Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002508.1 Hibiscus syriacus cultivar Beakdansim tig00005108_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: 68509
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:14275 original size:108 final size:108
Alignment explanation
Indices: 14086--14297 Score: 379
Period size: 108 Copynumber: 2.0 Consensus size: 108
14076 ACATTCTTGA
*
14086 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTTCGGTATGATTAGCAAATGGA
1 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
* *
14151 ATAATAACATTTCCATCTATCCTGTCATGGTCTTTTTTGTTGG
66 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTGTTGG
* *
14194 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGTGAGGGTTCTCCGGTATGATTAGCAAATGGA
1 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
14259 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTG
66 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTG
14298 ATGGCCTCAT
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (108 bp):
GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTGTTGG
Found at i:21046 original size:39 final size:38
Alignment explanation
Indices: 20988--21123 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 38
20978 CGAGTCAAAT
*
20988 ATATGCACCGTAA-TACTTACACATAAGGTCGTGCCAACC
1 ATATGCACCG-AAGTGCTTACACATAAGGTCGTGCC-ACC
*
21027 ATATGCACCAAAGTGCTTACACATAAGGTCGTGCTCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTGC-CACC
21066 ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTG-CCACC
*
21105 ATGTGCACCGAAGTGCTTA
1 ATATGCACCGAAGTGCTTA
21124 ATCGATATGC
Statistics
Matches: 90, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.02
39 86 0.96
40 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (38 bp):
ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCACC
Found at i:24092 original size:23 final size:23
Alignment explanation
Indices: 24043--24100 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
24033 TAAGCTACCA
*
24043 AAAGGCAGAGAAAAACTTGTCAC
1 AAAGGCAGAGAAAAACTTGCCAC
* *
24066 AAAGGCAGAGATAAA-TATGCCAT
1 AAAGGCAGAGAAAAACT-TGCCAC
*
24089 AAAGCCAGAGAA
1 AAAGGCAGAGAA
24101 CATGTTACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACTTGCCAC
Found at i:26574 original size:26 final size:26
Alignment explanation
Indices: 26522--26574 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
26512 ATACAATAAG
* *
26522 TGACATTTATTGAAATGTACCATTAA
1 TGACATGTATTGAAATGTACCAGTAA
* *
26548 TGACATGTATTTAAATGTACCGGTAA
1 TGACATGTATTGAAATGTACCAGTAA
26574 T
1 T
26575 TAAAATAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (26 bp):
TGACATGTATTGAAATGTACCAGTAA
Found at i:30639 original size:16 final size:16
Alignment explanation
Indices: 30618--30679 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
30608 TACCCGACCA
30618 GTTTTCAACCTGACTT
1 GTTTTCAACCTGACTT
* *
30634 GTTTTCAACCTGGCCT
1 GTTTTCAACCTGACTT
*
30650 GTTTTTAACCTGACTT
1 GTTTTCAACCTGACTT
*
30666 GTTTTTAACCTGAC
1 GTTTTCAACCTGAC
30680 CTGTAAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (16 bp):
GTTTTCAACCTGACTT
Found at i:30660 original size:32 final size:32
Alignment explanation
Indices: 30613--30683 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
30603 GGTATTACCC
*
30613 GACCAGTTTTCAACCTGACTTGTTTTCAACCT
1 GACCTGTTTTCAACCTGACTTGTTTTCAACCT
* * *
30645 GGCCTGTTTTTAACCTGACTTGTTTTTAACCT
1 GACCTGTTTTCAACCTGACTTGTTTTCAACCT
30677 GACCTGT
1 GACCTGT
30684 AAATGATCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (32 bp):
GACCTGTTTTCAACCTGACTTGTTTTCAACCT
Found at i:30987 original size:23 final size:24
Alignment explanation
Indices: 30950--30999 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
30940 ATGAAAATAA
30950 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
30974 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
30997 AAA
1 AAA
31000 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:31204 original size:49 final size:50
Alignment explanation
Indices: 31151--31253 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
31141 AGTGCTTATG
** * ** *
31151 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
31200 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
31249 GTTTA
1 GTTTA
31254 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:31263 original size:15 final size:15
Alignment explanation
Indices: 31243--31279 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
31233 TAATTTACTT
31243 TATATAGTTTATATA
1 TATATAGTTTATATA
31258 TATATAGTTTATATA
1 TATATAGTTTATATA
31273 TACTATA
1 TA-TATA
