Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003191.1 Hibiscus syriacus cultivar Beakdansim tig00006715_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: 77776
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:3650 original size:96 final size:96
Alignment explanation
Indices: 3486--3681 Score: 383
Period size: 96 Copynumber: 2.0 Consensus size: 96
3476 ATCATAGTTT
3486 AAAATCTAAAATGATATTGTCACATTATTATCACATTAACAAAAAGATTCATCTACGTCATCGTG
1 AAAATCTAAAATGATATTGTCACATTATTATCACATTAACAAAAAGATTCATCTACGTCATCGTG
3551 TCATTATTATAATTTAATAATCACGTTAACA
66 TCATTATTATAATTTAATAATCACGTTAACA
3582 AAAATCTAAAATGATATTGTCACATTATTATCACATTAACAAAAAGATTCATCTACGTCATCGTG
1 AAAATCTAAAATGATATTGTCACATTATTATCACATTAACAAAAAGATTCATCTACGTCATCGTG
*
3647 TCATTATTATAATTTAATGATCACGTTAACA
66 TCATTATTATAATTTAATAATCACGTTAACA
3678 AAAA
1 AAAA
3682 GATTCATCTA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (96 bp):
AAAATCTAAAATGATATTGTCACATTATTATCACATTAACAAAAAGATTCATCTACGTCATCGTG
TCATTATTATAATTTAATAATCACGTTAACA
Found at i:3697 original size:55 final size:55
Alignment explanation
Indices: 3611--3727 Score: 207
Period size: 55 Copynumber: 2.1 Consensus size: 55
3601 TCACATTATT
* *
3611 ATCACATTAACAAAAAGATTCATCTACGTCATCGTGTCATTATTATAATTTAATG
1 ATCACGTTAACAAAAAGATTCATCTAAGTCATCGTGTCATTATTATAATTTAATG
*
3666 ATCACGTTAACAAAAAGATTCATCTAAGTCATCGTGTCATTATTATAGTTTAATG
1 ATCACGTTAACAAAAAGATTCATCTAAGTCATCGTGTCATTATTATAATTTAATG
3721 ATCACGT
1 ATCACGT
3728 GTTATAACAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (55 bp):
ATCACGTTAACAAAAAGATTCATCTAAGTCATCGTGTCATTATTATAATTTAATG
Found at i:4212 original size:60 final size:60
Alignment explanation
Indices: 4140--4279 Score: 244
Period size: 60 Copynumber: 2.3 Consensus size: 60
4130 CAGGTGACCC
*
4140 TTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAATACCACTCTATAATTGAAGTACCA
1 TTTTATAACTTTTAATAGTCGAAGGACTCAACAAAATACCACTCTATAATTGAAGTACCA
* *
4200 TTTTATAACTTTTAATAGTCGAATGACTCAACAAAATACCACTCTATAGTTGAAGTACCA
1 TTTTATAACTTTTAATAGTCGAAGGACTCAACAAAATACCACTCTATAATTGAAGTACCA
*
4260 TTTTATAACATTTAATAGTC
1 TTTTATAACTTTTAATAGTC
4280 AAGTAACTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 76 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGAAGGACTCAACAAAATACCACTCTATAATTGAAGTACCA
Found at i:6294 original size:29 final size:30
Alignment explanation
Indices: 6248--6316 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
6238 ACCGGGTATA
6248 TATATATATATTTAAA-TTAAATATAAAAT
1 TATATATATATTTAAATTTAAATATAAAAT
* * * * *
6277 TATATGTATTTTTTAATTTAAATTTAAATT
1 TATATATATATTTAAATTTAAATATAAAAT
6307 TAT-TA-ATATT
1 TATATATATATT
6317 ATATATATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 4 0.12
29 14 0.44
30 14 0.44
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TATATATATATTTAAATTTAAATATAAAAT
Found at i:9105 original size:4 final size:4
Alignment explanation
Indices: 9096--9658 Score: 637
Period size: 4 Copynumber: 140.5 Consensus size: 4
9086 GTGTTATTAA
9096 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9144 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
9192 TATG TATG TATG TATG TATAG T-TT TTTT TAAG TATAG TA-A CATT TGATG
1 TATG TATG TATG TATG TAT-G TATG TATG TATG TAT-G TATG TATG T-ATG
* * * * * ** * * * *
9241 TAT- T-TT TAACTT TATTT TAT- TAATTA TATT TACC TA-A AATTT TATT
1 TATG TATG T-A-TG TA-TG TATG T-A-TG TATG TATG TATG TA-TG TATG
** ** * * * * * *
9287 TATG ATAAT- TCAAA TACA AAAG TCT- TGTG TTAT- TA-A TATA TATG
1 TATG -T-ATG T-ATG TATG TATG TATG TATG -TATG TATG TATG TATG
*
9331 TATG TATG TATG TATG TATG TATG TATG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9379 TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
