Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005318.1 Hibiscus syriacus cultivar Beakdansim tig00012038_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 125683
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3284 original size:2 final size:2
Alignment explanation
Indices: 3277--3310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3267 CATACTTTAA
3277 AT 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 AT
3311 TAAAAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3567 original size:59 final size:58
Alignment explanation
Indices: 3491--3602 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 58
3481 AATAGTCCCC
*
3491 CGATTATAGGTCATTGCTTTGTGAGTCTTCCA-ACTATTAAAAGTTACAAAATGGCCACT
1 CGATTATAGGTCATTGCTTTGTGAGTCCT-CAGACTATT-AAAGTTACAAAATGGCCACT
* * *
3550 CGATTATAGGAT-GTTGCTTTTTTAGTCCTCAGACTATTAAAGTTACAAAATGG
1 CGATTATAGG-TCATTGCTTTGTGAGTCCTCAGACTATTAAAGTTACAAAATGG
3603 TCACATGACT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 17 0.36
59 29 0.62
60 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (58 bp):
CGATTATAGGTCATTGCTTTGTGAGTCCTCAGACTATTAAAGTTACAAAATGGCCACT
Found at i:5588 original size:2 final size:2
Alignment explanation
Indices: 5576--5619 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5566 TATTTTATTT
5576 TA TA TA T- 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
5617 TA T
1 TA T
5620 CATACGTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6300 original size:46 final size:47
Alignment explanation
Indices: 6201--6564 Score: 472
Period size: 46 Copynumber: 7.9 Consensus size: 47
6191 TATGGCCTCT
* * * * *
6201 TTTCATGCCTTAATACATTCGTTCATGCATTTTTAGTGATGGCATAC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
* ** * * ** *
6248 ATTCATGTTTTAAAGTATCTTTTCATGCA-TTTTAGTTATGTCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
* *
6294 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATG-CATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
** *
6340 TTTCAAACCTTAATGCATCCTTTCATGCA-TTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
*
6386 TTT-ATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
*
6432 TTTTATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
*
6479 TTTCATGCCTTAATGCAT--GTTCATGCA-TTTTAATTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
* *
6523 TTTCATGCCTTAATGCACCCGTTCATGCTTTTTTAGTTATGA
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
6565 ATTCGGTTTA
Statistics
Matches: 276, Mismatches: 34, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
44 33 0.12
45 42 0.15
46 101 0.37
47 100 0.36
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (47 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCC
Found at i:6417 original size:91 final size:93
Alignment explanation
Indices: 6201--6564 Score: 445
Period size: 91 Copynumber: 3.9 Consensus size: 93
6191 TATGGCCTCT
* * * * * * ** * *
6201 TTTCATGCCTTAATACATTCGTTCATGCATTTTTAGTGATGGCATAC-ATTCATGTTTTAAAGTA
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAATTATGACAT-CTTTTCATGCCTTAATGCA
** *
6265 TCTTTTCATGCATTTTAGTTATGTCATCC
65 TCCGTTCATGCATTTTAGTTATGACATCC
* **
6294 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATG-CATCTTTTCAAACCTTAATGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAATTATGACATCTTTTCATGCCTTAATGCAT
*
6358 CCTTTCATGCATTTTAGTTATGACATCC
66 CCGTTCATGCATTTTAGTTATGACATCC
* *
6386 TTT-ATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCCTTTT-ATGCCTTAATGCA
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAATTATGACAT-CTTTTCATGCCTTAATGCA
6449 TCCGTTCATGCATTTTTAGTTATGACATCC
65 TCCGTTCATGCA-TTTTAGTTATGACATCC
* *
6479 TTTCATGCCTTAATGCAT--GTTCATGCA-TTTTAATTATGACATCCTTTCATGCCTTAATGCAC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAATTATGACATCTTTTCATGCCTTAATGCAT
*
6541 CCGTTCATGCTTTTTTAGTTATGA
66 CCGTTCATGC-ATTTTAGTTATGA
6565 ATTCGGTTTA
Statistics
Matches: 241, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
90 4 0.02
91 85 0.35
92 76 0.32
93 62 0.26
94 14 0.06
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (93 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAATTATGACATCTTTTCATGCCTTAATGCAT
CCGTTCATGCATTTTAGTTATGACATCC
Found at i:6439 original size:27 final size:27
Alignment explanation
Indices: 6400--6486 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 27
6390 TGCCTTAATG
