Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004647.1 Hibiscus syriacus cultivar Beakdansim tig00010417_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: 94906
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6486 original size:44 final size:43
Alignment explanation
Indices: 6419--6503 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 43
6409 ATTAACATGG
* *
6419 TGTTTTAAAAGAATTTTTAAAGAAACTAAGTCTTATTTTCAGA
1 TGTTTTAAAAGAATTTTTAAAGAAACCAAGTCTTACTTTCAGA
* *
6462 TGTTCTTAAATGAGTTTTTAAAGAAACCAAGTCTTACTTTCA
1 TGTT-TTAAAAGAATTTTTAAAGAAACCAAGTCTTACTTTCA
6504 AAGGTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (43 bp):
TGTTTTAAAAGAATTTTTAAAGAAACCAAGTCTTACTTTCAGA
Found at i:6970 original size:116 final size:116
Alignment explanation
Indices: 6824--7657 Score: 911
Period size: 116 Copynumber: 7.2 Consensus size: 116
6814 CATTTATGAG
** * * * * * *
6824 GAAGGGTTTTTAATGAGAATAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGATAAGATCTTT
1 GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
6889 TTCGAAACTCGGCACATCCATCACACAATGAAATGAATCAACATTTCATAA
66 TTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
* *
6940 GAAGGGTTCGTAATGGGAAGAACTCATCCAATGAGGAAGACGAAGTTCATAATGAGAAGAACTTG
1 GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *** * *
7005 TTCGAAACTCGACACATTTGTCACACAAGGAGATGAATCAATATTTTAGAA
66 TTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
* *
7056 G-AGGGTTCGTAATAAGAAGAACTCATCCAATGAGGAAGGAA-AAGTTCATAATAAGAAGAACTT
1 GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAA-GAAGAAGTTCATAATGAGAAGAACTT
* * * ** * ** *
7119 GTTCGAAACTTGGCAAATCTGTCACACAAGGATATGGTTCAACATTTCAAAA
65 GTTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
* * *
7171 GAGGGGTTTGTAATGAGATAG-ACTCATCC-A--ACGAAGAAGAAGTTCATAATGAGAAGAACTT
1 GAAGGGTTCGTAATGAGA-AGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * * * * *
7232 GTTCAGAACTCAGTATAT-CAGTCACATAAGGAGATGGATCAATATTTCAGAA
65 GTTCAAAACTCGGCACATCCA-TCACACAAGGAGATGAATCAACATTTCAGAA
* * * *
7284 GAAGGGTTCGTAATAAGAAAAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAAAACTTG
1 GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
7349 TTCAAAACTCGGCACATCCATCACACAAGGAGATGGATCACCATTTCAGAA
66 TTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
* * * * *
7400 GAAGGGTCCGTAAT-AGGAAGAACTCGTCCAACGAGGAAGAAAAAGTTCATAATAAGAAGAACTT
1 GAAGGGTTCGTAATGA-GAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * * * *
7464 ATTCAAAACTCGACACATCCTTCACACAAGGAGATGTATCAACATGTCTGAA
65 GTTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
* * *
7516 GAAGGGTTTGTAATGAGAAGAACTCACCCAATGAGGAAGAAGGAGTTCATAATGAGAAGAAC---
1 GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
7578 TTCAAAACT-GAACACATCCATCACACAAGGAGAT-AGACCAACATTTTAGAA
66 TTCAAAACTCG-GCACATCCATCACACAAGGAGATGA-ATCAACATTTCAGAA
* * *
7629 AAAGAGTTCATAATGAGAAGAACTCATCC
1 GAAGGGTTCGTAATGAGAAGAACTCATCC
7658 GACGAAGGGT
Statistics
Matches: 608, Mismatches: 96, Indels: 31
0.83 0.13 0.04
Matches are distributed among these distances:
112 5 0.01
113 152 0.25
114 1 0.00
115 100 0.16
116 345 0.57
117 5 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (116 bp):
GAAGGGTTCGTAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAAAACTCGGCACATCCATCACACAAGGAGATGAATCAACATTTCAGAA
Found at i:8039 original size:153 final size:153
Alignment explanation
Indices: 7757--8067 Score: 496
Period size: 153 Copynumber: 2.0 Consensus size: 153
7747 GAGGTGGATA
* *
7757 AATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAAGGGGTCCATAATGAGAATAACTAATCC
1 AATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAAGGGGTCCATAATGAAAAGAACTAATCC
*
7822 AACGAGGAAGAAGAAGTTCGTAATAAGAAGGGCTTATTCAACATGGGATCGTCCGTCACTCAAGG
66 AACGAGGAAGAAGAAGTTCGTAATAAGAAGGGCTTATTCAACATGGGATCGTCCGTCACGCAAGG
7887 AGGTGGATTAAAGAAAAGTTCAT
131 AGGTGGATTAAAGAAAAGTTCAT
* * * * * *
7910 AATGAAGAGTTCATAATGAGAATAACTTATTCGAAGAAGGGGTTCATAATGAAAAGAACTCATCC
1 AATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAAGGGGTCCATAATGAAAAGAACTAATCC
* *
7975 AACGAGGAAGAAGAAGTTCGTAATGAGAAGGGCTTGTTCAACATGGGATCGTCCGTCACGCAAGG
66 AACGAGGAAGAAGAAGTTCGTAATAAGAAGGGCTTATTCAACATGGGATCGTCCGTCACGCAAGG
* * *
8040 AGGTGGATTAACGAAGAGTTCGT
131 AGGTGGATTAAAGAAAAGTTCAT
8063 AATGA
1 AATGA
8068 GAAGAACTCA
Statistics
