Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 13 of 14
Found at i:1428930 original size:20 final size:18
Alignment explanation
Indices: 1428811--1428949 Score: 80
Period size: 16 Copynumber: 7.8 Consensus size: 18
1428801 TTTATACATG
1428811 TATTTGTATTAT-TTT-TA
1 TATTT-TATTATATTTATA
* * *
1428828 TATTATAATAATATTTAAA
1 TATT-TTATTATATTTATA
*
1428847 GTATTATA-TATATTTATA
1 -TATTTTATTATATTTATA
*
1428865 TAAATTTTAATATA-TTA-A
1 T--ATTTTATTATATTTATA
*
1428883 TAATTTA-TATA-TTATA
1 TATTTTATTATATTTATA
*
1428899 TATTTTAATATATTTATA
1 TATTTTATTATATTTATA
1428917 TATTTTGTATTATATTTAT-
1 TA-TTT-TATTATATTTATA
*
1428936 T-TTATATTATATTT
1 TATTTTATTATATTT
1428950 TAATTTATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 25
0.73 0.09 0.19
Matches are distributed among these distances:
15 7 0.07
16 22 0.22
17 15 0.15
18 21 0.21
19 14 0.14
20 19 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTTTATTATATTTATA
Found at i:1432291 original size:111 final size:108
Alignment explanation
Indices: 1432132--1432351 Score: 386
Period size: 111 Copynumber: 2.0 Consensus size: 108
1432122 TGGGGTTCTA
*
1432132 TAGGTTTTTGCTGCATTATGTTGTTTAGCTTTGTTTGCTCATGAAGTGGCCAGGGGTAATGAACA
1 TAGGTTTTTGCTGCATTATGTTGTTTAGCTGTGTTTGCTCATGAAGTGGCCAGGGGTAATGAACA
1432197 TATCATCTTTAGTTGTAATTGCTGCTACAATCCCAAACTTGTTCAG
66 TATCATCTTTAGTTGTAATTGCTG---CAATCCCAAACTTGTTCAG
*
1432243 TAGGTTTTTGCTGCATTATGTTGTTTAGCTGTGTTTGCTCATGGAGTGGCCAGGGGTAATGAACA
1 TAGGTTTTTGCTGCATTATGTTGTTTAGCTGTGTTTGCTCATGAAGTGGCCAGGGGTAATGAACA
*
1432308 TTTCATCTTTAGTTGTAATTGCTGCAATCCCAAACTTGTTCAG
66 TATCATCTTTAGTTGTAATTGCTGCAATCCCAAACTTGTTCAG
1432351 T
1 T
1432352 TTGGGAATTG
Statistics
Matches: 106, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
108 20 0.19
111 86 0.81
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (108 bp):
TAGGTTTTTGCTGCATTATGTTGTTTAGCTGTGTTTGCTCATGAAGTGGCCAGGGGTAATGAACA
TATCATCTTTAGTTGTAATTGCTGCAATCCCAAACTTGTTCAG
Found at i:1432446 original size:21 final size:21
Alignment explanation
Indices: 1432420--1432461 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1432410 GAGCCCAGGA
*
1432420 AGACCATTTAGTTTATCATGT
1 AGACCATTTAGTTTACCATGT
1432441 AGACCATTTAGTTTACCATGT
1 AGACCATTTAGTTTACCATGT
1432462 TGTAGGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (21 bp):
AGACCATTTAGTTTACCATGT
Found at i:1434155 original size:2 final size:2
Alignment explanation
Indices: 1434148--1434191 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1434138 TTAGCATACC
1434148 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1434190 CT
1 CT
1434192 TTTTTCATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1436583 original size:77 final size:77
Alignment explanation
Indices: 1436455--1436599 Score: 245
Period size: 77 Copynumber: 1.9 Consensus size: 77
1436445 ACAAAAGCTT
* *
1436455 TGGTAAAACAGCAATTCATTTTTCCAATGCTGCAATGTATGTATGTCTGTATGTATGTTTATGTG
1 TGGTAAAACAGCAATTCATTTTTCCAATGCTGCAATGTATGTATGTATGTATGTATGTCTATGTG
1436520 TGTGTGTGTTTG
66 TGTGTGTGTTTG
* * *
1436532 TGGTAAAACAGCAATTCATTTTTCCAATGCTGCTATGTATGTATGTATGTATGTCTGTCTGTGTG
1 TGGTAAAACAGCAATTCATTTTTCCAATGCTGCAATGTATGTATGTATGTATGTATGTCTATGTG
1436597 TGT
66 TGT
1436600 ATTAAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (77 bp):
TGGTAAAACAGCAATTCATTTTTCCAATGCTGCAATGTATGTATGTATGTATGTATGTCTATGTG
TGTGTGTGTTTG
Found at i:1437361 original size:24 final size:24
Alignment explanation
Indices: 1437334--1437400 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 24
1437324 TTGATAAAAC
*
1437334 TTAAATTTGATTTTTTATTTAATT
1 TTAAATTTGATTTTTTATTTAAGT
*
1437358 TTAAATTTGATTATTTATATTTGAGT
1 TTAAATTTGATT-TTT-TATTTAAGT
*
1437384 TTAAATTGAGATTTTTT
1 TTAAATT-TGATTTTTT
1437401 TTAATAGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.32
25 4 0.11
26 17 0.46
27 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (24 bp):
TTAAATTTGATTTTTTATTTAAGT
Found at i:1440044 original size:17 final size:18
Alignment explanation
Indices: 1440008--1440076 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 18
1439998 TATTTAAAAT
* *
1440008 ATTTTATAT-TTAAATAA
1 ATTTTAAATATTATATAA
1440025 ATTTTAATATATTA-AT-A
1 ATTTTAA-ATATTATATAA
1440042 A-TTTAAA-ATTATATAA
1 ATTTTAAATATTATATAA
1440058 ATTTTAAAATATTTATATA
1 ATTTT-AAATA-TTATATA
1440077 TTCATATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
14 4 0.09
15 3 0.07
16 7 0.16
17 11 0.26
18 7 0.16
19 4 0.09
20 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAATATTATATAA
Found at i:1440112 original size:29 final size:27
Alignment explanation
Indices: 1440049--1440112 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
1440039 ATAATTTAAA
1440049 ATTATATAAATTTTAAAATATTTATAT
1 ATTATATAAATTTTAAAATATTTATAT
* * *
1440076 ATTCATATCAAATTTTAATTATTTTTATGT
1 ATT-ATAT-AAATTTTAA-AATATTTATAT
1440106 ATTATAT
1 ATTATAT
1440113 TTATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 3 0.10
28 4 0.13
29 13 0.42
30 11 0.35
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTATATAAATTTTAAAATATTTATAT
Found at i:1440590 original size:21 final size:22
Alignment explanation
Indices: 1440556--1440597 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1440546 TAAAATTTTA
1440556 AAAAATAAATAAATTAATTAAT
1 AAAAATAAATAAATTAATTAAT
*
1440578 AAAAATTAA-AAATTAATTAA
1 AAAAATAAATAAATTAATTAA
1440598 ATTTTGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAATAAATAAATTAATTAAT
Found at i:1440874 original size:4 final size:4
Alignment explanation
Indices: 1440865--1440891 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1440855 CAACTTTGAA
1440865 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1440892 ATCTCATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1442133 original size:20 final size:21
Alignment explanation
Indices: 1442101--1442152 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
1442091 AGTTGAATTA
1442101 ATTTAATTAAAAATATTATTT
1 ATTTAATTAAAAATATTATTT
*
1442122 ATTTAA-TAAAAATTTTATTT
1 ATTTAATTAAAAATATTATTT
1442142 AAATTTAATTA
1 --ATTTAATTA
1442153 TAATATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 13 0.48
21 6 0.22
22 6 0.22
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATTAAAAATATTATTT
Found at i:1442336 original size:30 final size:26
Alignment explanation
Indices: 1442282--1442345 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1442272 TTAGTTAAAA
* *
1442282 TAAAAAAATTTTTATTTTTATTATAT
1 TAAATAAATTTTTATTTTAATTATAT
1442308 GTAAATAAATTTTTAATATTTAATTTATAT
1 -TAAATAAATTTTT-AT-TTTAA-TTATAT
*
1442338 CAAATAAA
1 TAAATAAA
1442346 CTATTAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 12 0.39
28 2 0.06
29 11 0.35
30 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAATAAATTTTTATTTTAATTATAT
Found at i:1442440 original size:27 final size:28
Alignment explanation
Indices: 1442402--1442459 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1442392 TTTTTAATTT
1442402 AAAATAAGAATTT-TTTAAATA-AATTAA
1 AAAATAAGAATTTATTTAAATATAA-TAA
*
1442429 AAAATAATAATTTATTTAAATATAATAA
1 AAAATAAGAATTTATTTAAATATAATAA
1442457 AAA
1 AAA
1442460 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 12 0.43
28 14 0.50
29 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATAAGAATTTATTTAAATATAATAA
Found at i:1442831 original size:12 final size:12
Alignment explanation
Indices: 1442804--1442836 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1442794 GTCACTTATA
1442804 ATTTAAATTTTT
1 ATTTAAATTTTT
1442816 -TTTAAATTTTT