6400 CATCCTTTCATGCATTTTTAGTTATGA
1 CATCCTTTCATGCATTTTTAGTTATGA
* *
6427 CATCCTTTTATGC---CTTA---ATG-
1 CATCCTTTCATGCATTTTTAGTTATGA
*
6447 CATCCGTTCATGCATTTTTAGTTATGA
1 CATCCTTTCATGCATTTTTAGTTATGA
6474 CATCCTTTCATGC
1 CATCCTTTCATGC
6487 CTTAATGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 11 0.23
21 3 0.06
23 3 0.06
24 3 0.06
26 3 0.06
27 24 0.51
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (27 bp):
CATCCTTTCATGCATTTTTAGTTATGA
Found at i:6459 original size:20 final size:20
Alignment explanation
Indices: 6436--6550 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
6426 ACATCCTTTT
6436 ATGCCTTAATGCATCCGTTC
1 ATGCCTTAATGCATCCGTTC
* *
6456 ATGCATTTTTAGTTATGACATCCTTTC
1 ATGC---CTTA---ATG-CATCCGTTC
6483 ATGCCTTAATGCAT--GTTC
1 ATGCCTTAATGCATCCGTTC
* *
6501 ATGCATTTTAATTATGACATCCTTTC
1 ATGC--CTT-A--ATG-CATCCGTTC
*
6527 ATGCCTTAATGCACCCGTTC
1 ATGCCTTAATGCATCCGTTC
6547 ATGC
1 ATGC
6551 TTTTTTAGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 30
0.65 0.08 0.27
Matches are distributed among these distances:
18 7 0.10
20 20 0.28
21 7 0.10
23 7 0.10
24 8 0.11
26 10 0.14
27 12 0.17
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGCCTTAATGCATCCGTTC
Found at i:8615 original size:35 final size:35
Alignment explanation
Indices: 8544--8643 Score: 186
Period size: 34 Copynumber: 2.9 Consensus size: 35
8534 AACTCTGAAA
8544 ATACCCTTATGTTGTAAGATAACAA-AATTGTAAG
1 ATACCCTTATGTTGTAAGATAACAAGAATTGTAAG
8578 ATACCCTTATGTTGTAAGATAACAAGAATTGTAAG
1 ATACCCTTATGTTGTAAGATAACAAGAATTGTAAG
8613 ATACCCTTATGTTGTAAGA-AACAAGAATTGT
1 ATACCCTTATGTTGTAAGATAACAAGAATTGT
8644 CCCTGGAAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
34 37 0.57
35 28 0.43
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (35 bp):
ATACCCTTATGTTGTAAGATAACAAGAATTGTAAG
Found at i:10306 original size:24 final size:24
Alignment explanation
Indices: 10279--10340 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
10269 TTCTGTTATA
*
10279 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
10303 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
10327 ATACTTGACCTGGA
1 ATACTTGACCTGGA
10341 ATATGTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:15630 original size:21 final size:21
Alignment explanation
Indices: 15606--15656 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
15596 TTGGAAACAA
15606 GCTCCACTGAGAAGTCTGCAT
1 GCTCCACTGAGAAGTCTGCAT
*
15627 GCTCCACTAAGAAGTCTGCAT
1 GCTCCACTGAGAAGTCTGCAT
15648 GCTCCACTG
1 GCTCCACTG
15657 TGTAATTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (21 bp):
GCTCCACTGAGAAGTCTGCAT
Found at i:17444 original size:47 final size:47
Alignment explanation
Indices: 17372--17745 Score: 436
Period size: 47 Copynumber: 8.0 Consensus size: 47
17362 TATGGCCTCT
* * *
17372 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTGATAACATAC
1 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
* * * * *
17419 TTTCATGTTTTAAAGTATCTTTTCATGCA-TTTTAGTTATGGCATTC
1 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
* * *
17465 TTTCAT-TCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGT-CTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
* *
17512 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATTC
1 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
* * * *
17559 TTTCATGCCTTAATGCATCCT-TTTATGCATTTTTAGTTATGGCATCC
1 TTTCATGTCTTAATGCAT-CTGTTCATGCATTTTTAGTTATGACATTC
** * * *
17606 TTTCATACCTTAATGCAT-TCATTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGTCTTAATGCATCT-GTTCATGCATTTTTAGTTATGACATTC
* *
17653 TTTCATGCCTTAATGCAT-TCGTTCATGCATTTTTAGTTATGACATCC
1 TTTCATGTCTTAATGCATCT-GTTCATGCATTTTTAGTTATGACATTC
* *
17700 TTTCATGCCTTAATGCATATGTTCATGCATTTTTAGTTATGA-ATTC
1 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
17746 GGTTTAGAGC
Statistics
Matches: 293, Mismatches: 27, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
45 2 0.01
46 38 0.13
47 251 0.86
48 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (47 bp):
TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATTC
Found at i:17587 original size:94 final size:94
Alignment explanation
Indices: 17372--17745 Score: 509
Period size: 94 Copynumber: 4.0 Consensus size: 94
17362 TATGGCCTCT
* * * * * ** * *
17372 TTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTGATAACATACTTTCATGTTTTAAAGTAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