Matches: 144, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
153 144 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.22
Consensus pattern (153 bp):
AATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAAGGGGTCCATAATGAAAAGAACTAATCC
AACGAGGAAGAAGAAGTTCGTAATAAGAAGGGCTTATTCAACATGGGATCGTCCGTCACGCAAGG
AGGTGGATTAAAGAAAAGTTCAT
Found at i:9883 original size:29 final size:30
Alignment explanation
Indices: 9851--9973 Score: 139
Period size: 29 Copynumber: 4.2 Consensus size: 30
9841 GTCAATAAAA
*
9851 TTTAGTTTTTTACACTTTA-GTCCCTAGAC
1 TTTAGATTTTTACACTTTAGGTCCCTAGAC
9880 TTTAGATTTTT-CA-TGCTTAGGTCCCTAGAC
1 TTTAGATTTTTACACT--TTAGGTCCCTAGAC
9910 TTTAGATTTTTACAC-TTAGGTCCCTAGAC
1 TTTAGATTTTTACACTTTAGGTCCCTAGAC
* *** *
9939 TTTAGAATTTTATGTTTTA-GTCCCTAAAC
1 TTTAGATTTTTACACTTTAGGTCCCTAGAC
9968 TTTAGA
1 TTTAGA
9974 CCTTTCACAT
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.01
28 2 0.02
29 53 0.65
30 24 0.29
31 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.46
Consensus pattern (30 bp):
TTTAGATTTTTACACTTTAGGTCCCTAGAC
Found at i:9914 original size:59 final size:58
Alignment explanation
Indices: 9846--9973 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 58
9836 TATTAGTCAA
* * *
9846 TAAAATTTAGTTTTTTACACTTTA-GTCCCTAGACTTTAGATTTTTCATG-CTTAGGTCCC
1 TAAACTTTAGATTTTTACAC-TTAGGTCCCTAGACTTTAGAATTTT-ATGTCTTA-GTCCC
* *
9905 TAGACTTTAGATTTTTACACTTAGGTCCCTAGACTTTAGAATTTTATGTTTTAGTCCC
1 TAAACTTTAGATTTTTACACTTAGGTCCCTAGACTTTAGAATTTTATGTCTTAGTCCC
9963 TAAACTTTAGA
1 TAAACTTTAGA
9974 CCTTTCACAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 21 0.34
59 40 0.66
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (58 bp):
TAAACTTTAGATTTTTACACTTAGGTCCCTAGACTTTAGAATTTTATGTCTTAGTCCC
Found at i:10981 original size:25 final size:26
Alignment explanation
Indices: 10939--11004 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
10929 TTAACTGAAA
* *
10939 AAATATTTTTTATGTTAACTT-A-TT
1 AAATATATTTTATATTAACTTAATTT
10963 AAATATATTTTATAATTAACTTAATTT
1 AAATATATTTTAT-ATTAACTTAATTT
*
10990 AAAAATATTTT-TATT
1 AAATATATTTTATATT
11005 TTTATTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.33
25 10 0.28
26 2 0.06
27 12 0.33
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (26 bp):
AAATATATTTTATATTAACTTAATTT
Found at i:10998 original size:27 final size:26
Alignment explanation
Indices: 10914--11000 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
10904 TTAAATGCAT
*
10914 AATATTTTATATATATTAACTGA--AAA
1 AATA-TTT-TATATATTAACTTATTAAA
* *
10940 AATATTTTTTATGTTAACTTATTAAA
1 AATATTTTATATATTAACTTATTAAA
*
10966 TATATTTTATA-ATTAACTTAATTTAAA
1 AATATTTTATATATTAACTT-A-TTAAA
10993 AATATTTT
1 AATATTTT
11001 TATTTTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.22
25 10 0.20
26 17 0.34
27 12 0.24
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
AATATTTTATATATTAACTTATTAAA
Found at i:11588 original size:8 final size:8
Alignment explanation
Indices: 11564--11604 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
11554 TTTTCATTTA
11564 ATTATATT
1 ATTATATT
*
11572 AAATATATT
1 -ATTATATT
11581 ATTATATT
1 ATTATATT
*
11589 AATATATT
1 ATTATATT
11597 ATTATATT
1 ATTATATT
11605 TAAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATTATATT
Found at i:11594 original size:16 final size:17
Alignment explanation
Indices: 11564--11604 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
11554 TTTTCATTTA
11564 ATTATATTAAATATATT
1 ATTATATTAAATATATT
11581 ATTATATT-AATATATT
1 ATTATATTAAATATATT
11597 ATTATATT
1 ATTATATT
11605 TAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATATTAAATATATT
Found at i:11607 original size:17 final size:17
Alignment explanation
Indices: 11564--11612 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
11554 TTTTCATTTA
*
11564 ATTATATTAAATATATT
1 ATTATATTTAATATATT
11581 ATTATA-TTAATATATT
1 ATTATATTTAATATATT
*
11597 ATTATATTTAAAATAT
1 ATTATATTTAATATAT
11613 AACTATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATTTAATATATT
Found at i:12152 original size:20 final size:19
Alignment explanation
Indices: 12112--12247 Score: 139
Period size: 20 Copynumber: 6.9 Consensus size: 19
12102 ATAACCAACG
* *
12112 AATTCACAACGCGAATTCA
1 AATTCGCAACACGAATTCA
12131 AATTCGCAACACGAACTTCA
1 AATTCGCAACACGAA-TTCA
*
12151 AATTCGCAACACGAACTCA
