Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012618.1 Corchorus capsularis cultivar CVL-1 contig12639, 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: 103598
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5770 original size:22 final size:22
Alignment explanation
Indices: 5562--5990 Score: 170
Period size: 22 Copynumber: 19.7 Consensus size: 22
5552 CTCCCTAAGG
* *
5562 AATTTTGA-AGACCTTAATATGA
1 AATTTTGATA-ACCTCACTATGA
* * *
5584 AATTTTGATAACTTCCCAATGA
1 AATTTTGATAACCTCACTATGA
* *
5606 AATTTTGATAACCAACACTTTGA
1 AATTTTGATAACC-TCACTATGA
* * *
5629 GATGTTGATAACCTC-CATACGA
1 AATTTTGATAACCTCAC-TATGA
* * * **
5651 TATATTGATAACCACGTTATGA
1 AATTTTGATAACCTCACTATGA
* * *
5673 AAATTTAAAAACCTC-CATATG-
1 AATTTTGATAACCTCAC-TATGA
* * * *
5694 AATTGTT-AGTAATCACATTCTGA
1 AATT-TTGA-TAACCTCACTATGA
* * *
5717 AATTTTGATTATCACACTAT-A
1 AATTTTGATAACCTCACTATGA
* * *
5738 AATTGTAATAACCTCACTATAA
1 AATTTTGATAACCTCACTATGA
* ** *
5760 AATTTTGATAAATCTTTCTATAA
1 AATTTTGAT-AACCTCACTATGA
* *
5783 AATTTTGATAAACCTCCCTATAA
1 AATTTTGAT-AACCTCACTATGA
* *
5806 AATTTTGATAACTTTC-TTATGA
1 AATTTTGATAAC-CTCACTATGA
*
5828 AATCTTGATAA-CT-AC----A
1 AATTTTGATAACCTCACTATGA
*
5844 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTCACTATGA
** *
5866 TTTTTTGATAACCTCATTATGA
1 AATTTTGATAACCTCACTATGA
* * *
5888 AATTTTGTTAATCTCCCTATGA
1 AATTTTGATAACCTCACTATGA
** *
5910 AATTTTGATCTGCAT-ACTATGA
1 AATTTTGAT-AACCTCACTATGA
* *
5932 AATTTTAATAACCCTC-TTATGA
1 AATTTTGATAA-CCTCACTATGA
* *
5954 AATTTTGA-AAACTAAACTATGA
1 AATTTTGATAACCT-CACTATGA
*
5976 AATTTTGATATCCTC
1 AATTTTGATAACCTC
5991 CCTGAAAATT
Statistics
Matches: 296, Mismatches: 85, Indels: 52
0.68 0.20 0.12
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 3 0.01
21 23 0.08
22 189 0.64
23 67 0.23
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCACTATGA
Found at i:5784 original size:23 final size:22
Alignment explanation
Indices: 5754--5838 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
5744 AATAACCTCA
5754 CTATAAAATTTTGATAAATCTTT
1 CTATAAAATTTTGATAAA-CTTT
**
5777 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTT
5800 CTATAAAATTTTGAT-AACTTT
1 CTATAAAATTTTGATAAACTTT
* *
5821 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
5839 CTACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 3 0.06
22 14 0.26
23 36 0.68
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTT
Found at i:5804 original size:46 final size:45
Alignment explanation
Indices: 5747--5838 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 45
5737 AAATTGTAAT
*
5747 AACCTCACTATAAAATTTTGATAAATCTTTC-TATAAAATTTTGATA
1 AACCTCACTATAAAATTTTGAT-AA-CTTTCTTATAAAATCTTGATA
* *
5793 AACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATA
1 AACCTCACTATAAAATTTTGATAACTTTCTTATAAAATCTTGATA
5838 A
1 A
5839 CTACAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 5 0.12
45 16 0.38
46 21 0.50
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.40
Consensus pattern (45 bp):
AACCTCACTATAAAATTTTGATAACTTTCTTATAAAATCTTGATA
Found at i:6289 original size:22 final size:22
Alignment explanation
Indices: 6085--6334 Score: 135
Period size: 22 Copynumber: 11.5 Consensus size: 22
6075 AGAAATACCA
6085 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
6108 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
6129 TTATAAAATTTTGTTGACCTCT
1 CTATGAAATTTTGATAATCACT
* *
6151 CTATGAAATTCTGATAATAACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
6174 -TATGTAATTTTGATAACCCCG
1 CTATGAAATTTTGATAATCACT
* *
6195 CTTTGAAATTTTGATAA-CAAT
1 CTATGAAATTTTGATAATCACT
*
6216 ACTATGAAATTTTGATAATC-TT
1 -CTATGAAATTTTGATAATCACT
6238 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
*
6263 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
6285 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* *
6305 CTATCAAATTTTGGTAATC-CT
1 CTATGAAATTTTGATAATCACT
6326 -TATGAAATT
1 CTATGAAATT
6335 GAGACTTTTA
Statistics
Matches: 174, Mismatches: 39, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.01
20 16 0.09
21 35 0.20
22 101 0.58
23 3 0.02
24 4 0.02
25 14 0.08
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:6369 original size:22 final size:22
Alignment explanation
Indices: 6198--6450 Score: 98
Period size: 22 Copynumber: 11.3 Consensus size: 22
6188 AACCCCGCTT
