Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1102
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: 83758
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:388 original size:26 final size:26
Alignment explanation
Indices: 335--396 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
325 AAAATCACAA
335 AAATAATATAAAATATAAATAAATAT
1 AAATAATATAAAATATAAATAAATAT
* **
361 AAATAATGTTAAAATATGCATAAA-AT
1 AAATAAT-ATAAAATATAAATAAATAT
387 AAAT-ATATAA
1 AAATAATATAA
397 CTAAAATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 3 0.10
25 2 0.06
26 13 0.42
27 13 0.42
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
AAATAATATAAAATATAAATAAATAT
Found at i:640 original size:15 final size:14
Alignment explanation
Indices: 612--654 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
602 AGAAAAAAAA
612 AAAGAAAGGAAAGGG
1 AAAGAAA-GAAAGGG
627 AAGAGAAAGAAA-GG
1 AA-AGAAAGAAAGGG
641 AAAGAAAGAGAAGG
1 AAAGAAAGA-AAGG
655 AAGCAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 7 0.28
16 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGGG
Found at i:662 original size:14 final size:13
Alignment explanation
Indices: 612--656 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
602 AGAAAAAAAA
612 AAAGAAAGGAAAGGG
1 AAAGAAA-GAAA-GG
627 AAGAGAAAGAAAGG
1 AA-AGAAAGAAAGG
641 AAAGAAAGAGAAGG
1 AAAGAAAGA-AAGG
655 AA
1 AA
657 GCAAAGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.25
14 10 0.36
15 6 0.21
16 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGG
Found at i:757 original size:15 final size:15
Alignment explanation
Indices: 737--765 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
727 TATTTTACAG
737 TTATATTTTATATTT
1 TTATATTTTATATTT
752 TTATATTTTATATT
1 TTATATTTTATATT
766 ATATTCATAT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATTTTATATTT
Found at i:3492 original size:2 final size:2
Alignment explanation
Indices: 3485--3514 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3475 AATAAAATGC
3485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3515 TGTTGATTAA
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):
AT
Found at i:3583 original size:34 final size:34
Alignment explanation
Indices: 3513--3697 Score: 246
Period size: 34 Copynumber: 5.5 Consensus size: 34
3503 ATATATATAT
* *
3513 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3546 ATTGTTGACTAAATGGGAAATTTGGTAGCTTATC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3580 ATTGTTGATTAAATAGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3614 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3648 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3682 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3698 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
33 13 0.10
34 117 0.90
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:4062 original size:19 final size:19
Alignment explanation
Indices: 4006--4068 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3996 TGGTTGTCGA
**
4006 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
4025 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
4044 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
4063 GTTACT
1 GGTACT
4069 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:8204 original size:34 final size:34
Alignment explanation
Indices: 8134--8318 Score: 246
Period size: 34 Copynumber: 5.5 Consensus size: 34
8124 AAGTGGGAGA
* *
8134 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
8167 ATTGTTGACTAAATGGGAAATTTGGTAGCTTATC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
8201 ATTGTTGATTAAATAGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
8235 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
8269 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
8303 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
8319 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
33 13 0.10
34 117 0.90
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:8607 original size:2 final size:2
Alignment explanation
Indices: 8600--8631 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8590 ATGCTCTAAC
8600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8632 CTCAGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9067 original size:20 final size:21
Alignment explanation
Indices: 9020--9099 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 21
9010 TTAACTTTAT
*
9020 TTATTTAATTTATGAATTAATT-
1 TTATTTTATTTAT--ATTAATTA
9042 TTATTTTATTTAT-TTAATTA
1 TTATTTTATTTATATTAATTA
* *
9062 TTATTTT-TTGATAATAATTA
1 TTATTTTATTTATATTAATTA
9082 TTAGTTTTATATTATATT
1 TTA-TTTTAT-TTATATT
9100 GCATTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.21
20 16 0.33
21 4 0.08
22 13 0.27
23 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTATTTTATTTATATTAATTA
Found at i:9987 original size:46 final size:46
Alignment explanation
Indices: 9933--10039 Score: 196
Period size: 46 Copynumber: 2.3 Consensus size: 46
9923 TTTTATATTA
9933 TAATTGTTTTATTTTGAAGTTAATTTCATTTTACCAAGTTCAAAAT
1 TAATTGTTTTATTTTGAAGTTAATTTCATTTTACCAAGTTCAAAAT
9979 TAATTGTTTTATTTTGAAGTTAATTTCATTTTACCAAGTTCAAAAT
1 TAATTGTTTTATTTTGAAGTTAATTTCATTTTACCAAGTTCAAAAT
* *
10025 TAATTTTTTTCTTTT
1 TAATTGTTTTATTTT
10040 AATTTTTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.54
Consensus pattern (46 bp):
TAATTGTTTTATTTTGAAGTTAATTTCATTTTACCAAGTTCAAAAT
Found at i:10122 original size:26 final size:27
Alignment explanation
Indices: 10082--10133 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
10072 TTTTGTTCTC
