Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015023.1 Corchorus olitorius cultivar O-4 contig15056, 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: 137382
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:740 original size:80 final size:80
Alignment explanation
Indices: 607--788 Score: 283
Period size: 80 Copynumber: 2.3 Consensus size: 80
597 AAATCAAACC
* * * *
607 TTTAAAGATAGGAATCGAAGGAGAAATTGGTTTTTTGTTTGATGAAAAGTTTTTGAAATTAGGAT
1 TTTAAAGATAGGAATCGAAGAAGAAATTGGATTTTCGTTTGATAAAAAGTTTTTGAAATTAGGAT
**
672 TTTGGTGGAAGAAGG
66 TTTGGCAGAAGAAGG
*
687 TTTAAAGATAGGAATCGAAGAAGAAATTGGATTTTCGTTTGATAAAAAGTTTTTGAAATTAGGGT
1 TTTAAAGATAGGAATCGAAGAAGAAATTGGATTTTCGTTTGATAAAAAGTTTTTGAAATTAGGAT
*
752 TTTGGCAGAAGAGGG
66 TTTGGCAGAAGAAGG
*
767 TTTAAAGAGAGGAATCGAAGAA
1 TTTAAAGATAGGAATCGAAGAA
789 TAAAAAAAGG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 93 1.00
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (80 bp):
TTTAAAGATAGGAATCGAAGAAGAAATTGGATTTTCGTTTGATAAAAAGTTTTTGAAATTAGGAT
TTTGGCAGAAGAAGG
Found at i:3606 original size:13 final size:13
Alignment explanation
Indices: 3573--3605 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3563 TTTTTGTGTC
3573 TTCTTTCTCTTCTT
1 TTCTTT-TCTTCTT
3587 TTCTTTTCTTCTT
1 TTCTTTTCTTCTT
3600 TT-TTTT
1 TTCTTTT
3606 TTTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTCTTCTT
Found at i:8612 original size:19 final size:20
Alignment explanation
Indices: 8573--8615 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
8563 AGCATCCGAT
8573 ACAATTAAAAGATAAAGAGTA
1 ACAATTAAAAGAT-AAGAGTA
*
8594 ACAATTAGAAGAT-AGAGTA
1 ACAATTAAAAGATAAGAGTA
8613 ACA
1 ACA
8616 CTATTGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (20 bp):
ACAATTAAAAGATAAGAGTA
Found at i:10550 original size:82 final size:82
Alignment explanation
Indices: 10404--10556 Score: 254
Period size: 82 Copynumber: 1.9 Consensus size: 82
10394 TCTGCTTACC
* *
10404 TAATTGTGAATTTTTATTCTTTAGGTAGCAAAGTGACAGTTTAGGTATAGTACAAATGCAAAATT
1 TAATTGTGAATTTTTATTCTTTAGGTACCAAAGTGACAGTTTAGGTATAATACAAATGCAAAATT
10469 CTAATAGTTCAGGTACA
66 CTAATAGTTCAGGTACA
* *
10486 TAATTTTGAATTTTTATTCTTTAGGTACCAAAGTGACAGTTTAGGTATAATACTAATGTC-AAAT
1 TAATTGTGAATTTTTATTCTTTAGGTACCAAAGTGACAGTTTAGGTATAATACAAATG-CAAAAT
10550 TCTAATA
65 TCTAATA
10557 ACCCTATTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
82 65 0.98
83 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (82 bp):
TAATTGTGAATTTTTATTCTTTAGGTACCAAAGTGACAGTTTAGGTATAATACAAATGCAAAATT
CTAATAGTTCAGGTACA
Found at i:10753 original size:2 final size:2
Alignment explanation
Indices: 10746--10776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10736 GGAAAAATCA
10746 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10777 ATGAGCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14672 original size:2 final size:2
Alignment explanation
Indices: 14665--14704 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14655 AAAAATAAGG
14665 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14705 AACAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19386 original size:21 final size:21
Alignment explanation
Indices: 19352--19480 Score: 159
Period size: 21 Copynumber: 6.1 Consensus size: 21
19342 AGTGACGACT
* *
19352 CCGATCATAAGGGGATCTCTC
1 CCGAGCATATGGGGATCTCTC
*
19373 ACGAGCATATGGGGATCTCTC
1 CCGAGCATATGGGGATCTCTC
* *
19394 CCGAGTATATGGGGATTTCTC
1 CCGAGCATATGGGGATCTCTC
* *
19415 CCGAACATATGGGGATTTCTC
1 CCGAGCATATGGGGATCTCTC
*
19436 CCGAGCATATGGGGACCTCTC
1 CCGAGCATATGGGGATCTCTC
* * *
19457 CCTAGAATACGGGGATCTCTC
1 CCGAGCATATGGGGATCTCTC