** *
17437 CTTTTCATGCA-TTTTAGTTATGGCATTC
66 CCGTTCATGCATTTTTAGTTATGACATTC
* *
17465 TTTCATTCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
17530 CCGTTCATGCATTTTTAGTTATGACATTC
66 CCGTTCATGCATTTTTAGTTATGACATTC
* * * *
17559 TTTCATGCCTTAATGCATCCTTTTATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
* * * *
17624 TCATTCATGCATTTTTAGTTATGGCATCC
66 CCGTTCATGCATTTTTAGTTATGACATTC
*
17653 TTTCATGCCTTAATGCATTCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
**
17718 ATGTTCATGCATTTTTAGTTATGA-ATTC
66 CCGTTCATGCATTTTTAGTTATGACATTC
17746 GGTTTAGAGC
Statistics
Matches: 248, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 66 0.27
94 182 0.73
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (94 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
CCGTTCATGCATTTTTAGTTATGACATTC
Found at i:17647 original size:141 final size:140
Alignment explanation
Indices: 17361--17740 Score: 555
Period size: 141 Copynumber: 2.7 Consensus size: 140
17351 TTAATTTCAT
* * * * * *
17361 TTATGGCCTCTTTTCATGTCTTAATGCATCTGTTCATGCATTTTTAGTGATAACATACTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATG
** * * * * *
17426 TTTTAAAGTATCTTTTCATGCA-TTTTAGTTATGGCATTCTTTCATTCCTTAATGCATCCGTTCA
66 CCTTAATGCATCTTTT-ATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCATTCA
17490 TGCATTTTTAG
130 TGCATTTTTAG
*
17501 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATTCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATG
*
17566 CCTTAATGCATCCTTTTATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATTCATTCA
66 CCTTAATGCAT-CTTTTATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCATTCA
17631 TGCATTTTTAG
130 TGCATTTTTAG
* *
17642 TTATGGCATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTTAGTTATGACATCCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATG
* *
17707 CCTTAATGCATATGTTCATGCATTTTTAGTTATG
66 CCTTAATGCATCT-TTTATGCATTTTTAGTTATG
17741 AATTCGGTTT
Statistics
Matches: 218, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
140 71 0.33
141 147 0.67
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.46
Consensus pattern (140 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATG
CCTTAATGCATCTTTTATGCATTTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCATTCAT
GCATTTTTAG
Found at i:18446 original size:20 final size:19
Alignment explanation
Indices: 18414--18452 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
18404 CTATTTACAC
*
18414 CTATAGTATCGATACCATT
1 CTATAGTACCGATACCATT
18433 CTATCAGTACCGATACCATT
1 CTAT-AGTACCGATACCATT
18453 GCCATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (19 bp):
CTATAGTACCGATACCATT
Found at i:19967 original size:25 final size:24
Alignment explanation
Indices: 19918--19967 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
19908 GTAAAATAGA
**
19918 TTTTTTAGAATTTTATTTATGATT
1 TTTTTTAGAATTTTATTTAAAATT
19942 TTTTTTA-AATTTTATATTTAAAATT
1 TTTTTTAGAA-TTT-TATTTAAAATT
19967 T
1 T
19968 AAATTATGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 2 0.09
24 10 0.45
25 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTTAGAATTTTATTTAAAATT
Found at i:24414 original size:21 final size:21
Alignment explanation
Indices: 24390--24431 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24380 AGTTTATTTT
24390 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
24411 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
24432 AACTTGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:24468 original size:33 final size:32
Alignment explanation
Indices: 24420--24496 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
24410 GTAAACTTTG
* * *
24420 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGAAAATATTTAAGTA
*
24452 TTTGAATTTATCGAACTTGAAAATATTTAAGTA
1 TTTCAA-TTATCGAACTTGAAAATATTTAAGTA
24485 TTTCAATTATCG
1 TTTCAATTATCG
24497 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGAAAATATTTAAGTA
Found at i:24948 original size:17 final size:18
Alignment explanation
Indices: 24907--24948 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
24897 ATCTGGTTTT
24907 TTTTTTTAAAAAAACCGG
1 TTTTTTTAAAAAAACCGG
24925 TTTTTTT-AAAAAACCGG
1 TTTTTTTAAAAAAACCGG
24942 TTTTTTT
1 TTTTTTT
24949 CAAACCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (18 bp):
TTTTTTTAAAAAAACCGG
Found at i:25494 original size:2 final size:2
