Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004813.1 Hibiscus syriacus cultivar Beakdansim tig00010848_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: 71171
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7357 original size:16 final size:16
Alignment explanation
Indices: 7336--7382 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
7326 TTACCCGACC
*
7336 TGTTTTCAACCTGACT
1 TGTTTTCAACCTGACA
7352 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
*
7368 TGTTTTTAACCTGAC
1 TGTTTTCAACCTGAC
7383 CCTTTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:7390 original size:15 final size:15
Alignment explanation
Indices: 7370--7398 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7360 ACCTGACATG
7370 TTTTTAACCTGACCC
1 TTTTTAACCTGACCC
7385 TTTTTAACCTGACC
1 TTTTTAACCTGACC
7399 TGTAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTTTAACCTGACCC
Found at i:7606 original size:21 final size:22
Alignment explanation
Indices: 7580--7624 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
7570 TAGACTATTA
7580 TATAAAATTATTT-AATAAAAT
1 TATAAAATTATTTAAATAAAAT
*
7601 TATAAAATTATTTAAATTAAAT
1 TATAAAATTATTTAAATAAAAT
7623 TA
1 TA
7625 GATAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAAAATTATTTAAATAAAAT
Found at i:7689 original size:21 final size:21
Alignment explanation
Indices: 7660--7700 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
7650 GGAAAATTAA
7660 TATAGTTTAATTTATATAAAT
1 TATAGTTTAATTTATATAAAT
*
7681 TATATTTTAATTTATATAAA
1 TATAGTTTAATTTATATAAA
7701 GAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATAGTTTAATTTATATAAAT
Found at i:10596 original size:102 final size:102
Alignment explanation
Indices: 10420--10748 Score: 511
Period size: 102 Copynumber: 3.3 Consensus size: 102
10410 AATGAACAAC
* * *
10420 CAACAGTAACAACAAATTAAATAGTTTATTTAAACTGTAAATAAAGGCAACTAACAACCTTATAA
1 CAACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
10485 AAGCAATCCGAATGAACAAACAACAACACAAACAAAT
66 AAGCAATCCGAATGAACAAACAACAACACAAACAAAT
* * * *
10522 CAACAGTAGCAACAAATTGAACAGTTTATTTAAACTATAAATAAAGGTAGCTAACAACCTTATAG
1 CAACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
10587 AAGTAATCCGAATGAA-AAAC--CAACACAAACAAAT
66 AAGCAATCCGAATGAACAAACAACAACACAAACAAAT
*
10621 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
1 CAACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
** * *
10686 AAGCAATTTGAATGAACAACCAACAACATAAACAAAT
66 AAGCAATCCGAATGAACAAACAACAACACAAACAAAT
*
10723 CAACAGTAGCTACAAATTAAACAGTT
1 CAACAGTAGCAACAAATTAAACAGTT
10749 GAGTTACCTC
Statistics
Matches: 206, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
99 87 0.42
100 3 0.01
101 4 0.02
102 112 0.54
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (102 bp):
CAACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
AAGCAATCCGAATGAACAAACAACAACACAAACAAAT
Found at i:11515 original size:21 final size:20
Alignment explanation
Indices: 11487--11530 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
11477 AGGGTTAAGA
*
11487 TTTAGATTTAAAGTTTATGG
1 TTTAGATTTAAAGTTTAGGG
*
11507 TTTATGATTTAAGGTTTAGGG
1 TTTA-GATTTAAAGTTTAGGG
11528 TTT
1 TTT
11531 TTATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTAGATTTAAAGTTTAGGG
Found at i:11703 original size:41 final size:42
Alignment explanation
Indices: 11651--11757 Score: 189
Period size: 42 Copynumber: 2.6 Consensus size: 42
