Statistics
Matches: 83, Mismatches: 13, Indels: 31
0.65 0.10 0.24
Matches are distributed among these distances:
14 23 0.28
16 16 0.19
17 9 0.11
18 7 0.08
19 28 0.34
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:77010 original size:33 final size:32
Alignment explanation
Indices: 76968--77092 Score: 173
Period size: 33 Copynumber: 3.8 Consensus size: 32
76958 TTAAATTCGC
76968 GTTGCGATTTTCATTTCGCATTGCGATTCCCTT
1 GTTGCGATTTTCATTTCGCATTGCGATTCCC-T
**
77001 GTTGCGATTTTCATTTCGCATTGCGAAATTAGC-
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCCT
*
77034 GTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCT
77066 CGTTGCGATTTTCA-TTCGCATTGCGAT
1 -GTTGCGATTTTCATTTCGCATTGCGAT
77093 AGTAATTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
31 4 0.05
32 13 0.15
33 63 0.75
35 4 0.05
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:77045 original size:66 final size:65
Alignment explanation
Indices: 76960--77091 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 65
76950 ACGCGAAATT
* *
76960 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTTGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCA-TTCGCATTGC
77025 G
65 G
*
77026 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGCATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTCGCATTGCG
77091 A
1 A
77092 TAGTAATTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 12 0.19
66 51 0.81
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTCGCATTGCG
Found at i:79317 original size:12 final size:12
Alignment explanation
Indices: 79300--79324 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79290 TCTTCGGGGA
79300 CTTTTTCTTCTT
1 CTTTTTCTTCTT
79312 CTTTTTCTTCTT
1 CTTTTTCTTCTT
79324 C
1 C
79325 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:80319 original size:20 final size:20
Alignment explanation
Indices: 80294--80342 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
80284 CTGTATATCA
80294 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCG
80314 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCG
80334 TTGCGAAAG
1 TTGCGAAAG
80343 GCAATCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (20 bp):
TTGCGAAAGTCAGAATCGCG
Found at i:80613 original size:19 final size:20
Alignment explanation
Indices: 80555--80624 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
80545 ATTCATTTGA
*
80555 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
80575 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
80595 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
80614 CTATCGCAACG
1 CTATCGCAACG
80625 ACAAAATCGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 17 0.35
20 32 0.65
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:80694 original size:19 final size:19
Alignment explanation
Indices: 80672--80714 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
80662 TTTCTCGTTA
80672 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
80691 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
80710 CGATT
1 CGATT
80715 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:80860 original size:14 final size:14
Alignment explanation
Indices: 80841--80874 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
80831 CATCAATTAA
80841 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
80855 ACAAATCATCTTTT
1 ACAAATCAACATTT
80869 ACAAAT
1 ACAAAT
80875 TAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:82770 original size:20 final size:20
Alignment explanation
Indices: 82747--82793 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
82737 GAAACTTAAA
82747 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * * *
82767 ATCGTAACGCGGAAATGGCT
1 ATCGCAACACGAAAATGACT
82787 ATCGCAA
1 ATCGCAA
82794 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:82802 original size:19 final size:19
Alignment explanation
Indices: 82759--82822 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
82749 CGCAACACGA
* *
82759 AAATGACTATCGTAACGCGG
1 AAATGACTATCGCAATGC-G
*
82779 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
82798 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
82817 AAATGA
1 AAATGA
82823 AATCGCAACG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:82823 original size:19 final size:19
Alignment explanation
Indices: 82787--82868 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
82777 GGAAATGGCT
82787 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
82806 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
82824 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
82838 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
82857 ATCGCAATGCGA
1 ATCGCAATGCGA
82869 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
14 10 0.19
16 4 0.07
18 10 0.19
19 30 0.56
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:82899 original size:14 final size:14
Alignment explanation