9425 TATG TGTG TGTG TATG TATG TATG TATG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9473 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9521 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9569 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9617 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
9659 CATGTTAACT
Statistics
Matches: 499, Mismatches: 37, Indels: 46
0.86 0.06 0.08
Matches are distributed among these distances:
2 3 0.01
3 12 0.02
4 458 0.92
5 20 0.04
6 6 0.01
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:9378 original size:227 final size:225
Alignment explanation
Indices: 8983--9429 Score: 858
Period size: 227 Copynumber: 2.0 Consensus size: 225
8973 AGAGCCACAT
8983 TAGTTTTTTTTAAGTATAGTAACATTTGATGTATTTTTAACTTTATTTTATTAATTATATTTACC
1 TAGTTTTTTTTAAGTATAGTAACATTTGATGTATTTTTAACTTTATTTTATTAATTATATTTACC
*
9048 TAAAATTTTATTTATGATAATTCAAATACAAAAGTCTTGTGTTATTAATATGTATGTATGTATGT
66 TAAAATTTTATTTATGATAATTCAAATACAAAAGTCTTGTGTTATTAATATATATGTATGTATGT
9113 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA
131 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATG--TGTA
9178 TGTATGTATGTATGTATGTATGTATGTATGTA
194 TGTATGTATGTATGTATGTATGTATGTATGTA
9210 TAGTTTTTTTTAAGTATAGTAACATTTGATGTATTTTTAACTTTATTTTATTAATTATATTTACC
1 TAGTTTTTTTTAAGTATAGTAACATTTGATGTATTTTTAACTTTATTTTATTAATTATATTTACC
9275 TAAAATTTTATTTATGATAATTCAAATACAAAAGTCTTGTGTTATTAATATATATGTATGTATGT
66 TAAAATTTTATTTATGATAATTCAAATACAAAAGTCTTGTGTTATTAATATATATGTATGTATGT
*
9340 ATGTATGTATGTATGTATGTGTGTATGTATGTATGTATGTATGTATGTATGTATGTATGTGTATG
131 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTGTATG
9405 TATGTATGTATGTATGTATGTATGT
196 TATGTATGTATGTATGTATGTATGT
9430 GTGTGTGTAT
Statistics
Matches: 218, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
225 31 0.14
227 187 0.86
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (225 bp):
TAGTTTTTTTTAAGTATAGTAACATTTGATGTATTTTTAACTTTATTTTATTAATTATATTTACC
TAAAATTTTATTTATGATAATTCAAATACAAAAGTCTTGTGTTATTAATATATATGTATGTATGT
ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTGTATG
TATGTATGTATGTATGTATGTATGTATGTA
Found at i:22552 original size:154 final size:157
Alignment explanation
Indices: 22244--22572 Score: 411
Period size: 154 Copynumber: 2.1 Consensus size: 157
22234 CAGATTCTAA
* * *
22244 TAAAAAGT-GACTTAAAATAAATCACAAATTAAATGAATAAGGAGATTATGAAAAATTGAAGGAC
1 TAAAAA-TAGACTTAAAATAAATCACAAATTAAATGAATAAGAAGATTATGAAAAATTAAAGGAA
* *
22308 TAAATTGAAAAATAAAAAAAATTGTTATCAAAAAAGGAATTGAAAGTACACATGTATTCTACTAT
65 TAAATTGAAAAATAAAAAAAATTATTATCAAAAAAGGAATTAAAAGTACACATGTATTCTACTAT
*
22373 GGCTTAGGAGCATATGGCTCAAA-TTTG
130 GGCTTAGGAGCATATAGCTCAAATTTTG
** * *
22400 ATAAAAA-A-ACTTAAAATAAATGTCGAATTTAA-GAAATAAGAAGATTATGAAAAATTAAAGGA
1 -TAAAAATAGACTTAAAATAAATCACAAATTAAATG-AATAAGAAGATTATGAAAAATTAAAGGA
** * * *
22462 ATAAATT-AAAAA-ATTAAAAATTATTATCAAAAAGATGAATTAAAAGTACACGTGTATTCTATT
64 ATAAATTGAAAAATAAAAAAAATTATTATCAAAAA-AGGAATTAAAAGTACACATGTATTCTACT
* * *
22525 ATGGTTTAGGAGCATGTAGTTCAAATTTTG
128 ATGGCTTAGGAGCATATAGCTCAAATTTTG
22555 TAAAAATAGACTTAAAAT
1 TAAAAATAGACTTAAAAT
22573 GAAGAGGAAT
Statistics
Matches: 148, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
153 18 0.12
154 58 0.39
155 57 0.39
156 9 0.06
157 6 0.04
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (157 bp):
TAAAAATAGACTTAAAATAAATCACAAATTAAATGAATAAGAAGATTATGAAAAATTAAAGGAAT
AAATTGAAAAATAAAAAAAATTATTATCAAAAAAGGAATTAAAAGTACACATGTATTCTACTATG
GCTTAGGAGCATATAGCTCAAATTTTG
Found at i:24330 original size:21 final size:21
Alignment explanation
Indices: 24304--24357 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
24294 TCTTTGAGTA
24304 TTATATAAGCTTAAGAAAAGC
1 TTATATAAGCTTAAGAAAAGC
*
24325 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGAAAAGC
24346 TTATATAAGCTT
1 TTATATAAGCTT
24358 TAAACATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (21 bp):