1 ATTTAAATTTTT
1442827 ATTT-AATTTT
1 ATTTAAATTTT
1442837 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTAAATTTTT
Found at i:1442966 original size:14 final size:14
Alignment explanation
Indices: 1442924--1442966 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1442914 AATTTTTTTT
1442924 ATTTTTAATAATTAA
1 ATTTTTAATAA-TAA
*
1442939 A-TTTAAATAA-AA
1 ATTTTTAATAATAA
1442951 ATTTTTAATAATAA
1 ATTTTTAATAATAA
1442965 AT
1 AT
1442967 AATAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 12 0.50
15 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTTAATAATAA
Found at i:1443605 original size:8 final size:7
Alignment explanation
Indices: 1443531--1443604 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
1443521 TTAAATGAAT
1443531 ATATATA
1 ATATATA
1443538 A-A-ATA
1 ATATATA
*
1443543 AGATAT-
1 ATATATA
1443549 ATATAT-
1 ATATATA
1443555 ATATATGA
1 ATATAT-A
1443563 ATATATA
1 ATATATA
*
1443570 AGT-TATT
1 A-TATATA
1443577 ATATATAA
1 ATATAT-A
*
1443585 ATACATA
1 ATATATA
1443592 ATATATA
1 ATATATA
1443599 AT-TATA
1 ATATATA
1443605 TTACATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
5 4 0.07
6 18 0.33
7 21 0.38
8 12 0.22
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:1443807 original size:49 final size:49
Alignment explanation
Indices: 1443750--1443845 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
1443740 GCACTCAAGT
* *
1443750 TTGTGAGGAAGATAAGGACCTACACAAATTTAGTTGGACCATTTTCGCA
1 TTGTGAGGAAGATAAGGACCTACACAAACTTACTTGGACCATTTTCGCA
1443799 TTGTGAGGAAGATAAGGACCTACACAAACTTACTTGGACCATTTTCG
1 TTGTGAGGAAGATAAGGACCTACACAAACTTACTTGGACCATTTTCG
1443846 TATACTTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (49 bp):
TTGTGAGGAAGATAAGGACCTACACAAACTTACTTGGACCATTTTCGCA
Found at i:1444752 original size:22 final size:22
Alignment explanation
Indices: 1444724--1444770 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1444714 GATTAAATGA
*
1444724 TGATTTGGTAGTTTGTCATTAT
1 TGATTTGGTAGTTTATCATTAT
* *
1444746 TGATTTGGTGGTTTATCATTGT
1 TGATTTGGTAGTTTATCATTAT
1444768 TGA
1 TGA
1444771 CTAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.04, G:0.26, T:0.53
Consensus pattern (22 bp):
TGATTTGGTAGTTTATCATTAT
Found at i:1444828 original size:34 final size:34
Alignment explanation
Indices: 1444790--1444895 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 34
1444780 AACTTTGGTA
*
1444790 GTTTGTTATTGTTGATTAAATGGGTGATTTAGTG
1 GTTTGTCATTGTTGATTAAATGGGTGATTTAGTG
* * * * ** * *
1444824 GTTTGTCATTCTTGACTAAAAGTGAAATTTAATA
1 GTTTGTCATTGTTGATTAAATGGGTGATTTAGTG
* * *
1444858 GTGTGCCATTGTTGATTAAATGGGTGATTTGGTG
1 GTTTGTCATTGTTGATTAAATGGGTGATTTAGTG
1444892 GTTT
1 GTTT
1444896 TTACCTAACC
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (34 bp):
GTTTGTCATTGTTGATTAAATGGGTGATTTAGTG
Found at i:1449346 original size:22 final size:22
Alignment explanation
Indices: 1449318--1449364 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1449308 GATTAAATGG
1449318 TGATTTGGTAGTTTACCATTGT
1 TGATTTGGTAGTTTACCATTGT
* *
1449340 TGATTTGGTGGTTTGCCATTGT
1 TGATTTGGTAGTTTACCATTGT
1449362 TGA
1 TGA
1449365 CTAAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.49
Consensus pattern (22 bp):
TGATTTGGTAGTTTACCATTGT
Found at i:1449422 original size:34 final size:34
Alignment explanation
Indices: 1449340--1449489 Score: 142
Period size: 34 Copynumber: 4.4 Consensus size: 34
1449330 TTACCATTGT
*
1449340 TGATTTGGTGGTTTGCCATTGTTGACTAAAT-GA
1 TGATTTGGTGGTTTGCCATTGTTGACTAAATGGG
** *
1449373 AAATTTTGGTAGTTTGCCATTGTTGA-TGAAATGGG
1 TGA-TTTGGTGGTTTGCCATTGTTGACT-AAATGGG
* * *
1449408 TGATTGGGTGGTTTGCTATTGTTGACTAAAAGGG
1 TGATTTGGTGGTTTGCCATTGTTGACTAAATGGG
** * * * * *
1449442 AAATTTGATAGTTTGACATTATTGATTAAATGGG
1 TGATTTGGTGGTTTGCCATTGTTGACTAAATGGG
1449476 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
1449490 TTACCTAACC
Statistics
Matches: 89, Mismatches: 24, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
33 2 0.02
34 84 0.94
35 3 0.03
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (34 bp):
TGATTTGGTGGTTTGCCATTGTTGACTAAATGGG
Found at i:1449454 original size:68 final size:68
Alignment explanation
Indices: 1449340--1449489 Score: 212
Period size: 68 Copynumber: 2.2 Consensus size: 68
1449330 TTACCATTGT
* * * *
1449340 TGATTTGGTGGTTTGCCATTGTTGACTAAATGAAAATTTTGGTAGTTTGCCATTGTTGATGAAAT
1 TGATTTGGTGGTTTGCCATTGTTGACTAAAGGAAAATTTTGATAGTTTGACATTATTGATGAAAT
1449405 GGG
66 GGG
* * * *
1449408 TGATTGGGTGGTTTGCTATTGTTGACTAAAAGGGAAA-TTTGATAGTTTGACATTATTGATTAAA
1 TGATTTGGTGGTTTGCCATTGTTGACT-AAAGGAAAATTTTGATAGTTTGACATTATTGATGAAA
1449472 TGGG
65 TGGG
1449476 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
1449490 TTACCTAACC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 65 0.90
69 7 0.10
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (68 bp):
TGATTTGGTGGTTTGCCATTGTTGACTAAAGGAAAATTTTGATAGTTTGACATTATTGATGAAAT
GGG
Found at i:1450396 original size:23 final size:23
Alignment explanation
Indices: 1450365--1450413 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1450355 GATCAAGAAA
* *
1450365 TTTATTTTTGATTTTTTTGGATT
1 TTTAGTTTTGAATTTTTTGGATT
*
1450388 TTTAGTTTTGAATTTTTTGGTTT
1 TTTAGTTTTGAATTTTTTGGATT
1450411 TTT
1 TTT
1450414 GTGAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.14, T:0.73
Consensus pattern (23 bp):
TTTAGTTTTGAATTTTTTGGATT
Found at i:1451071 original size:21 final size:21
Alignment explanation
Indices: 1451045--1451085 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1451035 GATTTATTGA
*
1451045 TTTATTAAAATTATTATTTAT
1 TTTATTAAAAATATTATTTAT
*
1451066 TTTATTAAAAATATTTTTTA
1 TTTATTAAAAATATTATTTA
1451086 AATTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTAAAAATATTATTTAT
Found at i:1451132 original size:21 final size:21
Alignment explanation
Indices: 1451100--1451150 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1451090 TTATAATTAA
*
1451100 ATTTAAA-TAAAAATATATT-
1 ATTTAAATTAAAAAAATATTG
*
1451119 ATTTAAATTAAAAAAATTTTG
1 ATTTAAATTAAAAAAATATTG
*
1451140 AATTAAATTAA
1 ATTTAAATTAA
1451151 GTCAACACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAAATTAAAAAAATATTG
Found at i:1451865 original size:90 final size:90
Alignment explanation
Indices: 1451702--1451875 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
1451692 ATTAATATTA
* * *
1451702 AATTTTATTTGATAGAAAAATATTAATTCTACCTTATATTTAGATTTGCTCATTGATTGAATCAT
1 AATTTTATTTGATAAAAAAATATTAATTCTACCTTACATTTAGATTTGCTCATTGATTGAATCAG
1451767 CCCCAAATAAGATATTAACTGCTAT
66 CCCCAAATAAGATATTAACTGCTAT
*
1451792 AATTTTATTTGATAAAAAAATATTAATTCTACTTTACATTTAGATTTGCTCATTGATTGAATCAG
1 AATTTTATTTGATAAAAAAATATTAATTCTACCTTACATTTAGATTTGCTCATTGATTGAATCAG
****
1451857 GTTTAAATAAGATATTAAC
66 CCCCAAATAAGATATTAAC
1451876 ACTTTATAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (90 bp):
AATTTTATTTGATAAAAAAATATTAATTCTACCTTACATTTAGATTTGCTCATTGATTGAATCAG
CCCCAAATAAGATATTAACTGCTAT
Found at i:1452699 original size:17 final size:18
Alignment explanation
Indices: 1452677--1452722 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1452667 TTAGCAATTT
1452677 AAATAATTAAAATTTT-A
1 AAATAATTAAAATTTTAA
**
1452694 AAATAATTTTAATTTTAA
1 AAATAATTAAAATTTTAA
1452712 AAATAATTAAA
1 AAATAATTAAA
1452723 TAATTACAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAATTAAAATTTTAA
Found at i:1452749 original size:31 final size:30
Alignment explanation
Indices: 1452711--1452795 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 30