31280 TATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:31281 original size:20 final size:20
Alignment explanation
Indices: 31252--31305 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
31242 TTATATAGTT
31252 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
31271 TATACTATATATGGTTTATA
1 TATACTATATATAGTTTATA
*
31291 CATACATATTATATA
1 TATAC-TA-TATATA
31306 AAATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 2 0.07
22 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:32869 original size:19 final size:18
Alignment explanation
Indices: 32829--32895 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
32819 CAAGGATTGA
*
32829 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
32849 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
32868 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
32886 TTTAGGGTTT
1 TTTAGGGTTT
32896 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:32888 original size:18 final size:18
Alignment explanation
Indices: 32848--32891 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
32838 TAAAGTTTAG
*
32848 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
32867 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
32885 GTTTAGG
1 GTTTAGG
32892 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:33307 original size:2 final size:2
Alignment explanation
Indices: 33300--33463 Score: 91
Period size: 2 Copynumber: 85.5 Consensus size: 2
33290 TGTTTCTTTA
*
33300 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T A- AT -T AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
33338 AT AC AT AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT AT AT AA
1 AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
33379 ACT AT AT AT -T TT AT AT A- AT TT AT AC AT AT AT AGT TT AT AT AC
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
33421 AT AT AT TT AT AT AT AT ACT AT AT -T A- AT AT AA AT A- AT AT TT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
33461 AT A
1 AT A
33464 AACTATATAC
Statistics
Matches: 122, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
1 12 0.10
2 102 0.84
3 8 0.07
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33410 original size:15 final size:15
Alignment explanation
Indices: 33301--33613 Score: 77
Period size: 15 Copynumber: 19.8 Consensus size: 15
33291 GTTTCTTTAA
*
33301 TATATATATATATATA
1 TATATATATATA-ATT
33317 TATATATTATATTAA-T
1 TATATA-TATA-TAATT
* * *
33333 TATACATACATATATA
1 TATATATATATA-ATT
*
33349 TACTATATTAGTATAAAT
1 TA-TATA-TA-TATAATT
*
33367 TATA-ATATATAAACTA
1 TATATATATAT-AA-TT
*
33383 TATATTTTATATAATT
1 TATA-TATATATAATT
* *
33399 TATACATATATAGTT
1 TATATATATATAATT
*
33414 TATATACATAT-ATT
1 TATATATATATAATT
33428 TATATATATACTATATT
1 TATATATATA-TA-ATT
* *
33445 AATATAAATA-ATATT
1 TATATATATATA-ATT
* *
33460 TATAAACTATATACTT
1 TATATA-TATATAATT
* * *
33476 TTTATAGTTTATACATA
1 TATATA-TATATA-ATT
*
33493 TATAGTTTATATACA--
1 TATA-TATATATA-ATT
* *
33508 TAGTTTATATATAGTT
1 TA-TATATATATAATT
* *
33524 CACATA-ATCATAATT
1 TATATATAT-ATAATT
**
33539 TATATATATATAGCT
1 TATATATATATAATT
*
33554 TATAATAATTATATAGTT
1 TAT-AT-A-TATATAATT
*
33572 TATA-ATATA-AATA
1 TATATATATATAATT
* * *
33585 TAGTTTATATGTAAACT
1 TA-TATATATAT-AATT
33602 TATATATATATA
1 TATATATATATA
33614 TATTATTTTT
Statistics
Matches: 213, Mismatches: 54, Indels: 61
0.65 0.16 0.19
Matches are distributed among these distances:
13 4 0.02
14 23 0.11
15 68 0.32
16 50 0.23
17 41 0.19
18 24 0.11
19 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:33487 original size:86 final size:86
Alignment explanation
Indices: 33342--33520 Score: 281
Period size: 86 Copynumber: 2.1 Consensus size: 86
33332 TTATACATAC
* *
33342 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATATTTTATATAATTTATACATA
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAATTTATACATA
33407 TATAGTTTATATACATATATTT
66 TATAGTTTATATACATA-ATTT
* *
33429 ATATATATACTATATTAATATAAATAAT-ATTTATAAACTATATACTTTT-TATAGTTTATACAT
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATA-TTTTATATAATTTATACAT
*
33492 ATATAGTTTATATACATAGTTT
65 ATATAGTTTATATACATAATTT
33514 ATATATA
1 ATATATA
33521 GTTCACATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
85 10 0.12
86 46 0.53
87 30 0.35
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (86 bp):
ATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAATTTATACATA
TATAGTTTATATACATAATTT
Found at i:33510 original size:13 final size:13
Alignment explanation
Indices: 33479--33518 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