11641 TAGTTTATAC
*
11651 ATACATGTACTATAAGTTACATATATA-TTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
11692 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
11734 ATACACATACTATAAGTTACATAT
1 ATACATATACTATAAGTTACATAT
11758 GGGAATAGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 26 0.41
42 37 0.59
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
Found at i:11718 original size:24 final size:24
Alignment explanation
Indices: 11684--11757 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 24
11674 TATATTTACA
*
11684 TTACATGTATACATATACTATAAG
1 TTACATATATACATATACTATAAG
* *
11708 TTACATATATA-GT-T--TA-CA-
1 TTACATATATACATATACTATAAG
* *
11726 TTACATGTATACACATACTATAAG
1 TTACATATATACATATACTATAAG
11750 TTACATAT
1 TTACATAT
11758 GGGAATAGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
18 10 0.28
19 1 0.03
20 3 0.08
22 3 0.08
23 2 0.06
24 17 0.47
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (24 bp):
TTACATATATACATATACTATAAG
Found at i:12107 original size:2 final size:2
Alignment explanation
Indices: 12100--12488 Score: 86
Period size: 2 Copynumber: 196.0 Consensus size: 2
12090 TGTTTCTTTA
* *
12100 AT AT AT AT AT AT -T ACT -T AT AT -T AGT -T AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
12140 AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT AT A- ACT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
12179 TT AT AT AGT TT AT AC AT AT AGT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * *
12223 AT AT AT A- AT AT A- AT AT AT TT AT AA ACT AT AT ACT TT TT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T
* * * * * *
12266 TT AT AC AT AT AT AGT TT AT AT AC AT AGT TT AT AT CT AT AGT -T
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * * * *
12308 CAC AT AA AC AT A- AT TT AT AT AT AGT TT AT A- AT AT AA AT AT AGT
1 -AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* * * * * * * *
12351 TT AT AA AT TT AT AT AC AT AGT TT AT AT AT AT AGT AC AC AT AA AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * *
12395 AT A- AT TT AT AT AT AT AGT TT AT A- AT A- AT -T AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
12435 A- AT AT AA AT AT AGT TT AT AT AT A- AT -T TT AT AT -T AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12474 AT CT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
12489 TTTTTCAATT
Statistics
Matches: 273, Mismatches: 71, Indels: 86
0.63 0.17 0.20
Matches are distributed among these distances:
1 23 0.08
2 229 0.84
3 21 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12199 original size:13 final size:13
Alignment explanation
Indices: 12181--12211 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12171 CTATATATTT
12181 ATATAGTTTATAC
1 ATATAGTTTATAC
*
12194 ATATAGTTTATAT
1 ATATAGTTTATAC
12207 ATATA
1 ATATA
12212 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (13 bp):
ATATAGTTTATAC
Found at i:12292 original size:13 final size:13
Alignment explanation
Indices: 12261--12337 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
12251 TATACTTTTT
*
12261 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
12276 ATAGTTTATATAC
1 ATAGTTTATATAC
12289 ATAGTTTATAT-C
1 ATAGTTTATATAC
* *
12301 TATAGTTCACATAAAC
1 -ATAGTT--TATATAC
*
12317 ATAATTTATAT--
1 ATAGTTTATATAC
12328 ATAGTTTATA
1 ATAGTTTATA
12338 ATATAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