10082 TTTTATTATAATTATTTTAATATATAG
1 TTTTATTATAATTATTTTAATATATAG
*
10109 TTTTATTAT-TTTATTTTAATATATA
1 TTTTATTATAATTATTTTAATATATA
10134 TAATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTATTATAATTATTTTAATATATAG
Found at i:10150 original size:26 final size:27
Alignment explanation
Indices: 10095--10174 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 27
10085 TATTATAATT
* *
10095 ATTTTAATATATAGT--TTTATTATTTT
1 ATTTTAATATATAGTAATTT-TTATATA
10121 ATTTTAATATATA-TAATTTTTATATA
1 ATTTTAATATATAGTAATTTTTATATA
* *
10147 ATTTATATTATAAATATTAATTTTTATA
1 ATTT-TA--ATATATAGTAATTTTTATA
10175 ATAAAAGAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
25 1 0.02
26 22 0.49
27 5 0.11
29 6 0.13
30 11 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTTTAATATATAGTAATTTTTATATA
Found at i:10168 original size:30 final size:30
Alignment explanation
Indices: 10101--10174 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
10091 AATTATTTTA
* *
10101 ATATAT-AGTTTTAT-TATTTTATTTTAAT
1 ATATATAATTTTTATATATTTTATTATAAT
10129 ATATATAATTTTTATATAATTTATATTATAA-
1 ATATATAATTTTTATAT-ATTT-TATTATAAT
10160 ATAT-TAATTTTTATA
1 ATATATAATTTTTATA
10175 ATAAAAGAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 6 0.15
29 7 0.17
30 12 0.30
31 8 0.20
32 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATATATAATTTTTATATATTTTATTATAAT
Found at i:10604 original size:33 final size:33
Alignment explanation
Indices: 10567--10655 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 33
10557 TTATTTTTAT
*
10567 TTATAGAAGTTTAAGATTTATTTTTT-AGTTTGA
1 TTATACAAGTTTAAGATTTATTTTTTGA-TTTGA
10600 TTATACAAGTTTAATAGGATTTATTTTTTGATTTGA
1 TTATACAAGTTT-A-A-GATTTATTTTTTGATTTGA
*
10636 TTATACAAGTTTAAAATTTA
1 TTATACAAGTTTAAGATTTA
10656 GGATTTGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
33 16 0.32
34 2 0.04
35 2 0.04
36 29 0.58
37 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (33 bp):
TTATACAAGTTTAAGATTTATTTTTTGATTTGA
Found at i:10628 original size:36 final size:36
Alignment explanation
Indices: 10581--10649 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
10571 AGAAGTTTAA
10581 GATTTATTTTTT-AGTTTGATTATACAAGTTTAATAG
1 GATTTATTTTTTGA-TTTGATTATACAAGTTTAATAG
10617 GATTTATTTTTTGATTTGATTATACAAGTTTAA
1 GATTTATTTTTTGATTTGATTATACAAGTTTAA
10650 AATTTAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.54
Consensus pattern (36 bp):
GATTTATTTTTTGATTTGATTATACAAGTTTAATAG
Found at i:10672 original size:33 final size:33
Alignment explanation
Indices: 10562--10676 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 33
10552 GTAATTTATT
* * * *
10562 TTTATTTATAGAAGTTTAAGATTTATTTTTTAG
1 TTTAATTATACAAGTTTAAAATTTATTTTTTGG
* *
10595 TTTGATTATACAAGTTTAATAGGATTTATTTTTTGA
1 TTTAATTATACAAGTTTAA-A--ATTTATTTTTTGG
* ***
10631 TTTGATTATACAAGTTTAAAATTTAGGATTTGG
1 TTTAATTATACAAGTTTAAAATTTATTTTTTGG
10664 TTTAATTATACAA
1 TTTAATTATACAA
10677 CTTTGAACTA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
33 37 0.54
35 1 0.01
36 30 0.44
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (33 bp):
TTTAATTATACAAGTTTAAAATTTATTTTTTGG
Found at i:10727 original size:17 final size:18
Alignment explanation
Indices: 10690--10742 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
10680 TGAACTAGAA
*
10690 AAAAAAAAAAGGAAAGGAG
1 AAAAAAAAAAGGAAA-AAG
* *
10709 AAGAAAAGAA-GAAAAAG
1 AAAAAAAAAAGGAAAAAG
10726 AAAAAAAAAAGGAAAAA
1 AAAAAAAAAAGGAAAAA
10743 AAATAGGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 10 0.36
18 10 0.36
19 8 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGGAAAAAG
Found at i:10740 original size:12 final size:12
Alignment explanation
Indices: 10720--10754 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
10710 AGAAAAGAAG
10720 AAAAA-GAAAAA
1 AAAAAGGAAAAA
10731 AAAAAGGAAAAA
1 AAAAAGGAAAAA
*
10743 AAATAGGAAAAA
1 AAAAAGGAAAAA
10755 TGTGGCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAAGGAAAAA
Found at i:18024 original size:20 final size:20
Alignment explanation
Indices: 17952--18026 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
17942 AAAAAGACAG
* *
17952 AATGTATCGATATATTGAAG
1 AATGTATCGATACATTGAAA
* * *
17972 AATGTATCGATATATTCATA
1 AATGTATCGATACATTGAAA
*
17992 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
18012 AATATATCGATACAT
1 AATGTATCGATACAT
18027 CTGGGTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:20811 original size:39 final size:39
Alignment explanation
Indices: 20768--20849 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
20758 GAATCCTTGA
* *
20768 ATTAGTCTCAT-TTTCTAAATTCCAATAAAAAATTTATAT
1 ATTAGTCACATATTT-TAAATTCCAATAAAAAATCTATAT
* * *
20807 ATTAGTCACATATTTTAGATTTCAATAAATAATCTATAT
1 ATTAGTCACATATTTTAAATTCCAATAAAAAATCTATAT
20846 ATTA
1 ATTA
20850 CTATTATCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.92
40 3 0.08
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (39 bp):
ATTAGTCACATATTTTAAATTCCAATAAAAAATCTATAT
Found at i:21322 original size:17 final size:17
Alignment explanation
Indices: 21290--21389 Score: 61
Period size: 16 Copynumber: 5.9 Consensus size: 17
21280 TCTATTTTAA
*
21290 TATATTTA-AAATATTT
1 TATATTTATATATATTT
21306 TATATTTATATATATTTT
1 TATATTTATATATA-TTT
* *
21324 TAAAATATTCATAT-TTTTT
1 T---ATATTTATATATATTT
21343 TATA-TTATATTATATTT
1 TATATTTATA-TATATTT
21360 TATA--TA-ATAT-TTT
1 TATATTTATATATATTT
*
21373 AATTATTTATATATATT
1 TA-TATTTATATATATT
21390 ATATTTGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
13 4 0.06
14 5 0.08
15 5 0.08
16 16 0.24
17 16 0.24
18 6 0.09
19 4 0.06
20 1 0.02
21 9 0.14
