Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001150.1 Hibiscus syriacus cultivar Beakdansim tig00002292_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: 83546
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:7583 original size:9 final size:8
Alignment explanation
Indices: 7569--7690 Score: 63
Period size: 9 Copynumber: 14.2 Consensus size: 8
7559 GGTTTGTATT
7569 ATATAATTA
1 ATATAA-TA
*
7578 ATATAAAAA
1 ATAT-AATA
7587 ATATAA-A
1 ATATAATA
*
7594 ATATTATA
1 ATATAATA
7602 TATATAATTA
1 -ATATAA-TA
*
7612 ATATAAAA
1 ATATAATA
7620 ATATAA-A
1 ATATAATA
7627 ATAGT-ATA
1 ATA-TAATA
7635 TATATAATTA
1 -ATATAA-TA
*
7645 ATATAAAA
1 ATATAATA
*
7653 AT-TAAAA
1 ATATAATA
7660 ATATATATA
1 ATATA-ATA
7669 TATATATATA
1 -ATATA-ATA
7679 TATATATATA
1 -ATATA-ATA
7689 AT
1 AT
7691 CGGGACGGGG
Statistics
Matches: 95, Mismatches: 6, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
7 18 0.19
8 18 0.19
9 34 0.36
10 25 0.26
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:7597 original size:25 final size:26
Alignment explanation
Indices: 7569--7634 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 26
7559 GGTTTGTATT
7569 ATATAAT-TAATATAAAAAATAT-AAA
1 ATATAATAT-ATATAAAAAATATAAAA
* **
7594 ATATTATATATATAATTAATATAAAA
1 ATATAATATATATAAAAAATATAAAA
*
7620 ATATAAAATAGTATA
1 ATATAATATA-TATA
7635 TATATAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 17 0.52
26 12 0.36
27 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
ATATAATATATATAAAAAATATAAAA
Found at i:7625 original size:33 final size:33
Alignment explanation
Indices: 7568--7674 Score: 171
Period size: 33 Copynumber: 3.2 Consensus size: 33
7558 AGGTTTGTAT
7568 TATATAATTAATATAAAAAATATAAAATATTATA
1 TATATAATTAATAT-AAAAATATAAAATATTATA
*
7602 TATATAATTAATATAAAAATATAAAATAGTATA
1 TATATAATTAATATAAAAATATAAAATATTATA
7635 TATATAATTAATATAAAAAT-TAAAAATATATATA
1 TATATAATTAATATAAAAATAT-AAAATAT-TATA
7669 TATATA
1 TATATA
7675 TATATATATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 1 0.01
33 44 0.64
34 24 0.35
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
TATATAATTAATATAAAAATATAAAATATTATA
Found at i:7667 original size:2 final size:2
Alignment explanation
Indices: 7660--7688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7650 AAAATTAAAA
7660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7689 ATCGGGACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8341 original size:21 final size:21
Alignment explanation
Indices: 8315--8362 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
8305 GAGAAATAAT
8315 GATACTACTAAATGGAGTATC
1 GATACTACTAAATGGAGTATC
8336 GATACTACTAAATGGAGTATC
1 GATACTACTAAATGGAGTATC
8357 GATACT
1 GATACT
8363 CTATGAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (21 bp):
GATACTACTAAATGGAGTATC
Found at i:11318 original size:30 final size:30
Alignment explanation
Indices: 11284--11346 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
11274 TAAAATTTAT
* * *
11284 TTTGAGGACTAAATTGAAATTTTAACTAAA
1 TTTGAGGACCAAAGTAAAATTTTAACTAAA
* *
11314 TTTGAGGACCAAAGTAAAATTTTGATTAAA
1 TTTGAGGACCAAAGTAAAATTTTAACTAAA
11344 TTT
1 TTT
11347 AGATCTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTGAGGACCAAAGTAAAATTTTAACTAAA
Found at i:24832 original size:25 final size:25
Alignment explanation
Indices: 24800--24934 Score: 75
Period size: 25 Copynumber: 5.3 Consensus size: 25
24790 ATATTTTATA
24800 TATATTAACTTTAAAAAAATATTTT
1 TATATTAACTTTAAAAAAATATTTT
**
24825 TATATTAAC-TT-ATTAAATATATTT
1 TATATTAACTTTAAAAAAATAT-TTT
24849 TATTATTAAC-TTAATTTAAAAATATTTT
1 TA-TATTAACTTTAA---AAAAATATTTT
* * *
24877 ATTTTTTAAATTT--AAAAATATTTAT
1 -TATATTAACTTTAAAAAAATATTT-T
* * *
24902 T-TTTTAAATTTAAAAATATATATTT
1 TATATTAACTTTAAAAAAATAT-TTT
*
24927 TATGTTAA
1 TATATTAA
24935 AATATTTTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 25
0.72 0.07 0.20
Matches are distributed among these distances:
23 17 0.19
24 18 0.20
25 28 0.32
26 8 0.09
28 8 0.09
29 9 0.10
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (25 bp):
TATATTAACTTTAAAAAAATATTTT
Found at i:24840 original size:27 final size:25
Alignment explanation
Indices: 24800--24876 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
24790 ATATTTTATA
*
24800 TATATTAACTT-TAAAAAAATATTTT
1 TATATTAACTTAT-TAAAAATATTTT
*
24825 TATATTAACTTATTAAATATA-TTT
1 TATATTAACTTATTAAAAATATTTT
24849 TATTATTAACTTAATTTAAAAATATTTT
1 TA-TATTAACTT-A-TTAAAAATATTTT
24877 ATTTTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.11
25 26 0.59
26 2 0.05
27 8 0.18
28 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTAACTTATTAAAAATATTTT
Found at i:24893 original size:23 final size:23
Alignment explanation
Indices: 24861--24927 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
24851 TTATTAACTT
24861 AATTTAAAAATATTTTATTTTTTA
1 AATTTAAAAATA-TTTATTTTTTA
24885 AATTTAAAAATATTTATTTTTTA
1 AATTTAAAAATATTTATTTTTTA
*
24908 AATTTAAAAATATATATTTT
1 AATTTAAAAATATTTATTTT
24928 ATGTTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 30 0.71
24 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTAAAAATATTTATTTTTTA
Found at i:24998 original size:30 final size:30
Alignment explanation
Indices: 24962--25059 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
24952 ATAAGATTAA
24962 AATATATTTAATAATTTAAAGTAATAATAT
1 AATATATTTAATAATTTAAAGTAATAATAT
* *
24992 AATATATTTAGTAAATT-AAGATAA-AATAT
1 AATATATTTAATAATTTAAAG-TAATAATAT
* *
25021 -ATATACTTTTAA-AATTTAAAATAATAATAA
1 AATATA--TTTAATAATTTAAAGTAATAATAT
25051 AATATATTT
1 AATATATTT
25060 TTAATAGGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
28 5 0.09
29 18 0.32
30 28 0.50
31 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
AATATATTTAATAATTTAAAGTAATAATAT
Found at i:24999 original size:59 final size:58
Alignment explanation
Indices: 24936--25060 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 58
24926 TTATGTTAAA
* * *
24936 ATATTTTA-AAATTAAGATAAGATTAAAATATA-TTTAATAATTTAAAGTAATAATATAAT
1 ATATTTTAGAAATTAAGATAA-AAT-AAATATACTTTAA-AATTTAAAATAATAATAAAAT
*
24995 ATA-TTTAGTAAATTAAGATAAAATATATATACTTTTAAAATTTAAAATAATAATAAAAT
1 ATATTTTAG-AAATTAAGATAAAATAAATATAC-TTTAAAATTTAAAATAATAATAAAAT
25054 ATATTTT
1 ATATTTT
25061 TAATAGGTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
58 10 0.18
59 27 0.47
60 20 0.35