19478 CCG
1 CCG
19481 TCGAATTGGG
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 92 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (21 bp):
CCGAGCATATGGGGATCTCTC
Found at i:19471 original size:63 final size:63
Alignment explanation
Indices: 19352--19480 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
19342 AGTGACGACT
* * * * *
19352 CCGATCATAAGGGGATCTCTCACGAGCATATGGGGATCTCTCCCGAGTATATGGGGATTTCTC
1 CCGAACATAAGGGGATCTCTCACGAGCATATGGGGACCTCTCCCGAGAATACGGGGATCTCTC
* * * *
19415 CCGAACATATGGGGATTTCTCCCGAGCATATGGGGACCTCTCCCTAGAATACGGGGATCTCTC
1 CCGAACATAAGGGGATCTCTCACGAGCATATGGGGACCTCTCCCGAGAATACGGGGATCTCTC
19478 CCG
1 CCG
19481 TCGAATTGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (63 bp):
CCGAACATAAGGGGATCTCTCACGAGCATATGGGGACCTCTCCCGAGAATACGGGGATCTCTC
Found at i:20083 original size:42 final size:42
Alignment explanation
Indices: 20024--20149 Score: 225
Period size: 42 Copynumber: 3.0 Consensus size: 42
20014 ACTTTACAGA
*
20024 AGGTGGTGTGCGTTCCATCTCGTATTTCCAGCTTTTTTCCTT
1 AGGTGGTGTGCGTTCCATCTCATATTTCCAGCTTTTTTCCTT
*
20066 AGGTGGTGTCCGTTCCATCTCATATTTCCAGCTTTTTTCCTT
1 AGGTGGTGTGCGTTCCATCTCATATTTCCAGCTTTTTTCCTT
*
20108 AGGTGGTGTGCGTTCCATCTCATATTTCCAGCCTTTTTCCTT
1 AGGTGGTGTGCGTTCCATCTCATATTTCCAGCTTTTTTCCTT
20150 TCCAAACTCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.44
Consensus pattern (42 bp):
AGGTGGTGTGCGTTCCATCTCATATTTCCAGCTTTTTTCCTT
Found at i:20446 original size:24 final size:24
Alignment explanation
Indices: 20418--20473 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
20408 CCCCTTCTCC
20418 ACCTCCCCTTTTCCATCAGAAACA
1 ACCTCCCCTTTTCCATCAGAAACA
20442 ACCTCCCCTTTTCCATCAGAAACA
1 ACCTCCCCTTTTCCATCAGAAACA
*
20466 ATCTCCCC
1 ACCTCCCC
20474 CTTCTCTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.45, G:0.04, T:0.25
Consensus pattern (24 bp):
ACCTCCCCTTTTCCATCAGAAACA
Found at i:20831 original size:15 final size:15
Alignment explanation
Indices: 20811--20849 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20801 ACGTGGTGGC
20811 TGCTGCTGTGATGGT
1 TGCTGCTGTGATGGT
*
20826 TGCTGCTCTGATGGT
1 TGCTGCTGTGATGGT
*
20841 TGTTGCTGT
1 TGCTGCTGT
20850 TGCTCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.15, G:0.36, T:0.44
Consensus pattern (15 bp):
TGCTGCTGTGATGGT
Found at i:24043 original size:21 final size:19
Alignment explanation
Indices: 24019--24071 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
24009 TATTAATATG
24019 ATCTAATTAATGACAATGGTA
1 ATCTAATT-ATGACAA-GGTA
*
24040 ATCTAATTAT--CAAGGTG
1 ATCTAATTATGACAAGGTA
24057 ATCTAATTTATGACA
1 ATCTAA-TTATGACA
24072 GTTCCAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
20 4 0.14
21 8 0.29
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (19 bp):
ATCTAATTATGACAAGGTA
Found at i:24060 original size:17 final size:17
Alignment explanation
Indices: 24002--24064 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
23992 TATGGTAATA
* **
24002 ATCTAATTATTAATATG
1 ATCTAATTATCAAGGTG
*
24019 ATCTAATTAATGACAATGGTA
1 ATCTAATT-AT--CAA-GGTG
24040 ATCTAATTATCAAGGTG
1 ATCTAATTATCAAGGTG
24057 ATCTAATT
1 ATCTAATT
24065 TATGACAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
17 19 0.51
18 5 0.14
20 4 0.11
21 9 0.24
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (17 bp):
ATCTAATTATCAAGGTG
Found at i:24081 original size:38 final size:38
Alignment explanation
Indices: 24001--24082 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 38
23991 CTATGGTAAT
* * **
24001 AATCTAATTATTAATATGATCTAATTAATGACAATGGT
1 AATCTAATTATCAAGATGATCTAATTAATGACAATGCC
* * * *
24039 AATCTAATTATCAAGGTGATCTAATTTATGACAGTTCC