**
6198 TGAAATTTTGATAACAAT-ACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
6220 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAACCTTCATA
* *
6242 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAACCT--TC-ATA
*
6266 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
6288 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* *
6308 TCAAATTTTGGTAATCCTT-ATGAAA
1 TGAAATTTTGATAA-CCTTCAT---A
*
6333 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
6356 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
6378 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTTCATA
* *
6400 TGAAATATT-AGTAACC-TCCTAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
6422 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
6444 TGAAATT
1 TGAAATT
6451 CTTAAACCTC
Statistics
Matches: 179, Mismatches: 28, Indels: 48
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.01
20 8 0.04
21 39 0.22
22 91 0.51
23 5 0.03
24 6 0.03
25 16 0.09
26 7 0.04
27 6 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:6597 original size:45 final size:45
Alignment explanation
Indices: 6496--6649 Score: 163
Period size: 44 Copynumber: 3.4 Consensus size: 45
6486 GATAACCTTT
* ***
6496 CTATGAAATTTTGATAATTAACTATCCTATGAAATTTCAATAACCA-A
1 CTATGAAATTTTGATAA-T--CTATCCAATGAAATTTTGGTAACCACA
* *
6543 CCTAAGAAATTTTAATAATCTGATCC-ATGAAATTTTGGTAACCACA
1 -CTATGAAATTTTGATAATCT-ATCCAATGAAATTTTGGTAACCACA
6589 CTATGAAATTTTGATAA-CT-TCCAAATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAATCTATCC-AATGAAATTTTGGTAACCACA
*
6633 CTATGGAATTTTGATAA
1 CTATGAAATTTTGATAA
6650 CCTGCTCATG
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
42 3 0.03
44 38 0.40
45 32 0.34
46 5 0.05
47 1 0.01
48 15 0.16
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (45 bp):
CTATGAAATTTTGATAATCTATCCAATGAAATTTTGGTAACCACA
Found at i:6626 original size:44 final size:44
Alignment explanation
Indices: 6569--6695 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 44
6559 AATCTGATCC
*
6569 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTCCAA
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCAA
* * **
6613 ATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTGCTC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCAA
* ** *
6657 ATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
6696 ACATAGAGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 71 0.99
45 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (44 bp):
ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCAA
Found at i:6696 original size:22 final size:22
Alignment explanation
Indices: 6483--6696 Score: 141
Period size: 22 Copynumber: 9.5 Consensus size: 22
6473 TGATAATCTC
* *
6483 TTTGATAACCTTTCTATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
6505 TTTGATAATTAACTATCCTATGAAAT
1 TTTG---A-TAACCATCCTATGAAAT
** * *
6531 TTCAATAACCAACCTAAGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
6553 TTTAATAATCTGATCC-ATGAAAT
1 TTTGATAA-C-CATCCTATGAAAT
*
6576 TTTGGTAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
* *
6598 TTTGATAA-CTTCCAAATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
6620 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
*
6642 TTTGATAACC-TGCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
6664 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
6686 TTTGATAACCA
1 TTTGATAACCA
6697 CATAGAGATA
Statistics
Matches: 146, Mismatches: 31, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 101 0.69
23 18 0.12
24 3 0.02
25 1 0.01
26 16 0.11
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:15184 original size:35 final size:32
Alignment explanation
Indices: 15118--15184 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
15108 AACAAAATAC
* *
15118 TACTACTATTAATTAATTTTTTTTTGTACAAA
1 TACTACTATTAATTAATTTTTTTTGGAACAAA
15150 TACTACTATTAATTAATTGTCTTTTTAGGAACAAA
1 TACTACTATTAATTAATT-T-TTTTT-GGAACAAA
15185 GTACGATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 5 0.17
35 6 0.20
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (32 bp):
TACTACTATTAATTAATTTTTTTTGGAACAAA
Found at i:25383 original size:5 final size:5
Alignment explanation
Indices: 25373--25406 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
25363 ACAAGAACAT
*