11 9 0.18
12 1 0.02
13 23 0.45
15 17 0.33
16 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:12369 original size:78 final size:80
Alignment explanation
Indices: 12280--12457 Score: 251
Period size: 78 Copynumber: 2.3 Consensus size: 80
12270 ACATATATAG
* *
12280 TTTATATACATAGTTTATATCTATAGTTCACATAAACATAA-TT-TATATATAGTTTATAAT-AT
1 TTTATATACATAGTTTATATATATAGTACACATAAACATAATTTATATATATAGTTTATAATAAT
12342 AAATATAGTTTATAAA
66 -AATATAGTTTATAAA
*
12358 TTTATATACATAGTTTATATATATAGTACACATAAATATAATTTATATATATAGTTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTACACATAAACATAATTTATATATATAGTTTATAATAAT
*
12423 TATATAGTTTAT-AA
66 AATATAGTTTATAAA
* *
12437 --TATAAATATAGTTTATATATA
1 TTTATATACATAGTTTATATATA
12458 ATTTTATATT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
77 19 0.21
78 38 0.42
79 4 0.04
80 28 0.31
81 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (80 bp):
TTTATATACATAGTTTATATATATAGTACACATAAACATAATTTATATATATAGTTTATAATAAT
AATATAGTTTATAAA
Found at i:12470 original size:15 final size:17
Alignment explanation
Indices: 12449--12488 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12439 TAAATATAGT
*
12449 TTATATATAAT-TTTATA
1 TTATATAT-ATCTATATA
12466 TTATATATATCTATATA
1 TTATATATATCTATATA
12483 TTATAT
1 TTATAT
12489 TTTTTCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATATATATCTATATA
Found at i:12482 original size:36 final size:36
Alignment explanation
Indices: 12317--12483 Score: 106
Period size: 36 Copynumber: 4.4 Consensus size: 36
12307 TCACATAAAC
* *
12317 ATAATTTATATATAGTTTATAAT-ATAAATATAGTTT
1 ATAATATATATATAGTTTATAATAAT-TATATAGTTT
* * * **
12353 ATAAATTTATATACATAGTTTATATATATAGTACACATA-AAT
1 AT-AA--TATATATATAGTTTATA-ATA-A-T-TATATAGTTT
12395 ATAATTTATATATATAGTTTATAATAATTATATAGTTT
1 ATAA--TATATATATAGTTTATAATAATTATATAGTTT
* *
12433 ATAATATAAATATAGTTTATATATAATTTTATA-TTAT
1 ATAATATATATATAGTTTATA-ATAATTATATAGTT-T
*
12470 ATATATCTATATAT
1 ATA-ATATATATAT
12484 TATATTTTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
36 20 0.19
37 20 0.19
38 14 0.13
39 16 0.15
40 5 0.05
41 20 0.19
42 4 0.04
43 6 0.06
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (36 bp):
ATAATATATATATAGTTTATAATAATTATATAGTTT
Found at i:16756 original size:44 final size:44
Alignment explanation
Indices: 16702--16786 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
16692 TTGGTAGAGC
*
16702 ATTATCTAAAATATTATTTTTTT-ACTGGAAATATTAATATCTGA
1 ATTATCTAAAATATTATTTTTTTAAC-GAAAATATTAATATCTGA
* *
16746 ATTATTTAAAATATTATTTTTTTAACGAAAATGTTAATATC
1 ATTATCTAAAATATTATTTTTTTAACGAAAATATTAATATC
16787 GAAAAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (44 bp):
ATTATCTAAAATATTATTTTTTTAACGAAAATATTAATATCTGA
Found at i:18042 original size:25 final size:26
Alignment explanation
Indices: 18008--18059 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
17998 TATTTTAACG
*
18008 TATTAAATCTAATACT-TTTAAAATA
1 TATTAAATCTAATACTAATTAAAATA
* *
18033 TATTATATCTTATACTAATTAAAATA
1 TATTAAATCTAATACTAATTAAAATA
18059 T
1 T
18060 TTTTAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTAAATCTAATACTAATTAAAATA
Found at i:18583 original size:34 final size:33
Alignment explanation
Indices: 18529--18646 Score: 104
Period size: 34 Copynumber: 3.7 Consensus size: 33
18519 TATTTTTGTG
*
18529 TTATAGTATA-A-ATATATATTACAATATTTAT