1 AATCTAATTATCAAGATGATCTAATTAATGACAATGCC
24077 AATCTA
1 AATCTA
24083 CTTTTATGAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (38 bp):
AATCTAATTATCAAGATGATCTAATTAATGACAATGCC
Found at i:30878 original size:30 final size:30
Alignment explanation
Indices: 30842--30899 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
30832 CCATGAATTT
* *
30842 ATAAGACTATAATTATTATTTT-TTTGAAAA
1 ATAAGACTAT-ATAATCATTTTATTTGAAAA
30872 ATAAGACTATATAATCATTTTATTTGAA
1 ATAAGACTATATAATCATTTTATTTGAA
30900 CATGAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
ATAAGACTATATAATCATTTTATTTGAAAA
Found at i:36542 original size:58 final size:58
Alignment explanation
Indices: 36472--36581 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
36462 ATTAATCAAA
* *
36472 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAAGAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTTCTTTATTAGATGTC-TAAA-AAAGACATTTTAGGACCAAGACT
* *
36530 TATCGAGTGACATGTTTTTTTATTAGATGTCTAAAAAAGACATTTTAGGACC
1 TATCAAGTGACATGTTTCTTTATTAGATGTCTAAAAAAGACATTTTAGGACC
36582 GAGGCATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 28 0.61
59 17 0.37
60 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (58 bp):
TATCAAGTGACATGTTTCTTTATTAGATGTCTAAAAAAGACATTTTAGGACCAAGACT
Found at i:38951 original size:24 final size:23
Alignment explanation
Indices: 38919--38964 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
38909 ACGTTTGCAC
38919 AAATACCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
38943 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
38965 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:39014 original size:39 final size:40
Alignment explanation
Indices: 38955--39035 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
38945 ATACCTAAGA
* *
38955 ATTTAATTAATGTAAGTATTTTAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
38994 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
39034 AT
1 AT
39036 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
Found at i:39030 original size:18 final size:18
Alignment explanation
Indices: 38971--39031 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
38961 TTAATGTAAG
38971 TATTTTAGTTATTATAGTA
1 TATTTTAGTTATTATA-TA
* * * * *
38990 TTACATTTAATTAATGTAAA
1 -TA-TTTTAGTTATTATATA
39010 TATTTTAGTTATTATATA
1 TATTTTAGTTATTATATA
39028 TATT
1 TATT
39032 ACATAGGAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
20 3 0.10
21 10 0.33
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTTTAGTTATTATATA
Found at i:39270 original size:6 final size:6
Alignment explanation
Indices: 39252--39293 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
39242 GTTTAGACTT
39252 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
39294 TAGGTATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:41641 original size:60 final size:60
Alignment explanation
Indices: 41576--41696 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
41566 CATTTAACAT
* * * *
41576 GATGACAATACAAGATTCAGTTAAGTTCACCATACCAAATAAGCACCACGATCAATAAAA
1 GATGACAATACAAAATTAAGTTAAGTTCACCATACCAAACAAGCACCACAATCAATAAAA
* * * *
41636 GATGACGATGCAAAATTAAGTTATGTTCACCATACCAAACAAGCACCCCAATCAATAAAA
1 GATGACAATACAAAATTAAGTTAAGTTCACCATACCAAACAAGCACCACAATCAATAAAA
41696 G
1 G
41697 TAAAACTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.20
Consensus pattern (60 bp):
GATGACAATACAAAATTAAGTTAAGTTCACCATACCAAACAAGCACCACAATCAATAAAA
Found at i:44191 original size:30 final size:30
Alignment explanation
Indices: 44152--44219 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
44142 AATGCAAGTG
*
