Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007412.1 Corchorus capsularis cultivar CVL-1 contig07433, 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: 35061
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:45 original size:18 final size:18
Alignment explanation
Indices: 19--54 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9 TATCAACTCC
*
19 TCACCAAACCAAGAAGAT
1 TCACAAAACCAAGAAGAT
*
37 TCACAAAACCAAGGAGAT
1 TCACAAAACCAAGAAGAT
55 AGTTTCTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (18 bp):
TCACAAAACCAAGAAGAT
Found at i:1626 original size:13 final size:13
Alignment explanation
Indices: 1608--1634 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1598 CTCTATAACC
1608 TCATAAATCATAT
1 TCATAAATCATAT
1621 TCATAAATCATAT
1 TCATAAATCATAT
1634 T
1 T
1635 TATTATATTT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:1777 original size:19 final size:18
Alignment explanation
Indices: 1748--1789 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1738 TGAGTAGTTT
* *
1748 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
1766 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
1785 TTAAA
1 TTAAA
1790 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:1793 original size:19 final size:19
Alignment explanation
Indices: 1753--1789 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1743 AGTTTTTAAG
*
1753 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
1772 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
1790 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:1992 original size:16 final size:15
Alignment explanation
Indices: 1961--2005 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1951 TTTAAGGATA
* *
1961 TTTAAGAATGTATTT
1 TTTAAGGATATATTT
*
1976 TTTAAAGGATTTATTT
1 TTT-AAGGATATATTT
1992 TTTAAGGATATATT
1 TTTAAGGATATATT
2006 ATGGATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTAAGGATATATTT
Found at i:3743 original size:30 final size:30
Alignment explanation
Indices: 3702--3774 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
3692 TTATGTATAG
* *
3702 GAAAATACCACGTGGACACTAACATGGTCT
1 GAAAATTCCACGTGGACACTAACATGGCCT
* *
3732 GAAAATTCCACGCGGACTCTAACATGGCCT
1 GAAAATTCCACGTGGACACTAACATGGCCT
*
3762 AAAAATTCCACGT
1 GAAAATTCCACGT
3775 AAGCATGACC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (30 bp):
GAAAATTCCACGTGGACACTAACATGGCCT
Found at i:4971 original size:16 final size:18
Alignment explanation
Indices: 4940--4972 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4930 CACTTCTCAA
4940 AAGCACTTTTTCCAAACC
1 AAGCACTTTTTCCAAACC
4958 AAGCA-TTTTT-CAAAC
1 AAGCACTTTTTCCAAAC
4973 TGCAATCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (18 bp):
AAGCACTTTTTCCAAACC
Found at i:7295 original size:9 final size:9
Alignment explanation
Indices: 7281--7310 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
7271 TATATAGAAA
7281 CAGTTATAC
1 CAGTTATAC
7290 CAGTTATAC
1 CAGTTATAC
7299 CAGTTATAC
1 CAGTTATAC
7308 CAG
1 CAG
7311 ACTTTCCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (9 bp):
CAGTTATAC
Found at i:12957 original size:22 final size:22
Alignment explanation
Indices: 12887--12995 Score: 87
Period size: 22 Copynumber: 4.8 Consensus size: 22