Alignment explanation
Indices: 25425--25477 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
25415 GTTTTAGCTT
25425 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
25467 TA TA TA TA TA T
1 TA TA TA TA TA T
25478 CAATCATCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26365 original size:16 final size:16
Alignment explanation
Indices: 26339--26380 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
26329 TTTGTTTTAC
*
26339 AATTTTATATTT-TTA
1 AATTTTTTATTTCTTA
*
26354 TATTTATTTATTTCTTA
1 AATTT-TTTATTTCTTA
26371 AATTTTTTAT
1 AATTTTTTAT
26381 ATTATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.18
16 11 0.50
17 7 0.32
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
AATTTTTTATTTCTTA
Found at i:34251 original size:65 final size:65
Alignment explanation
Indices: 34162--34351 Score: 256
Period size: 65 Copynumber: 2.9 Consensus size: 65
34152 TACACTCTTG
** * * *
34162 ATGCATCGATACACTCCTTATTTTATTAAAACATCGAATGCATTTTGTGTACCGATGCACAGACA
1 ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACA
* *
34227 ATGCATCGATATACTCCTGGTTTTATTGAAACATCGAATGCATTTTATGTACTGATGCACAAACA
1 ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACA
* * * * *
34292 ATGCATCGATACACTCCTGGCTCTT-TTGAAACATTGAATGTAATTAGTGTACTGATGCAC
1 ATGCATCGATACACTCCTGG-TTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCAC
34352 CCCAAGTGTA
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 107 0.97
66 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (65 bp):
ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACA
Found at i:35799 original size:12 final size:12
Alignment explanation
Indices: 35782--35817 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35772 AGGTAGACCT
*
35782 CGAGACGAAGAA
1 CGAGACAAAGAA
35794 CGAGACAAAGAA
1 CGAGACAAAGAA
*
35806 TGAGACAAAGAA
1 CGAGACAAAGAA
35818 AAACGTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.14, G:0.28, T:0.03
Consensus pattern (12 bp):
CGAGACAAAGAA
Found at i:40160 original size:23 final size:23
Alignment explanation
Indices: 40134--40204 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
40124 GAAAGTGTAC
40134 CGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCTTGAATGTGCAT
* * *
40157 CGATACA---CTATAAAAGTGCA-
1 CGATGCATTCCT-TGAATGTGCAT
*
40177 CTGATGCATTCCTTGAATGTGTAT
1 C-GATGCATTCCTTGAATGTGCAT
40201 CGAT
1 CGAT
40205 ACACTCAGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 3 0.09
21 13 0.37
23 16 0.46
24 3 0.09
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (23 bp):
CGATGCATTCCTTGAATGTGCAT
Found at i:40173 original size:44 final size:44
Alignment explanation
Indices: 40110--40209 Score: 155
Period size: 44 Copynumber: 2.3 Consensus size: 44
40100 GTGCAAAGTT
* * *
40110 CATCGATACACTGTGAAAGTGTACCGATGCATTCCTTGAATGTG
1 CATCGATACACTATAAAAGTGCACCGATGCATTCCTTGAATGTG
*
40154 CATCGATACACTATAAAAGTGCACTGATGCATTCCTTGAATGTG
1 CATCGATACACTATAAAAGTGCACCGATGCATTCCTTGAATGTG
*
40198 TATCGATACACT
1 CATCGATACACT
40210 CAGACGTGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
CATCGATACACTATAAAAGTGCACCGATGCATTCCTTGAATGTG
Found at i:40670 original size:17 final size:18
Alignment explanation
Indices: 40631--40667 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40621 TAAAAAAAAA
*
40631 ATTG-TTTTGATTTAATT
1 ATTGTTTTTAATTTAATT
40648 ATTGTTTTTAATTTAATT
1 ATTGTTTTTAATTTAATT
40666 AT
1 AT
40668 GTTGTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
ATTGTTTTTAATTTAATT
Found at i:42495 original size:13 final size:14
Alignment explanation
Indices: 42473--42507 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
42463 AGGGGGAGTA
42473 ATTTTC-AAAATTG
1 ATTTTCAAAAATTG
42486 A-TTTCAAAAATTG
1 ATTTTCAAAAATTG
42499 ATTTTCAAA
1 ATTTTCAAA
42508 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 9 0.45
14 7 0.35
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:42521 original size:13 final size:13
Alignment explanation
Indices: 42505--42533 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42495 ATTGATTTTC
42505 AAAGAAAATCTTA
1 AAAGAAAATCTTA
42518 AAAGAAAATCTTA
1 AAAGAAAATCTTA
42531 AAA
1 AAA
42534 TTACTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAGAAAATCTTA
Found at i:42909 original size:65 final size:65
Alignment explanation
Indices: 42832--43019 Score: 229
Period size: 65 Copynumber: 2.9 Consensus size: 65