44152 GGCTTGAGTTCAATCGAGCCTTATTTTTGA
1 GGCTCGAGTTCAATCGAGCCTTATTTTTGA
*
44182 GGCTCGAGTTCGATCGAGCCTTATTTTTGA
1 GGCTCGAGTTCAATCGAGCCTTATTTTTGA
44212 GGCTCGAG
1 GGCTCGAG
44220 CTTGGTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (30 bp):
GGCTCGAGTTCAATCGAGCCTTATTTTTGA
Found at i:45628 original size:6 final size:6
Alignment explanation
Indices: 45617--45642 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45607 TCTGGTGGCA
45617 TTCTAG TTCTAG TTCTAG TTCTAG TT
1 TTCTAG TTCTAG TTCTAG TTCTAG TT
45643 TAATGGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTCTAG
Found at i:50674 original size:3 final size:3
Alignment explanation
Indices: 50666--50709 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
50656 TGGAGCATAA
50666 ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
50710 TAATAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:58663 original size:16 final size:16
Alignment explanation
Indices: 58642--58675 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58632 CGAGTTCTAG
58642 ACCTGAAAAACCCAAA
1 ACCTGAAAAACCCAAA
**
58658 ACCTGAATGACCCAAA
1 ACCTGAAAAACCCAAA
58674 AC
1 AC
58676 TCGAATGACC
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:0.50, C:0.32, G:0.09, T:0.09
Consensus pattern (16 bp):
ACCTGAAAAACCCAAA
Found at i:58681 original size:16 final size:16
Alignment explanation
Indices: 58651--58685 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
58641 GACCTGAAAA
58651 ACCCAAAACCTGAATG
1 ACCCAAAACCTGAATG
58667 ACCCAAAA-CTCGAATG
1 ACCCAAAACCT-GAATG
58683 ACC
1 ACC
58686 TGAAGCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.43, C:0.34, G:0.11, T:0.11
Consensus pattern (16 bp):
ACCCAAAACCTGAATG
Found at i:59450 original size:22 final size:22
Alignment explanation
Indices: 59415--59461 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
59405 TTTTTAGTTG
* **
59415 AGTAAAATTATAAATGTAAAAT
1 AGTAAAATGATAAAAATAAAAT
*
59437 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
59459 AGT
1 AGT
59462 TATAAGGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:61410 original size:7 final size:7
Alignment explanation
Indices: 61400--61428 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
61390 TCCTCTACTC
61400 TCTCAAG
1 TCTCAAG
61407 TCTCAAG
1 TCTCAAG
61414 TCTCAAG
1 TCTCAAG
61421 TCTCAAG
1 TCTCAAG
61428 T
1 T
61429 TCCATGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (7 bp):
TCTCAAG
Found at i:64724 original size:25 final size:25
Alignment explanation
Indices: 64696--64752 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
64686 AATTAATTAC
64696 ATTA-ACAAGTACTATACTAATATAT
1 ATTATACAA-TACTATACTAATATAT
* * *
64721 ATTATATAATACTGTTCTAATATAT
1 ATTATACAATACTATACTAATATAT
*
64746 ATAATAC
1 ATTATAC
64753 TGTTCTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTATACAATACTATACTAATATAT
Found at i:64746 original size:20 final size:20
Alignment explanation
Indices: 64723--64768 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
64713 TAATATATAT
64723 TATATAATACTGTTCTAATA
1 TATATAATACTGTTCTAATA
64743 TATATAATACTGTTCTAATA
1 TATATAATACTGTTCTAATA
64763 TATATA
1 TATATA
64769 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATAATACTGTTCTAATA
Found at i:64765 original size:2 final size:2
Alignment explanation
Indices: 64760--64791 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
64750 TACTGTTCTA
64760 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64792 AAAGTTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71756 original size:21 final size:21
Alignment explanation
Indices: 71732--71798 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