TTATATAAGCTTAAGAAAAGC
Found at i:24893 original size:20 final size:22
Alignment explanation
Indices: 24848--24905 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
24838 GCATGGGTAG
24848 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
24872 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
24892 TGTATCGATGCACT
1 TGCATCGATGCACT
24906 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:25670 original size:12 final size:12
Alignment explanation
Indices: 25630--25671 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
25620 GCTATGAGAT
25630 TATATGAAATG-
1 TATATGAAATGA
25641 TGATATGAAAGTGTA
1 T-ATATGAAA-TG-A
25656 TATATGAAATGA
1 TATATGAAATGA
25668 TATA
1 TATA
25672 AAGATAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 13 0.48
13 4 0.15
14 8 0.30
15 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (12 bp):
TATATGAAATGA
Found at i:25824 original size:31 final size:32
Alignment explanation
Indices: 25739--25832 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 32
25729 ATTCGAGGGT
* *
25739 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTAAGGAACATATGGACAGTA
***
25771 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 TTACCTATGTTCTAAGGA-ACATATGGACAGTA
*
25803 -TATCTATGTTCTAAGGAACATATGGACAGT
1 TTACCTATGTTCTAAGGAACATATGGACAGT
25833 TGTCGAGGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 25 0.48
32 27 0.52
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:26773 original size:43 final size:43
Alignment explanation
Indices: 26726--26900 Score: 174
Period size: 43 Copynumber: 4.1 Consensus size: 43
26716 GCCATACTTG
* * * *
26726 CGCCGCAATAGGTAAAAATCTATAGCAGCGTTTTTGGAGCAAA
1 CGCCGCAAAAGGTCAATATCTATAGCAGCGTTTTTGGAACAAA
* * * * *
26769 CGCCGCAAAATGTCGATATCTATAGCGGCGTTTCT-GATCAAA
1 CGCCGCAAAAGGTCAATATCTATAGCAGCGTTTTTGGAACAAA
* * * * *
26811 CACCGCAAAAGGTCACTATTTATAGCGGCATTTTTGGAACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCAGCGTTTTTGGAACAAA
* * *
26854 TGCCGCAAAAGGTC-AGATCTATAGCAACGTTTTTGGATACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCAGCGTTTTTGGA-ACAAA
26897 CGCC
1 CGCC
26901 ACTAATTACC
Statistics
Matches: 105, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 51 0.49
43 54 0.51
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (43 bp):
CGCCGCAAAAGGTCAATATCTATAGCAGCGTTTTTGGAACAAA
Found at i:26835 original size:42 final size:42
Alignment explanation
Indices: 26743--26900 Score: 174
Period size: 42 Copynumber: 3.7 Consensus size: 42
26733 ATAGGTAAAA
* * *
26743 ATCTATAGCAGCGTTTTTGGAGCAAACGCCGCAAAATGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AT
* * *
26786 ATCTATAGCGGCGTTTCT-GATCAAACACCGCAAAAGGTCACT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCA-T
* * * *
26828 ATTTATAGCGGCATTTTTGGAACAAATGCCGCAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
**
26870 ATCTATAGCAACGTTTTTGGATACAAACGCC
1 ATCTATAGCGGCGTTTTTGGA-ACAAACGCC
26901 ACTAATTACC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 51 0.54
43 43 0.45
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
Found at i:27815 original size:27 final size:28
Alignment explanation
Indices: 27765--27821 Score: 98
Period size: 27 Copynumber: 2.0 Consensus size: 28
27755 ACCTATCAAA
27765 ATAAAGCACGTCTCATGAAAGTCATCCAT
1 ATAAAGCACG-CTCATGAAAGTCATCCAT
27794 ATAAAGCACG-TCATGAAAGTCATCCAT
1 ATAAAGCACGCTCATGAAAGTCATCCAT
27821 A
1 A
27822 AATGGTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 18 0.64
29 10 0.36
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (28 bp):
ATAAAGCACGCTCATGAAAGTCATCCAT
Found at i:31801 original size:16 final size:18
Alignment explanation
Indices: 31769--31803 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
31759 ATATAAAAAC
31769 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