1 AATTCGCAACACGAATTCA
*
12170 AATTTCGCAACAC-AGTTTCCA
1 AA-TTCGCAACACGA-ATT-CA
*
12191 AATTCGCAACACGAATTTA
1 AATTCGCAACACGAATTCA
* *
12210 GAATTCGCAACACAGAAGTAA
1 -AATTCGCAACAC-GAATTCA
*
12231 AATTCGCAACTCGAATT
1 AATTCGCAACACGAATT
12248 TGACAATTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
19 24 0.24
20 65 0.66
21 10 0.10
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (19 bp):
AATTCGCAACACGAATTCA
Found at i:12528 original size:22 final size:22
Alignment explanation
Indices: 12489--12543 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12479 TCTCTCACTC
* *
12489 TCTCCGGCGACATTCGTCCCCA
1 TCTCCGACGACATCCGTCCCCA
*
12511 TCTCCGACGATATCCGTCCCCA
1 TCTCCGACGACATCCGTCCCCA
* *
12533 TATTCGACGAC
1 TCTCCGACGAC
12544 CCCCCTCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.42, G:0.16, T:0.24
Consensus pattern (22 bp):
TCTCCGACGACATCCGTCCCCA
Found at i:13391 original size:22 final size:22
Alignment explanation
Indices: 13360--13421 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
13350 ATTAGAGATG
13360 AGGAA-GGATGTCGTCGGATAT
1 AGGAACGGATGTCGTCGGATAT
13381 AGGAACGGATGTCGTCGGATAT
1 AGGAACGGATGTCGTCGGATAT
* *
13403 AGAAACGGATGTCGCCGGA
1 AGGAACGGATGTCGTCGGA
13422 GAGAGTGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 5 0.13
22 33 0.87
ACGTcount: A:0.29, C:0.15, G:0.37, T:0.19
Consensus pattern (22 bp):
AGGAACGGATGTCGTCGGATAT
Found at i:13539 original size:20 final size:20
Alignment explanation
Indices: 13511--13558 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
13501 TCCAAAACAT
13511 TTGTGTTGCGAAAATAAAAG
1 TTGTGTTGCGAAAATAAAAG
* *
13531 TTGTTTTGCGAAATTAAAA-
1 TTGTGTTGCGAAAATAAAAG
13550 TTCGTGTTG
1 TT-GTGTTG
13559 TGAATTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGTGTTGCGAAAATAAAAG
Found at i:13639 original size:20 final size:20
Alignment explanation
Indices: 13616--13682 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
13606 GAAACGCGCT
13616 TTGCGAATTAGAAAATCTTG
1 TTGCGAATTAGAAAATCTTG
* *
13636 TTGCGAA-AATGAAACT-TGTG
1 TTGCGAATTA-GAAAATCT-TG
*
13656 TTGCGAATTTA-AAAATCGTG
1 TTGCGAA-TTAGAAAATCTTG
13676 TTGCGAA
1 TTGCGAA
13683 AAAGAAATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.05
20 34 0.92
22 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGCGAATTAGAAAATCTTG
Found at i:13649 original size:40 final size:40
Alignment explanation
Indices: 13585--13723 Score: 108
Period size: 40 Copynumber: 3.5 Consensus size: 40
13575 GTTGTGAAAA
* *
13585 TAAAATTCGCGTTGC-AAAATTGAAACGCGCT-TTGCGAA-T
1 TAAAAATCGTGTTGCGAAAA-TGAAACGCG-TGTTGCGAATT
* **
13624 TAGAAAATCTTGTTGCGAAAATGAAACTTGTGTTGCGAATT
1 TA-AAAATCGTGTTGCGAAAATGAAACGCGTGTTGCGAATT
* ** *
13665 TAAAAATCGTGTTGCGAAAAAGAAATTCGTATTGCGAA--
1 TAAAAATCGTGTTGCGAAAATGAAACGCGTGTTGCGAATT
*
13703 AAAAGAATTCGTGTTGCGAAA
1 TAAA-AA-TCGTGTTGCGAAA
13724 TTGTCAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
38 3 0.04
39 5 0.06
40 68 0.82
41 7 0.08
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (40 bp):
TAAAAATCGTGTTGCGAAAATGAAACGCGTGTTGCGAATT
Found at i:13680 original size:60 final size:60
Alignment explanation
Indices: 13513--13746 Score: 197
Period size: 60 Copynumber: 3.9 Consensus size: 60
13503 CAAAACATTT
* * * * *
13513 GTGTTGCGAAAATAAAAGTT-GTTTTGCGAAATTAAAATTCGTGTTGTGAATTCGGAAATC
1 GTGTTGCGAAAATAAAA-TTCGTGTTGCGAAATTAAAAATCGTGTTGCGAATTAGAAAATC
* * * * * **
13573 GAGTTGTGAAAATAAAATTCGCGTTGCAAAATTGAAACGCGCT-TTGCGAATTAGAAAATC
1 GTGTTGCGAAAATAAAATTCGTGTTGCGAAATTAAAAATCG-TGTTGCGAATTAGAAAATC
* * * ** *
13633 TTGTTGCGAAAATGAAACTT-GTGTTGCGAATTTAAAAATCGTGTTGCGAAAAAGAAATTC
1 GTGTTGCGAAAAT-AAAATTCGTGTTGCGAAATTAAAAATCGTGTTGCGAATTAGAAAATC
* * *
13693 GTATTGCGAAAA-AAGAATTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAATT
1 GTGTTGCGAAAATAA-AATTCGTGTTGCGAAA-T-TAAAAATCGTGTTGCGAATT
13747 TGGAAACTGT
Statistics
Matches: 134, Mismatches: 32, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
58 2 0.01
59 6 0.04
60 103 0.77
61 7 0.05
62 16 0.12
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (60 bp):
GTGTTGCGAAAATAAAATTCGTGTTGCGAAATTAAAAATCGTGTTGCGAATTAGAAAATC
Found at i:13694 original size:20 final size:19
Alignment explanation
Indices: 13634--13723 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 19
13624 TAGAAAATCT
*