33469 TATACTTTTT
*
33479 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
33494 ATAGTTTATATAC
1 ATAGTTTATATAC
33507 ATAGTTTATATA
1 ATAGTTTATATA
33519 TAGTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:33517 original size:24 final size:26
Alignment explanation
Indices: 33490--33546 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
33480 TAGTTTATAC
* * *
33490 ATATATAGTTTATAT-A-CATAGTTT
1 ATATATAGTTCACATAATCATAATTT
33514 ATATATAGTTCACATAATCATAATTT
1 ATATATAGTTCACATAATCATAATTT
33540 ATATATA
1 ATATATA
33547 TATAGCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 13 0.46
25 1 0.04
26 14 0.50
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAGTTCACATAATCATAATTT
Found at i:33585 original size:18 final size:18
Alignment explanation
Indices: 33540--33593 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
33530 ATCATAATTT
*
33540 ATATATATATAGCTTATA
1 ATATATATATAGTTTATA
33558 ATA-ATTATATAGTTTATA
1 ATATA-TATATAGTTTATA
*
33576 ATATAAATATAGTTTATA
1 ATATATATATAGTTTATA
33594 TGTAAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATATATATAGTTTATA
Found at i:44618 original size:16 final size:16
Alignment explanation
Indices: 44594--44664 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
44584 GGTATTACCC
*
44594 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
44610 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
44626 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
44642 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
44658 GACCTGT
1 GACCTGT
44665 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:44957 original size:23 final size:24
Alignment explanation
Indices: 44920--44969 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
44910 ATGAAAATAA
44920 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
44944 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
44967 AAA
1 AAA
44970 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:45174 original size:49 final size:50
Alignment explanation
Indices: 45121--45223 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
45111 AGTGCTTATG
** * ** *
45121 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
45170 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
45219 GTTTA
1 GTTTA
45224 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:45233 original size:15 final size:15
Alignment explanation
Indices: 45213--45249 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
45203 TAATTTACTT
45213 TATATAGTTTATATA
1 TATATAGTTTATATA
45228 TATATAGTTTATATA
1 TATATAGTTTATATA
45243 TACTATA
1 TA-TATA
45250 TATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:45251 original size:20 final size:20
Alignment explanation
Indices: 45222--45275 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
45212 TTATATAGTT
45222 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
45241 TATACTATATATGGTTTATA
1 TATACTATATATAGTTTATA
*
45261 CATACATATTATATA
1 TATAC-TA-TATATA
45276 AAATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 2 0.07
22 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:46711 original size:15 final size:17
Alignment explanation
Indices: 46677--46719 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
46667 TTTAATGATA
46677 TATATATACATATATAT
1 TATATATACATATATAT
*
46694 TATATATACATA-GT-T
1 TATATATACATATATAT
46709 TATATATACAT
1 TATATATACAT
46720 GTACTATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATATACATATATAT
Found at i:46843 original size:19 final size:18
Alignment explanation
Indices: 46803--46869 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
46793 CAAGGATTGA
*
46803 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
46823 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
46842 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
46860 TTTAGGGTTT
1 TTTAGGGTTT
46870 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:46862 original size:18 final size:18
Alignment explanation
Indices: 46822--46865 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
46812 TAAAGTTTAG
*
46822 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
46841 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
46859 GTTTAGG
1 GTTTAGG
46866 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:47282 original size:2 final size:2
Alignment explanation
Indices: 47275--47424 Score: 118
Period size: 2 Copynumber: 77.0 Consensus size: 2
47265 TGTTTCTTTA
47275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
47315 -T AT AC AT AC AT AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