25373 ATATA ATATA ATATG ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
25407 GTTTTTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:25634 original size:15 final size:12
Alignment explanation
Indices: 25601--25626 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25591 CCCATTTATT
25601 AAATGTTCTACC
1 AAATGTTCTACC
25613 AAATGTTCTACC
1 AAATGTTCTACC
25625 AA
1 AA
25627 TGAATGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAATGTTCTACC
Found at i:31786 original size:6 final size:6
Alignment explanation
Indices: 31777--31805 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31767 GTTGTTGTTG
31777 CTTCAT CTTCAT CTTCAT CTTCAT CTTCA
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCA
31806 ATTTCCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTCAT
Found at i:36430 original size:11 final size:11
Alignment explanation
Indices: 36394--36431 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
36384 TAAAAAAACA
36394 AAAAGAAAATG
1 AAAAGAAAATG
*
36405 AAAAAGAAAAAG
1 -AAAAGAAAATG
36417 AAAAGAAAATG
1 AAAAGAAAATG
36428 AAAA
1 AAAA
36432 TGAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (11 bp):
AAAAGAAAATG
Found at i:36435 original size:6 final size:6
Alignment explanation
Indices: 36387--36431 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
36377 AATGATTTAA
* * *
36387 AAAAAC AAAAAG AAAATG AAAAAG AAAAAG -AAAAG AAAATG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
36432 TGAATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:36589 original size:61 final size:61
Alignment explanation
Indices: 36489--36614 Score: 225
Period size: 61 Copynumber: 2.1 Consensus size: 61
36479 GTGCAAATGA
* *
36489 GTCCTTGAAGTGAACTTAGTGAGCAATTGAGTCCCTGAAGTGGAGTTAATTGAGCAATTGG
1 GTCCTTAAAGTGAACTTAGTGAGCAATTGAGTCCCTGAAGTGGAGTTAATTGAGCAATTAG
*
36550 GTCCTTAAAGTGAACTTAGTGAGCAATTGAGTCCTTGAAGTGGAGTTAATTGAGCAATTAG
1 GTCCTTAAAGTGAACTTAGTGAGCAATTGAGTCCCTGAAGTGGAGTTAATTGAGCAATTAG
36611 GTCC
1 GTCC
36615 CTAACTCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (61 bp):
GTCCTTAAAGTGAACTTAGTGAGCAATTGAGTCCCTGAAGTGGAGTTAATTGAGCAATTAG
Found at i:36608 original size:31 final size:30
Alignment explanation
Indices: 36481--36591 Score: 150
Period size: 30 Copynumber: 3.7 Consensus size: 30
36471 GGGCAAATGT
*
36481 GCAAATGAGTCCTTGAAGTGAACTTAGTGA
1 GCAATTGAGTCCTTGAAGTGAACTTAGTGA
* * * *
36511 GCAATTGAGTCCCTGAAGTGGAGTTAATTGA
1 GCAATTGAGTCCTTGAAGTGAACTT-AGTGA
* *
36542 GCAATTGGGTCCTTAAAGTGAACTTAGTGA
1 GCAATTGAGTCCTTGAAGTGAACTTAGTGA
36572 GCAATTGAGTCCTTGAAGTG
1 GCAATTGAGTCCTTGAAGTG
36592 GAGTTAATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
30 43 0.64
31 24 0.36
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
GCAATTGAGTCCTTGAAGTGAACTTAGTGA
Found at i:36658 original size:15 final size:15
Alignment explanation
Indices: 36640--36675 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
36630 TTTAAATATT
36640 TATATATTTTTTTAA
1 TATATATTTTTTTAA
36655 TATATA-TTTTTTAA
1 TATATATTTTTTTAA
36669 TATATAT
1 TATATAT
36676 ATATGATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATATTTTTTTAA
Found at i:36673 original size:16 final size:15
Alignment explanation
Indices: 36640--36677 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
36630 TTTAAATATT
*
36640 TATATATTTTTTTAA
1 TATATATTTTTTAAA
36655 TATATATTTTTTAATA
1 TATATATTTTTTAA-A
36671 TATATAT
1 TATATAT
36678 ATGATGTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATATTTTTTAAA
Found at i:43645 original size:17 final size:18
Alignment explanation
Indices: 43608--43645 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
43598 GTAATTCTCT
* *
43608 TCACAATCAAGGAAAAGA
1 TCACAAGCAAGGAAAAAA
43626 TCACAAGCAA-GAAAAAA
1 TCACAAGCAAGGAAAAAA
43643 TCA
1 TCA
43646 TAAATGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.58, C:0.18, G:0.13, T:0.11
Consensus pattern (18 bp):
TCACAAGCAAGGAAAAAA
Found at i:44588 original size:29 final size:29
Alignment explanation
Indices: 44490--44577 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
44480 GCGAGTCTAT
*
44490 TCCTAATATTTTCACTAACATGACTAAAG
1 TCCTAATCTTTTCACTAACATGACTAAAG
*
44519 TCCTAATCTTTTCAATAACATGACTAAAG
1 TCCTAATCTTTTCACTAACATGACTAAAG
44548 TCCTAATCTTTTCACTAACATGACTAAAG
1 TCCTAATCTTTTCACTAACATGACTAAAG
44577 T
1 T
44578 TCTTTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