13634 TGTTGCGAAAATGAAACTT-G
1 TGTTGCGAAAA--AAAATTCG
*
13654 TGTTGCGAATTTAAAAA-TCG
1 TGTTGCGAA--AAAAAATTCG
13674 TGTTGCGAAAAAGAAATTCG
1 TGTTGCGAAAAA-AAATTCG
*
13694 TATTGCGAAAAAAGAATTCG
1 TGTTGCGAAAAAA-AATTCG
13714 TGTTGCGAAA
1 TGTTGCGAAA
13724 TTGTCAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
18 2 0.03
19 5 0.08
20 51 0.86
22 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (19 bp):
TGTTGCGAAAAAAAATTCG
Found at i:15876 original size:39 final size:39
Alignment explanation
Indices: 15826--15932 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
15816 ATTTAAAAAT
* *
15826 AATTTAAAATGTTAATATGAAATAATTTGAGAAATTAAA
1 AATTTAGAATGTTAATGTGAAATAATTTGAGAAATTAAA
* * *
15865 AATTTAGAATGTT-ATGGTAGCAA-AATTTAAGAAATTAAG
1 AATTTAGAATGTTAAT-GT-GAAATAATTTGAGAAATTAAA
*
15904 TATTTAGAATGTTAGA-GTGAAATAATTTG
1 AATTTAGAATGTTA-ATGTGAAATAATTTG
15933 TAAATTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 5 0.09
39 46 0.84
40 3 0.05
41 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.16, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTGAGAAATTAAA
Found at i:34427 original size:34 final size:32
Alignment explanation
Indices: 34383--34473 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 32
34373 TTGTTTGTGC
* *
34383 AATAGAATAAAGAGTTAGTAAGTTATTAATAACA
1 AATA-AATAAA-AGTTAGTAAGTTAATAAGAACA
34417 GTAA-AAATAAAAAGTTAGTATA-TTAATAAGAACA
1 --AATAAAT-AAAAGTTAGTA-AGTTAATAAGAACA
*
34451 AATAAATAAAAGTTAGTATGTTA
1 AATAAATAAAAGTTAGTAAGTTA
34474 GTTTGAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
32 16 0.33
33 4 0.08
34 21 0.44
35 5 0.10
36 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (32 bp):
AATAAATAAAAGTTAGTAAGTTAATAAGAACA
Found at i:34482 original size:32 final size:32
Alignment explanation
Indices: 34382--34506 Score: 101
Period size: 32 Copynumber: 3.8 Consensus size: 32
34372 GTTGTTTGTG
* * * *
34382 CAATAGAATAAAGAGTTAGTAAGTTATTAATAA
1 CAATAAAATAAA-AGTTAGTATGTTAATAAGAA
* *
34415 CAGTAAAAATAAAAAGTTAGTATATTAATAAGAA
1 CAAT-AAAAT-AAAAGTTAGTATGTTAATAAGAA
* **
34449 CAA-ATAAATAAAAGTTAGTATGTTAGTTTGAA
1 CAATA-AAATAAAAGTTAGTATGTTAATAAGAA
*
34481 CAATAAAATAAATA-TTAGAATGTTAA
1 CAATAAAATAAA-AGTTAGTATGTTAA
34507 CAAGTTAGTA
Statistics
Matches: 74, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
32 40 0.54
33 9 0.12
34 22 0.30
35 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTATGTTAATAAGAA
Found at i:47418 original size:16 final size:18
Alignment explanation
Indices: 47397--47433 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
47387 ACTTGAATAT
47397 TATTTATAAC-ATTT-TG
1 TATTTATAACTATTTATG
*
47413 TATTTATTACTATTTATG
1 TATTTATAACTATTTATG
47431 TAT
1 TAT
47434 AAGAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
TATTTATAACTATTTATG
Found at i:48071 original size:35 final size:34
Alignment explanation
Indices: 48016--48109 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 34
48006 TGAAAGTATT
*
48016 AAAATGGTTTTTGAAA-TTTGGTAA-CCAACTTTG
1 AAAATGG-TTTTCAAAGTTTGGTAATCCAACTTTG
****
48049 AAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 --AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
48086 AAAATGGTTTTCAAAGTTTGGTAA
1 AAAATGGTTTTCAAAGTTTGGTAA
48110 ATATTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 9 0.18
35 35 0.69
36 2 0.04
37 5 0.10
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:48076 original size:21 final size:21
Alignment explanation
Indices: 48052--48111 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
48042 AACTTTGAAA
48052 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
48073 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
48087 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
48108 AAAT
1 AAAT
48112 ATTTATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:48158 original size:36 final size:36
Alignment explanation
Indices: 48045--48163 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
48035 GGTAACCAAC
*
48045 TTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
*
48082 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTTA
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
* * *
48117 TTTGAAAAATAGTTTTTCAAAGTTTGATAGATGTTT-
1 TTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTA
*
48153 GTTGAAAAATG
1 TTTGAAAAATG