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (58 bp):
ATATTTTAGAAATTAAGATAAAATAAATATACTTTAAAATTTAAAATAATAATAAAAT
Found at i:25124 original size:26 final size:26
Alignment explanation
Indices: 25083--25152 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
25073 TAAAGATAAC
25083 ATATATTT--TTAAATTAA-AAGAAA
1 ATATATTTAATTAAATTAATAAGAAA
* *
25106 ATATTTTTTAATTAAATTAATAATAAA
1 ATA-TATTTAATTAAATTAATAAGAAA
25133 ATATATTTAA-TAAATTAATA
1 ATATATTTAATTAAATTAATA
25153 TAAATATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.08
24 4 0.10
25 10 0.25
26 15 0.38
27 8 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
ATATATTTAATTAAATTAATAAGAAA
Found at i:25140 original size:50 final size:49
Alignment explanation
Indices: 25078--25185 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 49
25068 TTAGATAAAG
* * *
25078 ATAACATATATTT-TTAAATTAAAAGAAAATATTTTTTA-ATTAAATTAAT
1 ATAAAATATATTTAATAAATTAAAA-AAAATATTTCTTACATT-AATTAAT
* * *
25127 AATAAAATATATTTAATAAATTAATATAAATATTTCTTACATTAATTTAT
1 -ATAAAATATATTTAATAAATTAAAAAAAATATTTCTTACATTAATTAAT
25177 ATAAAATAT
1 ATAAAATAT
25186 TATAACTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 9 0.18
50 29 0.58
51 12 0.24
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (49 bp):
ATAAAATATATTTAATAAATTAAAAAAAATATTTCTTACATTAATTAAT
Found at i:25161 original size:21 final size:25
Alignment explanation
Indices: 25078--25159 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 25
25068 TTAGATAAAG
25078 ATAACATATATTT--TTAAATTAA-A
1 ATAA-ATATATTTAATTAAATTAATA
* *
25101 AGAAAATATTTTTTAATTAAATTAATA
1 A-TAAATA-TATTTAATTAAATTAATA
25128 ATAAAATATATTTAA-TAAATTAAT-
1 AT-AAATATATTTAATTAAATTAATA
25152 ATAAATAT
1 ATAAATAT
25160 TTCTTACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
23 10 0.20
24 8 0.16
25 9 0.18
26 15 0.31
27 7 0.14
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (25 bp):
ATAAATATATTTAATTAAATTAATA
Found at i:25173 original size:25 final size:24
Alignment explanation
Indices: 25094--25186 Score: 89
Period size: 26 Copynumber: 3.7 Consensus size: 24
25084 TATATTTTTA
* *
25094 AATTAAAAGAAAATATTTTTTAATT
1 AATTAATATAAAATA-TTTTTAATT
* *
25119 AAATTAATAATAAAATATATTTAATA
1 -AATTAAT-ATAAAATATTTTTAATT
25145 AATTAATAT-AAATATTTCTTACATT
1 AATTAATATAAAATATTT-TTA-ATT
*
25170 AATTTATATAAAATATT
1 AATTAATATAAAATATT
25187 ATAACTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 7 0.12
24 5 0.09
25 17 0.30
26 20 0.36
27 7 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (24 bp):
AATTAATATAAAATATTTTTAATT
Found at i:26322 original size:35 final size:36
Alignment explanation
Indices: 26264--26341 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
26254 ACAATAGTTA
*
26264 ATATATGTAACCTATAGTATACATATACATGTAAACT
1 ATATATGTAACCTATAG-ATACATATACATATAAACT
* * **
26301 ATATATGTAACTTATAG-TACATGTATGTATAAACT
1 ATATATGTAACCTATAGATACATATACATATAAACT
26336 ATATAT
1 ATATAT
26342 AGTATATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 20 0.56
37 16 0.44
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (36 bp):
ATATATGTAACCTATAGATACATATACATATAAACT
Found at i:26346 original size:20 final size:20
Alignment explanation
Indices: 26323--26420 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
26313 TATAGTACAT
*
26323 GTATGTATAAACTATATATA
1 GTATATATAAACTATATATA
26343 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
*
26363 -TATA-ACT-TA-TA-ATATA
1 GTATATA-TAAACTATATATA
*
26379 TGTATATATACAATCTATTTATA
1 -GTATATATA-AA-CTATATATA
* *
26402 TTTTATATAAACTATATAT
1 GTATATATAAACTATATAT
26421 GTAACCTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
16 5 0.08
17 2 0.03
18 7 0.11
19 6 0.10
20 27 0.44
21 2 0.03
22 9 0.15
23 4 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:26361 original size:57 final size:57
Alignment explanation
Indices: 26295--26432 Score: 172
Period size: 57 Copynumber: 2.4 Consensus size: 57
26285 CATATACATG
*
26295 TAAACTATATATGTAACTTATAGTACATGTATGTATA-AA-CTATATATAGTATATA
1 TAAACTATATATGTAACTTATAGTACATGTATATATACAATCTATATATAGTATATA
* * * * * *
26350 TAAACTATATATATATAACTTATAATATATGTATATATACAATCTATTTATATTTTATA
1 TAAAC--TATATATGTAACTTATAGTACATGTATATATACAATCTATATATAGTATATA
*
26409 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACTTATAGT
26433 TTATAAACAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
55 5 0.07
57 44 0.64
58 2 0.03
59 18 0.26
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (57 bp):
TAAACTATATATGTAACTTATAGTACATGTATATATACAATCTATATATAGTATATA
Found at i:26364 original size:15 final size:15
Alignment explanation
Indices: 26339--26378 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
26329 ATAAACTATA
26339 TATAGTATATATAAAC
1 TATA-TATATATAAAC
26355 TATATATATAT-AAC
1 TATATATATATAAAC
26369 T-TATA-ATATA
1 TATATATATATA
26379 TGTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 4 0.17
15 7 0.30
16 4 0.17
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:26451 original size:21 final size:20
Alignment explanation
Indices: 26427--26517 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
26417 ATATGTAACC
26427 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
**
26448 TATA-TTAGTGTACTATATAGTT
1 TATATTTA-TAAAC-A-ATAGTT
* * *
26470 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
26491 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
26512 TATATT
1 TATATT
26518 AATGTACTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 30 0.55
22 11 0.20
23 2 0.04
24 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:26541 original size:22 final size:21
Alignment explanation
Indices: 26442--26544 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
26432 TTTATAAACA
*
26442 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
26464 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
26485 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
26506 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
26528 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
26545 TAATTATATT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.10
21 23 0.34
22 34 0.51
23 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:26563 original size:15 final size:15
Alignment explanation
Indices: 26526--26819 Score: 70
Period size: 15 Copynumber: 18.5 Consensus size: 15