TCCTAATCTTTTCACTAACATGACTAAAG
Found at i:48131 original size:156 final size:154
Alignment explanation
Indices: 47825--48174 Score: 379
Period size: 156 Copynumber: 2.3 Consensus size: 154
47815 GAGCTTCTCA
* *
47825 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTATTCTAAGTCTGAATGAGCTGAAAT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTATTCTAAGTCTCAACGAGCTG-AAT
* * * *
47890 TTTTCCAAGGGTCTTATAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCC
65 TTTTCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCC
* * * *
47955 CCTTGATGGTGAACTAGGTTTCTCT
130 CCTAGATAGAGAACTAGGTTTCACT
**
47980 CC-CTAAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT-ATTCTAAGTCTCAACG-AGCTGA
* * *
48042 A-TTTTCCACCAGTAGACTTAGATTATCCCCATAA-AGCTATGGGAAAAATTCTAAGTAAAACCG
63 ATTTTTCCA--AG-AGACTTAGAATATCCACATAAGA-CTATGGAAAAAATTCTAAGTAAAACCG
** * * *
48105 AACT-TTCTAGCATAGAGAAGTTGGTTTGACT
124 AACTCCCCTAG-ATAGAGAACTAGGTTTCACT
* *
48136 CCTCAAACTGTCCTCAATTGAAAAACTAGCATAAGTTTT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTT
48175 CAAACTAAGT
Statistics
Matches: 162, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
153 7 0.04
154 2 0.01
155 45 0.28
156 107 0.66
157 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (154 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTATTCTAAGTCTCAACGAGCTGAATT
TTTCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCC
CTAGATAGAGAACTAGGTTTCACT
Found at i:49864 original size:17 final size:17
Alignment explanation
Indices: 49842--49896 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
49832 ACTTTTTATG
49842 CTTTATACTATTTAATC
1 CTTTATACTATTTAATC
* * *
49859 CTTTATA-TTTTTTATG
1 CTTTATACTATTTAATC
*
49875 CTTTATGCTATTTAATC
1 CTTTATACTATTTAATC
49892 CTTTA
1 CTTTA
49897 CAATTATGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (17 bp):
CTTTATACTATTTAATC
Found at i:49876 original size:33 final size:33
Alignment explanation
Indices: 49834--49896 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
49824 ATCCTCACAC
49834 TTTTTATGCTTTATACTATTTAATCCTTTATAT
1 TTTTTATGCTTTATACTATTTAATCCTTTATAT
*
49867 TTTTTATGCTTTATGCTATTTAATCCTTTA
1 TTTTTATGCTTTATACTATTTAATCCTTTA
49897 CAATTATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (33 bp):
TTTTTATGCTTTATACTATTTAATCCTTTATAT
Found at i:49888 original size:16 final size:16
Alignment explanation
Indices: 49836--49888 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
49826 CCTCACACTT
49836 TTTATGCTTTATACTA
1 TTTATGCTTTATACTA
* * *
49852 TTTAATCCTTTATATTT
1 TTT-ATGCTTTATACTA
*
49869 TTTATGCTTTATGCTA
1 TTTATGCTTTATACTA
49885 TTTA
1 TTTA
49889 ATCCTTTACA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (16 bp):
TTTATGCTTTATACTA
Found at i:50843 original size:14 final size:14
Alignment explanation
Indices: 50812--50843 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
50802 TATTTGATCA
50812 TGATATATACTATT
1 TGATATATACTATT
50826 TGATATATACTATT
1 TGATATATACTATT
50840 TGAT
1 TGAT
50844 CAGTGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (14 bp):
TGATATATACTATT
Found at i:51272 original size:11 final size:11
Alignment explanation
Indices: 51256--51280 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51246 AAGAAAATAT
51256 ATATCTATACC
1 ATATCTATACC
51267 ATATCTATACC
1 ATATCTATACC
51278 ATA
1 ATA
51281 GTATATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATCTATACC
Found at i:51499 original size:30 final size:31
Alignment explanation
Indices: 51443--51507 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
51433 AACTTTATGT
* *
51443 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
51474 TTTCCAATTGTA-CCTT-TTCTTTAAAACATA
1 TTTCCAATTGTACCCTTATT-TTTAAAACATA
51504 TTTC
1 TTTC
51508 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 11 0.35
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:51514 original size:31 final size:31
Alignment explanation
Indices: 51449--51514 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
51439 ATGTTTTCCG
* *
51449 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
51480 ATTGTA-CCTT-TTCTTTAAAACATATTTCTAA
1 ATTGTACCCTTATT-TTTAAAACATATTTC-AA
51511 ATTG
1 ATTG
51515 CCATTACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 11 0.35
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:51853 original size:19 final size:20