48164 ATAATGGGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 34 0.47
36 14 0.19
37 25 0.34
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
Found at i:52690 original size:35 final size:34
Alignment explanation
Indices: 52638--52767 Score: 100
Period size: 35 Copynumber: 3.7 Consensus size: 34
52628 TGAAAGTATT
**
52638 AAAATGGTTTTTGAAGTTTGGTAA-CCAACTTTG
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
****
52671 AAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 --AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
****
52708 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
*
52743 AAAAATAGTTTTTCAAAGTTTGGTA
1 -AAAAT-GGTTTTCAAAGTTTGGTA
52768 GATGTTTGTT
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
35 55 0.65
36 8 0.10
37 21 0.25
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:52698 original size:21 final size:21
Alignment explanation
Indices: 52674--52734 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
52664 AACTTTGAAA
52674 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
52695 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
52709 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
52730 AAATG
1 AAATG
52735 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:52765 original size:37 final size:37
Alignment explanation
Indices: 52666--52784 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
52656 TGGTAACCAA
52666 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
52703 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
52738 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
52775 -GTTGAAAAAT
1 CTTTGAAAAAT
52785 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:54758 original size:49 final size:49
Alignment explanation
Indices: 54686--54779 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
54676 GTTGATGTAT
54686 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGTGCC
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGTGCC
*
54735 CTATGCTTAAAAAATATGTAGTATAAAAATTATAAAACTTTTATG
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATG
54780 GGGCCTGGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (49 bp):
CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGTGCC
Found at i:65176 original size:18 final size:18
Alignment explanation
Indices: 65153--65187 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65143 ATTTTATACT
*
65153 ACATATTAACTTAAATTC
1 ACATATTAAATTAAATTC
65171 ACATATTAAATTAAATT
1 ACATATTAAATTAAATT
65188 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
ACATATTAAATTAAATTC
Found at i:65233 original size:16 final size:16
Alignment explanation
Indices: 65212--65244 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
65202 AAAAATATAT
*
65212 ATTTTAATTTATCTTA
1 ATTTTAATTTAACTTA
65228 ATTTTAATTTAACTTA
1 ATTTTAATTTAACTTA
65244 A
1 A
65245 ATAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAATTTAACTTA
Found at i:65259 original size:21 final size:21
Alignment explanation
Indices: 65191--65259 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
65181 TTAAATTAAA
*
65191 ATTTTAACATTAAA-AATATAT
1 ATTTTAAC-TTAAATAAAATAT
* ** * * *
65212 ATTTTAATTTATCTTAATTTT
1 ATTTTAACTTAAATAAAATAT
*
65233 AATTTAACTTAAATAAAATAT
1 ATTTTAACTTAAATAAAATAT
65254 ATTTTA
1 ATTTTA
65260 TTTTTACCTT
Statistics
Matches: 32, Mismatches: 15, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAACTTAAATAAAATAT
Found at i:65272 original size:43 final size:41
Alignment explanation
Indices: 65193--65298 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 41
65183 AAATTAAAAT
* *
65193 TTTAACATTAAAAATATATATTTTAATTTATCTTAATTTTAA
1 TTTAAC-TTAAAAAAATATATTTTAATTTACCTTAATTTTAA
*
65235 TTTAACTTAAATAAAATATATTTTATTTTTACCTTAATTTTAA
1 TTTAACTTAAA-AAAATATATTTTA-ATTTACCTTAATTTTAA
*
65278 TTTAACTTAAAAATATA-ATTT
1 TTTAACTTAAAAAAATATATTT
65299 ATTCTTGGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
41 9 0.16
42 23 0.40
43 26 0.45
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (41 bp):
TTTAACTTAAAAAAATATATTTTAATTTACCTTAATTTTAA
Found at i:65314 original size:30 final size:32
Alignment explanation
Indices: 65278--65336 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
65268 TTAATTTTAA
65278 TTTAACTTAAA-A-ATATAATTTATTCTTGGT
1 TTTAACTTAAATATATATAATTTATTCTTGGT
* *