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTATATATATTT
Found at i:21332 original size:37 final size:37
Alignment explanation
Indices: 21284--21393 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 37
21274 TTTTATTCTA
* *
21284 TTTTAATATATTTAAAATATTTTATATTTATATATAT
1 TTTTAAAATATTTAAATTATTTTATATTTATATATAT
* * *
21321 TTTTAAAATATTCATATTTTTTTATA-TTATATTATAT
1 TTTTAAAATATTTAAATTATTTTATATTTATA-TATAT
* *
21358 TTTATATAATATTTTAATTATTTATATATATTATAT
1 TTT-TAAAATATTTAAATTATTT-TATAT-TTATAT
21394 TTGAATTAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
36 5 0.09
37 29 0.50
38 14 0.24
39 4 0.07
40 1 0.02
41 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTTAAAATATTTAAATTATTTTATATTTATATATAT
Found at i:21346 original size:27 final size:28
Alignment explanation
Indices: 21284--21348 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
21274 TTTTATTCTA
* * *
21284 TTTTAATATATTTAAAATATTTTATATT
1 TTTTTATATTTTTAAAATATTTCATATT
* *
21312 TATATATATTTTTAAAATA-TTCATATT
1 TTTTTATATTTTTAAAATATTTCATATT
21339 TTTTTATATT
1 TTTTTATATT
21349 ATATTATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTATATTTTTAAAATATTTCATATT
Found at i:21352 original size:5 final size:5
Alignment explanation
Indices: 21328--21394 Score: 52
Period size: 5 Copynumber: 14.0 Consensus size: 5
21318 TATTTTTAAA
* * * * *
21328 ATATT CATATT TTTTT ATATT ATATT ATATT TTA-T ATAAT ATTTT A-ATT
1 ATATT -ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
21377 AT-TT ATA-T ATATT ATATT
1 ATATT ATATT ATATT ATATT
21395 TGAATTAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
4 14 0.29
5 29 0.60
6 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (5 bp):
ATATT
Found at i:24938 original size:2 final size:2
Alignment explanation
Indices: 24929--24962 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
24919 TATTCTTTTT
*
24929 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24963 TAAACACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28163 original size:325 final size:326
Alignment explanation
Indices: 27572--28552 Score: 1928
Period size: 326 Copynumber: 3.0 Consensus size: 326
27562 CTTCACCTGG
*
27572 ACTCATTAAAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
1 ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
*
27637 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAAAACAAAC
66 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAGAACAAAC
27702 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
131 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
27767 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
196 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
27832 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
261 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
27897 C
326 C
27898 ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
1 ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
*
27963 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAATAT-AAAAAATGCCAAGAACAAAC
66 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAGAACAAAC
28027 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
131 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
28092 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
196 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
28157 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
261 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
28222 C
326 C
28223 ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
1 ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
28288 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAGAACAAAC
66 GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAGAACAAAC
28353 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
131 ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
28418 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
196 CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
28483 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
261 GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
28548 C
326 C
28549 ACTC
1 ACTC
28553 CCTCAAGTCC
Statistics
Matches: 650, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
325 323 0.50
326 327 0.50
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (326 bp):
ACTCATTAGAGTTCCACATTCTATCCATTCTCTAAGTTAACATTGTTCATCATGTACAATGGCAT
GCATGTACACCACAATTGATAAGTCAAAAACAATAGCCAAAGATAAAAAAATGCCAAGAACAAAC
ACATCAACTAACTCCCACACCAAATCCATACAGGACTAGACTGATGCTTTTTCTCCAACTCTTCA
CTTCAATTTTCCAGACGTATCCATGTTTGACACATCTGACACCTCAAATTGGCGGGGCTTATGCA
GTCTTGACCCTCCAAATAAAAGGTAAAAACTTAGCCTACATGTCTTAAAACATACTAATATCCTA
C
Found at i:31919 original size:3 final size:3
Alignment explanation
Indices: 31911--31964 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
31901 CATCATAAAC
31911 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31959 ATT ATT
1 ATT ATT
31965 GCACATTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:37975 original size:21 final size:20
Alignment explanation
Indices: 37949--37988 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
37939 ATTTAAAAAA
*
37949 ATATTTTATATTAATATTTAT
1 ATATTTTAAATTAA-ATTTAT
37970 ATATTTTAAATTAAATTTA
1 ATATTTTAAATTAAATTTA
37989 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTTAAATTAAATTTAT
Found at i:40275 original size:2 final size:2
Alignment explanation
Indices: 40268--40300 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40258 CAAAGATGTG
40268 AT AT 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 AT AT A