* * * * *
47355 AT AT AA ACT AT AT AT -T TT AT AT A- AT TT AT AC AT AT AT AGT TT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
47397 AT AT AC AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47425 TAATATAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
1 8 0.07
2 103 0.88
3 6 0.05
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47331 original size:31 final size:31
Alignment explanation
Indices: 47284--47431 Score: 117
Period size: 31 Copynumber: 4.7 Consensus size: 31
47274 AATATATATA
*
47284 TATATATATATATATATATATATATATTAAT
1 TATACATATATATATATATATATATATTAAT
* *
47315 TATACATACATATATATACTATATTAGTATAAAT
1 TATACATATATATATATA-TATA-TA-TATTAAT
* *
47349 TATA-ATATATAAACTATATAT-TTTATATAATT
1 TATACATATATATA-TATATATATATAT-TAA-T
* * *
47381 TATACATATATAGTTTATATACATATATTTA-
1 TATACATATATA-TATATATATATATATTAAT
*
47412 TATATATATATAT-TA-ATATA
1 TATACATATATATATATATATA
47432 AATAATATTT
Statistics
Matches: 94, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.04
29 2 0.02
30 4 0.04
31 30 0.32
32 9 0.10
33 27 0.29
34 18 0.19
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (31 bp):
TATACATATATATATATATATATATATTAAT
Found at i:47445 original size:14 final size:15
Alignment explanation
Indices: 47372--47459 Score: 70
Period size: 15 Copynumber: 5.7 Consensus size: 15
47362 CTATATATTT
* *
47372 TATATAATTTATACA
1 TATATATTTTATAAA
* *
47387 TATATAGTTTATATA
1 TATATATTTTATAAA
* *
47402 CATATATTTATATATA
1 TATATATTT-TATAAA
*
47418 TATATATTAATATAAA
1 TATATATT-TTATAAA
47434 TA-ATATTTTATAAA
1 TATATATTTTATAAA
47448 CTATATACTTTT
1 -TATATA-TTTT
47460 TATAGTTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.10
15 27 0.45
16 23 0.38
17 4 0.07
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (15 bp):
TATATATTTTATAAA
Found at i:47452 original size:86 final size:86
Alignment explanation
Indices: 47324--47502 Score: 272
Period size: 86 Copynumber: 2.1 Consensus size: 86
47314 TTATACATAC
* *
47324 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATA-TTTTATATAATTTATACAT
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTT-TATAATTTATACAT
47388 ATATAGTTTATATACATATATTT
65 ATATAGTTTATATACATA-ATTT
* * *
47411 ATATATATA-TATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
*
47475 TATAGTTTATATACATAGTTT
66 TATAGTTTATATACATAATTT
47496 ATATATA
1 ATATATA
47503 GTTCACATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
85 10 0.12
86 62 0.73
87 13 0.15
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (86 bp):
ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
TATAGTTTATATACATAATTT
Found at i:47480 original size:15 final size:14
Alignment explanation
Indices: 47460--47560 Score: 70
Period size: 15 Copynumber: 7.1 Consensus size: 14
47450 ATATACTTTT
47460 TATAGTTTATACATA
1 TATAGTTTATA-ATA
47475 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
47488 CATAG-TT-T-ATA
1 TATAGTTTATAATA
*
47499 TATAGTTCACATAATCA
1 TATAGTT--TATAAT-A
47516 TA-A-TTTATATATA
1 TATAGTTTATA-ATA
*
47529 TATAGCTTATAATAA
1 TATAGTTTATAAT-A
47544 TTATAGTTTATAATA
1 -TATAGTTTATAATA
47559 TA
1 TA
47561 AATATAGTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 23
0.70 0.06 0.23
Matches are distributed among these distances:
11 8 0.12
12 3 0.04
13 13 0.19
14 7 0.10
15 20 0.29
16 15 0.22
17 3 0.04
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:47492 original size:13 final size:13
Alignment explanation
Indices: 47461--47500 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
47451 TATACTTTTT
*
47461 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
47476 ATAGTTTATATAC
1 ATAGTTTATATAC
47489 ATAGTTTATATA
1 ATAGTTTATATA
47501 TAGTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:47499 original size:24 final size:26
Alignment explanation
Indices: 47472--47528 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
47462 TAGTTTATAC
* * *
47472 ATATATAGTTTATAT-A-CATAGTTT
1 ATATATAGTTCACATAATCATAATTT
47496 ATATATAGTTCACATAATCATAATTT
1 ATATATAGTTCACATAATCATAATTT
47522 ATATATA
1 ATATATA
47529 TATAGCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 13 0.46
25 1 0.04
26 14 0.50
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAGTTCACATAATCATAATTT
Found at i:47554 original size:16 final size:17
Alignment explanation
Indices: 47521--47579 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 17
47511 AATCATAATT
* *
47521 TATATATATATAGCTTA
1 TATATAAATATAGTTTA
*
47538 TA-ATAATTATAGTTTA
1 TATATAAATATAGTTTA
47554 TAATATAAATATAGTTTA
1 T-ATATAAATATAGTTTA
*
47572 TATGTAAA
1 TATATAAA