65308 TTTAACTTAAATATTTATATTTTATTCTT
1 TTTAACTTAAATATATATAATTTATTCTT
65337 ATAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 1 0.04
32 13 0.52
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTAACTTAAATATATATAATTTATTCTTGGT
Found at i:65372 original size:28 final size:29
Alignment explanation
Indices: 65340--65418 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
65330 TATTCTTATA
*
65340 ATATTTTAAAATTAAGATAA-AATAAAAT
1 ATATTTTAAAATTAAAATAAGAATAAAAT
*
65368 ATATTTTTAAATTAAAATAAGAATAAAAT
1 ATATTTTAAAATTAAAATAAGAATAAAAT
* *
65397 ATAAATTTTTAAATAAAAATAA
1 AT--ATTTTAAAATTAAAATAA
65419 ACTATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.40
29 10 0.22
31 17 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
ATATTTTAAAATTAAAATAAGAATAAAAT
Found at i:65408 original size:31 final size:30
Alignment explanation
Indices: 65336--65419 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 30
65326 ATTTTATTCT
* *
65336 TATAATATTTTAAAATTAAGATAAAATAAAA
1 TATAA-ATTTTTAAATTAAAATAAAATAAAA
65367 TAT--ATTTTTAAATTAAAATAAGAATAAAA
1 TATAAATTTTTAAATTAAAATAA-AATAAAA
*
65396 TATAAATTTTTAAATAAAAATAAA
1 TATAAATTTTTAAATTAAAATAAA
65420 CTATATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 16 0.34
29 10 0.21
30 1 0.02
31 20 0.43
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TATAAATTTTTAAATTAAAATAAAATAAAA
Found at i:65546 original size:27 final size:30
Alignment explanation
Indices: 65435--65529 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
65425 TATTAAAATT
* * *
65435 TAAAATATAT-TTTTATGTTAAAGTACGAA
1 TAAAATATATATTTTAAGTTAAAATAAGAA
* * *
65464 TAAATTATATTTTTTAAGTTAAGATAAGAA
1 TAAAATATATATTTTAAGTTAAAATAAGAA
65494 TAAAATATATATTTTAAGTTAAAATAAGAA
1 TAAAATATATATTTTAAGTTAAAATAAGAA
65524 TAAAAT
1 TAAAAT
65530 GTATTTAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 9 0.16
30 48 0.84
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (30 bp):
TAAAATATATATTTTAAGTTAAAATAAGAA
Found at i:65604 original size:18 final size:18
Alignment explanation
Indices: 65571--65622 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
65561 TATATTTTTT
*
65571 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
65590 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
65608 TTTAAGTTAAGATGT
1 TTTAATTTAAGATGT
65623 ATTATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:66539 original size:43 final size:42
Alignment explanation
Indices: 66451--66550 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
66441 CGATGTTTGA
*
66451 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGCAG
* *
66493 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTGCAG-G-GG
1 GTGCATGGATGCACTGCAGGG-TGCATCGATGCACT--AGTGCAG
66536 GTGCATGGATGCACT
1 GTGCATGGATGCACT
66551 TTGACACCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
42 20 0.38
43 29 0.56
44 1 0.02
45 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.22
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGCAG
Found at i:66543 original size:22 final size:21
Alignment explanation
Indices: 66451--66550 Score: 116
Period size: 22 Copynumber: 4.7 Consensus size: 21
66441 CGATGTTTGA
*
66451 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
66471 GTGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
66493 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
66514 ATGCATGGATGCACTGCAGGGG
1 GTGCATGGATGCACTGCA-GGG
66536 GTGCATGGATGCACT
1 GTGCATGGATGCACT
66551 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.01
20 14 0.21
21 18 0.26
22 32 0.47
23 1 0.01
24 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:66651 original size:29 final size:29
Alignment explanation
Indices: 66630--66687 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
66620 AAACTTTGAA
66630 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
66659 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
66688 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:66677 original size:30 final size:30
Alignment explanation
Indices: 66630--66689 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
66620 AAACTTTGAA
66630 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
66659 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
66690 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:66833 original size:21 final size:21