1 TTATAGTATATATATATATATTACAATATATAT
* * *
18560 TATATAGTATATATATATTTATTATATTATATAT
1 T-TATAGTATATATATATATATTACAATATATAT
**
18594 TTATAGTAT-TATAT-TATA-TAGTATATATTAT
1 TTATAGTATATATATATATATTACAATATA-TAT
*
18625 TTATATTATATACTATAT-TATT
1 TTATAGTATATA-TATATATATT
18647 TATATTTCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
30 6 0.09
31 15 0.21
32 16 0.23
33 14 0.20
34 19 0.27
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (33 bp):
TTATAGTATATATATATATATTACAATATATAT
Found at i:18590 original size:16 final size:16
Alignment explanation
Indices: 18567--18720 Score: 75
Period size: 16 Copynumber: 9.8 Consensus size: 16
18557 TATTATATAG
18567 TATA-TATATATTTAT
1 TATATTATATATTTAT
18582 TATATTATATATTTA-
1 TATATTATATATTTAT
*
18597 TAGTATTATATTATATAGT
1 TA-TATTATA-TATTTA-T
*
18616 ATATATTATTTATATTA-
1 -TATATTATATAT-TTAT
*
18633 TATACTATATTATTTA-
1 TATATTATA-TATTTAT
18649 TAT-TTCATAGTATTTA-
1 TATATT-ATA-TATTTAT
*
18665 TATAGTATAT-TTATAT
1 TATATTATATATT-TAT
18681 TA-ATTATTATATTTTAT
1 TATATTA-TATA-TTTAT
18698 T-T-TTAT-T-TTTAT
1 TATATTATATATTTAT
18710 TA-ATTA-ATATT
1 TATATTATATATT
18721 GTTTTTATTT
Statistics
Matches: 110, Mismatches: 9, Indels: 41
0.69 0.06 0.26
Matches are distributed among these distances:
12 6 0.05
13 4 0.04
14 5 0.05
15 14 0.13
16 53 0.48
17 13 0.12
18 5 0.05
19 8 0.07
20 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (16 bp):
TATATTATATATTTAT
Found at i:18621 original size:44 final size:43
Alignment explanation
Indices: 18556--18693 Score: 144
Period size: 44 Copynumber: 3.2 Consensus size: 43
18546 ATTACAATAT
18556 TTATTATA-TAGTATA-TATATATTTATTATATTATATATTTATA
1 TTATTATATTA-TATAGTATATATTTATTATATTATATA-TTATA
* *
18599 GTATTATATTATATAGTATATA-TTATTTATATTATATACTATA
1 TTATTATATTATATAGTATATATTTA-TTATATTATATATTATA
* * *
18642 TTATTTATATT-TCATAGTATTTATATAGTATATT-TATATTA-A
1 TTA-TTATATTAT-ATAGTATATATTTATTATATTATATATTATA
18684 TTATTATATT
1 TTATTATATT
18694 TTATTTTTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
41 7 0.09
42 4 0.05
43 27 0.33
44 42 0.51
45 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (43 bp):
TTATTATATTATATAGTATATATTTATTATATTATATATTATA
Found at i:18636 original size:7 final size:7
Alignment explanation
Indices: 18557--18697 Score: 91
Period size: 7 Copynumber: 19.9 Consensus size: 7
18547 TTACAATATT
18557 TATTATA
1 TATTATA
*
18564 TAGTATA
1 TATTATA
18571 TA-TATA
1 TATTATA
18577 T-TTATTA
1 TATTA-TA
18584 TATTATA
1 TATTATA
18591 TATT-TA
1 TATTATA
*
18597 TAGTATTA
1 TATTA-TA
18605 TATTATA
1 TATTATA
*
18612 TAGTATA
1 TATTATA
18619 TATTATTTA
1 TATTA--TA
18628 TATTATA
1 TATTATA
*
18635 TACTATA
1 TATTATA
18642 TTATT-TA
1 -TATTATA
18649 TATTTCATA
1 TA-TT-ATA
18658 GTATT-TA
1 -TATTATA
18665 TA-TAGTA
1 TATTA-TA
18672 TATT-TA
1 TATTATA
18678 TATTA-A
1 TATTATA
18684 TTATTATA
1 -TATTATA
*
18692 TTTTAT
1 TATTAT
18698 TTTTATTTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
5 1 0.01
6 23 0.21
7 57 0.53
8 14 0.13
9 11 0.10
10 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:18698 original size:23 final size:23
Alignment explanation
Indices: 18615--18704 Score: 58
Period size: 23 Copynumber: 3.7 Consensus size: 23
18605 TATTATATAG
*
18615 TATATATTATTTATATT-ATATACT
1 TATATTTTATTTATATTAAT-TA-T
* *
18639 ATATTATTTATATTTCATAGTATTTA-
1 -TA-TATTT-TATTT-ATATTAATTAT
* *
18665 TATAGTATATTTATATTAATTAT