26516 TTAATGTACT
*
26526 ATATAGTTTATATTA
1 ATATAATTTATATTA
*
26541 ATGTTAA-TTATATTA
1 AT-ATAATTTATATTA
26556 ACTATAATTTATATTA
1 A-TATAATTTATATTA
* * * *
26572 ATATAGTATATTGTTT
1 ATATAATTTA-TATTA
*
26588 ATA-AACTATACTATTTTA
1 ATATAA-T-T--TATATTA
26606 ATATTAA-TTATATTA
1 ATA-TAATTTATATTA
*
26621 ACTATAGTTTATAAACTATA
1 A-TATAATTTAT--A-T-TA
26641 CTATATAATTTATA--A
1 --ATATAATTTATATTA
*
26656 CATATATTTTATATTA
1 -ATATAATTTATATTA
*
26672 ATATTAACTTTATA-GA
1 ATA-TAA-TTTATATTA
* *
26688 CTATATTTTATATTA
1 ATATAATTTATATTA
* *
26703 ATAATAATTACAAATTA
1 AT-ATAATT-TATATTA
*
26720 TAAACTATATTT-TATTA
1 -ATA-TA-ATTTATATTA
* *
26737 ATATAAGCTAATATTA
1 ATATAA-TTTATATTA
*
26753 ATATTATTTATATTA
1 ATATAATTTATATTA
* *
26768 ATATTAA-ATATTTTA
1 ATA-TAATTTATATTA
*
26783 ATATTAA-TTATAAT-
1 ATA-TAATTTATATTA
*
26797 ATATAA-TTATTTTA
1 ATATAATTTATATTA
26811 ATATTAATT
1 ATA-TAATT
26820 ATAAATAGTT
Statistics
Matches: 203, Mismatches: 42, Indels: 67
0.65 0.13 0.21
Matches are distributed among these distances:
13 8 0.04
14 24 0.12
15 72 0.35
16 51 0.25
17 17 0.08
18 10 0.05
19 7 0.03
20 4 0.02
21 9 0.04
22 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:26614 original size:65 final size:61
Alignment explanation
Indices: 26538--26673 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 61
26528 ATAGTTTATA
* * **
26538 TTAATGTTAATTATATTAACTATAATTTATATTAA-TATAGTATATTGTTTATAAACTATACTAT
1 TTAATATTAATTATATTAACTATAATTTATA--AACTATACTATATAATTTAT-AAC-ATA-TAT
26602 T
61 T
*
26603 TTAATATTAATTATATTAACTATAGTTTATAAACTATACTATATAATTTATAACATATATT
1 TTAATATTAATTATATTAACTATAATTTATAAACTATACTATATAATTTATAACATATATT
26664 TT-ATATTAAT
1 TTAATATTAAT
26674 ATTAACTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
60 8 0.12
61 6 0.09
62 3 0.05
63 5 0.08
64 14 0.22
65 29 0.45
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (61 bp):
TTAATATTAATTATATTAACTATAATTTATAAACTATACTATATAATTTATAACATATATT
Found at i:26740 original size:131 final size:132
Alignment explanation
Indices: 26491--26728 Score: 288
Period size: 131 Copynumber: 1.8 Consensus size: 132
26481 ACCTATAGTA
* * * *
26491 TATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAATTATATTA
1 TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATATTA
* ****
26556 ACTATAATTTATATTAATATAGTATATTGTTTATAAACTATACTATTTTAATATTAATTATATTA
66 ACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATTTTAATATTAATTATATTA
26621 AC
131 AC
* * *
26623 TATAGTTTATAAACTATACTATATAATTTAT-AAC-ATATATTTTATATTAATATTAACTT-TA-
1 TATAATTTATAAACTATACTATAT-ATTAATGAACTATATAGTTTATATTAATATTAA-TTATAT
*
26684 TAGACTATATTTTATATTAATAATAAT-TACAAATTATAAACTATA
64 TA-ACTATAATTTATATTAAT-ATAATATACAAATTATAAACTATA
26729 TTTTATTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
130 2 0.02
131 53 0.60
132 29 0.33
133 5 0.06
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (132 bp):
TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATATTA
ACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATTTTAATATTAATTATATTA
AC
Found at i:26763 original size:131 final size:131
Alignment explanation
Indices: 26490--26764 Score: 278
Period size: 131 Copynumber: 2.1 Consensus size: 131
26480 AACCTATAGT
* * * * *
26490 ATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAATTATATT
1 ATATTATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATATT
* **** *
26555 AACTATAATTTATATTAATATAGTATATTGTTTATAAACTATACTATTTTAATATTAATTATATT
66 AACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATTTTAATATTAATAATATT
26620 A
131 A
* *
26621 ACTA-TAGTTTATAAACTATACTATATAATTTAT-AAC-ATATATTTTATATTAATATTAACTT-
1 A-TATTA-TTTATAAACTATACTATAT-ATTAATGAACTATATAGTTTATATTAATATTAA-TTA
* *
26682 TA-TAGACTATATTTTATATTAATAATAAT-TACAAATTATAAACTATA-TTTTATTAATA-TAA
62 TATTA-ACTATAATTTATATTAAT-ATAATATACAAATTATAAACTATACTATT-TTAATATTAA
26743 GCTAATATTA
124 --TAATATTA
26753 ATATTATTTATA
1 ATATTATTTATA
26765 TTAATATTAA
Statistics
Matches: 119, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
130 8 0.07
131 69 0.58
132 37 0.31
133 5 0.04
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (131 bp):
ATATTATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATATT
AACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATTTTAATATTAATAATATT
A
Found at i:26805 original size:13 final size:12
Alignment explanation
Indices: 26781--26823 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
26771 TTAAATATTT
26781 TAATATTAATTA
1 TAATATTAATTA
26793 TAATATATAATTA
1 TAATAT-TAATTA
26806 TTTTAATATTAATTA
1 ---TAATATTAATTA
26821 TAA
1 TAA
26824 ATAGTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
15 6 0.22
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATTAATTA
Found at i:26816 original size:28 final size:30
Alignment explanation
Indices: 26750--26823 Score: 107
Period size: 28 Copynumber: 2.5 Consensus size: 30
26740 TAAGCTAATA
* *
26750 TTAATATTATTTATATTAATATTAAATATT
1 TTAATATTAATTATAATAATATTAAATATT
*
26780 TTAATATTAATTATAAT-ATA-TAATTATT
1 TTAATATTAATTATAATAATATTAAATATT
26808 TTAATATTAATTATAA
1 TTAATATTAATTATAA
26824 ATAGTTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 23 0.56
29 3 0.07
30 15 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAATATTAATTATAATAATATTAAATATT
Found at i:26820 original size:15 final size:15
Alignment explanation
Indices: 26750--26821 Score: 87
Period size: 15 Copynumber: 4.9 Consensus size: 15
26740 TAAGCTAATA
* *
26750 TTAATATTATTTATA
1 TTAATATTAATTATT
*
26765 TTAATATTAAATATT
1 TTAATATTAATTATT
26780 TTAATATTAATTA--
1 TTAATATTAATTATT
26793 -TAATATATAATTATT
1 TTAATAT-TAATTATT
26808 TTAATATTAATTAT
1 TTAATATTAATTAT
26822 AAATAGTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
12 6 0.12
13 6 0.12
15 31 0.63
16 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATTAATTATT
Found at i:26833 original size:28 final size:27
Alignment explanation
Indices: 26750--26833 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 27
26740 TAAGCTAATA
* *
26750 TTAATATTATTTATATTAATATTAAATATT
1 TTAATATTAATTATA--AATATT-ATTATT
*
26780 TTAATATTAATTATAATATATAATTATT
1 TTAATATTAATTATAA-ATATTATTATT
26808 TTAATATTAATTATAAATAGTTATTA
1 TTAATATTAATTATAAATA-TTATTA
26834 ATATAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.06
28 27 0.56
29 4 0.08
30 14 0.29