1452701 TTTAATTTTA
1452711 AAAATAATTAAATAATTACAATCCTTAATAT
1 AAAATAATTAAA-AATTACAATCCTTAATAT
* *
1452742 AAAATAATT--AAATTAC-AGCCTTAATTT
1 AAAATAATTAAAAATTACAATCCTTAATAT
*
1452769 AAAATAATTAAACAATTACAATACTTA
1 AAAATAATTAAA-AATTACAATCCTTA
1452796 GGAATTAGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 18 0.39
28 6 0.13
29 2 0.04
30 6 0.13
31 14 0.30
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAATAATTAAAAATTACAATCCTTAATAT
Found at i:1452938 original size:25 final size:23
Alignment explanation
Indices: 1452904--1452979 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 23
1452894 AATTAATCTA
1452904 AATAAATAAATTTATTGTCATTAAT
1 AATAAATAAATTTATT-T-ATTAAT
* *
1452929 AATAAATAAAATAATTT-TTAAT
1 AATAAATAAATTTATTTATTAAT
*
1452951 AATAAA-AAATATTATTATATTTAT
1 AATAAATAAAT-TTATT-TATTAAT
1452975 AATAA
1 AATAA
1452980 TATTATCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 3 0.07
22 15 0.35
23 1 0.02
24 10 0.23
25 14 0.33
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
AATAAATAAATTTATTTATTAAT
Found at i:1453150 original size:33 final size:32
Alignment explanation
Indices: 1453113--1453174 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1453103 GGTTTTAACA
* *
1453113 ATTTTTACGTAAA-ATTCATTAATCATTTTATTG
1 ATTTTTAAGTAAACA-T-ATTAATCAATTTATTG
1453146 ATTTTTAAGTAAACATATTAATCAATTTA
1 ATTTTTAAGTAAACATATTAATCAATTTA
1453175 ATATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 13 0.50
34 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTTTTAAGTAAACATATTAATCAATTTATTG
Found at i:1453257 original size:26 final size:27
Alignment explanation
Indices: 1453196--1453258 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
1453186 TATGAGTTAA
* *
1453196 AAAAATAATATTTTGATAATTTATTTC
1 AAAAATATTATTTTGATAATTTATGTC
*
1453223 AAGCTAATATTATTTTGATAATTTATGT-
1 AA--AAATATTATTTTGATAATTTATGTC
1453251 AAAAATAT
1 AAAAATAT
1453259 CGGTGTGCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 2 0.07
29 21 0.70
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (27 bp):
AAAAATATTATTTTGATAATTTATGTC
Found at i:1454572 original size:10 final size:8
Alignment explanation
Indices: 1454544--1454578 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1454534 ATTAAGTTAA
1454544 TTTAAATT
1 TTTAAATT
1454552 TTTAAATT
1 TTTAAATT
1454560 TTTAATTATT
1 TTTAA--ATT
1454570 TTTAAATT
1 TTTAAATT
1454578 T
1 T
1454579 AAATTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTAAATT
Found at i:1454583 original size:17 final size:18
Alignment explanation
Indices: 1454549--1454602 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1454539 GTTAATTTAA
*
1454549 ATTTTTAAATTTTTAATT
1 ATTTTTAAATTTTAAATT
1454567 ATTTTTAAA-TTTAAATT
1 ATTTTTAAATTTTAAATT
* *
1454584 A--ATTAAATTTTAATTT
1 ATTTTTAAATTTTAAATT
1454600 ATT
1 ATT
1454603 GAATTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.17
16 8 0.27
17 8 0.27
18 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTAAATTTTAAATT
Found at i:1454591 original size:15 final size:15
Alignment explanation
Indices: 1454522--1454608 Score: 52
Period size: 15 Copynumber: 5.7 Consensus size: 15
1454512 AAGCGAGTTC
* *
1454522 AATTAATTTTGAATT
1 AATTAAATTTAAATT
1454537 AAGTT-AATTTAAATT
1 AA-TTAAATTTAAATT
* *
1454552 -TTTAAATTTTTAATT
1 AATTAAA-TTTAAATT
*
1454567 ATTTTTAAATTTAAATT
1 A--ATTAAATTTAAATT
*
1454584 AATTAAATTTTAATT
1 AATTAAATTTAAATT
* *
1454599 TATTGAATTT
1 AATTAAATTT
1454609 GATTATTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 37 0.65
16 2 0.04
17 8 0.14
18 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
AATTAAATTTAAATT
Found at i:1454598 original size:21 final size:21
Alignment explanation
Indices: 1454561--1454600 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1454551 TTTTAAATTT
*
1454561 TTAATTATTTTTAAATTTAAA
1 TTAATTAATTTTAAATTTAAA
1454582 TTAATTAAATTTT-AATTTA
1 TTAATT-AATTTTAAATTTA
1454601 TTGAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTAATTTTAAATTTAAA
Found at i:1455621 original size:245 final size:245
Alignment explanation
Indices: 1455134--1455609 Score: 785
Period size: 245 Copynumber: 1.9 Consensus size: 245
1455124 ACAGCCAGAT
** *
1455134 ATGCCTGTGTGCTTCATAAGTATATTTCAATTTCTTTAAAAAATACACTCGTTGCCTCTGCATTA
1 ATGCCTGTGTGCTTCATAAGTATATTTCAACATCTTTAAAAAATACACTCGTTGCCTCTACATTA
* * * *
1455199 GTCTCCAGTAAGTATATTTCAATTTGTAGATTGTATTCATTTGTATTTTGCTTTTCATGTTGCAG
66 GTCTCCAGTAAGTATATTTCAATTTGTACATGGTATTCACTTGTATTTTGCCTTTCATGTTGCAG
* * *
1455264 AAAATAATTCAACTGTTCCTGTTATAAAAGTTGCAGGAGGTAATGTACATACTACATAGTCATCG
131 AAAATAATTCAACTGTTCATGTTATAAAAGTTGCAGCAGGTAATGTACATACTACATAGTCATCA
*
1455329 AGCTGATTTGTTTTCATCTTTAATTAGCAATTTAAACAGCAGTTACAAAA
196 AGCTGATTTGTTTTCATCTTCAATTAGCAATTTAAACAGCAGTTACAAAA
* *
1455379 ATGCCTGTGTGCTTCATAAGTATTTTTCAGCATCTTTAAAAAATACACTCGTTGCCTCTACATTA
1 ATGCCTGTGTGCTTCATAAGTATATTTCAACATCTTTAAAAAATACACTCGTTGCCTCTACATTA
*
1455444 GTCTCCAGTAAGTATATTTCAATTTGTTCATGGTATTCACTTGTATTTTGCCTTTCATGTTGCAG
66 GTCTCCAGTAAGTATATTTCAATTTGTACATGGTATTCACTTGTATTTTGCCTTTCATGTTGCAG
*
1455509 AAAATAATTCGACTGCTT-ATGTTATAAAAGTTGCAGCAGGTAATGTACATACTACATAGTCATC
131 AAAATAATTCAACTG-TTCATGTTATAAAAGTTGCAGCAGGTAATGTACATACTACATAGTCATC
1455573 AAGCTGATTTGTTTTCATCTTCAATTAG-AGATTTAAA
195 AAGCTGATTTGTTTTCATCTTCAATTAGCA-ATTTAAA
1455610 TGACAGTTAC
Statistics
Matches: 214, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
244 1 0.00
245 211 0.99
246 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (245 bp):
ATGCCTGTGTGCTTCATAAGTATATTTCAACATCTTTAAAAAATACACTCGTTGCCTCTACATTA
GTCTCCAGTAAGTATATTTCAATTTGTACATGGTATTCACTTGTATTTTGCCTTTCATGTTGCAG
AAAATAATTCAACTGTTCATGTTATAAAAGTTGCAGCAGGTAATGTACATACTACATAGTCATCA
AGCTGATTTGTTTTCATCTTCAATTAGCAATTTAAACAGCAGTTACAAAA
Found at i:1461552 original size:18 final size:19
Alignment explanation
Indices: 1461529--1461567 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1461519 AATTAAATAA
*
1461529 AAAAATATTTTTTTAA-TT
1 AAAAATATTATTTTAAGTT
1461547 AAAAATATTATTTTAAGTT
1 AAAAATATTATTTTAAGTT
1461566 AA
1 AA
1461568 GCCAAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAAAATATTATTTTAAGTT
Found at i:1462338 original size:12 final size:13
Alignment explanation
Indices: 1462314--1462347 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1462304 ATTAAACAAT
1462314 TTTTTTAATTTTA
1 TTTTTTAATTTTA
*
1462327 TTTTTTAATTTAA
1 TTTTTTAATTTTA
1462340 TATTTTTA
1 T-TTTTTA
1462348 TATAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTAATTTTA
Found at i:1463642 original size:2 final size:2
Alignment explanation
Indices: 1463637--1463669 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1463627 ATCTATCTTT
1463637 TA TA TA 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 TA TA TA T
1463670 TAAGTGAGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1463744 original size:17 final size:17
Alignment explanation
Indices: 1463701--1463745 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1463691 AGATTGAATT
1463701 AATTTGAATT-TTTTTA
1 AATTTGAATTATTTTTA
* *
1463717 ATTTTTAAATTATTTTTA
1 A-ATTTGAATTATTTTTA
1463735 AATTTGAATTA
1 AATTTGAATTA
1463746 ATTAAGTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
AATTTGAATTATTTTTA
Found at i:1468687 original size:16 final size:15
Alignment explanation
Indices: 1468647--1468688 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1468637 TATATAATTT
1468647 TAATAATA-AATAAC
1 TAATAATATAATAAC
*
1468661 TATTAAGTATAATAAC