42822 CACTCTTGAT
*
42832 GCATCGATACACTCCTTATTTTATTAAAACATCGAATGCATTTTGTGTACCGATGCACAGACAAT
1 GCATCGATACACTCCTTATTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACAA-
42897 C
65 C
* ** * * *
42898 -CATCGATACACTCATGGTTTTATTGAAACATCGAATACATTTTGTGTACCGATACACATACAAC
1 GCATCGATACACTCCTTATTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACAAC
* * * *
42962 GCATCGATACACT-CATATCTCTT-TTGAAACATCGAATGTAATTAGTGTACCGATGCAC
1 GCATCGATACACTCCTTAT-T-TTATTGAAACATCGAATGCATTTTGTGTACCGATGCAC
43020 CCCAAGTGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
64 2 0.02
65 99 0.96
66 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (65 bp):
GCATCGATACACTCCTTATTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACAAC
Found at i:45070 original size:23 final size:23
Alignment explanation
Indices: 45038--45106 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
45028 AATTAGGTCC
45038 TTATTTTATGTTTATTTTATTTT
1 TTATTTTATGTTTATTTTATTTT
* *
45061 TTATTCTATGTTT-TTACTATTTT
1 TTATTTTATGTTTATT-TTATTTT
* *
45084 TTATTTTTTG-TTAGTTTATTTT
1 TTATTTTATGTTTATTTTATTTT
45106 T
1 T
45107 AAAATTCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 11 0.29
23 27 0.71
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.75
Consensus pattern (23 bp):
TTATTTTATGTTTATTTTATTTT
Found at i:51777 original size:11 final size:11
Alignment explanation
Indices: 51763--51821 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
51753 AAGAGACAAA
*
51763 AAGAAATAAAG
1 AAGAAAGAAAG
51774 AAG--AGAAAG
1 AAGAAAGAAAG
* *
51783 AA-AAAAAACAA
1 AAGAAAGAA-AG
*
51794 AAGAAAGAGAG
1 AAGAAAGAAAG
51805 AAGAAAGAAAG
1 AAGAAAGAAAG
51816 AAGAAA
1 AAGAAA
51822 AAAATAGATC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
9 7 0.19
10 3 0.08
11 23 0.62
12 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:51813 original size:15 final size:14
Alignment explanation
Indices: 51763--51820 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
51753 AAGAGACAAA
*
51763 AAGAAATAAAGAAG
1 AAGAAAGAAAGAAG
*
51777 -AGAAAGAAA-AAA
1 AAGAAAGAAAGAAG
*
51789 AACAAAAGAAAGAGAG
1 AA-GAAAGAAAGA-AG
51805 AAGAAAGAAAGAAG
1 AAGAAAGAAAGAAG
51819 AA
1 AA
51821 AAAAATAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 11 0.31
15 10 0.29
16 3 0.09
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
AAGAAAGAAAGAAG
Found at i:58563 original size:18 final size:20
Alignment explanation
Indices: 58540--58579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
58530 TGTATTTACC
58540 TTTATA-TCTT-ACTTGTTT
1 TTTATAGTCTTAACTTGTTT
58558 TTTATATGTCTTAACTTGTTT
1 TTTATA-GTCTTAACTTGTTT
58579 T
1 T
58580 CTTTTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTATAGTCTTAACTTGTTT
Found at i:61286 original size:21 final size:21
Alignment explanation
Indices: 61253--61350 Score: 70
Period size: 23 Copynumber: 4.5 Consensus size: 21
61243 CGTAGAATTT
**
61253 TCCCGAAAAACCACATATATG
1 TCCCGAAGGACCACATATATG
* *
61274 TCCCGAAGGACCACGTAGAGATG
1 TCCCGAAGGACCAC--ATATATG
* * *
61297 TCCCGAAAGACCAAATAGATTTG
1 TCCCGAAGGACCACAT--ATATG
*
61320 TCCCTAAGGACCACATATATG
1 TCCCGAAGGACCACATATATG
* *
61341 TTCCAAAGGA
1 TCCCGAAGGA
61351 TATGTCCTAA
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
21 25 0.43
23 33 0.57
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:61301 original size:23 final size:23
Alignment explanation
Indices: 61271--61336 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
61261 AACCACATAT
*
61271 ATGTCCCGAAGGACCACGTAGAG
1 ATGTCCCGAAGGACCACATAGAG
* * *
61294 ATGTCCCGAAAGACCAAATAGAT
1 ATGTCCCGAAGGACCACATAGAG
* *
61317 TTGTCCCTAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
61337 TATGTTCCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
ATGTCCCGAAGGACCACATAGAG
Found at i:65787 original size:28 final size:28
Alignment explanation
Indices: 65727--65788 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
65717 TGCAAGAAGC
65727 CAACCTGAAACACATTACGTCCCCAAAT
1 CAACCTGAAACACATTACGTCCCCAAAT
* * *
65755 TAACCTGAAACACATTATC-TTCCCAAGT
1 CAACCTGAAACACATTA-CGTCCCCAAAT
65783 CAACCT
1 CAACCT
65789 AAGCCTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.37, C:0.34, G:0.06, T:0.23
Consensus pattern (28 bp):
CAACCTGAAACACATTACGTCCCCAAAT
Found at i:66541 original size:13 final size:14
Alignment explanation
Indices: 66520--66548 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