31787 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
31803 A
1 A
31804 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:31983 original size:32 final size:30
Alignment explanation
Indices: 31918--32006 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
31908 ATATAAATAT
* *
31918 ATATATATATATAATAACACTAATAAAAAA
1 ATATACATATATAATAAAACTAATAAAAAA
* *
31948 ATATACATATATAATAAAATTAATAGAAAGTA
1 ATATACATATATAATAAAACTAATA-AAA-AA
* *
31980 ATATGCATATATAACAAGAA-TAATAAA
1 ATATACATATATAATAA-AACTAATAAA
32007 GTAGGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 22 0.44
31 5 0.10
32 21 0.42
33 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (30 bp):
ATATACATATATAATAAAACTAATAAAAAA
Found at i:32008 original size:30 final size:29
Alignment explanation
Indices: 31947--32009 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 29
31937 CTAATAAAAA
31947 AATATACATATATAATAAAATTAATAGAAAGT
1 AATATACATATATAATAAAA-TAAT--AAAGT
* *
31979 AATATGCATATATAACAAGAATAATAAAGT
1 AATATACATATATAATAA-AATAATAAAGT
32009 A
1 A
32010 GGAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.21
32 20 0.71
33 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.29
Consensus pattern (29 bp):
AATATACATATATAATAAAATAATAAAGT
Found at i:32416 original size:37 final size:36
Alignment explanation
Indices: 32373--32474 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
32363 ATAGTAGAAC
32373 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
32410 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
32444 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
32475 TATGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:33329 original size:105 final size:105
Alignment explanation
Indices: 33022--33958 Score: 1488
Period size: 105 Copynumber: 9.0 Consensus size: 105
33012 CATTGTTCCA
* * * ** * * *
33022 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
33087 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
33128 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
33188 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
33228 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGATAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
33293 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
33333 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
33398 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
33438 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
33503 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
33543 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
33608 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
33648 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
33713 ATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
33753 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
33818 AGCAGTCCCTTCGTCGTGAAGTTAAAATTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
33858 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
33923 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
33959 CCTCGAGTGC
Statistics
Matches: 781, Mismatches: 44, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
100 84 0.11
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 611 0.78
106 74 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:34691 original size:68 final size:65
Alignment explanation
Indices: 34601--34758 Score: 199
Period size: 68 Copynumber: 2.4 Consensus size: 65
34591 AAGATATCTG
* * ** *
34601 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
34666 TT
64 TT
* * * *
34668 TGTGTTTCAAGAGTAACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
34733 T
65 T
*
34734 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
34759 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:34736 original size:67 final size:65