40301 CACACGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42848 original size:28 final size:28
Alignment explanation
Indices: 42812--42867 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
42802 TAATTATCAA
42812 TAAAAATAATT-TTAAATT-AAATTTTAT
1 TAAAAATAATTATT-AATTAAAATTTTAT
*
42839 TAAATAATAATTATTTATTAAAATTTTAT
1 TAAA-AATAATTATTAATTAAAATTTTAT
42868 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 10 0.40
29 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAAAATAATTATTAATTAAAATTTTAT
Found at i:43711 original size:21 final size:22
Alignment explanation
Indices: 43687--43734 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
43677 TAAATTCATC
43687 ATTTAAAAATAA-AATAAAATA
1 ATTTAAAAATAATAATAAAATA
43708 ATTTAAAAATAATTAATAAAATA
1 ATTTAAAAATAA-TAATAAAATA
43731 ATTT
1 ATTT
43735 TTGAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTTAAAAATAATAATAAAATA
Found at i:43730 original size:12 final size:12
Alignment explanation
Indices: 43699--43733 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
43689 TTAAAAATAA
43699 AATAAAATAATT
1 AATAAAATAATT
*
43711 TA-AAAATAATT
1 AATAAAATAATT
43722 AATAAAATAATT
1 AATAAAATAATT
43734 TTTGAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAAAATAATT
Found at i:43777 original size:18 final size:19
Alignment explanation
Indices: 43750--43785 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
43740 TTAATATTTT
43750 TAAATATATTAATTAAAAA
1 TAAATATATTAATTAAAAA
43769 TAAAT-TATTAATTAAAA
1 TAAATATATTAATTAAAA
43786 TTGAAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATATATTAATTAAAAA
Found at i:44496 original size:34 final size:33
Alignment explanation
Indices: 44448--44668 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
44438 TGGTAAAAAC
*
44448 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
44481 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
44515 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
44549 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
44583 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
44617 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
44651 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
44669 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:44564 original size:68 final size:67
Alignment explanation
Indices: 44450--44668 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
44440 GTAAAAACCA
* * *
44450 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
44515 CAC
65 CAC
* * * *
44518 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
44583 CTC
65 CAC
* * * * *
44586 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
44651 CA-
65 CAC
44653 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
44669 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:44592 original size:102 final size:101
Alignment explanation
Indices: 44448--44668 Score: 361
Period size: 102 Copynumber: 2.2 Consensus size: 101
44438 TGGTAAAAAC
* *
44448 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
44513 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
44549 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
44614 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
44651 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
44669 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:48761 original size:19 final size:19
Alignment explanation
Indices: 48734--48796 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
48724 TCACGTGTAC
* *
48734 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
48753 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
***
48772 AGTACATATATACGTGAAT
1 AGTACCCGTATACGTGAAT
48791 AGTACC
1 AGTACC
48797 TCGACAACCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:49142 original size:34 final size:33
Alignment explanation
Indices: 49094--49313 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 33
49084 TGGTAAAAAC
*
49094 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
49127 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
49161 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
49195 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
49229 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
49263 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
49297 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
49314 ATTAGGCTTC
Statistics
Matches: 159, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 132 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:49210 original size:68 final size:67
Alignment explanation
Indices: 49096--49313 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 67
49086 GTAAAAACCA
* * *
49096 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
49161 CAC
65 CAC
* * * *
49164 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
49229 CTC
65 CAC
* * * * *
49232 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
49297 CA-
65 CAC
49299 CCATTTAATCAACAA
1 CCATTTAATCAACAA
49314 ATTAGGCTTC
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 16 0.12
68 113 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:49273 original size:102 final size:101
Alignment explanation
Indices: 49094--49313 Score: 359
Period size: 102 Copynumber: 2.2 Consensus size: 101
49084 TGGTAAAAAC
* *
49094 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
49159 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
49195 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
49260 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