1 TAATAA-TATAATAAC
1468677 TAATCAATATAA
1 TAAT-AATATAA
1468689 ATATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 14 0.61
17 2 0.09
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (15 bp):
TAATAATATAATAAC
Found at i:1468743 original size:23 final size:24
Alignment explanation
Indices: 1468702--1468751 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1468692 TATTTTTAAT
1468702 TAAATGTTATAATCTTTATTAAAA
1 TAAATGTTATAATCTTTATTAAAA
*
1468726 TAAATGTTCA-AATC-TTATTACAA
1 TAAATGTT-ATAATCTTTATTAAAA
1468749 TAA
1 TAA
1468752 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 11 0.46
24 12 0.50
25 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAATGTTATAATCTTTATTAAAA
Found at i:1472903 original size:20 final size:20
Alignment explanation
Indices: 1472878--1472915 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1472868 ATTTTTAATT
* *
1472878 ATAAAAATATATTAATATAA
1 ATAAAAAAAAATTAATATAA
1472898 ATAAAAAAAAATTAATAT
1 ATAAAAAAAAATTAATAT
1472916 TACTATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAAAAAATTAATATAA
Found at i:1473469 original size:22 final size:23
Alignment explanation
Indices: 1473438--1473501 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
1473428 ATTTTTAATT
1473438 TAAAT-TTAATTATAA-AATATA
1 TAAATATTAATTATAATAATATA
*
1473459 TAAATATTAA-TATAATAATATT
1 TAAATATTAATTATAATAATATA
*
1473481 TTAATATT-ATTATGAATAATA
1 TAAATATTAATTAT-AATAATA
1473502 AAATTGTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 11 0.30
22 19 0.51
23 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATATTAATTATAATAATATA
Found at i:1474326 original size:2 final size:2
Alignment explanation
Indices: 1474319--1474347 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1474309 AGAATGATAC
1474319 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
1474348 GTCACTGGTA
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:1474614 original size:13 final size:13
Alignment explanation
Indices: 1474598--1474656 Score: 68
Period size: 13 Copynumber: 4.6 Consensus size: 13
1474588 TAAGTAATCG
1474598 TAATAAATATTAA
1 TAATAAATATTAA
*
1474611 TAATAAATATAAA
1 TAATAAATATTAA
*
1474624 TAATAAATAATAA
1 TAATAAATATTAA
*
1474637 TTATAAA-A-TAA
1 TAATAAATATTAA
1474648 TAATTAAAT
1 TAA-TAAAT
1474657 TATAATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 29 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAAATATTAA
Found at i:1474629 original size:7 final size:7
Alignment explanation
Indices: 1474598--1474650 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
1474588 TAAGTAATCG
1474598 TAATAAA
1 TAATAAA
*
1474605 T-ATTAA
1 TAATAAA
1474611 TAATAAA
1 TAATAAA
1474618 T-ATAAA
1 TAATAAA
1474624 TAATAAA
1 TAATAAA
1474631 TAAT-AA
1 TAATAAA
*
1474637 TTATAAAA
1 TAAT-AAA
1474645 TAATAA
1 TAATAA
1474651 TTAAATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 16 0.42
7 17 0.45
8 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
TAATAAA
Found at i:1474853 original size:14 final size:14
Alignment explanation
Indices: 1474834--1474891 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1474824 AAAATATTAT
1474834 TAAAATTAATTATAA
1 TAAAA-TAATTATAA
*
1474849 T-AAAT-ATCTTTAA
1 TAAAATAAT-TATAA
*
1474862 TAAAAAAATTATAA
1 TAAAATAATTATAA
1474876 -AATAATAATTATAA
1 TAA-AATAATTATAA
1474890 TA
1 TA
1474892 TTATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.06
13 8 0.24
14 20 0.59
15 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATAATTATAA
Found at i:1475173 original size:7 final size:7
Alignment explanation
Indices: 1475142--1475184 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1475132 TATAATTTAT
1475142 TTTTAAA
1 TTTTAAA
*
1475149 ATTTAATA
1 TTTTAA-A
*
1475157 TTTAATAA
1 TTTTA-AA
1475165 TTTTAAA
1 TTTTAAA
1475172 TTTTAAA
1 TTTTAAA
1475179 TTTTAA
1 TTTTAA
1475185 TATTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 20 0.67
8 9 0.30
9 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTTAAA
Found at i:1475193 original size:14 final size:15
Alignment explanation
Indices: 1475143--1475196 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 15
1475133 ATAATTTATT
1475143 TTTAAAA-TTTAATA
1 TTTAAAATTTTAATA
1475157 TTTAATAATTTTAA-A
1 TTTAA-AATTTTAATA
*
1475172 TTTTAAATTTTAATA
1 TTTAAAATTTTAATA
1475187 -TTAAAATTTT
1 TTTAAAATTTT
1475197 TATTATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 22 0.63
15 8 0.23
16 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAAATTTTAATA
Found at i:1475400 original size:13 final size:12
Alignment explanation
Indices: 1475376--1475438 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1475366 AAAAATTACA
1475376 ATTAATTTTTAT
1 ATTAATTTTTAT
1475388 ATTAATATTTTAT
1 ATTAAT-TTTTAT
1475401 A-T-ATTTTTAT
1 ATTAATTTTTAT
* *
1475411 AATTAA-ATTTAA
1 -ATTAATTTTTAT
* *
1475423 ATAAATTTTTTT
1 ATTAATTTTTAT
1475435 ATTA
1 ATTA
1475439 TTAAATAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
10 6 0.15
11 7 0.18
12 18 0.46
13 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTAATTTTTAT
Found at i:1475430 original size:24 final size:23
Alignment explanation
Indices: 1475379--1475438 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1475369 AATTACAATT
*
1475379 AATTTTTATATTAATATTTTATA
1 AATTTTTATATTAATATTTAATA
*
1475402 TATTTTTATAATTAA-ATTTAAATA
1 AATTTTTAT-ATTAATATTT-AATA
*
1475426 AATTTTTTTATTA
1 AATTTTTATATTA
1475439 TTAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTTATATTAATATTTAATA
Found at i:1475907 original size:23 final size:23
Alignment explanation
Indices: 1475881--1475954 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 23
1475871 ATAAAATTAT
1475881 TAATTATTATATTTAATATAATA
1 TAATTATTATATTTAATATAATA
**
1475904 TAATTATATTATAAGTAATAT-AT-
1 TAA-T-TATTATATTTAATATAATA
*
1475927 TAATT-TAAT-TTTAA-ATAATA
1 TAATTATTATATTTAATATAATA
1475947 T-ATTATTA
1 TAATTATTA
1475955 AATTATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 6 0.15
21 1 0.03
22 1 0.03
23 6 0.15
24 3 0.08
25 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TAATTATTATATTTAATATAATA
Found at i:1475911 original size:20 final size:19
Alignment explanation
Indices: 1475881--1475935 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1475871 ATAAAATTAT
1475881 TAAT-TATTATATTTAATA
1 TAATATATTATATTTAATA
*
1475899 TAATATAATTATATTATAA-G
1 TAATAT-ATTATATT-TAATA
1475919 TAATATATTA-ATTTAAT
1 TAATATATTATATTTAAT
1475936 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 7 0.22
19 5 0.16
20 14 0.44
21 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATATATTATATTTAATA
Found at i:1476381 original size:20 final size:19
Alignment explanation
Indices: 1476333--1476370 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1476323 TTACAATTAA
*
1476333 AATTAATTTAAAAATAAAT
1 AATTAAATTAAAAATAAAT
*
1476352 AATTACATTAAAAATAAAT
1 AATTAAATTAAAAATAAAT
1476371 TTAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTAAATTAAAAATAAAT
Found at i:1480897 original size:2 final size:2
Alignment explanation
Indices: 1480827--1480888 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
1480817 TCATATCTTG
*
1480827 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
1480869 CT CA CT CT CT TT CG CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
1480889 GTTTCTCTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.02, C:0.47, G:0.03, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1485700 original size:24 final size:24
Alignment explanation