Indices: 82880--82937 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
82870 TTGTGTTTCG
82880 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
82894 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
82910 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
82926 CGTTGTGATTTT
1 CGTTGCGATTTT
82938 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:82918 original size:32 final size:33
Alignment explanation
Indices: 82875--82953 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
82865 GCGATTTGTG
*
82875 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
82907 TTTCGCATTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
82940 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
82954 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:82962 original size:19 final size:20
Alignment explanation
Indices: 82938--82981 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
82928 TTGTGATTTT
*
82938 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTACGATAGC
* *
82957 CATTTCCGCGTTACGATAGT
1 CATTTCCGCATTACGATAGC
82977 CATTT
1 CATTT
82982 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:83500 original size:18 final size:18
Alignment explanation
Indices: 83474--83518 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
83464 GTCGATCAGA
*
83474 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
83492 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
83510 TGATGGCTC
1 TGATGGCTC
83519 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:85181 original size:22 final size:22
Alignment explanation
Indices: 85154--85197 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
85144 GATGGAGATA
*
85154 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
85176 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
85198 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:85411 original size:20 final size:20
Alignment explanation
Indices: 85386--85437 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
85376 ATTATGTATT
85386 ATCGCGTTGCGAAAGTCAAA
1 ATCGCGTTGCGAAAGTCAAA
**
85406 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAAA
*
85426 ATCTCGTTGCGA
1 ATCGCGTTGCGA
85438 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAAA
Found at i:85471 original size:20 final size:20
Alignment explanation
Indices: 85446--85492 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
85436 GATTTTGTAT
85446 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
85466 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
85486 TATCGCA
1 TATCGCA
85493 ACGACACTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:85471 original size:61 final size:61
Alignment explanation
Indices: 85371--85489 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
85361 GAAAATCGCA
* *
85371 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAAAATCGCGTTGCGAAAGTCAGTATCTCG
1 TTGCGATTATGTATTATCGCATTGCGAAAGTCAAAATCGCATTGCGAAAGTCAGTATCTCG
* * * *
85432 TTGCGATTTTGTATTATCGCATTGCGATAGT-AAGTATCGCATTGCGATAGTCAGTATC
1 TTGCGATTATGTATTATCGCATTGCGAAAGTCAA-AATCGCATTGCGAAAGTCAGTATC
85490 GCAACGACAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 2 0.04
61 49 0.96
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (61 bp):
TTGCGATTATGTATTATCGCATTGCGAAAGTCAAAATCGCATTGCGAAAGTCAGTATCTCG
Found at i:85548 original size:21 final size:21
Alignment explanation
Indices: 85508--85548 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
85498 ACTGTAGACC
**
85508 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
85529 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
85549 GCGAATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:86161 original size:2 final size:2
Alignment explanation
Indices: 86154--86179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86144 AGTATGTATG
86154 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
86180 AATACCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93469 original size:35 final size:36
Alignment explanation
Indices: 93402--93470 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
93392 TATATATATA
* *
93402 TATATATATTTTTTAAAAATTTAAATTCATAAAATT
1 TATATATATTTTTTAAAAATTAAAAATCATAAAATT
93438 TATATAT-TTTTTTACAAAATTAAAAAT-ATAAAA
1 TATATATATTTTTTA-AAAATTAAAAATCATAAAA
93471 GGTTTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
TATATATATTTTTTAAAAATTAAAAATCATAAAATT
Found at i:93824 original size:19 final size:19
Alignment explanation
Indices: 93800--93847 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
93790 ATGTGGATTC
93800 CATTCCCATGGGAATCCCA
1 CATTCCCATGGGAATCCCA
93819 CATTCCCATGGGAATCCCA
1 CATTCCCATGGGAATCCCA
93838 CATTCCCATG
1 CATTCCCATG
93848 TTTGGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (19 bp):
CATTCCCATGGGAATCCCA
Found at i:95975 original size:14 final size:14
Alignment explanation
Indices: 95958--95995 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
95948 TAAATATTAT
95958 AAAATAATTTAATA