49297 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
49314 ATTAGGCTTC
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:49864 original size:13 final size:12
Alignment explanation
Indices: 49846--49894 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
49836 TTTTGTTAAA
49846 TATATAAATATTT
1 TATATAAATA-TT
49859 TATATAAATA-T
1 TATATAAATATT
*
49870 TAAATAAATATT
1 TATATAAATATT
*
49882 AATAT-AATATT
1 TATATAAATATT
49893 TA
1 TA
49895 ATATTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 17 0.55
12 4 0.13
13 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATAAATATT
Found at i:49897 original size:22 final size:24
Alignment explanation
Indices: 49849--49897 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
49839 TGTTAAATAT
*
49849 ATAAATATTTTATATAAATATTAA
1 ATAAATATTTAATATAAATATTAA
*
49873 ATAAATA-TTAATAT-AATATTTA
1 ATAAATATTTAATATAAATATTAA
49895 ATA
1 ATA
49898 TTTAATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 6 0.26
24 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATATTTAATATAAATATTAA
Found at i:49936 original size:68 final size:66
Alignment explanation
Indices: 49816--49954 Score: 149
Period size: 68 Copynumber: 2.1 Consensus size: 66
49806 TTTTAATTTA
* * * *
49816 AATAAATATTTATATTATAATTTTGTTAAATATATAAATATTTTATATAAATATTAAAT-AAATA
1 AATAAATATTTATATTATAATTTAGTTAAATATATAAATATTTTAAAAAAATAAT-AATGAAATA
49880 TT
65 TT
* * *
49882 AATATAATATTTAATATT-TAATTTCAG-TATAATATATAATTTTTTTAAAAAAATAATAATGTA
1 AATA-AATATTT-ATATTATAATTT-AGTTA-AATATATAAATATTTTAAAAAAATAATAATGAA
49945 ATATT
62 ATATT
49950 AATAA
1 AATAA
49955 TTTTTTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
66 4 0.07
67 19 0.31
68 38 0.62
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (66 bp):
AATAAATATTTATATTATAATTTAGTTAAATATATAAATATTTTAAAAAAATAATAATGAAATAT
T
Found at i:50210 original size:20 final size:20
Alignment explanation
Indices: 50187--50236 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
50177 ATAAAGTAAT
50187 AAAATTAAAATTAAAATTTA
1 AAAATTAAAATTAAAATTTA
*** *
50207 AAAATTATTTTTAATATTTA
1 AAAATTAAAATTAAAATTTA
*
50227 AAAAATAAAA
1 AAAATTAAAA
50237 AAATAAATTT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTAAAATTAAAATTTA
Found at i:50315 original size:21 final size:20
Alignment explanation
Indices: 50291--50361 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
50281 ATATTAAAAT
50291 TATATTAAATATAAATAATAA
1 TATATTAAATAT-AATAATAA
* *
50312 TATATAAAATAT-TTAATAA
1 TATATTAAATATAATAATAA
* * *
50331 TA-AATAAAAATAATAATAT
1 TATATTAAATATAATAATAA
50350 TATAATTAAATA
1 TAT-ATTAAATA
50362 CTACTCTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
21 17 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATTAAATATAATAATAA
Found at i:50319 original size:38 final size:35
Alignment explanation
Indices: 50277--50354 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 35
50267 ATTTTATTTA
*
50277 ATAAATATTAAAATTATATTAAATATAAATAATAATA-T
1 ATAAATATT-AAA-TA-A-TAAATAAAAATAATAATATT
*
50315 ATAAAATATTTAATAATAAATAAAAATAATAATATT
1 AT-AAATATTAAATAATAAATAAAAATAATAATATT
50351 ATAA
1 ATAA
50355 TTAAATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
35 19 0.53
36 4 0.11
37 2 0.06
38 4 0.11
39 7 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (35 bp):
ATAAATATTAAATAATAAATAAAAATAATAATATT
Found at i:50344 original size:16 final size:16
Alignment explanation
Indices: 50275--50348 Score: 67
Period size: 16 Copynumber: 4.3 Consensus size: 16
50265 ATATTTTATT
*
50275 TAATAAATATTAAAATTA
1 TAATAAATA--AAAATAA
* *
50293 TATTAAATATAAATAA
1 TAATAAATAAAAATAA
*
50309 TAATATATAAAATATTTAA
1 TAATAAATAAAA-A--TAA
50328 TAATAAATAAAAATAA
1 TAATAAATAAAAATAA
50344 TAATA
1 TAATA
50349 TTATAATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
16 22 0.48
17 1 0.02
18 9 0.20
19 14 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAAATAAAAATAA
Found at i:50347 original size:19 final size:18
Alignment explanation
Indices: 50304--50348 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
50294 ATTAAATATA
*
50304 AATAATAATATATAAAAT
1 AATAATAATAAATAAAAT
*
50322 ATTTAATAATAAATAAAAAT
1 A-ATAATAATAAAT-AAAAT
50342 AATAATA
1 AATAATA
50349 TTATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAATAAATAAAAT
Found at i:50360 original size:19 final size:18
Alignment explanation
Indices: 50302--50361 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
50292 ATATTAAATA
*
50302 TAAATAATAATATATAAAA
1 TAAATAATAATATAT-AAT
** *
50321 TATTTAATAATAAATAA-
1 TAAATAATAATATATAAT
50338 -AAATAATAATATTATAAT
1 TAAATAATAATA-TATAAT
50356 TAAATA
1 TAAATA
50362 CTACTCTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 9 0.28
17 4 0.12
18 2 0.06
19 17 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATAATAATATATAAT
Found at i:51237 original size:19 final size:19
Alignment explanation
Indices: 51213--51251 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
51203 TGAATCAATC
51213 TCTCATGGATCTATATTTT
1 TCTCATGGATCTATATTTT
*
51232 TCTCATGGATCTCTATTTT
1 TCTCATGGATCTATATTTT
51251 T
1 T
51252 TCACTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (19 bp):
TCTCATGGATCTATATTTT
Found at i:52005 original size:6 final size:6
Alignment explanation
Indices: 51985--52022 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
51975 TTGATAAAAT
**
51985 TTTAAA TTTTTA TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
52023 AATTAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:53469 original size:2 final size:2
Alignment explanation
Indices: 53462--53507 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