Indices: 1485679--1485735 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1485669 TCATATATAG
**
1485679 ATATTTTTTATTTAATAAATATTA
1 ATATTTTTTAAATAATAAATATTA
1485703 ATATTTTTTAAATAATAAA-A-TA
1 ATATTTTTTAAATAATAAATATTA
1485725 A-A-TTTTTAAAT
1 ATATTTTTTAAAT
1485736 TTTTTCTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 1 0.03
22 3 0.10
23 1 0.03
24 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTTTTAAATAATAAATATTA
Found at i:1486311 original size:19 final size:19
Alignment explanation
Indices: 1486287--1486325 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1486277 ATTTTCTTTA
*
1486287 CTTTACTGTACTCTTAATT
1 CTTTACTGTACTATTAATT
*
1486306 CTTTACTGTAGTATTAATT
1 CTTTACTGTACTATTAATT
1486325 C
1 C
1486326 AATGATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (19 bp):
CTTTACTGTACTATTAATT
Found at i:1487234 original size:2 final size:2
Alignment explanation
Indices: 1487227--1487256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1487217 AGACATGAAC
1487227 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
1487257 GCCACACCCA
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:1489568 original size:2 final size:2
Alignment explanation
Indices: 1489561--1489596 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1489551 TTTTCCACAA
1489561 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
1489597 GAATCATGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1490367 original size:3 final size:3
Alignment explanation
Indices: 1490359--1490416 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
1490349 CAACCAATTT
*
1490359 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1490407 ATA ATA ATA A
1 ATA ATA ATA A
1490417 AGCATACGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1491879 original size:15 final size:15
Alignment explanation
Indices: 1491846--1491911 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
1491836 ATTGTTTCAT
*
1491846 TATTTAAAAATTAATTA
1 TATTTAATAATT-A-TA
*
1491863 TATTTAATATTTATA
1 TATTTAATAATTATA
* *
1491878 TATTTTATAATTAAA
1 TATTTAATAATTATA
*
1491893 T-TTTAATAAATATA
1 TATTTAATAATTATA
1491907 TATTT
1 TATTT
1491912 TATTAATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.28
15 18 0.45
16 1 0.03
17 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAATAATTATA
Found at i:1491906 original size:29 final size:30
Alignment explanation
Indices: 1491855--1491922 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
1491845 TTATTTAAAA
* **
1491855 ATTAATTATA-TTTAATATTTATATATTTT
1 ATTAATTAAATTTTAATAAATATATATTTT
1491884 A-TAATTAAATTTTAATAAATATATATTTT
1 ATTAATTAAATTTTAATAAATATATATTTT
1491913 ATTAA-TAAAT
1 ATTAATTAAAT
1491923 AATAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 24 0.71
30 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTAATTAAATTTTAATAAATATATATTTT
Found at i:1491919 original size:19 final size:19
Alignment explanation
Indices: 1491895--1491955 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1491885 TAATTAAATT
*
1491895 TTAATAAATATATATTTTA
1 TTAATAAATATATAATTTA
1491914 TTAATAAATA-ATAATTTA
1 TTAATAAATATATAATTTA
1491932 --AACTAAATATATTAAATTTA
1 TTAA-TAAATATA-T-AATTTA
1491952 TTAA
1 TTAA
1491956 ATTTTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 6 0.17
18 8 0.23
19 11 0.31
20 6 0.17
22 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATAAATATATAATTTA
Found at i:1493448 original size:20 final size:21
Alignment explanation
Indices: 1493415--1493462 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1493405 CATCATCAAC
* *
1493415 ATTTTATTAGTATT-TAAATA
1 ATTTTTTTAATATTATAAATA
* *
1493435 ATTTTTTTAATATTATTAATC
1 ATTTTTTTAATATTATAAATA
1493456 ATTTTTT
1 ATTTTTT
1493463 ATTTACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTTTTTAATATTATAAATA
Found at i:1493725 original size:2 final size:2
Alignment explanation
Indices: 1493718--1493771 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1493708 ACATTCGAGC
1493718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1493760 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1493772 ATTTAGTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1494903 original size:19 final size:19
Alignment explanation
Indices: 1494879--1494921 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1494869 TGAATTTAAT
*
1494879 TTTAATA-TAAATAATCAAA
1 TTTAATATTAAAT-ATAAAA
1494898 TTTAATATTAAATATAAAA
1 TTTAATATTAAATATAAAA
1494917 TTTAA
1 TTTAA
1494922 AATTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATATTAAATATAAAA
Found at i:1495040 original size:8 final size:8
Alignment explanation
Indices: 1495027--1495099 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 8
1495017 AACTTAAATT
1495027 TTTATATA
1 TTTATATA
1495035 TTTATATA
1 TTTATATA
1495043 TTTATTAATA
1 TTTA-T-ATA
1495053 TTTTTATATA
1 --TTTATATA
1495063 TTT-T-TA
1 TTTATATA
1495069 -TTA-ATA
1 TTTATATA
*
1495075 ATTA-ATA
1 TTTATATA
1495082 -TTATATA
1 TTTATATA
1495089 TTTATATA
1 TTTATATA
1495097 TTT
1 TTT
1495100 TTTAATTTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
5 2 0.04
6 7 0.12
7 10 0.18
8 25 0.45
9 1 0.02
10 6 0.11
11 1 0.02
12 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:1496660 original size:16 final size:16
Alignment explanation
Indices: 1496606--1496663 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
1496596 TGGAGTTGTC
1496606 TTAAATT-TTTTAATTT
1 TTAAATTATTTTAA-TT
**
1496622 TTAAATTATTTTTAAGC
1 TTAAATTA-TTTTAATT
*
1496639 TCAAATTATTTTAATT
1 TTAAATTATTTTAATT
1496655 TTAAATTAT
1 TTAAATTAT
1496664 AATATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 21 0.62
17 7 0.21
18 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTTAATT
Found at i:1496691 original size:9 final size:9
Alignment explanation
Indices: 1496679--1496704 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1496669 AAAAATTAAA
1496679 AAATTTTAT
1 AAATTTTAT
1496688 AAATTTTAT
1 AAATTTTAT
1496697 AAATTTTA
1 AAATTTTA
1496705 AATTTAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAATTTTAT
Found at i:1496757 original size:18 final size:17
Alignment explanation
Indices: 1496719--1496758 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1496709 TAGTAAATAA
*
1496719 ATTTTTTTTAATTTCTG
1 ATTTTTTTTAATTTCTC
*
1496736 ATTTATTTTTAATTTGTC
1 ATTT-TTTTTAATTTCTC
1496754 ATTTT
1 ATTTT
1496759 AGATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (17 bp):
ATTTTTTTTAATTTCTC
Found at i:1498406 original size:25 final size:26
Alignment explanation
Indices: 1498366--1498414 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1498356 GATTCATAAA
*
1498366 TTTATTTTATTGTTAA-ATAATTAATT
1 TTTATTTAATTGTTAACA-AATTAATT
1498392 TTTATTTAATT-TTAACAAATTAA
1 TTTATTTAATTGTTAACAAATTAA
1498415 ACATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTATTTAATTGTTAACAAATTAATT
Found at i:1498472 original size:24 final size:25
Alignment explanation
Indices: 1498417--1498472 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1498407 CAAATTAAAC
1498417 ATATAAATAGTATTAAAATATTAAT
1 ATATAAATAGTATTAAAATATTAAT
* * * *
1498442 ATA-AAATATTTTTAATATTTTAAT
1 ATATAAATAGTATTAAAATATTAAT
1498466 A-ATAAAT
1 ATATAAAT
1498473 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 22 0.85
25 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATAAATAGTATTAAAATATTAAT
Found at i:1499536 original size:12 final size:12
Alignment explanation
Indices: 1499496--1499538 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1499486 TATTAATAAC