1 TATATTTTATTTATATTAATTAT
*
18688 TATATTTTATTTTTATT
1 TATATTTTATTTATATT
18705 TTTATTAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
22 8 0.16
23 19 0.38
24 3 0.06
25 4 0.08
26 4 0.08
27 5 0.10
28 6 0.12
29 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TATATTTTATTTATATTAATTAT
Found at i:18711 original size:25 final size:25
Alignment explanation
Indices: 18674--18731 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
18664 ATATAGTATA
* *
18674 TTTATATTAATT-ATTATATTTTATT
1 TTTATTTTAATTAATTA-ATATTATT
* *
18699 TTTATTTTTATTAATTAATATTGTT
1 TTTATTTTAATTAATTAATATTATT
18724 TTTATTTT
1 TTTATTTT
18732 CAGATCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATTTTAATTAATTAATATTATT
Found at i:26598 original size:16 final size:16
Alignment explanation
Indices: 26573--26637 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
26563 CCAACATTTA
26573 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
26589 CGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
26605 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
26621 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26637 T
1 T
26638 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:34962 original size:16 final size:16
Alignment explanation
Indices: 34938--34971 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
34928 TATCGCCGAT
*
34938 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
34954 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
34970 CG
1 CG
34972 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:40715 original size:16 final size:17
Alignment explanation
Indices: 40688--40720 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40678 TATCGCCGAC
40688 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
40705 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
40721 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:43408 original size:29 final size:29
Alignment explanation
Indices: 43366--43426 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
43356 GATCGAGTCC
43366 CACTGAAGGAACTTATAACGGAGGTATTT
1 CACTGAAGGAACTTATAACGGAGGTATTT
* *
43395 CACTGAGGGAACTTATAACGGAGGTCTTT
1 CACTGAAGGAACTTATAACGGAGGTATTT
43424 CAC
1 CAC
43427 GAAAGTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (29 bp):
CACTGAAGGAACTTATAACGGAGGTATTT
Found at i:45117 original size:32 final size:33
Alignment explanation
Indices: 45054--45192 Score: 190
Period size: 33 Copynumber: 4.2 Consensus size: 33
45044 CAGCCAACTA
*
45054 AAACAGATGGGACTATAGCAAAAGAAGTTTAAT
1 AAACAGATGGGACTATAGCAAGAGAAGTTTAAT
*
45087 GAACAGATGGGACTAT-GCAAGAGAAGTTTAAT
1 AAACAGATGGGACTATAGCAAGAGAAGTTTAAT
* * * *
45119 AAACAGATGGAACTATAGAAAGAAAAGTTCAAT
1 AAACAGATGGGACTATAGCAAGAGAAGTTTAAT
*
45152 AAACAGATGAGACTACATAGCAAGAGAAGTTTAAT
1 AAACAGATGGGACT--ATAGCAAGAGAAGTTTAAT
45187 AAACAG
1 AAACAG
45193 CCAACTAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 29 0.32
33 40 0.44
35 22 0.24
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (33 bp):
AAACAGATGGGACTATAGCAAGAGAAGTTTAAT
Found at i:45135 original size:65 final size:67
Alignment explanation
Indices: 45054--45192 Score: 194
Period size: 65 Copynumber: 2.1 Consensus size: 67
45044 CAGCCAACTA
* * * * *
45054 AAACAGATGGGACTATAGCAAA-AGAAGTTTAATGAACAGATGGGACT-AT-GCAAGAGAAGTTT
1 AAACAGATGGAACTATAG-AAAGAAAAGTTCAATAAACAGATGAGACTAATAGCAAGAGAAGTTT