Alignment explanation
Indices: 34601--34995 Score: 249
Period size: 65 Copynumber: 5.8 Consensus size: 65
34591 AAGATATCTG
* * * * **
34601 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
34666 TT
64 TT
* * *
34668 TGTGTTTCAAGAGTAACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
34733 T
65 T
* * *
34734 TTGTTTCAAGGGAAACTGTCTCAAGAT-AGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAG-TGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-
** *
34797 AGACAAA-ACT
55 ATTCAAAGATT
* * * * * * * * * * *
34807 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACATAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * **
34872 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAT-TGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAAT-TC-A-A-A
34936 GATGAAAT
62 GAT----T
* * *
34944 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAAT
34996 TGTCTCAAGA
Statistics
Matches: 258, Mismatches: 47, Indels: 41
0.75 0.14 0.12
Matches are distributed among these distances:
64 7 0.03
65 84 0.33
66 10 0.04
67 24 0.09
68 34 0.13
70 1 0.00
72 54 0.21
73 39 0.15
74 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:34785 original size:36 final size:35
Alignment explanation
Indices: 34734--35014 Score: 245
Period size: 36 Copynumber: 8.0 Consensus size: 35
34724 TTCAAAGGTT
* *
34734 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
34770 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
34805 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACATAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAA
* * **
34843 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
34872 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * *
34907 TTTATTTCAAGGGAAATTGTCTCAAGATAGATGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGA-CAAAA
*
34944 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
34979 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
35015 CTCTTCTAGT
Statistics
Matches: 199, Mismatches: 30, Indels: 32
0.76 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 10 0.05
36 128 0.64
37 34 0.17
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:34844 original size:138 final size:137
Alignment explanation
Indices: 34682--34995 Score: 405
Period size: 138 Copynumber: 2.3 Consensus size: 137
34672 TTTCAAGAGT
* * * *
34682 AACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
* *
34747 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
34811 TCCAAAAGA
129 TCCAAAAGA
* * * * * * *
34820 AACTGTCTCAAGGGAGACATAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
* * * ** * *
34885 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAGATGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
34950 CAAGAGA
131 CAAAAGA
*
34957 AACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAT
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT
34996 TGTCTCAAGA
Statistics
Matches: 149, Mismatches: 26, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
137 48 0.32
138 101 0.68
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (137 bp):
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:35971 original size:22 final size:22
Alignment explanation
Indices: 35945--35993 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
35935 TTGTGTTTGG
* *
35945 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
35967 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
35989 TCAAA
1 TCAAA
35994 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:36000 original size:22 final size:22
Alignment explanation
Indices: 35957--36000 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35947 AAAGGTTTGG
* * *
35957 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
35979 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