1499496 TAATATTTATTA
1 TAATATTTATTA
* *
1499508 TAATTAATTATAA
1 TAA-TATTTATTA
*
1499521 TAATATTTATTT
1 TAATATTTATTA
1499533 TAATAT
1 TAATAT
1499539 AAAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAATATTTATTA
Found at i:1500252 original size:24 final size:26
Alignment explanation
Indices: 1500221--1500272 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
1500211 TACTCATATT
1500221 TATATTTATTATA-AT-TAATTATAA
1 TATATTTATTATATATGTAATTATAA
*
1500245 TATATTTATTATATTTGTAATTATAA
1 TATATTTATTATATATGTAATTATAA
1500271 TA
1 TA
1500273 AATAAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.52
25 1 0.04
26 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TATATTTATTATATATGTAATTATAA
Found at i:1501572 original size:21 final size:20
Alignment explanation
Indices: 1501521--1501572 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1501511 ATTAGATTAG
*
1501521 ATTTAAATTAATTTAAAAATA
1 ATTTAAATT-ATTTAAAAAAA
**
1501542 ATTTTTATTATTTAAATAAAA
1 ATTTAAATTATTTAAA-AAAA
1501563 ATTTAAATTA
1 ATTTAAATTA
1501573 AATAAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATTATTTAAAAAAA
Found at i:1501581 original size:15 final size:14
Alignment explanation
Indices: 1501551--1501593 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1501541 AATTTTTATT
1501551 ATTT-AAAT-AAAA
1 ATTTAAAATAAAAA
*
1501563 ATTTAAATTAAATAA
1 ATTTAAAATAAA-AA
1501578 ATTTAAAATAAAAA
1 ATTTAAAATAAAAA
1501592 AT
1 AT
1501594 ATATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 6 0.23
15 13 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTTAAAATAAAAA
Found at i:1501706 original size:16 final size:16
Alignment explanation
Indices: 1501681--1501742 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
1501671 AATTTAAATT
*
1501681 TAAATTTTAAAAATAA
1 TAAATATTAAAAATAA
*
1501697 TAAATATTAATAATAAA
1 TAAATATTAAAAAT-AA
*
1501714 AAAATTAAATTATAAAATAA
1 TAAA-T--ATTA-AAAATAA
1501734 TAAATATTA
1 TAAATATTA
1501743 TATCATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
16 12 0.33
17 9 0.25
18 1 0.03
19 1 0.03
20 9 0.25
21 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATATTAAAAATAA
Found at i:1502145 original size:20 final size:19
Alignment explanation
Indices: 1502117--1502154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1502107 ATTTAATAAA
1502117 TTTTAAATTTATTTTTAAT
1 TTTTAAATTTATTTTTAAT
*
1502136 TTTTATAATTTTTTTTTAA
1 TTTTA-AATTTATTTTTAA
1502155 AAAAAACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAAATTTATTTTTAAT
Found at i:1503673 original size:33 final size:35
Alignment explanation
Indices: 1503617--1503681 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
1503607 ATAAATTAAA
1503617 ATAAATATTAAATATAATTGATAATTAATAAATAT
1 ATAAATATTAAATATAATTGATAATTAATAAATAT
*
1503652 ATAAAT-TT-AATTTAATTGATAATTAATAAA
1 ATAAATATTAAATATAATTGATAATTAATAAA
1503682 AATTAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 21 0.72
34 2 0.07
35 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (35 bp):
ATAAATATTAAATATAATTGATAATTAATAAATAT
Found at i:1503689 original size:21 final size:19
Alignment explanation
Indices: 1503663--1503705 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1503653 TAAATTTAAT
*
1503663 TTAATTGATAATTAATAAAAA
1 TTAATTAATAA-T-ATAAAAA
*
1503684 TTAATTAATCATATAAAAA
1 TTAATTAATAATATAAAAA
1503703 TTA
1 TTA
1503706 TTTTTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 1 0.05
21 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAATTAATAATATAAAAA
Found at i:1503727 original size:23 final size:22
Alignment explanation
Indices: 1503704--1503756 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1503694 ATATAAAAAT
1503704 TATTTTTTATCAACTCAATT-A
1 TATTTTTTATCAACTCAATTAA
* *
1503725 -ATTTTTTATCAATTCGATTAA
1 TATTTTTTATCAACTCAATTAA
1503746 TATTCTTTTAT
1 TATT-TTTTAT
1503757 ATACCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 17 0.63
21 1 0.04
22 3 0.11
23 6 0.22
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTTATCAACTCAATTAA
Found at i:1503730 original size:20 final size:20
Alignment explanation
Indices: 1503701--1503746 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1503691 ATCATATAAA
1503701 AATT-ATTTTTTATCAACTC
1 AATTAATTTTTTATCAACTC
*
1503720 AATTAATTTTTTATCAATTC
1 AATTAATTTTTTATCAACTC
*
1503740 GATTAAT
1 AATTAAT
1503747 ATTCTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTAATTTTTTATCAACTC
Found at i:1504466 original size:33 final size:32
Alignment explanation
Indices: 1504424--1504523 Score: 98
Period size: 35 Copynumber: 3.0 Consensus size: 32
1504414 GAAAGGAGAA
*
1504424 AAAAAATTATGTATTTGTAT-TATTTTTTTATAT
1 AAAATATTAT-TATTT-TATATATTTTTTTATAT
1504457 AAAATATTA-TATTTTTATATATTTTTTCTATATT
1 AAAATATTATTA-TTTTATATATTTTTT-TATA-T
*
1504491 AATAAT-TTATTTATTTTATATATATTTTTATAT
1 AA-AATATTA-TTATTTTATATATTTTTTTATAT
1504524 GTACATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
31 5 0.09
32 11 0.19
33 13 0.22
34 10 0.17
35 17 0.29
36 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (32 bp):
AAAATATTATTATTTTATATATTTTTTTATAT
Found at i:1504489 original size:26 final size:24
Alignment explanation
Indices: 1504460--1504523 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 24
1504450 TTTATATAAA
*
1504460 ATATTATATTTTTATATATTTTTTCT
1 ATATTATATTTTTATAT-TTATTT-T
**
1504486 ATATTA-ATAATT-TATTTATTTT
1 ATATTATATTTTTATATTTATTTT
1504508 ATA-TATATTTTTATAT
1 ATATTATATTTTTATAT
1504524 GTACATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
21 2 0.06
22 8 0.26
23 8 0.26
24 3 0.10
25 4 0.13
26 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATTATATTTTTATATTTATTTT
Found at i:1504536 original size:37 final size:36
Alignment explanation
Indices: 1504469--1504557 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 36
1504459 AATATTATAT
*
1504469 TTTTATATATTTTTTCTATATTAATAATTTAT-TTA
1 TTTTATATATATTTTCTATATTAATAATTTATATTA
1504504 TTTTATATATATTTT-TATATGTACATATATTTATATTA
1 TTTTATATATATTTTCTATAT-TA-ATA-ATTTATATTA
*
1504542 TGTGTATAT-TATTTTC
1 T-TTTATATATATTTTC
1504558 AAGTAATGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
34 5 0.11
35 16 0.35
36 3 0.07
37 6 0.13
38 10 0.22
39 6 0.13
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (36 bp):
TTTTATATATATTTTCTATATTAATAATTTATATTA
Found at i:1504691 original size:24 final size:23
Alignment explanation
Indices: 1504647--1504692 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1504637 TTTTTACACG
* *
1504647 TTAATTATTTATTTATCTATATT
1 TTAATTATTCATGTATCTATATT
*
1504670 TTAATATATTCATGTATTTATAT
1 TTAAT-TATTCATGTATCTATAT
1504693 CGTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAATTATTCATGTATCTATATT
Found at i:1505224 original size:49 final size:50
Alignment explanation
Indices: 1505164--1505289 Score: 129
Period size: 49 Copynumber: 2.6 Consensus size: 50
1505154 ATTTAAAATA
* * *
1505164 TTATTTATATATATATTTTTATATATTAATAAT-T-TATTTTA-TTTTATG
1 TTATTTTTATATATATTTTTATATAAT-ATAATGTGTATATTATTTTTATG
* *
1505212 TATATTTTTATATATATGTGTAT-TAATATAATGTGTATATTATTTTTATG
1 T-TATTTTTATATATATTTTTATATAATATAATGTGTATATTATTTTTATG
*
1505262 TTATATTTTAAATAT-TTTTTATA-AATAT
1 TTAT-TTTTATATATATTTTTATATAATAT
1505290 TTTTTATGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.08
48 5 0.08
49 37 0.58
50 17 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (50 bp):
TTATTTTTATATATATTTTTATATAATATAATGTGTATATTATTTTTATG
Found at i:1505648 original size:33 final size:34