Alignment explanation
Indices: 51826--51863 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
51816 TACTATTATT
51826 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
51846 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
51864 AATATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:52130 original size:45 final size:43
Alignment explanation
Indices: 52061--52160 Score: 105
Period size: 45 Copynumber: 2.3 Consensus size: 43
52051 TAGTTATTAT
52061 AATTTCATGAGGAGGTTATCAAAAT-TCAATA-GTGTGGTTACCAA
1 AATTTCAT-AGGAGGTTATCAAAATCTC-ATAGGT-TGGTTACCAA
* * **
52105 AATTTCATAGGATCGGTTATTAAAATCTCTTAGGTTGGTTATTAA
1 AATTTCATAGGA--GGTTATCAAAATCTCATAGGTTGGTTACCAA
52150 AATTTCATAGG
1 AATTTCATAGG
52161 GTGGTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 4 0.08
44 8 0.17
45 32 0.67
46 4 0.08
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (43 bp):
AATTTCATAGGAGGTTATCAAAATCTCATAGGTTGGTTACCAA
Found at i:52165 original size:22 final size:22
Alignment explanation
Indices: 52037--52167 Score: 104
Period size: 22 Copynumber: 5.9 Consensus size: 22
52027 TATGATTGTC
* * *
52037 AAAATTTCATAAGATAGTTATT
1 AAAATTTCATAGGGTGGTTATT
* * *
52059 ATAATTTCAT-GAGGAGGTTATC
1 AAAATTTCATAG-GGTGGTTATT
* **
52081 AAAA-TTCAATAGTGTGGTTACC
1 AAAATTTC-ATAGGGTGGTTATT
*
52103 AAAATTTCATAGGATCGGTTATT
1 AAAATTTCATAGGGT-GGTTATT
* * *
52126 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGGTGGTTATT
52148 AAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGGTGGTTA
52168 ATTATCACAA
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
21 3 0.04
22 60 0.71
23 21 0.25
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGGTGGTTATT
Found at i:52255 original size:22 final size:22
Alignment explanation
Indices: 52230--52326 Score: 83
Period size: 22 Copynumber: 4.4 Consensus size: 22
52220 AGGTTATAAG
*
52230 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
52252 AATTTCATTAG-GAGGTT-ACTAA
1 AATTTCA-TAGTGAGGTTAAC-AA
* * * *
52274 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
* *
52296 AATTTTATAGT-ACGGTTATCAA
1 AATTTCATAGTGA-GGTTAACAA
52318 AATTTCATA
1 AATTTCATA
52327 TGAATGTTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
21 5 0.08
22 52 0.85
23 4 0.07
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:52268 original size:44 final size:42
Alignment explanation
Indices: 52219--52326 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 42
52209 AAATGTCAGC
* *
52219 GAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAG
1 GAGGTTATAA-AATTTCATAGGGAGGTTAACAAAATTTCA-TAG
* * * *
52263 GAGGTTACTAATATTTCATGGGGAGGTTATCAAAATTTTATAG
1 GAGGTTA-TAAAATTTCATAGGGAGGTTAACAAAATTTCATAG
*
52306 TACGGTTATCAAAATTTCATA
1 GA-GGTTAT-AAAATTTCATA
52327 TGAATGTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
43 5 0.10
44 44 0.85
45 3 0.06
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (42 bp):
GAGGTTATAAAATTTCATAGGGAGGTTAACAAAATTTCATAG
Found at i:52412 original size:22 final size:23
Alignment explanation
Indices: 52377--52430 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
52367 TGATAGAAGG
*
52377 TTATCAAATCTCATAGAG-T-GA
1 TTATCAAATTTCATAGAGATCGA
52398 TTATCGAAATTTCATAGAGATCGGA
1 TTATC-AAATTTCATAGAGATC-GA
52423 TTATCAAA
1 TTATCAAA
52431 ATTTATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 1 0.04
24 3 0.11
25 7 0.25
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (23 bp):
TTATCAAATTTCATAGAGATCGA
Found at i:52636 original size:22 final size:22
Alignment explanation
Indices: 52608--52902 Score: 137
Period size: 22 Copynumber: 13.6 Consensus size: 22
52598 TCAGGGATGA
52608 TATCAAAATTTCATATGAAAGT
1 TATCAAAATTTCATATGAAAGT
**
52630 TATCAAAATTTCATA-GTTTAGT
1 TATCAAAATTTCATATG-AAAGT
* * *
52652 TTTCAAAATTTCACATGAGAGT
1 TATCAAAATTTCATATGAAAGT
* *
52674 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAAGT
* * **
52695 AGATCAAAATTCCATA-GGGAGAT
1 -TATCAAAATTTCATATGAAAG-T
* * *
52718 TAACAAAATTTCACAATG-AGGT
1 TATCAAAATTTCA-TATGAAAGT
** * * *
52740 TATCAAAAAGTCATAGGGAGGT
1 TATCAAAATTTCATATGAAAGT
52762 TATCAAAATTT--T-T---AGT
1 TATCAAAATTTCATATGAAAGT
* * *
52778 TATCAAGATTTCATAAGAAAAT
1 TATCAAAATTTCATATGAAAGT
* * *
52800 TATCAAAATTTTATAGGGAAGTT
1 TATCAAAATTTCATATGAAAG-T
* * *
52823 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAA-AGT