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAATATTAATTATAAATATTATTATT
Found at i:28631 original size:7 final size:7
Alignment explanation
Indices: 28619--28645 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28609 GTTGGACCGA
28619 CTTGTTC
1 CTTGTTC
28626 CTTGTTC
1 CTTGTTC
28633 CTTGTTC
1 CTTGTTC
28640 CTTGTT
1 CTTGTT
28646 AGTTATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.15, T:0.59
Consensus pattern (7 bp):
CTTGTTC
Found at i:29455 original size:23 final size:23
Alignment explanation
Indices: 29425--29484 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
29415 TGCTTTCTTA
29425 ATGC-ATGATGCTTGCTGAAGTG
1 ATGCAATGATGCTTGCTGAAGTG
*
29447 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAAGTG
* * *
29470 GTACATTGATGCTTG
1 ATGCAATGATGCTTG
29485 TCGGTTGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.35
Consensus pattern (23 bp):
ATGCAATGATGCTTGCTGAAGTG
Found at i:30053 original size:12 final size:13
Alignment explanation
Indices: 30036--30069 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
30026 TAATTTAGTG
30036 ATTATAAATAA-A
1 ATTATAAATAAGA
30048 ATTATAATATAAGA
1 ATTATAA-ATAAGA
30062 ATTATAAA
1 ATTATAAA
30070 GAATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 5 0.25
14 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:30116 original size:14 final size:14
Alignment explanation
Indices: 30092--30130 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
30082 ATATAAAAAT
30092 CAAATTTATAATATA
1 CAAA-TTATAATATA
30107 CAAATTATAATATA
1 CAAATTATAATATA
30121 -AGAATTATAA
1 CA-AATTATAA
30131 AAAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (14 bp):
CAAATTATAATATA
Found at i:30144 original size:19 final size:19
Alignment explanation
Indices: 30115--30159 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30105 TACAAATTAT
30115 AATAT-AAGAATTATAAAA
1 AATATAAAGAATTATAAAA
* **
30133 AATATAAAGAATTGTAATT
1 AATATAAAGAATTATAAAA
30152 AATATAAA
1 AATATAAA
30160 AACTAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (19 bp):
AATATAAAGAATTATAAAA
Found at i:30214 original size:27 final size:26
Alignment explanation
Indices: 30163--30215 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
30153 ATATAAAAAC
* *
30163 TAAATTTAATTATCATAAGTTTATTA
1 TAAATTTAAATAACATAAGTTTATTA
30189 TAAATTTAAAATAACATAA-TTATATTA
1 TAAATTT-AAATAACATAAGTT-TATTA
30216 ATTGTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAATTTAAATAACATAAGTTTATTA
Found at i:30316 original size:16 final size:16
Alignment explanation
Indices: 30297--30335 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
30287 TGAGTCAATT
*
30297 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
30313 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
30329 ACAGGTC
1 ACAGGTC
30336 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:31189 original size:22 final size:20
Alignment explanation
Indices: 31146--31197 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
31136 ATATCATTAT
* *
31146 TTATATTATTTTTTAATTAAA
1 TTATATT-TTTTTGAATAAAA
31167 TCTATATTTTTATTGAATAAAA
1 T-TATATTTTT-TTGAATAAAA
31189 TTAATATTT
1 TT-ATATTT
31198 CTTTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATATTTTTTTGAATAAAA
Found at i:34066 original size:2 final size:2
Alignment explanation
Indices: 34059--34097 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
34049 TCCCTCCAAT
* *
34059 TA TA TA TA TC TA TA TA TC TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34098 GAATGTCTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35013 original size:3 final size:3
Alignment explanation
Indices: 35007--35032 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34997 GGAGGAGGAG
35007 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
35033 GGAGTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35052 original size:5 final size:5
Alignment explanation
Indices: 35042--35078 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
35032 AGGAGTTGCT
*
35042 TTTTC TTTTC TTTTC TTATC TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
35079 TGGTTCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:42059 original size:16 final size:17
Alignment explanation
Indices: 42028--42061 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42018 AGATATTATT
*
42028 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
42045 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
42061 T
1 T
42062 AATAAAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:46193 original size:2 final size:2
Alignment explanation
Indices: 46188--46234 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
46178 GCAAAAAAGT
46188 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
46230 AG AG A
1 AG AG A
46235 CCTCGAGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48196 original size:28 final size:28
Alignment explanation
Indices: 48156--48212 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
48146 GAAAGAAGAT
48156 TCAGTCATGCTCTTACCTTCATCTTTTC
1 TCAGTCATGCTCTTACCTTCATCTTTTC
*
48184 TCAGTCATGCTCTTACCTTTATCTTTTC
1 TCAGTCATGCTCTTACCTTCATCTTTTC
48212 T
1 T
48213 TTGTTTCTTT
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:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (28 bp):
TCAGTCATGCTCTTACCTTCATCTTTTC
Found at i:49844 original size:5 final size:5
Alignment explanation
Indices: 49834--49867 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
49824 CAGAATCCTA
*
49834 CTTCT CTTCT CTTCT CTTCT ATTCT CTTCT CTTC
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTC
49868 CTTGACAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTCT
Found at i:50524 original size:20 final size:19
Alignment explanation
Indices: 50501--50607 Score: 67
Period size: 19 Copynumber: 5.5 Consensus size: 19
50491 TTTCGTCCCC
50501 TATATATATATATTTTTAAT
1 TATATATATAT-TTTTTAAT
* *
50521 TATAT-TTTATTTATTTATT
1 TATATATATATTT-TTTAAT
* *
50540 TACTATAT-TCCTTTTTTATT
1 TA-TATATAT-ATTTTTTAAT
*
50560 TATAT-TATATTATTTTTAT
1 TATATATATATT-TTTTAAT
* * * *
50579 TATATATATCTTATATCAT
1 TATATATATATTTTTTAAT
50598 TATATATATA
1 TATATATATA
50608 CATGTATAGA
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
18 5 0.07
19 38 0.55
20 22 0.32
21 4 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATATATATTTTTTAAT
Found at i:50547 original size:22 final size:22