Alignment explanation
Indices: 1505603--1505667 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1505593 GTCTTAATTT
* * *
1505603 ATTTTATATTTTATATAAATTTTTTATATATTAA
1 ATTTTATATTTTAAATAAATTTATTAAATATTAA
*
1505637 ATTTTA-ATTTTAAATATATTTATTAAATATT
1 ATTTTATATTTTAAATAAATTTATTAAATATT
1505668 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
ATTTTATATTTTAAATAAATTTATTAAATATTAA
Found at i:1505838 original size:30 final size:30
Alignment explanation
Indices: 1505802--1505864 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1505792 TTTTTATATA
*
1505802 TTATATTTATATTTA-AAATATTATATAAAT
1 TTATATTTA-ATTTACAAATAATATATAAAT
* *
1505832 TTATATTTAATTTACTATTAATATATAAAT
1 TTATATTTAATTTACAAATAATATATAAAT
1505862 TTA
1 TTA
1505865 AATAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TTATATTTAATTTACAAATAATATATAAAT
Found at i:1505937 original size:23 final size:23
Alignment explanation
Indices: 1505902--1505946 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1505892 TATTACATAA
1505902 ATTTTAATATAAATATATATTTTT
1 ATTTTAATATAAAT-TATATTTTT
*
1505926 ATTTT-ATTTAAATTATATTTT
1 ATTTTAATATAAATTATATTTT
1505947 AATTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTAATATAAATTATATTTTT
Found at i:1506739 original size:16 final size:16
Alignment explanation
Indices: 1506714--1506747 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1506704 TTTTAAAATT
* *
1506714 TATATTTACATATAAA
1 TATATATACACATAAA
1506730 TATATATACACATAAA
1 TATATATACACATAAA
1506746 TA
1 TA
1506748 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATATACACATAAA
Found at i:1506852 original size:18 final size:18
Alignment explanation
Indices: 1506823--1506863 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
1506813 AAAAAATAAA
*
1506823 ATTAAAATATAT-TA-AT
1 ATTAATATATATATATAT
1506839 ATTAATATATATATATAT
1 ATTAATATATATATATAT
1506857 ATTAATA
1 ATTAATA
1506864 CTAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATATATATATATAT
Found at i:1506871 original size:26 final size:25
Alignment explanation
Indices: 1506828--1506904 Score: 93
Period size: 26 Copynumber: 3.1 Consensus size: 25
1506818 ATAAAATTAA
* * * *
1506828 AATATATTAATATTAATATATATAT
1 AATATATTAATACTAAAATAAAAAT
1506853 -ATATATTAATACTAAAATAAAAAT
1 AATATATTAATACTAAAATAAAAAT
*
1506877 AACAATATTAATACTAAAATAAAAAT
1 AA-TATATTAATACTAAAATAAAAAT
1506903 AA
1 AA
1506905 CAATATTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.44
25 1 0.02
26 24 0.53
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATATTAATACTAAAATAAAAAT
Found at i:1506905 original size:26 final size:26
Alignment explanation
Indices: 1506855--1506911 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1506845 ATATATATAT
1506855 ATATTAATACTAAAATAAAAATAACA
1 ATATTAATACTAAAATAAAAATAACA
1506881 ATATTAATACTAAAATAAAAATAACA
1 ATATTAATACTAAAATAAAAATAACA
1506907 ATATT
1 ATATT
1506912 GGCTCGTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (26 bp):
ATATTAATACTAAAATAAAAATAACA
Found at i:1507272 original size:20 final size:19
Alignment explanation
Indices: 1507247--1507296 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1507237 TTATATTTTA
1507247 TATTTATTTAATATTAAAAT
1 TATTTATTTAA-ATTAAAAT
*
1507267 TATTTATTTTTAAATTTAAAT
1 TATTTA--TTTAAATTAAAAT
1507288 T-TTTATTTA
1 TATTTATTTA
1507297 TTTTTACTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
20 10 0.37
21 8 0.30
22 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATTTAAATTAAAAT
Found at i:1507413 original size:24 final size:23
Alignment explanation
Indices: 1507348--1507417 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 23
1507338 TGATAATTTT
1507348 AAATATG-ATATAATTATAAATAA
1 AAATATGAATATAA-TATAAATAA
*
1507371 AAATAATTAAAATATAATATGAAATAA
1 AAAT-A-T-GAATATAATAT-AAATAA
1507398 AAATATGAATATAATATAAA
1 AAATATGAATATAATATAAA
1507418 AATATAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 7 0.17
24 11 0.28
25 2 0.05
26 4 0.10
27 16 0.40
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATATGAATATAATATAAATAA
Found at i:1507421 original size:13 final size:13
Alignment explanation
Indices: 1507379--1507443 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
1507369 AAAAATAATT
1507379 AAAATATAATAT-
1 AAAATATAATATA
* *
1507391 GAAATA-AAAATA
1 AAAATATAATATA
**
1507403 TGAATATAATATA
1 AAAATATAATATA
1507416 AAAATATAATTATA
1 AAAATATAA-TATA
1507430 TAAAATAT-ATATA
1 -AAAATATAATATA
1507443 A
1 A
1507444 TATTTATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 4 0.10
12 10 0.24
13 16 0.38
14 5 0.12
15 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:1507475 original size:21 final size:23
Alignment explanation
Indices: 1507432--1507480 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
1507422 TAATTATATA
1507432 AAATATATATAATATTTATTATT
1 AAATATATATAATATTTATTATT
*
1507455 TAATATAT-TAA-ATTT-TATATT
1 AAATATATATAATATTTAT-TATT
1507476 AAATA
1 AAATA
1507481 AATGTGTACG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 3 0.13
23 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATATATAATATTTATTATT
Found at i:1514703 original size:2 final size:2
Alignment explanation
Indices: 1514696--1514721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1514686 TTGTATTTAA
1514696 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
1514722 TTGTTCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1515017 original size:19 final size:19
Alignment explanation
Indices: 1514968--1515017 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1514958 CTCATTTTAT
*
1514968 TATTTA-AAATAATATTAA
1 TATTTATAATTAATATTAA
* *
1514986 TAAATTAT-TTTAATATTAA
1 T-ATTTATAATTAATATTAA
1515005 TATTTATAATTAA
1 TATTTATAATTAA
1515018 ATTTAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTATAATTAATATTAA
Found at i:1517443 original size:3 final size:3
Alignment explanation
Indices: 1517430--1517474 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1517420 ATATCAGATT
*
1517430 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1517475 TATGTGAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1520879 original size:3 final size:3
Alignment explanation
Indices: 1520873--1520897 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1520863 TATATTTATA
1520873 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1520898 TAAGTGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1521523 original size:42 final size:42
Alignment explanation
Indices: 1521461--1521545 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1521451 CTTACTTTAG
*
1521461 CATGCAAATGCCTCAGAGCTCATATGACCATTAATTATCCTT
1 CATGCAAATGCCTCAAAGCTCATATGACCATTAATTATCCTT
* *
1521503 CATGCAAATGCCTGAAAGCTCATATGACCTTTAATTATCCTT
1 CATGCAAATGCCTCAAAGCTCATATGACCATTAATTATCCTT
1521545 C
1 C
1521546 GGGTAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (42 bp):
CATGCAAATGCCTCAAAGCTCATATGACCATTAATTATCCTT
Found at i:1521737 original size:16 final size:16
Alignment explanation
Indices: 1521718--1521771 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1521708 TAAAAATAAC
1521718 ATTAATTTTTAATATT
1 ATTAATTTTTAATATT
*** *
1521734 ATTAAATTAAAAATAAT
1 ATT-AATTTTTAATATT
*
1521751 ATTTATTTTTAATATT
1 ATTAATTTTTAATATT
1521767 ATTAA
1 ATTAA
1521772 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTAATTTTTAATATT
Found at i:1521738 original size:28 final size:29
Alignment explanation
Indices: 1521690--1521772 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 29