47580 CTTATATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 12 0.34
17 9 0.26
18 14 0.40
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (17 bp):
TATATAAATATAGTTTA
Found at i:47556 original size:13 final size:13
Alignment explanation
Indices: 47459--47557 Score: 51
Period size: 13 Copynumber: 7.1 Consensus size: 13
47449 TATATACTTT
47459 TTATAGTTTATACA
1 TTATAGTTTATA-A
47473 TATATAGTTTAT-A
1 T-TATAGTTTATAA
*
47486 TACATAGTTTAT-A
1 T-TATAGTTTATAA
*
47499 -TATAGTTCACATAA
1 TTATAGTT--TATAA
* *
47513 TCATAATTTATATA
1 TTATAGTTTATA-A
47527 TATATAGCTTATAATAA
1 T-TATAG-TT-T-ATAA
47544 TTATAGTTTATAA
1 TTATAGTTTATAA
47557 T
1 T
47558 ATAAATATAG
Statistics
Matches: 67, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
11 6 0.09
13 23 0.34
14 5 0.07
15 20 0.30
16 7 0.10
17 3 0.04
18 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (13 bp):
TTATAGTTTATAA
Found at i:58597 original size:16 final size:16
Alignment explanation
Indices: 58573--58643 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
58563 GGTATTACCC
*
58573 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
58589 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
58605 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
58621 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
58637 GACCTGT
1 GACCTGT
58644 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:58950 original size:23 final size:24
Alignment explanation
Indices: 58913--58962 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
58903 ATGAAAATAA
58913 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
58937 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
58960 AAA
1 AAA
58963 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:59165 original size:49 final size:50
Alignment explanation
Indices: 59112--59214 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
59102 AGTGCTTATG
** * ** *
59112 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
59161 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
59210 GTTTA
1 GTTTA
59215 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:59224 original size:15 final size:15
Alignment explanation
Indices: 59204--59240 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
59194 TAATTTACTT
59204 TATATAGTTTATATA
1 TATATAGTTTATATA
59219 TATATAGTTTATATA
1 TATATAGTTTATATA
59234 TACTATA
1 TA-TATA
59241 TATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:59242 original size:20 final size:20
Alignment explanation
Indices: 59213--59266 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
59203 TTATATAGTT
59213 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
59232 TATACTATATATGGTTTATA
1 TATACTATATATAGTTTATA
*
59252 CATACATATTATATA
1 TATAC-TA-TATATA
59267 AAATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 2 0.07
22 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:60700 original size:15 final size:17
Alignment explanation
Indices: 60666--60708 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
60656 TTTAATGATA
60666 TATATATACATATATAT
1 TATATATACATATATAT
*
60683 TATATATACATA-GT-T
1 TATATATACATATATAT
60698 TATATATACAT
1 TATATATACAT
60709 GTACTATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATATACATATATAT
Found at i:60832 original size:19 final size:18
Alignment explanation
Indices: 60792--60858 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
60782 CAAGGATTGA
*
60792 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
60812 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
60831 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
60849 TTTAGGGTTT
1 TTTAGGGTTT
60859 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:60851 original size:18 final size:18
Alignment explanation
Indices: 60811--60854 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
60801 TAAAGTTTAG
*
60811 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
60830 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
60848 GTTTAGG
1 GTTTAGG
60855 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:60958 original size:2 final size:2
Alignment explanation
Indices: 60951--60980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60941 ATATGGTTTT
60951 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
60981 CATAGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61275 original size:2 final size:2
Alignment explanation
Indices: 61268--61407 Score: 98
Period size: 2 Copynumber: 72.0 Consensus size: 2
61258 TGTTTCTTTA
*