Alignment explanation
Indices: 50521--50594 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 22
50511 TATTTTTAAT
50521 TATATTTTATTTATTTAT-TTA
1 TATATTTTATTTATTTATATTA
*
50542 CTATATTCCTTTTTTATTTATATTA
1 -TATATT--TTATTTATTTATATTA
* *
50567 TATTATTTTTATTATATATATCTTA
1 TA-TA-TTTTATT-TATTTATATTA
50592 TAT
1 TAT
50595 CATTATATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.14
24 18 0.43
25 16 0.38
26 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTTATTTATTTATATTA
Found at i:50574 original size:14 final size:14
Alignment explanation
Indices: 50555--50594 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
50545 TATTCCTTTT
50555 TTATTTATATTATA
1 TTATTTATATTATA
*
50569 TTATTTTTATTATA
1 TTATTTATATTATA
50583 TATATCTTATAT
1 T-TAT-TTATAT
50595 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:50773 original size:19 final size:19
Alignment explanation
Indices: 50716--50774 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
50706 TCTATTTTTG
* *
50716 TTTTTATTTATTTATA-TA
1 TTTTTATTTTTTTCTATTA
* *
50734 TATATTATATTTTTACT-TTA
1 T-TTTTAT-TTTTTTCTATTA
50754 TTTTTATTTTTTTCTATTA
1 TTTTTATTTTTTTCTATTA
50773 TT
1 TT
50775 ATTTTTCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 8 0.26
19 15 0.48
20 8 0.26
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTTTTCTATTA
Found at i:50915 original size:18 final size:17
Alignment explanation
Indices: 50892--50925 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50882 ATTTTTATTC
50892 CTTTTTAATTTCTTTTAT
1 CTTTTT-ATTTCTTTTAT
*
50910 CTTTTTATTTTTTTTA
1 CTTTTTATTTCTTTTA
50926 CTCCATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTTATTTCTTTTAT
Found at i:50989 original size:18 final size:17
Alignment explanation
Indices: 50960--51004 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
50950 TGTGTCTTTG
*
50960 TTTTTTAATATTTTATTCA
1 TTTTTTTAT-TTTTATT-A
50979 TTTTGTTTATTTTTATTA
1 TTTT-TTTATTTTTATTA
50997 TTTTTTTA
1 TTTTTTTA
51005 CGTGTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 11 0.46
20 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTTTTATTA
Found at i:52956 original size:27 final size:26
Alignment explanation
Indices: 52911--52961 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
52901 ACATTTCATG
*
52911 CATTTTTGCATTTTGCATATACATTT
1 CATTTTTGCATTTTGCATAAACATTT
52937 CATTTTTAAGCATTTT-CATAAACAT
1 CATTTTT--GCATTTTGCATAAACAT
52962 GAAATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (26 bp):
CATTTTTGCATTTTGCATAAACATTT
Found at i:55420 original size:110 final size:108
Alignment explanation
Indices: 55222--55480 Score: 299
Period size: 110 Copynumber: 2.4 Consensus size: 108
55212 GCTTCCTAGT
** * *
55222 TTCAGAGCCAATTTCAACTTCACAGTGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTCA
* * * * *
55287 TAACGAAGGGGTGACTGATTGTCAATAAACAACTTT-TCAGTTTC
66 CAACGAAGGGGAGACTGACTGTCAACAAACAA-TTTCCCAG-TTC
* * * * *
55331 ATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGAACTCGAGACAACAGAAGCTCAACTTC
1 -TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTC
* * *
55396 ACAGCGAAGGGGAGGCTGGCTGTCAACAAACAATTTCCCAGTTC
65 ACAACGAAGGGGAGACTGACTGTCAACAAACAATTTCCCAGTTC
* *
55440 -T-AGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCG
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
55481 GAACAATACT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
106 35 0.28
107 1 0.01
109 6 0.05
110 84 0.67
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (108 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTCA
CAACGAAGGGGAGACTGACTGTCAACAAACAATTTCCCAGTTC
Found at i:56803 original size:20 final size:20
Alignment explanation
Indices: 56780--56849 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
56770 TATATATATA
*
56780 TATTTTTAATTATATTTTTT
1 TATTTATAATTATATTTTTT
**
56800 TATTTACTATATT-CCTTTTTT
1 TATTTA-TA-ATTATATTTTTT
56821 TATTTAT-ATTATATTATTTT
1 TATTTATAATTATATT-TTTT
56841 TATTATATA
1 TATT-TATA
56850 TCTTATATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 14 0.36
21 17 0.44
22 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTATAATTATATTTTTT
Found at i:56833 original size:23 final size:22
Alignment explanation
Indices: 56792--56857 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
56782 TTTTTAATTA
56792 TATTTTTTTATTTACTA-TAT-T
1 TATTTTTTTATTTA-TATTATAT
**
56813 CCTTTTTTTATTTATATTATAT
1 TATTTTTTTATTTATATTATAT
* *
56835 TATTTTTATTATATATCTTATAT
1 TATTTTT-TTATTTATATTATAT
56858 CATTATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 6 0.17
23 13 0.36
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTTTTATTTATATTATAT
Found at i:56839 original size:14 final size:15
Alignment explanation
Indices: 56821--56901 Score: 83
Period size: 16 Copynumber: 5.2 Consensus size: 15
56811 TTCCTTTTTT
56821 TATTTATATTATAT-
1 TATTTATATTATATA
*
56835 TATTTTTATTATATA
1 TATTTATATTATATA
*
56850 TCTTATATCATTATATA
1 TATT-TAT-ATTATATA
*
56867 TATATATATATATATA
1 TATTTATAT-TATATA
*
56883 TATATATATATATATA
1 TATTTATAT-TATATA
56899 TAT
1 TAT
56902 AGATGTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.22
15 5 0.09
16 30 0.52
17 10 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:56866 original size:2 final size:2
Alignment explanation
Indices: 56844--56902 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
56834 TTATTTTTAT
*
56844 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
56885 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
56903 GATGTATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.04
2 49 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56957 original size:18 final size:18
Alignment explanation
Indices: 56934--56996 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
56924 TTACTATGTA
56934 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* * **
56952 TATATTTATACGTTTTTA-
1 TATATTTTTTC-TTAATAT
56970 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
*
56988 TCTATTTTT
1 TATATTTTT
56997 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 4 0.12
18 26 0.76
19 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:57010 original size:36 final size:36
Alignment explanation
Indices: 56934--57052 Score: 122
Period size: 36 Copynumber: 3.3 Consensus size: 36
56924 TTACTATGTA
*
56934 TATATTTTTTCTTAATATTATATTTATACGTTTTTA--