66510 TTATAATTAC
66520 ATTATTATATTATT
1 ATTATTATATTATT
66534 ATTA-TATATTATT
1 ATTATTATATTATT
66547 AT
1 AT
66549 AACTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATATTATT
Found at i:66555 original size:10 final size:10
Alignment explanation
Indices: 66520--66549 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
66510 TTATAATTAC
66520 ATTATTATATT
1 ATTATTATA-T
66531 ATTATTATAT
1 ATTATTATAT
66541 ATTATTATA
1 ATTATTATA
66550 ACTTATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTATTATAT
Found at i:74810 original size:2 final size:2
Alignment explanation
Indices: 74803--74875 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
74793 TTTTTATGAT
74803 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
74845 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 T
74876 GTGTGTGTGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74880 original size:2 final size:2
Alignment explanation
Indices: 74875--74985 Score: 222
Period size: 2 Copynumber: 55.5 Consensus size: 2
74865 TATATATATA
74875 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
74917 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
74959 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
74986 ATACTCTTGT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 109 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:80417 original size:52 final size:54
Alignment explanation
Indices: 80356--80605 Score: 217
Period size: 57 Copynumber: 4.5 Consensus size: 54
80346 TCAAGGGTTT
*
80356 AGCCTAATTTTTGGGGGTTTCTTGATG-TTTTCAAATAAGTTTTT-AGAAACTA
1 AGCCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATAAGTTTTTAAGAAACTA
* * *
80408 AGCCTAATTTTCAAGGGTTTCTTGATGATGATTTTC-AATGAA-TTTCTTAAAATAAGCTA
1 AGCCTAATTTTTAGGGGTTTC-T--TGATGATTTTCAAAT-AAGTTT-TTAAGA-AA-CTA
* * * *
80467 AGCCCTAATTTTTAGGGGGTTTATTAATG-TTTTCAAATGAGTTTTTATG-AACTA
1 AG-CCTAATTTTTA-GGGGTTTCTTGATGATTTTCAAATAAGTTTTTAAGAAACTA
* * *
80521 AGCCTGATTTTTAGGGGTTTCTTGATGATTATCACCA-AAGCTTTTTTAAAGAAACTA
1 AGCCTAATTTTTAGGGGTTTCTTGATGATTTTCA-AATAAG--TTTTT-AAGAAACTA
* *
80578 AGGCTAATTTTTAGGGGTTCCTTGATGA
1 AGCCTAATTTTTAGGGGTTTCTTGATGA
80606 CAACTGAAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 33
0.75 0.10 0.16
Matches are distributed among these distances:
52 30 0.19
53 18 0.11
54 6 0.04
55 18 0.11
56 11 0.07
57 41 0.26
58 12 0.08
59 5 0.03
60 11 0.07
61 6 0.04
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (54 bp):
AGCCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATAAGTTTTTAAGAAACTA
Found at i:85263 original size:32 final size:32
Alignment explanation
Indices: 85193--85265 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
85183 CCTAAGGTGA
*
85193 CCCTTGGGTAGGCTCTGAGGCCCCAAGAAACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
** **
85225 TTCTTGGGTAGGCTCTCAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
85257 CCCTTGGGT
1 CCCTTGGGT
85266 TAATCATGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
Found at i:85614 original size:2 final size:2
Alignment explanation
Indices: 85607--85636 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
85597 TTGTTTTAAA
85607 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
85637 TCATTGGTTT
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:87594 original size:14 final size:14
Alignment explanation
Indices: 87577--87603 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87567 AAAAAAAATA
87577 ATATTTAAAATTTG
1 ATATTTAAAATTTG
87591 ATATTTAAAATTT
1 ATATTTAAAATTT
87604 ATTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATATTTAAAATTTG
Found at i:91025 original size:16 final size:16
Alignment explanation
Indices: 91000--91054 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
90990 CTCTCAAACC
* *
91000 CTTTTCAATTTTCAAT
1 CTTTTAAATTTTAAAT
91016 CTTTTAAATTTTAAAT
1 CTTTTAAATTTTAAAT
91032 -TTTTAATATTATTAAAT
1 CTTTTAA-ATT-TTAAAT
91049 CATTTT
1 C-TTTT
91055 GTGGTAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 6 0.18
16 17 0.52
17 6 0.18
19 4 0.12
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
CTTTTAAATTTTAAAT
Found at i:91032 original size:23 final size:24
Alignment explanation
Indices: 91001--91048 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
90991 TCTCAAACCC
* *
91001 TTTTCAATTTTCAATCTT-TTAAA
1 TTTTAAATTTTCAATATTATTAAA
*