36001 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:36655 original size:23 final size:22
Alignment explanation
Indices: 36629--36715 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 22
36619 TTTTTGTCCC
36629 TTTTTCTTTTTGATTTTTGCTTT
1 TTTTTCTTTTTG-TTTTTGCTTT
* *
36652 TTTTTC-TTTTGTTATTGTTTCT
1 TTTTTCTTTTTGTTTTTGCTT-T
*
36674 CTTTTTCTTTGT-TTTTTGCTTT
1 -TTTTTCTTTTTGTTTTTGCTTT
36696 TTTGCTTCTTTTCT-TTTTTG
1 TTT--TTCTTTT-TGTTTTTG
36716 TTCTTGATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
21 10 0.19
22 7 0.13
23 25 0.48
24 10 0.19
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTTT
Found at i:36714 original size:16 final size:16
Alignment explanation
Indices: 36643--36720 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 16
36633 TCTTTTTGAT
36643 TTTTGCTTTTTT-TTC
1 TTTTGCTTTTTTGTTC
*
36658 TTTTG--TTATTGTTTC
1 TTTTGCTTTTTTG-TTC
*
36673 TCTTT--TTCTTTGTT-
1 T-TTTGCTTTTTTGTTC
36687 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
36704 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
36719 TT
1 TT
36721 GATTGGATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
13 7 0.14
14 1 0.02
15 22 0.43
16 17 0.33
17 4 0.08
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:39928 original size:16 final size:18
Alignment explanation
Indices: 39896--39930 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
39886 ATATAAAAAC
39896 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
39914 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
39930 A
1 A
39931 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:39942 original size:22 final size:20
Alignment explanation
Indices: 39908--39950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
39898 AAAATATAGG
39908 ATAAATATAAAAATAGATAA
1 ATAAATATAAAAATAGATAA
*
39928 ATAAATGAGTAAAAATATATAA
1 ATAAAT-A-TAAAAATAGATAA
39950 A
1 A
39951 AAAGTAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
ATAAATATAAAAATAGATAA
Found at i:39956 original size:18 final size:19
Alignment explanation
Indices: 39935--39979 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
39925 TAAATAAATG
39935 AGTAAAA-ATATATAAAAA
1 AGTAAAACATATATAAAAA
* *
39953 AGTAAAAGCATATATATATA
1 AGTAAAA-CATATATAAAAA
39973 AGTAAAA
1 AGTAAAA
39980 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AGTAAAACATATATAAAAA
Found at i:39967 original size:20 final size:20
Alignment explanation
Indices: 39942--39979 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39932 ATGAGTAAAA
39942 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
39962 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
39980 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:40554 original size:37 final size:36
Alignment explanation
Indices: 40511--40612 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
40501 ATAGTAGAAC
40511 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
40548 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
* *
40582 TCTATCATATTTTTAGGAGTTTGATTCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
40613 TAGGACGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 31 0.53
37 28 0.47
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:43758 original size:31 final size:29
Alignment explanation
Indices: 43720--43778 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
43710 AAATTACGCG
43720 TTTAGTACCTAAACTATCAGTTTTAGTTCAT
1 TTTAGTACCTAAACTATCA-TTTT-GTTCAT
*
43751 TTTAGTACCTAAACTTTCATTTTGTTCA
1 TTTAGTACCTAAACTATCATTTTGTTCA
43779 AAACCATGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 18 0.67
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTAGTACCTAAACTATCATTTTGTTCAT
Found at i:46271 original size:29 final size:31
Alignment explanation
Indices: 46214--46273 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