1 TATATTTTTTCTTAATATTATATTTTTA--TTTTTATT
*
56970 TATATTTTTTCTTAATATTCTATTTTTATTTTTATT
1 TATATTTTTTCTTAATATTATATTTTTATTTTTATT
* * *
57006 TATATATATAT-ATATATATTATATTTTTA-TTTTATT
1 TATAT-TTTTTCTTA-ATATTATATTTTTATTTTTATT
57042 T-TATTTTTTCT
1 TATATTTTTTCT
57053 GTTATTGTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
34 9 0.13
35 3 0.04
36 41 0.59
37 16 0.23
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (36 bp):
TATATTTTTTCTTAATATTATATTTTTATTTTTATT
Found at i:57148 original size:36 final size:35
Alignment explanation
Indices: 57076--57148 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
57066 TAATATCATG
* * *
57076 TATATCTTTATTTTTTTATTTGTTTTACTTAGTAT
1 TATATATTTATTTTTTTATTTGTTTTACTAAATAT
*
57111 TATATATTTATTATTTTTATTTGTTTTAGTAAATAT
1 TATATATTTATT-TTTTTATTTGTTTTACTAAATAT
57147 TA
1 TA
57149 CTTTATATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (35 bp):
TATATATTTATTTTTTTATTTGTTTTACTAAATAT
Found at i:57208 original size:17 final size:18
Alignment explanation
Indices: 57176--57210 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57166 ATTTTTATTT
57176 CTTTTTAATTTCTTTTAC
1 CTTTTTAATTTCTTTTAC
*
57194 CTTTTTTATTT-TTTTAC
1 CTTTTTAATTTCTTTTAC
57211 TCCATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTAATTTCTTTTAC
Found at i:57286 original size:12 final size:12
Alignment explanation
Indices: 57269--57298 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57259 TTCATTTTAT
57269 TTATTTTTATTA
1 TTATTTTTATTA
57281 TTATTTTTATTA
1 TTATTTTTATTA
57293 TT-TTTT
1 TTATTTT
57299 ACGTGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:57316 original size:9 final size:9
Alignment explanation
Indices: 57262--57332 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
57252 CATTTTATTC
*
57262 ATTTTATTT
1 ATTTTTTTT
*
57271 ATTTTTATT
1 ATTTTTTTT
*
57280 ATTATTTTT
1 ATTTTTTTT
57289 ATTATTTTTT
1 ATT-TTTTTT
57299 ACGTGTTTTTTT
1 A--T-TTTTTTT
57311 ATTTTTTCTT
1 ATTTTTT-TT
* *
57321 GTTTTATTT
1 ATTTTTTTT
57330 ATT
1 ATT
57333 ATTCTCACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 26 0.53
10 14 0.29
12 8 0.16
13 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:57323 original size:18 final size:19
Alignment explanation
Indices: 57284--57332 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
57274 TTTATTATTA
57284 TTTTTATTATTTTTTACGTG
1 TTTTT-TTATTTTTTACGTG
*
57304 TTTTTTTATTTTTT-CTTG
1 TTTTTTTATTTTTTACGTG
57322 TTTTATTTATT
1 TTTT-TTTATT
57333 ATTCTCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTTTTTACGTG
Found at i:57853 original size:40 final size:40
Alignment explanation
Indices: 57798--57879 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
57788 AATCTGGAGC
57798 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
1 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
57838 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
1 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
57878 GT
1 GT
57880 GAGCAAAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (40 bp):
GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
Found at i:67480 original size:95 final size:94
Alignment explanation
Indices: 67323--67530 Score: 258
Period size: 95 Copynumber: 2.2 Consensus size: 94
67313 ATTTCAAATT
* *
67323 AGATCAATTTTGTTTCAATTGCAAAAAATTAAAAAAATTTCGAAAACTATCTCAAGCAAGACGAA
1 AGATCAATTTTGTTTCAAGTGAAAAAAATTAAAAAAATTTCGAAAACTATCTCAAGCAAGACGAA
*
67388 ATTTGTTTTTAG-GAAAACAATCTCAAGTG
66 ATTTGTTTTGAGAG-AAACAATCTCAAGTG
* * * * * *
67417 AGATCAATTTTGTTTCAAGTGTAAAAAAATT-CAAAATTTGTTGAAAATTGTCTTAAGCAAGACG
1 AGATCAATTTTGTTTCAAGTG-AAAAAAATTAAAAAAATT-TCGAAAACTATCTCAAGCAAGACG
* * *
67481 AAATTTGTTTTGAGAGGAATAATCTCAATTG
64 AAATTTGTTTTGAGAGAAACAATCTCAAGTG
*
67512 GGATCAATTTTGTTTCAAG
1 AGATCAATTTTGTTTCAAG
67531 AAATACTATT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
94 26 0.27
95 71 0.72
96 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (94 bp):
AGATCAATTTTGTTTCAAGTGAAAAAAATTAAAAAAATTTCGAAAACTATCTCAAGCAAGACGAA
ATTTGTTTTGAGAGAAACAATCTCAAGTG
Found at i:69799 original size:3 final size:3
Alignment explanation
Indices: 69791--69847 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
69781 AGGTTCTAAT
* *
69791 TTA TTA TTAA CTTA TTA TTA TTTA TTA TTA TTA TTA TTA -TA CTA ATA
1 TTA TTA TT-A -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
69838 TTA TT- TTA TT
1 TTA TTA TTA TT
69848 TTCATATTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.09
3 36 0.77
4 5 0.11
5 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:71642 original size:19 final size:19
Alignment explanation
Indices: 71598--71653 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
71588 TAATGGTAAT
* *
71598 TTTTATTTTTATAATATTTCA
1 TTTTATTTTT-T-ATTTTTAA
71619 TTTTATTTTTTATTTTTAA
1 TTTTATTTTTTATTTTTAA
* *
71638 TTTTAATTTTCATTTT
1 TTTTATTTTTTATTTT
71654 GTTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.65
20 1 0.03
21 10 0.32
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTTATTTTTAA
Found at i:71903 original size:19 final size:18
Alignment explanation
Indices: 71858--71903 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
71848 ATTTTCTTTT
*
71858 AATAATTAATATAGAATA
1 AATAATTAATATACAATA
*
71876 AATCAATTAATATTCAATA
1 AAT-AATTAATATACAATA
71895 AATAGATTA
1 AATA-ATTA
71904 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
AATAATTAATATACAATA
Found at i:72242 original size:13 final size:14
Alignment explanation
Indices: 72215--72243 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
72205 ATAATTATTT
72215 TTTTAAAATAATTG
1 TTTTAAAATAATTG
72229 TTTTAAAA-AATTG
1 TTTTAAAATAATTG
72242 TT
1 TT
72244 ATGACAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTAAAATAATTG
Found at i:72591 original size:37 final size:37
Alignment explanation
Indices: 72497--72601 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
72487 CATTTTCGTC
72497 CTACTAGGATTTAAATTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTTAAATTCCTAAAAATAGGATAAAATT
* ** * * * * *
72534 TTGTTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAATTCCTAAAAATAGGATAAAATT
* *
72571 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTTAAATTCCTAAAAATAGGAT
72602 CCACAAGCAC
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTTAAATTCCTAAAAATAGGATAAAATT