53452 TGACTTGAAT
53462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TGA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
53503 TA TA T
1 TA TA T
53508 TAATTAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57617 original size:6 final size:6
Alignment explanation
Indices: 57600--57657 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
57590 TTGGTAAAAA
* *
57600 TTTAATT TTTAAT TTTAAAT TATAAAAT TTAAAAT TTTAAT TTTAAT TTTAAT
1 TTTAA-T TTTAAT TTT-AAT T-T-TAAT TT-TAAT TTTAAT TTTAAT TTTAAT
57653 TTTAA
1 TTTAA
57658 ATTAAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
6 24 0.52
7 17 0.37
8 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTAAT
Found at i:58412 original size:16 final size:16
Alignment explanation
Indices: 58387--58422 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
58377 TTTTTATTTC
58387 TTTTAAAATA-AAATA
1 TTTTAAAATATAAATA
58402 TTTTAAAAATATAAATA
1 TTTT-AAAATATAAATA
58419 TTTT
1 TTTT
58423 TCGCTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAATATAAATA
Found at i:58610 original size:19 final size:19
Alignment explanation
Indices: 58582--58618 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58572 CTTAGATTTA
* *
58582 TATTTGTTTAAGTTTAAAT
1 TATTTATTTAAATTTAAAT
58601 TATTTATTTAAATTTAAA
1 TATTTATTTAAATTTAAA
58619 AATTAAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTTATTTAAATTTAAAT
Found at i:60834 original size:30 final size:31
Alignment explanation
Indices: 60776--60834 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
60766 TTGTTATTTG
* * *
60776 ATTGAATTTTGTTGCTTAATTTTAATTTTTT
1 ATTGAATTTTGTTACTCAAATTTAATTTTTT
*
60807 ATTGAA-TTTGTTACTCAAATTTGATTTT
1 ATTGAATTTTGTTACTCAAATTTAATTTT
60835 GAAAGATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (31 bp):
ATTGAATTTTGTTACTCAAATTTAATTTTTT
Found at i:60869 original size:20 final size:20
Alignment explanation
Indices: 60844--60890 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
60834 TGAAAGATTT
60844 GAAGATAAAATTAATTTATA
1 GAAGATAAAATTAATTTATA
60864 GAAGAT-AAATTAATTTATA
1 GAAGATAAAATTAATTTATA
*
60883 GAATATAA
1 GAAGATAA
60891 GAACAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (20 bp):
GAAGATAAAATTAATTTATA
Found at i:61188 original size:17 final size:17
Alignment explanation
Indices: 61166--61198 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61156 ATATAATGAT
61166 AAATATCAATAA-AAATA
1 AAATAT-AATAATAAATA
61183 AAATATAATAATAAAT
1 AAATATAATAATAAAT
61199 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATATAATAATAAATA
Found at i:62392 original size:23 final size:24
Alignment explanation
Indices: 62347--62392 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
62337 ATCGTATGCG
**
62347 TTATATTTTAAATTTTTAATAATT
1 TTATATTTTAAATTAATAATAATT
*
62371 TTATA-TTTAAATTAATAGTAAT
1 TTATATTTTAAATTAATAATAAT
62393 GGGTTCGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATTTTAAATTAATAATAATT
Found at i:63817 original size:28 final size:28
Alignment explanation
Indices: 63750--63834 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
63740 TTTAATTTTT
*
63750 TATAATTTTTAATTATTAATTAAAAATAA
1 TATAAGTTTTAATT-TTAATTAAAAATAA
63779 TATAAGTTTTAATTTT-ATTAAATAATAA
1 TATAAGTTTTAATTTTAATTAAA-AATAA
* * *
63807 T-TAGGTATTTAAATTTTTATTTAAAATA
1 TATAAGT-TTT-AATTTTAATTAAAAATA
63835 GGTTATAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 10 0.20
28 11 0.22
29 23 0.47
30 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TATAAGTTTTAATTTTAATTAAAAATAA
Found at i:64880 original size:22 final size:20
Alignment explanation
Indices: 64855--64898 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
64845 TACATAAAAT
*
64855 AAAATAAATTATTAATATATAA
1 AAAAT-AATTA-TAAAATATAA
64877 AAAATAATTATAAAATATAA
1 AAAATAATTATAAAATATAA
64897 AA
1 AA
64899 TTTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 5 0.24
22 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATAATTATAAAATATAA
Found at i:64898 original size:18 final size:22
Alignment explanation
Indices: 64853--64899 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 22
64843 TATACATAAA
64853 ATAAAATAAATTATTAATATAT
1 ATAAAATAAATTATTAATATAT
*
64875 AAAAAAT-AATTA-TAA-A-AT
1 ATAAAATAAATTATTAATATAT
64893 ATAAAAT
1 ATAAAAT
64900 TTTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 3 0.13
21 5 0.22
22 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAAATAAATTATTAATATAT
Found at i:64973 original size:16 final size:15
Alignment explanation
Indices: 64934--64973 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
64924 AAATATATAA
64934 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
*
64949 TTTTCTTTTCATTTTC
1 TTTTTTTTTC-TTTTC
64965 TTTTTTTTT
1 TTTTTTTTT
64974 TCAACCTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:64974 original size:5 final size:5
Alignment explanation
Indices: 64934--64972 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
64924 AAATATATAA
*
64934 TTTTT TTTTC TTTTC TTTTC TTTTC ATTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTT
64973 TTCAACCTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:64974 original size:11 final size:11
Alignment explanation
Indices: 64934--64975 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
64924 AAATATATAA
64934 TTTTTTTTTC-
1 TTTTTTTTTCT
*
64944 TTTTCTTTTCT
1 TTTTTTTTTCT
**
64955 TTTCATTTTCT
1 TTTTTTTTTCT
64966 TTTTTTTTTC
1 TTTTTTTTTC
64976 AACCTACCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:65399 original size:4 final size:4
Alignment explanation