Alignment explanation
Indices: 66800--66839 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66790 TTGTTTAATG
*
66800 AAAAAGATGTCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
66821 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
66840 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:67066 original size:25 final size:24
Alignment explanation
Indices: 67032--67080 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
67022 TAAACAACCT
*
67032 AATAAATATATCAATTTTTTAAATA
1 AATAAATATATCAA-ATTTTAAATA
67057 AATAAATATATCAAATTTTAAATA
1 AATAAATATATCAAATTTTAAATA
67081 GAAAAACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAAATATATCAAATTTTAAATA
Found at i:69043 original size:25 final size:24
Alignment explanation
Indices: 68980--69052 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
68970 GGAATCAAGC
*
68980 TTTCAATAAGATAAATCATTCATA
1 TTTCAATAAGATAAAACATTCATA
***
69004 AGCCAAATCAA-ATAAAACATTCATA
1 TTTC-AAT-AAGATAAAACATTCATA
*
69029 TTTCAAGTAAGATAAAACAATCAT
1 TTTCAA-TAAGATAAAACATTCAT
69053 GTGCACATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
24 5 0.14
25 30 0.81
26 2 0.05
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (24 bp):
TTTCAATAAGATAAAACATTCATA
Found at i:70438 original size:21 final size:20
Alignment explanation
Indices: 70412--70460 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
70402 CAAACTAAAG
*
70412 TATCAAACCTTAAGTCATATA
1 TATCAAACCTTAA-TCAAATA
**
70433 TATCAATATTTTAATCAAATA
1 TATCAA-ACCTTAATCAAATA
70454 TATCAAA
1 TATCAAA
70461 TCTCATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (20 bp):
TATCAAACCTTAATCAAATA
Found at i:72396 original size:13 final size:13
Alignment explanation
Indices: 72378--72438 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
72368 CGCAATGTAA
*
72378 GTCATAATTGCGC
1 GTCATAAATGCGC
*
72391 GTCATAAATGCGT
1 GTCATAAATGCGC
72404 GTCATAAATGCGC
1 GTCATAAATGCGC
*
72417 ATCATAAATGCGC
1 GTCATAAATGCGC
72430 GTCATAAAT
1 GTCATAAAT
72439 TTATGACGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:73551 original size:16 final size:16
Alignment explanation
Indices: 73530--73563 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
73520 CGCCGCATGC
73530 TTTTCCATTTTTCTCT
1 TTTTCCATTTTTCTCT
*
73546 TTTTCCCTTTTTCTCT
1 TTTTCCATTTTTCTCT
73562 TT
1 TT
73564 GCAACCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCCATTTTTCTCT
Found at i:78325 original size:2 final size:2
Alignment explanation
Indices: 78318--78371 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
78308 TCAATCTACA
78318 AT AT AT AT -T 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 AT AT AT AT
78359 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
78372 ATTTACGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78552 original size:13 final size:13
Alignment explanation
Indices: 78534--78582 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
78524 GCTCAATGAA
*
78534 CGTCATAAATACG
1 CGTCATAAATGCG
*
78547 CGTCATAAATGTG
1 CGTCATAAATGCG
*
78560 TGTCATAAATGCG
1 CGTCATAAATGCG
78573 CGTCATAAAT
1 CGTCATAAAT
78583 TTATGACGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:78557 original size:26 final size:26
Alignment explanation
Indices: 78528--78582 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
78518 AATGACGCTC
78528 AATGAACGTCATAAATACGCGTCATA
1 AATGAACGTCATAAATACGCGTCATA
*** *
78554 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATACGCGTCATA
78580 AAT
1 AAT
78583 TTATGACGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (26 bp):
AATGAACGTCATAAATACGCGTCATA
Found at i:79644 original size:60 final size:60
Alignment explanation
Indices: 79523--79635 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
79513 TTTTGTCACC
* *
79523 TTTAATAGTTGAGGGACTTAACAAAGTAGCACATTACAATCGAGTGACCATTTTATAACT
1 TTTAATAGTTGAGGGACTCAACAAAGTAGCACATTACAATCGAGGGACCATTTTATAACT
* * * * * *
79583 TTTAATAGTTTATGGTCTCAACAAAGTAGCGACA-TATAGTTGAGGGACCATTT
1 TTTAATAGTTGAGGGACTCAACAAAGTAGC-ACATTACAATCGAGGGACCATTT
79636 GTGTACTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 41 0.93
61 3 0.07
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (60 bp):
TTTAATAGTTGAGGGACTCAACAAAGTAGCACATTACAATCGAGGGACCATTTTATAACT
Found at i:81202 original size:2 final size:2
Alignment explanation