71722 AAATTCTTGT
71732 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
71753 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
71774 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
71795 AAAT
1 AAAT
71799 CTTGATTCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:71779 original size:42 final size:41
Alignment explanation
Indices: 71720--71799 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 41
71710 GCTAAGTCTT
71720 GAAAATTCTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTGTAAATTAAGAAATACTCAACTCAAATCATA
71761 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTC-TTGTAAATTAAGAAATACTCAACTCAAATC
71800 TTGATTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
41 8 0.21
42 30 0.79
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (41 bp):
GAAAATTCTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:71943 original size:56 final size:56
Alignment explanation
Indices: 71866--71979 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
71856 TTTATTTTGT
*
71866 AGAATAATTAAGTAGAAATAGGGGGATGGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
71922 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
71978 AG
1 AG
71980 GAAACGGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:75214 original size:25 final size:24
Alignment explanation
Indices: 75186--75247 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
75176 GTGGATTGTA
*
75186 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
75211 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
75235 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
75248 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:87658 original size:16 final size:17
Alignment explanation
Indices: 87637--87670 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
87627 TAGTTGACTT
87637 CCTTACT-ATTTATTAC
1 CCTTACTAATTTATTAC
87653 CCTTACTCAATTTATTAC
1 CCTTACT-AATTTATTAC
87671 TCTAATAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (17 bp):
CCTTACTAATTTATTAC
Found at i:93432 original size:336 final size:331
Alignment explanation
Indices: 92820--94008 Score: 1424
Period size: 336 Copynumber: 3.6 Consensus size: 331
92810 CCTTTGTTAC
* * * * *
92820 CAAAAACCGTGATGGTTAATATACGATTTCGGTTAAAATTTTGCAAAAATTTACCGGAAAGAATT
1 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAATT
* * * *
92885 T-TCCTAAATTTTTTTGCCATGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAA
66 TCTCCTCAA-TTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTG-AA
* * * *
92949 GGGGCTTTTCACTCTTCTAATATCGGTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGA
129 -GGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGA
* *
93014 AACATGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATATGGTTGAGATTTGGTTAGATG
193 AACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT-GTTGAGATTTGGTTAGATG
* * *
93079 GATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATACAAAACAGAGTCGGGAC-CCCGAAT
257 GATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGTCGGG-CTCCGGAA-
93143 CGCGTTTTTAGT
320 CGCGTTTTTAGT
* * * *
93155 CAAAAACTGTGATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACACGAAA-CATT
1 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAATT
* ** * * * **
93219 TCTCATCAATTTCCGGCCACCATATTCATAAAAAAATATATAACTCAATGTTAAAAAGATTGAAG
66 TCTCCTCAATTTTTGGCCACGATACTCAT-AAAAAATATATAACTCAACGCCAAAAAGATTGAAG
* * *
93284 GGCTTCTCACGCTTCTAATATTGTATTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATTG
130 GGCTTCTCACGCTTCTAATATCG---TTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCG
** * * * * *
93349 AAACCGGATTGAGATGCTCGTTAAAAGAAATCCTTAAATCCAATGTATCTGAGATTTCGTTAGAT
192 AAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGT-TGAGATTTGGTTAGAT
* * * * * *
93414 AGATATAGATATTTCAATGAGTCTTGACGCAAAAAATCATGCAAAACTGAGATGGGGCTACGGAA
256 GGATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAG-TCGGGCTCCGGAA
* **
93479 CGTGTTTTTAAC
320 CGCGTTTTTAGT
* * * *
93491 CAAAAACCGTGATAGTTAGTACACGATTTCGACTAAAATTTTGTAAAAGTTGACCCGAAAGAA-T
1 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAATT
* * * * *
93555 T-TCCTCAATTTTTGGCCATGGTACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAG
66 TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
* * * * *
93619 ACTAT-TCGCGTTTCTAATATCCTTTTTCCTA-TTTTTCCGAATTAA-TTCTCAATTGAATCGAA
131 GCT-TCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT-AATTAAATCGAA
* * * * * *
93681 ACATGATTTATATGCTCGTAAAAACAAATTCTTAAATTCAATGTGGGTAAGATTTGGTTAGATGG
194 ACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT-GTTGAGATTTGGTTAGATGG
**
93746 ATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAAACAGGGCTCCGGAACG
258 ATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGTC-GGGCTCCGGAACG
93811 CGTTTTTAGT
322 CGTTTTTAGT
* * **
93821 CAAAAACTGTGATGGTTACTACACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAA-AATT
1 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAATT
* * * **
93885 TCTCCTCAATTTTGGGCCACAATACTAATAAAAAATATATAACTCAACGCCAAAAAGACAGAAGG
66 TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
* *
93950 GCTTCTCAGGCTTCTAATATCGCTTTTCCTATCTTTTTCCGAATTAATTTCTAATTAAA
131 GCTTCTCACGCTTCTAATATCGTTTTTCCTAT-TTTTTCCGAATTAATTTCTAATTAAA
94009 AATTATATTT
Statistics
Matches: 709, Mismatches: 126, Indels: 40
0.81 0.14 0.05
Matches are distributed among these distances:
329 6 0.01
330 194 0.27
331 84 0.12
333 41 0.06
334 69 0.10
335 107 0.15
336 199 0.28
337 9 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (331 bp):
CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAATT
TCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
GCTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGTTGAGATTTGGTTAGATGGATA
TAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGTCGGGCTCCGGAACGCGTT
TTTAGT
Found at i:96590 original size:3 final size:3
Alignment explanation
Indices: 96582--96615 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
96572 TAGATAATTA
*
96582 CCT CCT CCT CCT CCT CCT CAT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
96616 TTCTTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.65, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:102576 original size:22 final size:23
Alignment explanation
Indices: 102548--102594 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
102538 TCTATAGTAT
102548 AGTACTAATCAATAAAAAGA-AA
1 AGTACTAATCAATAAAAAGAGAA
*
102570 AGTACTAATCAATTAAAAGAGAA
1 AGTACTAATCAATAAAAAGAGAA
102593 AG
1 AG
102595 ATAAAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.19
Consensus pattern (23 bp):
AGTACTAATCAATAAAAAGAGAA
Found at i:107642 original size:20 final size:20
Alignment explanation
Indices: 107617--107656 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
107607 AATAACTGGA
107617 TTACTAAAT-ACCGCCCCCTT
1 TTACT-AATCACCGCCCCCTT
*
107637 TTACTAGTCACCGCCCCCTT
1 TTACTAATCACCGCCCCCTT
107657 GGACTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.20, C:0.42, G:0.07, T:0.30
Consensus pattern (20 bp):
TTACTAATCACCGCCCCCTT
Found at i:107951 original size:20 final size:20
Alignment explanation
Indices: 107926--107964 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