Indices: 65392--65435 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
65382 TAAATAAATT
65392 TTTA TTTA --TA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T
65436 GTTTCATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
4 31 0.84
5 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:65446 original size:11 final size:9
Alignment explanation
Indices: 65391--65446 Score: 71
Period size: 8 Copynumber: 6.1 Consensus size: 9
65381 ATAAATAAAT
65391 TTTTATTTA
1 TTTTATTTA
65400 TATTTATTTA
1 T-TTTATTTA
65410 -TTTATTTA
1 TTTTATTTA
65418 -TTTATTTA
1 TTTTATTTA
65426 TTTTATTTA
1 TTTTATTTA
65435 TGTTTCATTTA
1 T-TTT-ATTTA
65446 T
1 T
65447 ATTCATTAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.37
9 10 0.23
10 11 0.26
11 6 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:68887 original size:17 final size:18
Alignment explanation
Indices: 68860--68896 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
68850 CATTTTTAGG
68860 ATTAGGGGGTCGATTTTA
1 ATTAGGGGGTCGATTTTA
68878 ATTA-GGGGTCGATTTTA
1 ATTAGGGGGTCGATTTTA
68895 AT
1 AT
68897 CGGTCAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (18 bp):
ATTAGGGGGTCGATTTTA
Found at i:73666 original size:78 final size:77
Alignment explanation
Indices: 73560--73978 Score: 381
Period size: 78 Copynumber: 5.4 Consensus size: 77
73550 TATAATCTAA
** * * *
73560 ATGAAAGTTCATACATGACCTTGGAGACTTGATATTAATGTAATATCACCTAAGTAACTCTAATA
1 ATGAAAGTTCCCACATGACC-TAGAGACTTGATATTAATGTAATATCACCTAAATAACCCTAATA
* *
73625 GATATGTATCAAC
65 GACATGTATCGAC
* * * * * *
73638 ACGAAAGTTCACACACGATCCTAGAGACTTGATTTTAATGTAATATAACCTAAGTAACCCTAATA
1 ATGAAAGTTCCCACATGA-CCTAGAGACTTGATATTAATGTAATATCACCTAAATAACCCTAATA
* *
73703 AACATATATCGAC
65 GACATGTATCGAC
* * * *
73716 ATGAAAGTTCCCACATGACTTTAGAGACTTGGTATTAATATAATATCACCT-AATAAGCCTTAAT
1 ATGAAAGTTCCCACATGAC-CTAGAGACTTGATATTAATGTAATATCACCTAAATAA-CCCTAAT
*
73780 AGACATGTCTCGAC
64 AGACATGTATCGAC
* *** * * * * * *
73794 ATAAAAGTTTTTACATGACTCTAAAGACTCGATATTAATGTAATGTTACCAAAATAACCCTAATG
1 ATGAAAGTTCCCACATGAC-CTAGAGACTTGATATTAATGTAATATCACCTAAATAACCCTAATA
** *
73859 GACAAATATCAAC
65 GACATGTATCGAC
* * * * * * **
73872 ATAAAAGTTCCCACATGACCTTAGAGACTTGGTGTTAATGTGATATTACTTAAATAACTTTAATA
1 ATGAAAGTTCCCACATGACC-TAGAGACTTGATATTAATGTAATATCACCTAAATAACCCTAATA
73937 GACATGTATCGAC
65 GACATGTATCGAC
* *
73950 GTGAAAGTTCTCACATGACCCTAGAGACT
1 ATGAAAGTTCCCACATGA-CCTAGAGACT
73979 CGAATAAAAT
Statistics
Matches: 273, Mismatches: 62, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
77 6 0.02
78 258 0.95
79 9 0.03
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (77 bp):
ATGAAAGTTCCCACATGACCTAGAGACTTGATATTAATGTAATATCACCTAAATAACCCTAATAG
ACATGTATCGAC
Found at i:73852 original size:156 final size:155
Alignment explanation
Indices: 73560--73981 Score: 479
Period size: 156 Copynumber: 2.7 Consensus size: 155
73550 TATAATCTAA
** * *
73560 ATGAAAGTTCATACATGACCTTGGAGACTTGATATTAATGTAATATCACCTAAGTAA-CTCTAAT
1 ATGAAAGTTCCCACATGACCTTAGAGACTTGGTATTAATGTAATATCACCTAA-TAACCT-TAAT
* * * * * * *
73624 AGATATGTATCAACACGAAAGTTCACACACGA-TCCTAGAGACTTGATTTTAATGTAATATAACC
64 AGACATGTATCGACATGAAAGTTCTCACATGACT-CTAGAGACTCGATATTAATGTAATATAACC
* * * *
73688 TAAGTAACCCTAATAAACATATATCGAC
128 AAAATAACCCTAATAAACAAATATCAAC
* *
73716 ATGAAAGTTCCCACATGACTTTAGAGACTTGGTATTAATATAATATCACCTAATAAGCCTTAATA
1 ATGAAAGTTCCCACATGACCTTAGAGACTTGGTATTAATGTAATATCACCTAATAA-CCTTAATA
* * * * * * *
73781 GACATGTCTCGACATAAAAGTTTTTACATGACTCTAAAGACTCGATATTAATGTAATGTTACCAA
65 GACATGTATCGACATGAAAGTTCTCACATGACTCTAGAGACTCGATATTAATGTAATATAACCAA
**
73846 AATAACCCTAATGGACAAATATCAAC
130 AATAACCCTAATAAACAAATATCAAC
* * * * * *
73872 ATAAAAGTTCCCACATGACCTTAGAGACTTGGTGTTAATGTGATATTACTTAAATAACTTTAATA
1 ATGAAAGTTCCCACATGACCTTAGAGACTTGGTATTAATGTAATATCACCT-AATAACCTTAATA
* *
73937 GACATGTATCGACGTGAAAGTTCTCACATGACCCTAGAGACTCGA
65 GACATGTATCGACATGAAAGTTCTCACATGACTCTAGAGACTCGA
73982 ATAAAATAAC
Statistics
Matches: 221, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
155 3 0.01
156 210 0.95
157 8 0.04
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (155 bp):
ATGAAAGTTCCCACATGACCTTAGAGACTTGGTATTAATGTAATATCACCTAATAACCTTAATAG
ACATGTATCGACATGAAAGTTCTCACATGACTCTAGAGACTCGATATTAATGTAATATAACCAAA
ATAACCCTAATAAACAAATATCAAC
Found at i:74205 original size:60 final size:59
Alignment explanation
Indices: 74130--74241 Score: 134
Period size: 59 Copynumber: 1.9 Consensus size: 59
74120 TTAGACTATG
* * **
74130 TAAAATAACCCAAATGGCCTAAAAAATGTATGAAAATTGTTAAATGATCCCTAGATTGTA
1 TAAAATAACCCAAAT-GACTAAAAAATATATGAAAATTAATAAATGATCCCTAGATTGTA
** * **
74190 TAAAATAACTTAAATGATTGTAAAATATATGAAAATTAATAAATGATCCCTA
1 TAAAATAACCCAAATGACTAAAAAATATATGAAAATTAATAAATGATCCCTA
74242 ATATGAATGA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 30 0.70
60 13 0.30
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (59 bp):
TAAAATAACCCAAATGACTAAAAAATATATGAAAATTAATAAATGATCCCTAGATTGTA
Found at i:75942 original size:21 final size:21
Alignment explanation
Indices: 75909--75949 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
75899 CTAAGTAAAA
75909 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
75930 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
75950 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:76014 original size:20 final size:19
Alignment explanation
Indices: 75989--76059 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
75979 ACCCTGAAAA
75989 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
76009 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