46204 CAATTTAAGG
*
46214 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
46245 CAAAATG-TATTTGGACTT-AATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
46274 TGAAGGGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGATATTTGGACTTGAATTGAATTTA
Found at i:46298 original size:21 final size:21
Alignment explanation
Indices: 46272--46313 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
46262 TAATTGAATT
*
46272 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46293 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46314 CCCCATTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:46381 original size:20 final size:22
Alignment explanation
Indices: 46343--46382 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
46333 TTTGAGTATA
46343 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
46365 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
46383 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:46635 original size:34 final size:32
Alignment explanation
Indices: 46596--46665 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
46586 TTTTGTAAAG
*
46596 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
46630 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
46662 GGGA
1 GGGA
46666 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:47742 original size:28 final size:27
Alignment explanation
Indices: 47686--47744 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
47676 ATAACCTGAT
* * *
47686 AATTTTAAATTTTTTATTTAAAATCAA
1 AATTTTAAATTATATATTTAAAATAAA
47713 AATTTTAAAATTATATATTTTAAAA-AAA
1 AATTTT-AAATTATATA-TTTAAAATAAA
47741 AATT
1 AATT
47745 AAAACACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 14 0.52
29 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTTTAAATTATATATTTAAAATAAA
Found at i:51331 original size:20 final size:21
Alignment explanation
Indices: 51265--51331 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
51255 TCGAATGATG
51265 CATTTAGTACCTAAACTATTA
1 CATTTAGTACCTAAACTATTA
* *
51286 GTATTTTTAG-A-GTAAACTA-TA
1 -CA--TTTAGTACCTAAACTATTA
51307 CATTTAGTACCTAAACTATTA
1 CATTTAGTACCTAAACTATTA
51328 -ATTT
1 CATTT
51332 TGATATGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 12 0.33
21 4 0.11
22 8 0.22
23 1 0.03
24 5 0.14
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (21 bp):
CATTTAGTACCTAAACTATTA
Found at i:57536 original size:95 final size:93
Alignment explanation
Indices: 57342--57536 Score: 236
Period size: 95 Copynumber: 2.1 Consensus size: 93
57332 TTTTGTCAAT
**
57342 TTGATATTGGCTACATTAGCTTATGGTTTGTACGGGTATGCTATCAACATATCCTTACTGGTTGT
1 TTGATATTGGCTACATTAGCTTATGGTTTAAACGGGTATGCTATCAACATATCCTTACTGGTTGT
* *
57407 AGCATGAAAGCAAAAATTATCCTACTCGAT
66 AGCACGAAAGCAAAAATTA--CTACTCGAC
* *
57437 TTGATATTGGCTGCGTTAGCTTATGGTTTAAACGGGTATGCTATCGAACATGGTTATCCTTACTG
1 TTGATATTGGCTACATTAGCTTATGGTTTAAACGGGTATGCTATC-AACA----TATCCTTACTG
57502 GTTGTAGCACGAAAG-AAAAAGTTA-T-C-CGAC
61 GTTGTAGCACGAAAGCAAAAA-TTACTACTCGAC
57532 TTGAT
1 TTGAT
57537 TTTTCTCCAG
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
95 49 0.56
96 5 0.06
97 1 0.01
99 5 0.06
100 28 0.32
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (93 bp):
TTGATATTGGCTACATTAGCTTATGGTTTAAACGGGTATGCTATCAACATATCCTTACTGGTTGT
AGCACGAAAGCAAAAATTACTACTCGAC
Found at i:58527 original size:20 final size:20
Alignment explanation
Indices: 58502--58547 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
58492 AACTGGATAC
58502 GTGTCGTCTGAGCTAATGTT
1 GTGTCGTCTGAGCTAATGTT
58522 GTGTCGTCTGAGCTAATGTT
1 GTGTCGTCTGAGCTAATGTT
*
58542 GGGTCG
1 GTGTCG
58548 GCTTGATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.35, T:0.37
Consensus pattern (20 bp):
GTGTCGTCTGAGCTAATGTT
Found at i:61109 original size:7 final size:7
Alignment explanation