45116 AAT
65 AAT
45119 AAACAGATGGAACTATAGAAAGAAAAGTTCAATAAACAGATGAGACTACATAGCAAGAGAAGTTT
1 AAACAGATGGAACTATAGAAAGAAAAGTTCAATAAACAGATGAGACTA-ATAGCAAGAGAAGTTT
45184 AAT
65 AAT
45187 AAACAG
1 AAACAG
45193 CCAACTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
64 3 0.05
65 38 0.58
67 2 0.03
68 22 0.34
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (67 bp):
AAACAGATGGAACTATAGAAAGAAAAGTTCAATAAACAGATGAGACTAATAGCAAGAGAAGTTTA
AT
Found at i:48315 original size:15 final size:15
Alignment explanation
Indices: 48287--48333 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
48277 ATTAATATTC
*
48287 AATGATTT-GATAATT
1 AATGATTTAG-TAATG
48302 AATGATTTAGTAATG
1 AATGATTTAGTAATG
48317 ATATGATTTAGTAATG
1 A-ATGATTTAGTAATG
48333 A
1 A
48334 TTACTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
AATGATTTAGTAATG
Found at i:48316 original size:26 final size:25
Alignment explanation
Indices: 48287--48394 Score: 80
Period size: 27 Copynumber: 4.3 Consensus size: 25
48277 ATTAATATTC
48287 AATGATTTGATAATTAATGATTTAGT
1 AATGATTTGATAATTAAT-ATTTAGT
* * * *
48313 AATGATATGATTTAGTAATGATTACTAAT
1 AATGATTTGA-TAATTAAT-ATT--TAGT
*
48342 AATGATTT-ATTATTAATA-TT--T
1 AATGATTTGATAATTAATATTTAGT
* *
48363 AATGATTTGATACTAAATATTTAGT
1 AATGATTTGATAATTAATATTTAGT
48388 AATGATT
1 AATGATT
48395 AGTAATAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
21 9 0.14
22 7 0.11
23 3 0.05
25 9 0.14
26 10 0.15
27 17 0.26
28 1 0.02
29 10 0.15
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
AATGATTTGATAATTAATATTTAGT
Found at i:48324 original size:16 final size:16
Alignment explanation
Indices: 48303--48334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48293 TTGATAATTA
48303 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
48319 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
48335 TACTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:48419 original size:24 final size:23
Alignment explanation
Indices: 48387--48456 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
48377 AAATATTTAG
* *
48387 TAATGATTAGTAATAATGAAATTA-
1 TAATAATTACTAATAATG--ATTAC
48411 TAATAATTACTAATAATGATTAC
1 TAATAATTACTAATAATGATTAC
* *
48434 TAATAATTATTTAATAATAATTA
1 TAATAATTA-CTAATAATGATTA
48457 AATATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.10
23 9 0.22
24 27 0.68
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (23 bp):
TAATAATTACTAATAATGATTAC
Found at i:48528 original size:16 final size:16
Alignment explanation
Indices: 48487--48529 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
48477 TCAATTTAAA
48487 TCGAATTTATAAATAG
1 TCGAATTTATAAATAG
* *
48503 TTGAACTTATAACA-AG
1 TCGAATTTATAA-ATAG
48519 TCGAATTTATA
1 TCGAATTTATA
48530 GTTATAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (16 bp):
TCGAATTTATAAATAG
Found at i:48542 original size:22 final size:22
Alignment explanation
Indices: 48509--48550 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
48499 ATAGTTGAAC
48509 TTATAACAAGTCGAATTTATAG
1 TTATAACAAGTCGAATTTATAG
48531 TTATAA-ATAGTCGAATTTAT
1 TTATAACA-AGTCGAATTTAT
48551 TCTTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATAACAAGTCGAATTTATAG
Found at i:48613 original size:17 final size:15
Alignment explanation
Indices: 48579--48618 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
48569 AGAGACATGC
48579 ATATTTAATATTATA
1 ATATTTAATATTATA