Found at i:73378 original size:18 final size:19
Alignment explanation
Indices: 73352--73387 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
73342 TTTTTGGTTT
*
73352 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
73370 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
73388 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:73431 original size:2 final size:2
Alignment explanation
Indices: 73424--73450 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73414 TTTACTCATT
73424 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
73451 TAATATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73473 original size:20 final size:21
Alignment explanation
Indices: 73450--73492 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
73440 TATATATATA
73450 TTAATATTT-CATTTATTT-TT
1 TTAAT-TTTCCATTTATTTATT
*
73470 TTAATTTTCCTTTTATTTATT
1 TTAATTTTCCATTTATTTATT
73491 TT
1 TT
73493 TTACTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
TTAATTTTCCATTTATTTATT
Found at i:77993 original size:183 final size:183
Alignment explanation
Indices: 77458--77994 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
77448 ATTAAATCCG
*
77458 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGTAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
77523 ATAGATTATGTTCAAACTATGACACTACTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
77588 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAATGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
77641 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
77706 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
77771 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
77824 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAACCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* ** * *
77889 ATATATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCATTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
77953 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
77995 TAAACCTGAT
Statistics
Matches: 341, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 340 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:79223 original size:71 final size:77
Alignment explanation
Indices: 79138--79293 Score: 202
Period size: 72 Copynumber: 2.1 Consensus size: 77
79128 AGATGATATC
* * * *
79138 TCACTCAA-ATTTGTTTTTCTT-AAGCATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAG
1 TCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAG
79199 AA-G-ATTT-ATT
65 AATGCATTTAATT
*
79209 TCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGA
1 TCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGA
79273 ATGCATTTAATT
66 ATGCATTTAATT
79285 TCACTCAAG
1 TCACTCAAG
79294 GCTGATTTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
71 20 0.27
72 26 0.36
73 10 0.14
74 1 0.01
75 4 0.05
76 12 0.16
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (77 bp):
TCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGA
ATGCATTTAATT
Found at i:79261 original size:36 final size:36
Alignment explanation
Indices: 79167--79261 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
79157 TTAAGCATAC
* *
79167 TTTGTCTCACTTGAGACTGTTTTTCTCGAAAGAAGA
1 TTTGTCTCACTTGAGACTGTTTTTCTCAAAACAAGA
* * ** * *
79203 TTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGA
1 TTTGTCTCACTTGAGACTGTTTTTCTCAAAACAAGA
* *
79239 TTTGTCTCGCTTGAGACCGTTTT
1 TTTGTCTCACTTGAGACTGTTTT
79262 CACTCGAAAG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTGTCTCACTTGAGACTGTTTTTCTCAAAACAAGA
Found at i:79341 original size:73 final size:72
Alignment explanation
Indices: 79171--79343 Score: 165
Period size: 73 Copynumber: 2.4 Consensus size: 72
79161 GCATACTTTG
* * * * *
79171 TCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTGATTTTCTT-AAAC
*
79235 AAGATTTG
65 AAGATTTA
* *
79243 TCTCGCTTGAGACCGTTTTCACTCGAAAGAATGCATTTAATTTCACTCAAGGCTGATTTT-TT-A
1 TCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTGATTTTCTTAA
*
79306 AGAAGATTTTA
63 ACAAGA-TTTA
* * *
79317 TCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TCTCGCTTGAGACAGTTTTCACTCGAAA
79344 CAGAAAATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
72 17 0.20
73 27 0.32
74 16 0.19
75 6 0.07
76 18 0.21
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (72 bp):
TCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTGATTTTCTTAAACA
AGATTTA
Found at i:79457 original size:39 final size:39
Alignment explanation
Indices: 79400--79474 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
79390 CCTTGAAATT
* *
79400 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* *
79439 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
79475 TAACATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:79609 original size:102 final size:102
Alignment explanation
Indices: 79377--79690 Score: 463
Period size: 101 Copynumber: 3.1 Consensus size: 102
79367 ATAGTTTCTC
* *
79377 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAG-AAA-
79442 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT-AACA
64 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
79480 TTGAAAACATTTCCCTTGAAATG-ATTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
* * *
79544 TATCTCCCTTGAGACAATTTCTCTTGAAATATAAACA
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * *
79581 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAATC-GAATTT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
** *
79645 TGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
79682 TTGAAAACA
1 TTGAAAACA
79691 ATTTAACGAA
Statistics
Matches: 191, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
100 31 0.16
101 75 0.39
102 63 0.33
103 22 0.12
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:79643 original size:36 final size:36
Alignment explanation
Indices: 79590--79665 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
79580 ATTGAAAACA
* *
79590 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
*
79626 TTTCCCTTG-AATCGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAT-GAATTTTATCTCCCTTGAGACAG
79662 TTTC
1 TTTC
79666 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
Found at i:80168 original size:209 final size:209
Alignment explanation
Indices: 79865--80494 Score: 878
Period size: 209 Copynumber: 3.0 Consensus size: 209