76028 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
76049 GTATCGATACA
1 GTATCGATACA
76060 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:76155 original size:10 final size:10
Alignment explanation
Indices: 76136--76166 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
76126 AATCTCATTT
76136 TCACTGTTCA
1 TCACTGTTCA
*
76146 TCACTATTCA
1 TCACTGTTCA
76156 TCACTGTTCA
1 TCACTGTTCA
76166 T
1 T
76167 GTATCGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:76182 original size:22 final size:22
Alignment explanation
Indices: 76154--76210 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
76144 CATCACTATT
*
76154 CATCACTGTTCATGTATCGATG
1 CATCACTGTTCATGTATCGATA
*
76176 CATCACTTTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
76198 CATCACTGTTCAT
1 CATCACTGTTCAT
76211 AGGTCACTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:76318 original size:13 final size:13
Alignment explanation
Indices: 76300--76325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76290 ACATATTTGT
76300 GTGTATCGATACA
1 GTGTATCGATACA
76313 GTGTATCGATACA
1 GTGTATCGATACA
76326 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:76867 original size:34 final size:35
Alignment explanation
Indices: 76804--76870 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
76794 CTAAGTGATT
76804 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
76840 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
76871 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:78558 original size:84 final size:84
Alignment explanation
Indices: 78385--78545 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 84
78375 ACTCAAAGAA
* * * * * *
78385 GAAAATAAATCAATAAGTGTAGAGAATGATTTTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
*
78450 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
78469 GAAAATAAATCAATGAGTTTAGAAAATAATTCTT-TTAAAAAGAAAATAAATGAAATAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATT-TTCTTAAAAAGAAAATAAATGAAATAGAGAAGA
78533 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
78546 GCAAGTGGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 5 0.08
84 58 0.89
85 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:79717 original size:18 final size:18
Alignment explanation
Indices: 79682--79719 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79672 TTAAATGATT
* *
79682 TTTTTTTTCAATTTTTGA
1 TTTTTTTTCAAATATTGA
79700 TTTTTTTTCAAATATTGA
1 TTTTTTTTCAAATATTGA
79718 TT
1 TT
79720 AATCTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTTTTCAAATATTGA
Found at i:80080 original size:13 final size:13
Alignment explanation
Indices: 80062--80086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80052 TTTTCCAGAT
80062 TGTATCGATACAA
1 TGTATCGATACAA
80075 TGTATCGATACA
1 TGTATCGATACA
80087 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:80921 original size:30 final size:32
Alignment explanation
Indices: 80885--80952 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
80875 GGGTGACAAC
* *
80885 GTATTAAGGGGGAGAGTTTGTATAAA-TTTT-
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
80915 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
80947 GTATTA
1 GTATTA
80953 GTTGTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 24 0.71
31 4 0.12
32 6 0.18
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (32 bp):
GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
Found at i:81713 original size:21 final size:21
Alignment explanation
Indices: 81680--81720 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
81670 CTAAGTAAAA
81680 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
81701 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
81721 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:81785 original size:20 final size:19
Alignment explanation
Indices: 81760--81830 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
81750 ACCCTGAAAA
81760 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
81780 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
81799 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
81820 GTATCGATACA
1 GTATCGATACA
81831 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:81926 original size:10 final size:10
Alignment explanation
Indices: 81907--81937 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
81897 AATCTCATTT
81907 TCACTGTTCA
1 TCACTGTTCA
*
81917 TCACTATTCA
1 TCACTGTTCA
81927 TCACTGTTCA
1 TCACTGTTCA
81937 T
1 T
81938 GTATCGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:81953 original size:22 final size:22
Alignment explanation
Indices: 81925--81981 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
81915 CATCACTATT
*
81925 CATCACTGTTCATGTATCGATG
1 CATCACTGTTCATGTATCGATA
*
81947 CATCACTTTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
81969 CATCACTGTTCAT
1 CATCACTGTTCAT
81982 AGGTCACTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:82089 original size:13 final size:13
Alignment explanation
Indices: 82071--82096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82061 ACATATTTGT
82071 GTGTATCGATACA
1 GTGTATCGATACA
82084 GTGTATCGATACA
1 GTGTATCGATACA
82097 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:82638 original size:34 final size:35
Alignment explanation
Indices: 82575--82641 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
82565 CTAAGTGATT
82575 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
82611 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
82642 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Done.