*
48594 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
48611 ATATTTAA
1 ATATTTAA
48619 CATAACCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:49071 original size:24 final size:23
Alignment explanation
Indices: 49008--49111 Score: 88
Period size: 24 Copynumber: 4.4 Consensus size: 23
48998 TAAATTATAT
49008 TTAATTATT-TAATT-ATTATTAA
1 TTAATTATTATAATTCATTATT-A
*
49030 ATAATTATTAGTAA-TCATTATTA
1 TTAATTATTA-TAATTCATTATTA
*
49053 TTAATTATTATAATTTCATTAGTA
1 TTAATTATTATAA-TTCATTATTA
* * *
49077 TTAATCATTACTAAATCATTAGTA
1 TTAATTATTA-TAATTCATTATTA
*
49101 TCAAATTATTA
1 T-TAATTATTA
49112 AATATTAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
22 11 0.16
23 11 0.16
24 36 0.53
25 10 0.15
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (23 bp):
TTAATTATTATAATTCATTATTA
Found at i:49132 original size:59 final size:60
Alignment explanation
Indices: 49068--49185 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 60
49058 TATTATAATT
* * *
49068 TCATTAGTATTAATCATTACTAAATCATT-AGTATCAAATTATTAAATATTAATAATAAA
1 TCATTAGTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
* *
49127 TCATTATTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTTATAATAA
1 TCATTAGTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAA
49186 TGAACTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 27 0.51
60 26 0.49
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (60 bp):
TCATTAGTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
Found at i:49168 original size:15 final size:15
Alignment explanation
Indices: 49148--49176 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49138 AATCATTACT
49148 AAATCATTAAATATC
1 AAATCATTAAATATC
49163 AAATCATTAAATAT
1 AAATCATTAAATAT
49177 TTATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:56569 original size:17 final size:17
Alignment explanation
Indices: 56547--56622 Score: 88
Period size: 17 Copynumber: 4.7 Consensus size: 17
56537 TAATAATAGT
56547 ATGGTGATATATTTTAA
1 ATGGTGATATATTTTAA
56564 ATGGTGATATATTTTAA
1 ATGGTGATATATTTTAA
* **
56581 AT-GTAATA-ATAGT--
1 ATGGTGATATATTTTAA
*
56594 ATGGTTATATATTTTAA
1 ATGGTGATATATTTTAA
56611 ATGGTGATATAT
1 ATGGTGATATAT
56623 ATGACATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.04
14 5 0.10
15 6 0.12
16 5 0.10
17 30 0.62
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
ATGGTGATATATTTTAA
Found at i:56583 original size:47 final size:47
Alignment explanation
Indices: 56532--56622 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
56522 TTTATATTAA
56532 AAATGTAATAATAGTATGGTGATATATTTTAAATGGTGATATATTTT
1 AAATGTAATAATAGTATGGTGATATATTTTAAATGGTGATATATTTT
*
56579 AAATGTAATAATAGTATGGTTATATATTTTAAATGGTGATATAT
1 AAATGTAATAATAGTATGGTGATATATTTTAAATGGTGATATAT
56623 ATGACATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (47 bp):
AAATGTAATAATAGTATGGTGATATATTTTAAATGGTGATATATTTT
Found at i:64104 original size:16 final size:15
Alignment explanation
Indices: 64084--64130 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
64074 TATTTTTTTC
64084 AAATAATGATAATAA
1 AAATAATGATAATAA
*
64099 ACAATAA-GTATAATTA
1 A-AATAATG-ATAATAA
64115 AAA-AATGATAATAA
1 AAATAATGATAATAA
64129 AA
1 AA
64131 TTACCTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.37
15 5 0.19
16 12 0.44
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (15 bp):
AAATAATGATAATAA
Done.