79855 ATATCGTGAC
* * * *
79865 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
79929 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
64 CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * *
79994 TTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
128 TTCACGATGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
80059 AC-ACGAAGGATATTGG
193 ACAACGAAGGATATTGG
* * *
80075 ACTTCAGTCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
80140 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
80205 CACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCAC
130 CACGATGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCAC
80270 AACGAAGGATATTGG
195 AACGAAGGATATTGG
* *
80285 ACTCCAGACAACGCAAGTTCAAC-TCTATGACGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTC-ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC
* * * * ** *
80346 -ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAATTGAGACAACACAAGTTCAACTT
65 AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* ** * * ** *
80410 CACAATGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCA
130 CACGATGAAGGGACCGCTGCTTGTCAA-AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
80475 CGACGGAGGATATTGG
194 CAACGAAGGATATTGG
80491 ACTC
1 ACTC
80495 GGAACAATGC
Statistics
Matches: 380, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
205 78 0.21
206 51 0.13
207 1 0.00
208 3 0.01
209 139 0.37
210 106 0.28
211 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (209 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGATGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGG
Found at i:80230 original size:105 final size:104
Alignment explanation
Indices: 79865--80494 Score: 860
Period size: 105 Copynumber: 6.0 Consensus size: 104
79855 ATATCGTGAC
* * * * *
79865 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
79929 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
79971 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
80036 ATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGG
66 A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
80075 ACTTCAGTCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
80140 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
80180 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
80245 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
80285 ACTCCAGACAACGCAAGTTCAAC-TCTATGACGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTC-ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCC
* * *
80346 -ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGA
65 AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * * ** * *
80385 AATTGAGACAACACAAGTTCAACTTCACAATGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
80450 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
80491 ACTC
1 ACTC
80495 GGAACAATGC
Statistics
Matches: 474, Mismatches: 39, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
100 73 0.15
101 6 0.01
102 3 0.01
103 5 0.01
104 103 0.22
105 204 0.43
106 78 0.16
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:81083 original size:37 final size:37
Alignment explanation
Indices: 81034--81134 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
81024 CATTTTCGTC
* *
81034 CTAGGA-TCAAACTCCTAAAAATAGGATAAAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTCTA
* *
81070 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTCTA
* * * *
81107 CTAAGATTTAAATTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
81135 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 6 0.11
37 50 0.89
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTCTA
Found at i:81893 original size:18 final size:19
Alignment explanation
Indices: 81867--81902 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
81857 TGTTGTTTTT
*
81867 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
81885 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
81903 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:81971 original size:8 final size:8
Alignment explanation
Indices: 81955--82027 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
81945 TATATATATA
81955 TTATATTTT
1 TTAT-TTTT
81964 TTATTTTTT
1 TTA-TTTTT
*
81973 TTATTTAT
1 TTATTTTT
*
81981 TT-TTTAT
1 TTATTTTT
81988 TTATTTTT
1 TTATTTTT
*
81996 TTA-TTCT
1 TTATTTTT
*
82003 TCATTTTT
1 TTATTTTT
* *
82011 TCATTTAT
1 TTATTTTT
*
82019 TCATTTTT
1 TTATTTTT
82027 T
1 T
82028 CTCTGACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
7 12 0.22
8 31 0.57
9 10 0.19
10 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (8 bp):
TTATTTTT
Found at i:81974 original size:11 final size:11
Alignment explanation
Indices: 81967--82000 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
81957 ATATTTTTTA
81967 TTTTTTTTATT
1 TTTTTTTTATT
*
81978 TATTTTTTATT
1 TTTTTTTTATT
81989 TATTTTTTTATT
1 T-TTTTTTTATT
82001 CTTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:82017 original size:19 final size:18
Alignment explanation
Indices: 81969--82020 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
81959 ATTTTTTATT
* *
81969 TTTTTTATTTATTTTTTA
1 TTTTTTATTTATTCTTCA
*
81987 TTTATTTTTTTATTCTTCA
1 TTT-TTTATTTATTCTTCA
82006 TTTTTTCATTTATTC
1 TTTTTT-ATTTATTC
82021 ATTTTTTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTATTTATTCTTCA
Found at i:82021 original size:16 final size:16
Alignment explanation
Indices: 81983--82028 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
81973 TTATTTATTT
* *
81983 TTTATTTATTTTTTTA
1 TTTATTCATTTTTTCA
*
81999 -TTCTTCATTTTTTCA
1 TTTATTCATTTTTTCA
82014 TTTATTCATTTTTTC
1 TTTATTCATTTTTTC
82029 TCTGACATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTCATTTTTTCA
Found at i:83315 original size:25 final size:24
Alignment explanation
Indices: 83287--83364 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
83277 TAAAAATAAT
83287 TTTTTTAAATTAAGTTAATAAAATA
1 TTTTTTAAATTAA-TTAATAAAATA
* *
83312 TTTTTAATAATTAATATAA-AAAACA
1 TTTTTTA-AATTAAT-TAATAAAATA
* *
83337 TTTCTTAAAGTTAACTATATAAAATA
1 TTTTTTAAA-TTAATTA-ATAAAATA
83363 TT
1 TT
83365 ATAAATGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
24 4 0.10
25 22 0.52
26 16 0.38
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (24 bp):
TTTTTTAAATTAATTAATAAAATA
Done.