1 AAAATAATTTAATA
95972 AAAATAATTTAATA
1 AAAATAATTTAATA
*
95986 AATATAATTT
1 AAAATAATTT
95996 TTAATTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATAATTTAATA
Found at i:96612 original size:35 final size:35
Alignment explanation
Indices: 96562--96638 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
96552 CAAAAAGTTT
* *
96562 ATTACTAAACTTTATATAACTGTATAATAACTTAA
1 ATTATTAAACTTTATATAACTATATAATAACTTAA
*
96597 ATTATTAAAGTTTATATAACTATATAATAACTTAA
1 ATTATTAAACTTTATATAACTATATAATAACTTAA
96632 ATTATTA
1 ATTATTA
96639 TATGATAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (35 bp):
ATTATTAAACTTTATATAACTATATAATAACTTAA
Found at i:96646 original size:20 final size:20
Alignment explanation
Indices: 96617--96657 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
96607 TTTATATAAC
96617 TATATAATAACTTAAATTAT
1 TATATAATAACTTAAATTAT
* *
96637 TATATGATAACTTATATTAT
1 TATATAATAACTTAAATTAT
96657 T
1 T
96658 GTTTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATAATAACTTAAATTAT
Found at i:99803 original size:30 final size:31
Alignment explanation
Indices: 99768--99829 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
99758 TTTTATATAT
* *
99768 TATTCAACGAGTTTAAAGTTCAAATT-TCAA
1 TATTCAACAAGGTTAAAGTTCAAATTATCAA
**
99798 TATTCAACAAGGTTGCAGTTCAAATTATCAA
1 TATTCAACAAGGTTAAAGTTCAAATTATCAA
99829 T
1 T
99830 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (31 bp):
TATTCAACAAGGTTAAAGTTCAAATTATCAA
Found at i:100952 original size:20 final size:19
Alignment explanation
Indices: 100929--100966 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
100919 TCCCCGCAGT
*
100929 TTTTTTAAACGGGTACGGG
1 TTTTTTAAACGGGGACGGG
100948 TTTTTTAAACGGGGACGGG
1 TTTTTTAAACGGGGACGGG
100967 GACGGGGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.34
Consensus pattern (19 bp):
TTTTTTAAACGGGGACGGG
Found at i:101746 original size:2 final size:2
Alignment explanation
Indices: 101739--101797 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
101729 ATGTCAATGT
101739 TA TA TA 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
101781 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
101798 TTAAGATCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101975 original size:2 final size:2
Alignment explanation
Indices: 101963--101998 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
101953 CGGTCCTATC
*
101963 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101999 CATTTGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:107046 original size:2 final size:2
Alignment explanation
Indices: 107039--107172 Score: 100
Period size: 2 Copynumber: 70.0 Consensus size: 2
107029 GCTATAAATC
*
107039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * *
107080 AT A- AT AG AT TT AT -T AT TT AA AT TT AT -T TT AA AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
107119 AT AA AT AA AA AT AT AT -T AA AT AT -T 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 AT AT AT
107159 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
107173 TTACGTTTTT
Statistics
Matches: 101, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
1 6 0.06
2 95 0.94
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107111 original size:11 final size:11
Alignment explanation
Indices: 107095--107124 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
107085 AGATTTATTA
107095 TTTAAATTTAT
1 TTTAAATTTAT
107106 TTTAAATTTAT
1 TTTAAATTTAT
107117 TTATAAAT
1 TT-TAAAT
107125 AAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:114262 original size:19 final size:19
Alignment explanation
Indices: 114222--114268 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
114212 ATGAATTGTT
* *
114222 TTTAATAATTTTATTTTAA
1 TTTAATAATCTAATTTTAA
114241 TTTAATAATCTAATATTT-A
1 TTTAATAATCTAAT-TTTAA
*
114260 TTTATTAAT
1 TTTAATAAT
114269 ATCTATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATAATCTAATTTTAA
Found at i:116396 original size:2 final size:2
Alignment explanation
Indices: 116391--116417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116381 ACACAATCCA
116391 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 A
116418 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:117053 original size:15 final size:17
Alignment explanation
Indices: 117035--117073 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
117025 ATAGAAAATA
117035 TTAAAATATAT-AT-AT
1 TTAAAATATATAATAAT
117050 TTAAAATATATAATAAT
1 TTAAAATATATAATAAT
117067 TTAAAAT
1 TTAAAAT
117074 TTTATAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.50
16 2 0.09
17 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATATATAATAAT
Found at i:119862 original size:2 final size:2
Alignment explanation
Indices: 119855--119888 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
119845 AAATAATTGA
119855 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
119889 TCTTAGGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.