Indices: 81195--81228 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
81185 ATTATCTTGG
81195 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
81229 TAATAATTTG
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:81769 original size:37 final size:38
Alignment explanation
Indices: 81727--81846 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 38
81717 AATATATACT
81727 AAAAAACCATATAATATTATATTTTC-AAATATGTTTTC
1 AAAAAA-CATATAATATTATATTTTCAAAATATGTTTTC
** * * *
81765 AAAAATTATATATTATATATATGTTTCCAAAAAATTTGTTTTA
1 AAAAAACATATAATAT-TATAT-TTT-C--AAAATATGTTTTC
*
81808 AAAAAAC-TAT-ATA-TATGTTTTCAAAATATGTTTTC
1 AAAAAACATATAATATTATATTTTCAAAATATGTTTTC
81843 AAAA
1 AAAA
81847 CTATATTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
35 15 0.23
37 9 0.14
38 13 0.20
39 7 0.11
40 1 0.02
41 2 0.03
42 3 0.05
43 15 0.23
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (38 bp):
AAAAAACATATAATATTATATTTTCAAAATATGTTTTC
Found at i:81834 original size:35 final size:33
Alignment explanation
Indices: 81778--81888 Score: 107
Period size: 36 Copynumber: 3.2 Consensus size: 33
81768 AATTATATAT
* *
81778 TATATATATGTTTCCAAAAAATTTGTTTTAAAAAAAC
1 TATATATATGTTTTC--AAAATATGTTTT--AAAAAC
*
81815 TATATATATGTTTTCAAAATATGTTTTCAAAAC
1 TATATATATGTTTTCAAAATATGTTTTAAAAAC
*
81848 TATATTATATACGTTTTCAAAA-ATCGTTTTTAAAAC
1 TATA-TATAT--GTTTTCAAAATAT-GTTTTAAAAAC
81884 TATAT
1 TATAT
81889 GTCGAGACGT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
33 9 0.14
34 5 0.08
35 14 0.21
36 24 0.36
37 14 0.21
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.44
Consensus pattern (33 bp):
TATATATATGTTTTCAAAATATGTTTTAAAAAC
Found at i:81838 original size:13 final size:13
Alignment explanation
Indices: 81820--81846 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
81810 AAAACTATAT
81820 ATATGTTTTCAAA
1 ATATGTTTTCAAA
81833 ATATGTTTTCAAA
1 ATATGTTTTCAAA
81846 A
1 A
81847 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:81864 original size:36 final size:34
Alignment explanation
Indices: 81810--81888 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 34
81800 TTGTTTTAAA
81810 AAAACTATA-TATATGTTTTCAAAATAT-GTTTTC
1 AAAACTATATTATATGTTTTCAAAA-ATCGTTTTC
*
81843 AAAACTATATTATATACGTTTTCAAAAATCGTTTTT
1 AAAACTATATTATAT--GTTTTCAAAAATCGTTTTC
81879 AAAACTATAT
1 AAAACTATAT
81889 GTCGAGACGT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 9 0.22
34 5 0.12
35 2 0.05
36 25 0.61
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (34 bp):
AAAACTATATTATATGTTTTCAAAAATCGTTTTC
Found at i:81899 original size:37 final size:36
Alignment explanation
Indices: 81824--81901 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
81814 CTATATATAT
* *
81824 GTTTTCAAAATATGTTTTCAAAACTATATTATATAC
1 GTTTTCAAAATATGTTTTCAAAACTATATTAGAGAC
* *
81860 GTTTTCAAAA-ATCGTTTTTAAAACTATATGTCGAGAC
1 GTTTTCAAAATAT-GTTTTCAAAACTATAT-TAGAGAC
81897 GTTTT
1 GTTTT
81902 TTGCCCGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 2 0.06
36 25 0.69
37 9 0.25
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (36 bp):
GTTTTCAAAATATGTTTTCAAAACTATATTAGAGAC
Found at i:82364 original size:20 final size:20
Alignment explanation
Indices: 82306--82357 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
82296 CTATTATAAT
*
82306 ATTATATTATAATCATATAG
1 ATTAAATTATAATCATATAG
82326 ATTAAATTATAATCATATAG
1 ATTAAATTATAATCATATAG
82346 ATTAAATTATAA
1 ATTAAATTATAA
82358 ATTTATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (20 bp):
ATTAAATTATAATCATATAG
Found at i:83991 original size:35 final size:35
Alignment explanation
Indices: 83937--84073 Score: 186
Period size: 35 Copynumber: 3.9 Consensus size: 35
83927 TGATCTGATC
83937 TTGCTTCACTACTCTTTTGTGAAGGC-TGAATTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTG-ATTGCA
* * *
83972 TTGCTTCACAACTCCTTTGTGAAGGCTTGATTACA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
* * *
84007 TTACTTCACTACTCTTTTGTTAAAGCTTGATTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
* *
84042 TTGATTCACTACTCTTTTGTGAAGTCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
84074 CAAATAACTT
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 85 0.98
36 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (35 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
Done.