107916 CATATAAAAT
*
107926 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
107946 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
107965 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:119090 original size:25 final size:24
Alignment explanation
Indices: 119062--119118 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
119052 GTGGATTGTA
*
119062 AAATAACTTTAACAATAAAGATATT
1 AAATAAATTTAACAATAAA-ATATT
* *
119087 AAATAAATTTAAGAATTAAATATT
1 AAATAAATTTAACAATAAAATATT
119111 AAA-AAATT
1 AAATAAATT
119119 CAAGACTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTTAACAATAAAATATT
Found at i:119183 original size:16 final size:16
Alignment explanation
Indices: 119158--119192 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
119148 GATCAAGAAA
119158 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
* *
119174 ACCCAGAACCCGAGTG
1 ACCCAAAACCCGAATG
119190 ACC
1 ACC
119193 TGAGGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.40, G:0.17, T:0.06
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:119976 original size:130 final size:130
Alignment explanation
Indices: 119789--120041 Score: 411
Period size: 132 Copynumber: 1.9 Consensus size: 130
119779 AAATATTTTT
* * *
119789 AAAAATTTTAATATATCTAAATTTTTTATTAAATTAGTAAAATGGTAAAAATAAAATAGGTAT-A
1 AAAAATTCTAATATATATAAATTTTTTATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA
119853 -AATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTC
66 GAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTC
* * *
119917 AAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTAT
1 AAAAATTCTAATATATATAA-ATTTTTT-ATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
*
119982 AAGAATATTAGGTTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
64 AAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
120042 TTAAACAATG
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
128 18 0.16
129 6 0.05
130 33 0.29
131 1 0.01
132 56 0.49
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (130 bp):
AAAAATTCTAATATATATAAATTTTTTATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA
GAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTC
Found at i:120845 original size:88 final size:89
Alignment explanation
Indices: 120731--120896 Score: 237
Period size: 90 Copynumber: 1.9 Consensus size: 89
120721 AGTAAAATGG
*
120731 TAAAAATAAAATAGGCATAAAAATATTAGATTTAA-TAAGAT-AAAAATAGAGTTTTTAATTGAG
1 TAAAAATAAAATAGGCATAAAAATATTAGACTTAATTAA-ATAAAAAATAGAGTTTTTAATTGAG
120794 TAAAACTATAAAAATAGTTTACTGC
65 TAAAACTATAAAAATAGTTTACTGC
** ** *
120819 TAAAAATAAAATAGTTATAAGGATATTAGACTTAATTAAATAAAAAAATAGAGTTTTTAGTTGAG
1 TAAAAATAAAATAGGCATAAAAATATTAGACTTAATTAAAT-AAAAAATAGAGTTTTTAATTGAG
*
120884 TAAAATTATAAAA
65 TAAAACTATAAAA
120897 CTTTAAATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 32 0.47
89 3 0.04
90 33 0.49
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (89 bp):
TAAAAATAAAATAGGCATAAAAATATTAGACTTAATTAAATAAAAAATAGAGTTTTTAATTGAGT
AAAACTATAAAAATAGTTTACTGC
Found at i:121015 original size:20 final size:22
Alignment explanation
Indices: 120990--121035 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
120980 TTTAATATAG
120990 TATAGATAGA-TAGATATAA-A
1 TATAGATAGATTAGATATAATA
*
121010 TATAGATAGATTATATATAATA
1 TATAGATAGATTAGATATAATA
121032 TATA
1 TATA
121036 TTATAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 8 0.35
22 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (22 bp):
TATAGATAGATTAGATATAATA
Found at i:127198 original size:27 final size:27
Alignment explanation
Indices: 127150--127210 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