91024 TTTTAAATTTTTAATATTATTAAA
1 TTTTAAATTTTCAATATTATTAAA
91048 T
1 T
91049 CATTTTGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAAATTTTCAATATTATTAAA
Found at i:92565 original size:15 final size:16
Alignment explanation
Indices: 92527--92567 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
92517 CCAAAGCCTC
*
92527 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
92543 TGAATCATTCAGCACT
1 TGAATCATTCAACACT
92559 T-AATCATTC
1 TGAATCATTC
92568 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:95138 original size:3 final size:3
Alignment explanation
Indices: 95130--95165 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
95120 TCAGTAATTA
95130 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
95166 TCTTAAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:95782 original size:30 final size:31
Alignment explanation
Indices: 95748--95813 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
95738 AGTACGATTT
95748 TAAAAAAAAACAAAA-TAAAAGTTTATGTAC
1 TAAAAAAAAACAAAACTAAAAGTTTATGTAC
** *
95778 TAAAACGAATCAAAACTAAAAGTTTATGTAC
1 TAAAAAAAAACAAAACTAAAAGTTTATGTAC
95809 TAAAA
1 TAAAA
95814 GCGGAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.59, C:0.09, G:0.08, T:0.24
Consensus pattern (31 bp):
TAAAAAAAAACAAAACTAAAAGTTTATGTAC
Found at i:98817 original size:60 final size:61
Alignment explanation
Indices: 98686--98832 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 61
98676 TGTATGACCC
* * * *
98686 TCATTTTAAATTAG-TCTTTAAACTTTTAAATATTCTAATTTCATCCCTAAACTATGACTAT
1 TCATTCTAAATTAGTTC-TCAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGAATAT
* * * *
98747 T-ATTCAAAATTAGTTCTCAAACTTTTGATTATT-TCAATTTCATCCCCAAATTATGAAT-T
1 TCATTCTAAATTAGTTCTCAAACTTTTAAATATTCT-AATTTCATCCCCAAACTATGAATAT
** *
98806 TCATTCTAAATTCCTCCTCAAACTTTT
1 TCATTCTAAATTAGTTCTCAAACTTTT
98833 TGAACATTCC
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.04
60 65 0.92
61 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (61 bp):
TCATTCTAAATTAGTTCTCAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGAATAT
Found at i:100521 original size:20 final size:19
Alignment explanation
Indices: 100496--100563 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
100486 ACCGTTTTAG
*
100496 GTTGACTCAATTCAGTTCGA
1 GTTGACTC-ATTCGGTTCGA
* * *
100516 GTTGACGCGGTTCGGTCCGA
1 GTTGACTC-ATTCGGTTCGA
*
100536 GTTAACTCATATCGGTTCGA
1 GTTGACTCAT-TCGGTTCGA
100556 GTTGACTC
1 GTTGACTC
100564 GAACAGATTC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (19 bp):
GTTGACTCATTCGGTTCGA
Found at i:104888 original size:20 final size:20
Alignment explanation
Indices: 104865--104905 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
104855 GGTTGACTTA
104865 GTTCGGTTCAT-GTTGACTCG
1 GTTCGG-TCATAGTTGACTCG
*
104885 GTTCGGTCCTAGTTGACTCG
1 GTTCGGTCATAGTTGACTCG
104905 G
1 G
104906 ACCGGTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.10, C:0.22, G:0.32, T:0.37
Consensus pattern (20 bp):
GTTCGGTCATAGTTGACTCG
Found at i:108011 original size:31 final size:31
Alignment explanation
Indices: 107962--108021 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
107952 ACTCGTGAGC
107962 TTTCGAGTCGAGTCGAGCTT-CAATTTTTTA
1 TTTCGAGTCGAGTCGAGCTTACAATTTTTTA
*
107992 TTTCGAGTTCGAGTTGAGCTTGACAATTTT
1 TTTCGAG-TCGAGTCGAGCTT-ACAATTTT
108022 AAGCTCATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 12 0.46
33 7 0.27
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (31 bp):
TTTCGAGTCGAGTCGAGCTTACAATTTTTTA
Found at i:108048 original size:72 final size:66
Alignment explanation
Indices: 107894--108052 Score: 183
Period size: 72 Copynumber: 2.3 Consensus size: 66
107884 GAGTTCAAGT
*
107894 CTTTTGAGCTCAAGTCGAGCTTCAATTTTTGATTTCGAGTCGAACTTGAAAATTTTAAACTCGTG
1 CTTTTGAG-TCAAGTCGAGCTTCAATTTTTGATTTCGAGTCGAACTTGAAAATTTTAAACTCATG
107959 AG
65 AG
* * * * *
107961 CTTTCGAGTCGAGTCGAGCTTCAATTTTTTATTTCGAGTTCGAGTTGAGCTTGACAATTTTAAGC
1 CTTTTGAGTCAAGTCGAGCTTCAATTTTTGATTTCGAG-TCGA----A-CTTGAAAATTTTAAAC
108026 TCATGAG
60 TCATGAG
* *
108033 TTTTTGAGTCTAGTCGAGCT
1 CTTTTGAGTCAAGTCGAGCT
108053 CAACTCGGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
66 28 0.36
67 11 0.14
71 1 0.01
72 37 0.48
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (66 bp):
CTTTTGAGTCAAGTCGAGCTTCAATTTTTGATTTCGAGTCGAACTTGAAAATTTTAAACTCATGA
G
Found at i:112488 original size:30 final size:30