* *
52846 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAAGT
* **
52868 TATCACAATTTCATAGTGTGA-T
1 TATCAAAATTTCATA-TGAAAGT
52890 TATCAAAATTTCA
1 TATCAAAATTTCA
52903 GAGTGTGATT
Statistics
Matches: 205, Mismatches: 50, Indels: 36
0.70 0.17 0.12
Matches are distributed among these distances:
16 12 0.06
18 1 0.00
20 1 0.00
21 6 0.03
22 143 0.70
23 39 0.19
24 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAAGT
Found at i:52701 original size:66 final size:66
Alignment explanation
Indices: 52608--52747 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 66
52598 TCAGGGATGA
* * ** **
52608 TATCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCAC-ATGAG
1 TATCAAAATTTCATATGAAAGTGATCAAAATTCCATAG-GGAGATTAACAAAATTTCACAATGAG
52671 AGT
65 -GT
* *
52674 TATCAAAATTTCATA-GTATGTAGATCAAAATTCCATAGGGAGATTAACAAAATTTCACAATGAG
1 TATCAAAATTTCATATGAAAGT-GATCAAAATTCCATAGGGAGATTAACAAAATTTCACAATGAG
52738 GT
65 GT
52740 TATCAAAA
1 TATCAAAA
52748 AGTCATAGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 6 0.10
66 52 0.83
67 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (66 bp):
TATCAAAATTTCATATGAAAGTGATCAAAATTCCATAGGGAGATTAACAAAATTTCACAATGAGG
T
Found at i:52702 original size:44 final size:44
Alignment explanation
Indices: 52584--52730 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 44
52574 TTTTATTATG
* * * * *
52584 GAGTAATCAAAATTTCA-GGGATG-ATATCAAAATTTCATATGA
1 GAGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCACATGA
* *
52626 AAGTTATCAAAATTTCATAGT-T-TAGTTTTCAAAATTTCACATGA
1 GAGTTATCAAAATTTCATAGTATGTAG--ATCAAAATTTCACATGA
*
52670 GAGTTATCAAAATTTCATAGTATGTAGATCAAAA-TTC-CATAGG
1 GAGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCACAT-GA
*
52713 GAGATTAACAAAATTTCA
1 GAG-TTATCAAAATTTCA
52731 CAATGAGGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
42 20 0.23
43 8 0.09
44 54 0.63
45 1 0.01
46 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (44 bp):
GAGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCACATGA
Found at i:52827 original size:23 final size:22
Alignment explanation
Indices: 52799--53064 Score: 117
Period size: 22 Copynumber: 12.0 Consensus size: 22
52789 CATAAGAAAA
*
52799 TTATCAAAATTTTATAGGGAAGT
1 TTATCAAAATTTCATAGGG-AGT
* *
52822 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAG-T
* *
52845 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGGGAGT
* * * *
52867 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGGGAGT
* * * *
52889 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGGGAGT
*
52911 TTA-CTAACAA-TTCATATGGAGGT
1 TTATC-AA-AATTTCATAGGGA-GT
* * ** * *
52934 TT-TTAAATTTTCATAATGTGG
1 TTATCAAAATTTCATAGGGAGT
* * * *
52955 TTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATAGGGAGT
* * ** *
52977 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-GGAGT
*
53000 TTATCAAAATTTCATTAGGAAG-
1 TTATCAAAATTTCA-TAGGGAGT
* **
53022 TTATCAAAATTTTATATTGAGT
1 TTATCAAAATTTCATAGGGAGT
* * *
53044 TTTTCAAAATTCCTTAGGGAG
1 TTATCAAAATTTCATAGGGAG
53065 ATTAACCGAA
Statistics
Matches: 185, Mismatches: 48, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
21 9 0.05
22 114 0.62
23 59 0.32
24 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGT
Found at i:52907 original size:22 final size:22
Alignment explanation
Indices: 52608--53014 Score: 130
Period size: 22 Copynumber: 18.6 Consensus size: 22
52598 TCAGGGATGA
**
52608 TATCAAAATTTCATA-TGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
*
52630 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
52652 TTTCAAAATTTCACA-TGAGAGT
1 TATCAAAATTTCATAGTGTGA-T
*
52674 TATCAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * * *
52695 AGATCAAAATTCCATAGGGAGAT
1 -TATCAAAATTTCATAGTGTGAT
* * * * *
52718 TAACAAAATTTCACAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * *
52740 TATCAAAAAGTCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
52762 TATCAAAATTT--T--T-AG-T
1 TATCAAAATTTCATAGTGTGAT
* ***
52778 TATCAAGATTTCATAAG-AAAAT
1 TATCAAAATTTCAT-AGTGTGAT
* * * *
52800 TATCAAAATTTTATAGGGAAGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
52823 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* * *
52846 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
52868 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