Indices: 61097--61135 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
61087 CAATTTGATT
61097 ATGAATA
1 ATGAATA
61104 ATGAATA
1 ATGAATA
61111 ATGAATA
1 ATGAATA
61118 ATGAATA
1 ATGAATA
61125 ATGAAT-
1 ATGAATA
61131 ATGAA
1 ATGAA
61136 GACTGTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (7 bp):
ATGAATA
Found at i:65686 original size:39 final size:39
Alignment explanation
Indices: 65643--65764 Score: 217
Period size: 39 Copynumber: 3.1 Consensus size: 39
65633 CATGCTTCCG
*
65643 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCC
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
65682 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
* *
65721 CAGCAAATGCCAGCAGGCCAGATGGGTTCAATGTACCCT
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
65760 CAGCA
1 CAGCA
65765 GCAGATTTAC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.27, C:0.30, G:0.29, T:0.15
Consensus pattern (39 bp):
CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
Found at i:68366 original size:165 final size:163
Alignment explanation
Indices: 68047--68355 Score: 460
Period size: 165 Copynumber: 1.9 Consensus size: 163
68037 TCGGATATGA
** * *
68047 AACAGTTTTCTTTTAGAATTGAATATACTTGTGTCTAGAGACATACTTGTATTCAATATTCTCCT
1 AACAGTTTTCTTTTA-AATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACCT
* *
68112 TTGAATCCTGGGTACATTGTTGTTTTGATTTTTTCTGAATTATGTAGCCTTCTTTTGTATAGGGA
65 TTGAATCCTGGGTACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTTGTATAGGGA
*
68177 CCGTCGGAGACACCGATCGAAGGCGCAGATATAT
130 CCATCGGAGACACCGATCGAAGGCGCAGATATAT
* * *
68211 AACAGTTTT-TTTT-AATTGAATATACTCATGTCTAGATACTTACTTATATTCGATATTCACCTT
1 AACAGTTTTCTTTTAAATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACCTT
68274 TGAATCCTGGGTACATACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTTGTATAG
66 TGAATCCTGGG----TACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTTGTATAG
*
68339 GGACCATCTGAGACACC
127 GGACCATCGGAGACACC
68356 TTACGAAGGC
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
161 54 0.42
163 4 0.03
164 9 0.07
165 63 0.48
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (163 bp):
AACAGTTTTCTTTTAAATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACCTT
TGAATCCTGGGTACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTTGTATAGGGAC
CATCGGAGACACCGATCGAAGGCGCAGATATAT
Found at i:71879 original size:51 final size:51
Alignment explanation
Indices: 71803--71903 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
71793 TGTTACTGGG
71803 GCAGATTAGCTCATTAAAAGAACATTTATTTTGAGTTTCACTGTCTAATTA
1 GCAGATTAGCTCATTAAAAGAACATTTATTTTGAGTTTCACTGTCTAATTA
71854 GCAGATTAGCTCATTAAAAGAACATTTATTTTGAGTTTCACTGTCTAATT
1 GCAGATTAGCTCATTAAAAGAACATTTATTTTGAGTTTCACTGTCTAATT
71904 TGATACATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (51 bp):
GCAGATTAGCTCATTAAAAGAACATTTATTTTGAGTTTCACTGTCTAATTA
Found at i:73009 original size:28 final size:28
Alignment explanation
Indices: 72977--73033 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
72967 ATTCTACAAG
*
72977 TAAAGGCTTCAACTTTTATTTATTTATT
1 TAAAGACTTCAACTTTTATTTATTTATT
73005 TAAAGACTTCAACTTTTATTTATTTATT
1 TAAAGACTTCAACTTTTATTTATTTATT
73033 T
1 T
73034 TCACACCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (28 bp):
TAAAGACTTCAACTTTTATTTATTTATT
Found at i:75586 original size:21 final size:23
Alignment explanation
Indices: 75543--75596 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
75533 ATCTTAGGAT
*
75543 TCATG-CATATTGATTACATTGC
1 TCATGACATATTGATTACAATGC
75565 T-ATGA-ATATTGTATTA-AATGC
1 TCATGACATATTG-ATTACAATGC
75586 TCATGACATAT
1 TCATGACATAT
75597 CTAATTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 14 0.52
22 9 0.33
23 4 0.15
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
TCATGACATATTGATTACAATGC
Done.