61268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT -T AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
61307 AC AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT AT AT AA ACT
1 AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
61347 AT AT AT -T TT AT AT A- AT TT AT AC AT AT AT TT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
61387 AT TT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT A-T AT AT
61408 TAATATAAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
1 8 0.07
2 92 0.86
3 7 0.07
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61407 original size:86 final size:87
Alignment explanation
Indices: 61309--61487 Score: 256
Period size: 86 Copynumber: 2.1 Consensus size: 87
61299 AATTACATAC
* *
61309 ATATATACTATATTAGTATAAATTATAATATATAAACTATATA-TTTTATATAATTTATAC-ATA
1 ATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTT-TATAATTTATACAATA
61372 TA-TTTATATACATATATTTATAT
65 TAGTTTATATACATA-ATTTATAT
* * *
61395 ATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATATA
1 ATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACA-ATA
*
61460 TAGTTTATATACATAGTTTATAT
65 TAGTTTATATACATAATTTATAT
61483 ATATA
1 ATATA
61488 GTTCACATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
86 50 0.60
87 4 0.05
88 17 0.20
89 12 0.14
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (87 bp):
ATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACAATAT
AGTTTATATACATAATTTATAT
Found at i:61475 original size:13 final size:13
Alignment explanation
Indices: 61443--61515 Score: 74
Period size: 13 Copynumber: 5.3 Consensus size: 13
61433 ATATACTTTT
61443 TATAGTTTATACATA
1 TATAGTTTAT--ATA
61458 TATAGTTTATATA
1 TATAGTTTATATA
*
61471 CATAGTTTATATA
1 TATAGTTTATATA
* *
61484 TATAGTTCACATAA
1 TATAGTTTATAT-A
*
61498 TCATAATTTATATA
1 T-ATAGTTTATATA
61512 TATA
1 TATA
61516 TATAGCTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 27 0.55
14 4 0.08
15 18 0.37
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:61477 original size:28 final size:29
Alignment explanation
Indices: 61444--61517 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
61434 TATACTTTTT
* *
61444 ATAGTTTATACATATATAGTTTATAT-A-C
1 ATAGTTTATA-ATATATAGTTCACATAATC
61472 ATAGTTTAT-ATATATAGTTCACATAATC
1 ATAGTTTATAATATATAGTTCACATAATC
*
61500 ATAATTTATATATATATA
1 ATAGTTTATA-ATATATA
61518 TAGCTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
28 18 0.46
30 7 0.18
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (29 bp):
ATAGTTTATAATATATAGTTCACATAATC
Found at i:61545 original size:15 final size:15
Alignment explanation
Indices: 61443--61562 Score: 65
Period size: 13 Copynumber: 7.7 Consensus size: 15
61433 ATATACTTTT
61443 TATAGTTTATACA-TA
1 TATAGTTTATA-ATTA
61458 TATAGTTTAT-A-TA
1 TATAGTTTATAATTA
*
61471 CATAGTTTAT-A-TA
1 TATAGTTTATAATTA
* *
61484 TATAGTTCACATAATCA
1 TATAGTT--TATAATTA
61501 TA-A-TTTATATATATA
1 TATAGTTTATA-AT-TA
61516 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAATTA
61534 TATAGTTTATAATATAAA
1 TATAGTTTATAAT-T--A
61552 TATAGTTTATA
1 TATAGTTTATA
61563 TGTAAACTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
13 24 0.28
14 2 0.02
15 22 0.26
16 5 0.06
17 5 0.06
18 21 0.25
19 3 0.04
20 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATAATTA
Found at i:61554 original size:18 final size:18
Alignment explanation
Indices: 61504--61562 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
61494 ATAATCATAA
61504 TTTAT-ATATATATATAG
1 TTTATAATATATATATAG
*
61521 CTTATAATA-ATTATATAG
1 TTTATAATATA-TATATAG
*
61539 TTTATAATATAAATATAG
1 TTTATAATATATATATAG
61557 TTTATA
1 TTTATA
61563 TGTAAACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.14
18 30 0.83
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTATAATATATATATAG
Found at i:61563 original size:15 final size:15
Alignment explanation
Indices: 61443--61563 Score: 63
Period size: 15 Copynumber: 7.8 Consensus size: 15
61433 ATATACTTTT
* *
61443 TATAGTTTATACATA
1 TATAGTTTATATAAA
61458 TATAGTTTATAT--A
1 TATAGTTTATATAAA
*
61471 CATAGTTTATAT--A
1 TATAGTTTATATAAA
* *
61484 TATAGTTCACAT-AA
1 TATAGTTTATATAAA
*
61498 TCATAATTTATATATATA
1 T-ATAGTTTATATA-A-A
*
61516 TATAGCTTATAATAATTA
1 TATAGTTTAT-ATAA--A
61534 TATAGTTTATAATATAAA
1 TATAG-TT-T-ATATAAA
61552 TATAGTTTATAT
1 TATAGTTTATAT
61564 GTAAACTTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 20
0.73 0.09 0.17
Matches are distributed among these distances:
13 22 0.26
14 2 0.02
15 23 0.27
16 1 0.01
17 11 0.13
18 18 0.21
19 1 0.01
20 5 0.06
21 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATATAAA
Done.