52890 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
52912 TA-CTAACAA-TTCATA-TG-GAGGT
1 TATC-AA-AATTTCATAGTGTGA--T
* * * * *
52934 TTTTAAATTTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTGAT
* *
52956 TATCAATATATCATA-TG-GAGGT
1 TATCAAAATTTCATAGTGTGA--T
* * *
52978 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
53001 TATCAAAATTTCAT
1 TATCAAAATTTCAT
53015 TAGGAAGTTA
Statistics
Matches: 293, Mismatches: 63, Indels: 57
0.71 0.15 0.14
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 4 0.01
21 11 0.04
22 202 0.69
23 59 0.20
24 2 0.01
25 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:53025 original size:45 final size:44
Alignment explanation
Indices: 52944--53028 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
52934 TTTTAAATTT
* *
52944 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACATC
* *
52988 TCATAGTGTTGGTTATCAAAATTTCAT-TAGGAAGTTATCAA
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAA
53029 AATTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACATC
Found at i:57534 original size:33 final size:33
Alignment explanation
Indices: 57489--57555 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
57479 TATGTACCTC
57489 GCAACACACCATTCTTCTTCATCAATCTGTTCA
1 GCAACACACCATTCTTCTTCATCAATCTGTTCA
*
57522 GCAACACGCCATTCTTCTTCATCAATCTGTTCA
1 GCAACACACCATTCTTCTTCATCAATCTGTTCA
57555 G
1 G
57556 GTTATTTCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (33 bp):
GCAACACACCATTCTTCTTCATCAATCTGTTCA
Found at i:63884 original size:15 final size:15
Alignment explanation
Indices: 63864--63894 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63854 TGTATTGCAT
63864 TTTTATTTTGTTTTC
1 TTTTATTTTGTTTTC
*
63879 TTTTATTTTTTTTTC
1 TTTTATTTTGTTTTC
63894 T
1 T
63895 CCCAAATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTATTTTGTTTTC
Found at i:68345 original size:64 final size:63
Alignment explanation
Indices: 68207--68346 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 63
68197 AAACAAAGAG
* *
68207 GTCTATTGTCCATTATTTAACGGCATCCACGCTTTCTAACGGAATTAATGCACAAGATATATA
1 GTCTATTGTCCATTATTTAACGGCATCCAAGCTTTCTAACGGAATTAATGCACAAGATAGATA
* ** * * *
68270 GTTTTATTGTCCATTATTTAATTGCATCCAAG-TTATGTAACGGAATTAATGTACATG-TCAAGA
1 G-TCTATTGTCCATTATTTAACGGCATCCAAGCTT-TCTAACGGAATTAATGCACAAGAT--AGA
68333 TA
62 TA
*
68335 GTCTAGTGTCCA
1 GTCTATTGTCCA
68347 AATTTGAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
63 4 0.06
64 54 0.86
65 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (63 bp):
GTCTATTGTCCATTATTTAACGGCATCCAAGCTTTCTAACGGAATTAATGCACAAGATAGATA
Found at i:72703 original size:54 final size:55
Alignment explanation
Indices: 72594--72705 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 55
72584 AATGGATGGA
* * *
72594 AATCATTAATATTAAGATACCACCTTTGATATAAAAATAGAGAAATTATATGAGG
1 AATCATTAACATTAAGATACCACCTTTAATATAAAAATAGAGAAATTATAGGAGG
72649 AATCATTAACATTAAGATACCACC-TTAATATAAAAATAGAGAAATTATAGGAGG
1 AATCATTAACATTAAGATACCACCTTTAATATAAAAATAGAGAAATTATAGGAGG
72703 AAT
1 AAT
72706 ATACGTGATC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 31 0.57
55 23 0.43
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (55 bp):
AATCATTAACATTAAGATACCACCTTTAATATAAAAATAGAGAAATTATAGGAGG
Found at i:73721 original size:21 final size:21
Alignment explanation
Indices: 73695--73737 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
73685 AGGCGGCGAA
73695 TAGGAAATCCAGAAGGTGATG
1 TAGGAAATCCAGAAGGTGATG
*
73716 TAGGAATTCCAGAAGGTGATG
1 TAGGAAATCCAGAAGGTGATG
73737 T
1 T
73738 GGTTTGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (21 bp):
TAGGAAATCCAGAAGGTGATG
Found at i:79796 original size:56 final size:56
Alignment explanation
Indices: 79717--79871 Score: 249
Period size: 56 Copynumber: 2.8 Consensus size: 56
79707 TCGTTTTTTT
* * *
79717 TTATAAAACAATTCCAGACTTTTCCTTCCTCTCTCCTTT-TTCCTTCAAGTCAATCAA
1 TTATCAAA-AATTCTAGAGTTTTCCTTCCTCTCT-CTTTCTTCCTTCAAGTCAATCAA
79774 TTATCAAAAATTCTAGAGTTTTCCTTCCTCTCTCTTTCTTCCTTCAAGTCAATCAA
1 TTATCAAAAATTCTAGAGTTTTCCTTCCTCTCTCTTTCTTCCTTCAAGTCAATCAA
*
79830 TTATCAAAAATTCTAGAGTTTTCCTTCGTCTCTCTTTCTTCC
1 TTATCAAAAATTCTAGAGTTTTCCTTCCTCTCTCTTTCTTCC
79872 GTTTCCTTCC
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
55 4 0.04
56 82 0.88
57 7 0.08
ACGTcount: A:0.24, C:0.28, G:0.05, T:0.43