127140 ATTACCAAAA
* * *
127150 TACCCGTGATGGACAAATTTACTATAT
1 TACCCCTGATGGACAAAATTACGATAT
* * *
127177 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATAT
127204 TACCCCT
1 TACCCCT
127211 ATAATGAGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATAT
Found at i:130997 original size:11 final size:11
Alignment explanation
Indices: 130964--130990 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
130954 GTATAAAATC
130964 AAATAATATCT
1 AAATAATATCT
130975 AAATAATATCT
1 AAATAATATCT
130986 AAATA
1 AAATA
130991 TAATCTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATCT
Found at i:135191 original size:33 final size:33
Alignment explanation
Indices: 135153--135218 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
135143 AACAACTTCT
* * *
135153 GGTGTCAACAGTAATTATAATTTACCAGAGTGA
1 GGTGTCAAAAATAATTATAATTTACCAAAGTGA
*
135186 GGTGTCAAAAATAATTTTAATTTACCAAAGTGA
1 GGTGTCAAAAATAATTATAATTTACCAAAGTGA
135219 CAACTTCTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (33 bp):
GGTGTCAAAAATAATTATAATTTACCAAAGTGA
Found at i:135231 original size:41 final size:41
Alignment explanation
Indices: 135186--135326 Score: 210
Period size: 41 Copynumber: 3.4 Consensus size: 41
135176 ACCAGAGTGA
*
135186 GGTGTCAAAAATAATTTTAATTTACCAAAGTGACAACTTCT
1 GGTGTCAAAAGTAATTTTAATTTACCAAAGTGACAACTTCT
* *
135227 GGTGTCAAAGGTAATTTTAATTTACCAAGGTGACAACTTCT
1 GGTGTCAAAAGTAATTTTAATTTACCAAAGTGACAACTTCT
* ***
135268 AGTGTCTGTAGTAATTTTAATTTACCAAAGTGACAACTTCT
1 GGTGTCAAAAGTAATTTTAATTTACCAAAGTGACAACTTCT
*
135309 GGTGTCAAAGGTAATTTT
1 GGTGTCAAAAGTAATTTT
135327 CAATATTATT
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (41 bp):
GGTGTCAAAAGTAATTTTAATTTACCAAAGTGACAACTTCT
Found at i:136667 original size:56 final size:54
Alignment explanation
Indices: 136568--136673 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 54
136558 TTGAACCTGA
* * *
136568 TAATTTAATTTAAGGGTCTTAACGACTTATCTTGAATTGATAATTTGATAACTT
1 TAATTTAATTCAAGGGTCTTAACGACTGATCTTAAATTGATAATTTGATAACTT
*
136622 TAATTTGATTCAAGGGTCTTTAACGACATGATCTTAAATTGATAATTTGATA
1 TAATTTAATTCAAGGGTC-TTAACGAC-TGATCTTAAATTGATAATTTGATA
136674 TGATAAGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 16 0.35
55 8 0.17
56 22 0.48
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (54 bp):
TAATTTAATTCAAGGGTCTTAACGACTGATCTTAAATTGATAATTTGATAACTT
Found at i:136738 original size:24 final size:24
Alignment explanation
Indices: 136676--136740 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 24
136666 ATTTGATATG
* *
136676 ATAAGCAACGACAATTCTTCAAGA
1 ATAAGCAGCAACAATTCTTCAAGA
*
136700 ATAAGCAGCATCAACAATTTTTCAAGA
1 ATAAGCAG---CAACAATTCTTCAAGA
136727 ATAAGCAGCAACAA
1 ATAAGCAGCAACAA
136741 ATAAATTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 13 0.37
27 22 0.63
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (24 bp):
ATAAGCAGCAACAATTCTTCAAGA
Found at i:136826 original size:79 final size:79
Alignment explanation
Indices: 136732--136885 Score: 272
Period size: 79 Copynumber: 1.9 Consensus size: 79
136722 CAAGAATAAG
* *
136732 CAGCAACAAATAAATTCTTGAAAAATAAACAGCAATTCTCCTTGGATCTTTTCCTTTGATAATAA
1 CAGCAACAAATAAATTCTTGAAAAATAAACAACAATTCTCCTTAGATCTTTTCCTTTGATAATAA
136797 TAATTCTCCTTAGA
66 TAATTCTCCTTAGA
* *
136811 CAGCAACAAATAAATTCTTGAAAAATAAACAACAATTCTCTTTAGATCTTTTTCTTTGATAATAA
1 CAGCAACAAATAAATTCTTGAAAAATAAACAACAATTCTCCTTAGATCTTTTCCTTTGATAATAA
136876 TAATTCTCCT
66 TAATTCTCCT
136886 AGAAACTCCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (79 bp):
CAGCAACAAATAAATTCTTGAAAAATAAACAACAATTCTCCTTAGATCTTTTCCTTTGATAATAA
TAATTCTCCTTAGA
Done.