1521680 AAATAAAATA
* *
1521690 ATTATTTTTTAAAAATT-TTAAAAATAAC
1 ATTAATTTTTAAATATTATTAAAAATAAC
*
1521718 ATTAATTTTTAATATTATTAAATTAAAAATAAT
1 ATTAATTTTTAA-A-TATT--ATTAAAAATAAC
*
1521751 ATTTATTTTT-AATATTATTAAA
1 ATTAATTTTTAAATATTATTAAA
1521773 TTTAAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
28 17 0.37
29 1 0.02
30 7 0.15
31 1 0.02
32 1 0.02
33 19 0.41
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTAATTTTTAAATATTATTAAAAATAAC
Found at i:1521744 original size:33 final size:33
Alignment explanation
Indices: 1521707--1521782 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
1521697 TTTAAAAATT
1521707 TTAAAAATAACATTAATTTTTAATATTATTAAA
1 TTAAAAATAACATTAATTTTTAATATTATTAAA
* *
1521740 TTAAAAATAATATTTATTTTTAATATTATTAAA
1 TTAAAAATAACATTAATTTTTAATATTATTAAA
*
1521773 TTTAAAATAA
1 TTAAAAATAA
1521783 AAATGATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
TTAAAAATAACATTAATTTTTAATATTATTAAA
Found at i:1521748 original size:17 final size:17
Alignment explanation
Indices: 1521728--1521781 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1521718 ATTAATTTTT
*
1521728 AATATTATTAAATTAAA
1 AATATTATTAAATTTAA
* * **
1521745 AATAATATT-TATTTTT
1 AATATTATTAAATTTAA
1521761 AATATTATTAAATTTAA
1 AATATTATTAAATTTAA
1521778 AATA
1 AATA
1521782 AAAATGATAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTATTAAATTTAA
Found at i:1522974 original size:12 final size:12
Alignment explanation
Indices: 1522957--1522995 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1522947 TTGTGTTATG
1522957 TTTATATTATTT
1 TTTATATTATTT
**
1522969 TTTATATTCGTT
1 TTTATATTATTT
*
1522981 TTTGTATTATTT
1 TTTATATTATTT
1522993 TTT
1 TTT
1522996 GTATATTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1522996 original size:12 final size:12
Alignment explanation
Indices: 1522961--1523003 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1522951 GTTATGTTTA
*
1522961 TATTATTTTTTA
1 TATTATTTTTTG
**
1522973 TATTCGTTTTTG
1 TATTATTTTTTG
1522985 TATTATTTTTTG
1 TATTATTTTTTG
1522997 TA-TATTT
1 TATTATTT
1523004 AAAGTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTG
Found at i:1523209 original size:23 final size:22
Alignment explanation
Indices: 1523183--1523236 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1523173 TATTATATTT
* *
1523183 ATATTATTTTATATATATTTAAA
1 ATATTATTTAAT-TATATATAAA
*
1523206 ATATT-TTTAATTTTATATAAA
1 ATATTATTTAATTATATATAAA
*
1523227 ATTTTATTTA
1 ATATTATTTA
1523237 TTAATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTATTTAATTATATATAAA
Found at i:1523233 original size:39 final size:35
Alignment explanation
Indices: 1523175--1523290 Score: 86
Period size: 35 Copynumber: 3.3 Consensus size: 35
1523165 TATGTTTATA
* *
1523175 TTATATTTATAT-TATTTTATATATATTTAAAATATTT
1 TTAT-TTTATATAAATTTTATATATATTT-AAATA-AT
1523212 TTAATTTTATATAAAATTTTAT-T-TA-TT-AATAAT
1 TT-ATTTTATAT-AAATTTTATATATATTTAAATAAT
1523245 TTATTTTATATAAATTTTAATATTATATTT--AT-AT
1 TTATTTTATATAAATTTT-ATA-TATATTTAAATAAT
1523279 TATATTTTATAT
1 T-TATTTTATAT
1523291 GGTATAAGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
31 7 0.10
32 11 0.16
33 3 0.04
34 8 0.12
35 14 0.21
36 4 0.06
37 11 0.16
38 3 0.04
39 7 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (35 bp):
TTATTTTATATAAATTTTATATATATTTAAATAAT
Found at i:1523236 original size:16 final size:16
Alignment explanation
Indices: 1523217--1523263 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
1523207 TATTTTTAAT
1523217 TTTATATAAAATTTTA
1 TTTATATAAAATTTTA
1523233 TTTAT-TAATAA-TTTA
1 TTTATATAA-AATTTTA
1523248 TTT-TATATAAATTTTA
1 TTTATATA-AAATTTTA
1523264 ATATTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 14 0.52
16 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATAAAATTTTA
Found at i:1523256 original size:32 final size:28
Alignment explanation
Indices: 1523181--1523283 Score: 95
Period size: 28 Copynumber: 3.6 Consensus size: 28
1523171 TATATTATAT
* *
1523181 TTATA-TTATTTTATATATATTTAAAATA
1 TTATATTTATTTTATATAAATTT-TAATA
* *
1523209 TT-T-TTAATTTTATATAAAATTTTATTTA
1 TTATATTTATTTTATAT-AAATTTTA-ATA
1523237 TTAATAATTTATTTTATATAAATTTTAATA
1 TT-AT-ATTTATTTTATATAAATTTTAATA
*
1523267 TTATATTTATATTATAT
1 TTATATTTATTTTATAT
1523284 TTTATATGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
27 12 0.20
28 23 0.38
29 2 0.03
30 5 0.08
31 8 0.13
32 11 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATATTTATTTTATATAAATTTTAATA
Found at i:1523272 original size:17 final size:16
Alignment explanation
Indices: 1523210--1523263 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1523200 TTTAAAATAT
1523210 TTTTAATTTTATATAAAA
1 TTTT-ATTTTATAT-AAA
1523228 TTTTA-TTTAT-TAATA
1 TTTTATTTTATATAA-A
*
1523243 ATTTATTTTATATAAA
1 TTTTATTTTATATAAA
1523259 TTTTA
1 TTTTA
1523264 ATATTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 2 0.06
15 6 0.19
16 15 0.48
17 4 0.13
18 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTTTATATAAA
Found at i:1523273 original size:24 final size:24
Alignment explanation
Indices: 1523237--1523287 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1523227 ATTTTATTTA
1523237 TTAATAATTTATTT-TATATAAATT
1 TTAATAATTTATTTATAT-TAAATT
*
1523261 TTAAT-ATTATATTTATATTATATT
1 TTAATAATT-TATTTATATTAAATT
1523285 TTA
1 TTA
1523288 TATGGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 18 0.75
25 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAATAATTTATTTATATTAAATT
Found at i:1523282 original size:11 final size:11
Alignment explanation
Indices: 1523164--1523290 Score: 69
Period size: 11 Copynumber: 12.1 Consensus size: 11
1523154 TAAAAAATTT
*
1523164 TTATGTTTATA
1 TTATATTTATA
1523175 TTATATTTATA
1 TTATATTTATA
1523186 TTAT-TTTATA
1 TTATATTTATA
1523196 -TATATTTA-A
1 TTATATTTATA
*
1523205 -AATATTT-T-
1 TTATATTTATA
*
1523213 TAAT-TTTATA
1 TTATATTTATA
* *
1523223 TAAAATTT-TA
1 TTATATTTATA
*
1523233 TT-TATTAATAA
1 TTATATTTAT-A
1523244 TT-TATTT-TA
1 TTATATTTATA
*
1523253 TATAAATTTTAATA
1 T-TATA-TTT-ATA
1523267 TTATATTTATA
1 TTATATTTATA
1523278 TTATATTTTATA
1 TTATA-TTTATA
1523290 T
1 T
1523291 GGTATAAGAA
Statistics
Matches: 93, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
8 3 0.03
9 19 0.20
10 19 0.20
11 33 0.35
12 13 0.14
13 3 0.03
14 3 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1523849 original size:7 final size:7
Alignment explanation
Indices: 1523837--1523863 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1523827 AAAACATAAT
1523837 AATTTTA
1 AATTTTA
1523844 AATTTTA
1 AATTTTA
1523851 AATTTTA
1 AATTTTA
1523858 AATTTT
1 AATTTT
1523864 TACATTTGTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:1523919 original size:2 final size:2
Alignment explanation
Indices: 1523912--1523938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1523902 GCCTTTTGTA
1523912 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 A
1523939 GCTACCCATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1526254 original size:26 final size:28
Alignment explanation
Indices: 1526225--1526288 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
1526215 TGTAATATTT
* *
1526225 TTTAATTTTTTAAA-TATTT-TTTTATA
1 TTTAATTTTTAAAATTATTTATTTAATA
*
1526251 TTTAA-TATTAAAATTATTTATTTAATA
1 TTTAATTTTTAAAATTATTTATTTAATA
1526278 TTTAATTTTTA
1 TTTAATTTTTA
1526289 TTTAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 6 0.19
26 10 0.32
27 11 0.35
28 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTAATTTTTAAAATTATTTATTTAATA
Done.