Alignment explanation
Indices: 112452--112513 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
112442 TCGGGTACAT
112452 AAAGCAATTCTCATCTCCAGCACTAACCAG
1 AAAGCAATTCTCATCTCCAGCACTAACCAG
112482 AAAGCAATTCTCATCTCCAGCACTAACCAG
1 AAAGCAATTCTCATCTCCAGCACTAACCAG
112512 AA
1 AA
112514 CCTACATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.19
Consensus pattern (30 bp):
AAAGCAATTCTCATCTCCAGCACTAACCAG
Found at i:114930 original size:54 final size:54
Alignment explanation
Indices: 114862--114964 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
114852 TGAATATAAC
* * *
114862 ATCAAAAATTAGTTTCATTCCCAC-CTTAATATCTTTATTTGAATGATACTTTTG
1 ATCAAAAATCAGTTTCATTCCCACAC-GAATACCTTTATTTGAATGATACTTTTG
* * *
114916 ATCAAAAATCAGTTTCTTTCCTACACGAATACCTTTATTTGACTGATAC
1 ATCAAAAATCAGTTTCATTCCCACACGAATACCTTTATTTGAATGATAC
114965 CTTCAATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (54 bp):
ATCAAAAATCAGTTTCATTCCCACACGAATACCTTTATTTGAATGATACTTTTG
Found at i:119157 original size:20 final size:20
Alignment explanation
Indices: 119134--119212 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
119124 AATTTGTAAA
119134 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
119154 TCGCAACACAAAAGTTAAAT
1 TCGCAACACAGAAGTCAAAT
*
119174 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
119194 TCGCAACATAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
119213 GCGCGTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:119360 original size:22 final size:22
Alignment explanation
Indices: 119335--119385 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
119325 CTACGGCGAC
*
119335 ATCCGTCCCCATCTCCGACGTA
1 ATCCGTCCCCATCTCCGACGAA
* *
119357 ATCCGTTCTCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
119379 ATCCGTC
1 ATCCGTC
119386 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.25
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:119772 original size:19 final size:20
Alignment explanation
Indices: 119744--119815 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
119734 AACACGAAAA
* *
119744 TCGCAATGCGAATTT-AGTT
1 TCGCATTGCGAATTTCATTT
*
119763 TCGCATTGCGATTTTCATTT
1 TCGCATTGCGAATTTCATTT
*
119783 TCGCATTGCGATTTTCATTT
1 TCGCATTGCGAATTTCATTT
119803 TCGCATTGCGAAT
1 TCGCATTGCGAAT
119816 GTAAGTTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
19 13 0.27
20 35 0.73
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (20 bp):
TCGCATTGCGAATTTCATTT
Found at i:119786 original size:20 final size:20
Alignment explanation
Indices: 119761--119813 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
119751 GCGAATTTAG
119761 TTTCGCATTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
119781 TTTCGCATTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
119801 TTTCGCATTGCGA
1 TTTCGCATTGCGA
119814 ATGTAAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:121990 original size:21 final size:21
Alignment explanation
Indices: 121960--122057 Score: 106
Period size: 21 Copynumber: 4.7 Consensus size: 21
121950 GATGCACCAG
121960 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
121981 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * * *
122002 CCACCATTCAAGAGGCCCATG
1 TCATCGTTCAAGAGGCCCCTC
* *
122023 TGATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
122044 ACACCGTTCAAGAG
1 TCATCGTTCAAGAG
122058 CCTGATTCAC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:122033 original size:42 final size:42
Alignment explanation
Indices: 121966--122057 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
121956 CCAGTCATCG
* *
121966 TTCAAGAGGCCCCTCTCATCATTCAAGAGGCCCCTCCCACCA
1 TTCAAGAGGCCCATCTCATCATTCAAGAGGCCCCTCACACCA
* * * * *
122008 TTCAAGAGGCCCATGTGATCGTTCAAGAGGTCCCTCACACCG
1 TTCAAGAGGCCCATCTCATCATTCAAGAGGCCCCTCACACCA
122050 TTCAAGAG
1 TTCAAGAG
122058 CCTGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCCATCTCATCATTCAAGAGGCCCCTCACACCA
Found at i:123791 original size:20 final size:20
Alignment explanation
Indices: 123764--123821 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
123754 AAAATTGAAA
*
123764 TACGAATTTGACTTTTGCGT
1 TACGAATTTGACTTTCGCGT
* *
123784 TGCGAATTTAACTTTCGCGT
1 TACGAATTTGACTTTCGCGT
*
123804 TACGAATTTGTCTTTCGC
1 TACGAATTTGACTTTCGC
123822 ATCATTCGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (20 bp):
TACGAATTTGACTTTCGCGT
Done.