Consensus pattern (56 bp):
TTATCAAAAATTCTAGAGTTTTCCTTCCTCTCTCTTTCTTCCTTCAAGTCAATCAA
Found at i:84686 original size:16 final size:16
Alignment explanation
Indices: 84637--84686 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
84627 GGCCATTAAT
*
84637 ATAATTAATATGATTA
1 ATAACTAATATGATTA
*
84653 ACAACTAATATGATTA
1 ATAACTAATATGATTA
84669 ATAACTAATATGATTA
1 ATAACTAATATGATTA
84685 AT
1 AT
84687 GGGAAAGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATAACTAATATGATTA
Found at i:85012 original size:27 final size:27
Alignment explanation
Indices: 84943--85015 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
84933 AAGTGAACTT
*
84943 AAAATGACCAAAATACCCCCTAAATGCA
1 AAAATGACCAAAAT-GCCCCTAAATGCA
* **
84971 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTAAATGCA
84998 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
85016 TTATGTGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 27 0.66
28 14 0.34
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATGCA
Found at i:88115 original size:33 final size:33
Alignment explanation
Indices: 88059--88122 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
88049 CTAATGACAA
* *
88059 CAGAGTTTTGGAGAGACTCCCGAATATTACAGT
1 CAGAGTTTGGGAGAGACTACCGAATATTACAGT
** *
88092 CAGAGTTTGGGAGAGTTTACCGAATGTTACA
1 CAGAGTTTGGGAGAGACTACCGAATATTACA
88123 AGTCCTAGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (33 bp):
CAGAGTTTGGGAGAGACTACCGAATATTACAGT
Found at i:94950 original size:48 final size:48
Alignment explanation
Indices: 94896--94994 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
94886 TTGTTTGTTT
* *
94896 GATACTTTGTTAAGTAGGTTATTTAAGCTCATTTCTTAGTTTGGGTTG
1 GATACTTTGTTAAGTAGGTTATTTAAGCTAATTTCTTAGTTTGGATTG
94944 GATACTTTGTTAAGTAGGTTATTTAAGCTAATTTCTTAGTTTGGATTG
1 GATACTTTGTTAAGTAGGTTATTTAAGCTAATTTCTTAGTTTGGATTG
94992 GAT
1 GAT
94995 TCTCATATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.47
Consensus pattern (48 bp):
GATACTTTGTTAAGTAGGTTATTTAAGCTAATTTCTTAGTTTGGATTG
Found at i:95128 original size:21 final size:21
Alignment explanation
Indices: 95104--95173 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
95094 ATGGTTACCG
95104 AAATTTCACATAAGGTTATCA
1 AAATTTCACATAAGGTTATCA
*
95125 AAA-TT-ACATAGGATTGTTATCA
1 AAATTTCACATA--A-GGTTATCA
*
95147 AAATTTCA-ATTGAGGTTATCA
1 AAATTTCACA-TAAGGTTATCA
95168 AAATTT
1 AAATTT
95174 TAAATGATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
19 5 0.12
20 2 0.05
21 17 0.43
22 11 0.28
23 3 0.08
24 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (21 bp):
AAATTTCACATAAGGTTATCA
Found at i:95191 original size:21 final size:22
Alignment explanation
Indices: 95140--95219 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
95130 ACATAGGATT
*
95140 GTTATCAAAA-TTTCAATTGA-G
1 GTTAT-AAAATTTTCAAATGATG
95161 GTTATCAAAATTTT-AAATGATG
1 GTTAT-AAAATTTTCAAATGATG
* *
95183 GTTTTAAAATTTTCAAATGGTG
1 GTTATAAAATTTTCAAATGATG
*
95205 GTTATCAAATTTTCA
1 GTTATAAAATTTTCA
95220 TAAGACAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 23 0.45
22 28 0.55
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
GTTATAAAATTTTCAAATGATG
Found at i:102040 original size:14 final size:14
Alignment explanation
Indices: 102021--102049 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
102011 AACCATGAAA
102021 AGGCAGAAAGTTTC
1 AGGCAGAAAGTTTC
102035 AGGCAGAAAGTTTC
1 AGGCAGAAAGTTTC
102049 A
1 A
102050 TTGAAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (14 bp):
AGGCAGAAAGTTTC
Found at i:102138 original size:12 final size:12
Alignment explanation
Indices: 102114--102162 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
102104 TGCTCCACAC
*
102114 AGTAAAAATAAT
1 AGTAATAATAAT
*
102126 AGTAATAAGAAT
1 AGTAATAATAAT
102138 AAG-AATAATAAT
1 -AGTAATAATAAT
*
102150 AATAATAATAAT
1 AGTAATAATAAT
102162 A
1 A
102163 TAAAAAGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 1 0.03
12 28 0.90
13 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
AGTAATAATAAT
Found at i:102149 original size:3 final size:3
Alignment explanation
Indices: 102120--102162 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
102110 ACACAGTAAA
* * *
102120 AAT AAT AGT AAT AAG AAT AAG AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
102163 TAAAAAGTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Done.