12877 TAAATATTCA
* *
12887 TATGAAATTTTGATAAACACGTAC
1 TATGAAATTATGAT-AACTC-TAC
*
12911 TATGAAATTATAATAACCTCT-C
1 TATGAAATTATGATAA-CTCTAC
*
12933 TATGAAATTATGATAACTATAC
1 TATGAAATTATGATAACTCTAC
* *
12955 TATTAAAATTTTGATAAC-CTAC
1 TA-TGAAATTATGATAACTCTAC
* *
12977 TTATGATATTTTGATAACT
1 -TATGAAATTATGATAACT
12996 TTCGTATTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
21 3 0.04
22 35 0.50
23 18 0.26
24 14 0.20
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
TATGAAATTATGATAACTCTAC
Found at i:13009 original size:22 final size:21
Alignment explanation
Indices: 12932--13009 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
12922 AATAACCTCT
* *
12932 CTATGAAATTATGATAACTATA
1 CTATTAAATTTTGATAACT-TA
*
12954 CTATTAAAATTTTGATAACCTA
1 CTATT-AAATTTTGATAACTTA
* * *
12976 CTTATGATATTTTGATAACTTT
1 C-TATTAAATTTTGATAACTTA
12998 CGTATTAAATTT
1 C-TATTAAATTT
13010 CAAGAACCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 29 0.66
23 15 0.34
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (21 bp):
CTATTAAATTTTGATAACTTA
Found at i:13054 original size:22 final size:23
Alignment explanation
Indices: 13018--13078 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
13008 TTCAAGAACC
* *
13018 TTTCTATGCAA-TTTTGTTAACT
1 TTTCTATGAAATTTTTGTTAACA
*
13040 TTTCTATG-AATTTTTTTTAACA
1 TTTCTATGAAATTTTTGTTAACA
* *
13062 TGTCTAAGAAATTTTTG
1 TTTCTATGAAATTTTTG
13079 AAAACCCCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.06
22 23 0.72
23 7 0.22
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (23 bp):
TTTCTATGAAATTTTTGTTAACA
Found at i:13141 original size:44 final size:44
Alignment explanation
Indices: 13093--14100 Score: 309
Period size: 44 Copynumber: 23.3 Consensus size: 44
13083 CCCCACTACA
* * *
13093 AAATTTTGATAACCTCCCAATGAAATTTTGATAATAACGCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
** * * *
13137 AAATTTTGATAATGTCCTTGTGAAATGTTTG-TAAGCACACTAT-
1 AAATTTTGATAACCTCCCTATGAAAT-TTTGATAATCACACTATG
* * *
13180 AAACTTTTGAGAA-CTCCCTATGAAATGTT-AGTAATCACACTGTG
1 AAA-TTTTGATAACCTCCCTATGAAATTTTGA-TAATCACACTATG
* ** * * *
13224 AAATTTTGATAATCAATTAATCACAGATGGAATTTTGATAATCTCACTATA
1 AAATTTTGATAA-C-----CTC-CCTATGAAATTTTGATAATCACACTATG
* * * ** * *
13275 AAATCTTGATAAACATTCCTACAAAATTTTGATAAAGCACACTATA
1 AAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AATCACACTATG
* * * *
13321 AAATTTCGATAACCTCCTTATGAAGTTTTGATAACCAC-CTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
** *
13364 ATTTTTTGATAACCT-CCTATGAAATTTTG--AA-CAAAACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATC-ACACTATG
* * *
13405 AAATTTTGATAA--TCCCTATGAAATTTTGACATTTA-ACTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACAC-TATG
** * * * * *
13447 AAATTTCAATAACCTCCTTAT-AACATTTTGGTAACCTTCA-TAGG
1 AAATTTTGATAACCTCCCTATGAA-ATTTTGATAATC-ACACTATG
* * * *
13491 AAATTTTGATAA-CTCCACAATAAAATTTTAATAA-C-C-CT-CG
1 AAATTTTGATAACCTCC-CTATGAAATTTTGATAATCACACTATG
* * * * **
13531 TAA-TTTGGT-ACCTACACC-ATGAAATTTTGAGAACCTTTA-TATG
1 AAATTTTGATAACCT-C-CCTATGAAATTTTGATAATC-ACACTATG
** * * *
13574 AAA---T-ACCA-CACCCTA--AAATTTTGATAACCACACTCTG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * *
13611 AAATTTTGATAACCTCCATATGAAAATTTG---AT-ACTCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * * * * * *
13651 AAATTTTGTTAACGTCTCGATGAAATTTTCATAACCATC-CTAAG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCA-CACTATG
* * * * *
13695 AAATTTTG-TAACCTCCATATGAAATTTTGAAAACCACACCATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * * * ** *
13738 AAATTGTGATGACCTCACTATGAGATTTTGATAAAAACGCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * * * * * * *
13782 AAGTTTTGATAACGTCGCTTTGAAATTTTGATAACCTCCCTATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * * ** *
13826 AAATTTTGATAA-CTGCACTGTAAAATTTTGATAACTTTC-TTATG
1 AAATTTTGATAACCT-CCCTATGAAATTTTGATAA-TCACACTATG
** *
13870 AAATTTTGATAATTTGATCTCTATGAAATTTTG---AT-A-A-TA-G
1 AAATTTTGATAA---CCTCCCTATGAAATTTTGATAATCACACTATG
* * *
13910 --ATTTTGATAACCTCCTTATGAAATTTTGATAACCACACTATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
* * * * * * **
13952 AAATTATGATAACATCCCTATTAGATATTGATAACATCCTTATAAAATTG
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT-A-AT-C--ACACTA-TG
* * * * * * *
14002 AGATTTTTATATCCTTCTTACGATCATTTTG-TAA-C-CACTATG
1 AAATTTTGATAACCTCCCTATGA-AATTTTGATAATCACACTATG
* * *
14044 AAATTTTGATAACCTCCCTATAAAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACAC-TATG
14088 AAATTTTGATAAC
1 AAATTTTGATAAC
14101 TATACTACGA
Statistics
Matches: 694, Mismatches: 187, Indels: 166
0.66 0.18 0.16
Matches are distributed among these distances:
35 14 0.02
36 1 0.00
37 19 0.03
38 14 0.02
39 24 0.03
40 56 0.08
41 35 0.05
42 58 0.08
43 95 0.14
44 244 0.35
45 37 0.05
46 23 0.03
47 13 0.02
48 2 0.00
49 4 0.01
50 18 0.03
51 34 0.05
52 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAATCACACTATG
Found at i:13236 original size:22 final size:21
Alignment explanation
Indices: 13093--13238 Score: 86
Period size: 22 Copynumber: 6.7 Consensus size: 21
13083 CCCCACTACA
*
13093 AAATTTTGATAACCTC-CCAATG
1 AAATTTTGATAA--TCACCTATG
*
13115 AAATTTTGATAATAACGCTATG
1 AAATTTTGATAATCAC-CTATG
** *
13137 AAATTTTGATAATGTCCTTGTG
1 AAATTTTGATAATCACC-TATG
*
13159 AAATGTTTG-TAAGCACACTAT-
1 AAAT-TTTGATAATCAC-CTATG
*
13180 AAACTTTTGAGAACTC-CCTATG
1 AAA-TTTTGATAA-TCACCTATG
* *
13202 AAATGTT-AGTAATCACACTGTG
1 AAATTTTGA-TAATCAC-CTATG
13224 AAATTTTGATAATCA
1 AAATTTTGATAATCA
13239 ATTAATCACA
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.04
21 19 0.20
22 66 0.69
23 7 0.07
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAATCACCTATG
Found at i:13323 original size:23 final size:22
Alignment explanation
Indices: 13254--13433 Score: 81
Period size: 21 Copynumber: 8.4 Consensus size: 22
13244 TCACAGATGG
* *
13254 AATTTTGATAATCTCACTATAA
1 AATTTTGATAAACACACTATAA
* *
13276 AATCTTGATAAACATTC-CTACAA
1 AATTTTGATAAACA--CACTATAA
13299 AATTTTGATAAAGCACACTATAA
1 AATTTTGATAAA-CACACTATAA
* * * *
13322 AATTTCGATAACCTC-CTTATGA
1 AATTTTGATAAACACAC-TATAA
* * *
13344 AGTTTTGATAACCAC-CTATGA
1 AATTTTGATAAACACACTATAA
** * * *
13365 TTTTTTGATAACCTC-CTATGA
1 AATTTTGATAAACACACTATAA
*
13386 AATTTTGA-ACAA-A-ACTATGA
1 AATTTTGATA-AACACACTATAA
* *
13406 AATTTTGATAATC-C-CTATGA
1 AATTTTGATAAACACACTATAA
13426 AATTTTGA
1 AATTTTGA
13434 CATTTAACTT
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
20 30 0.24
21 32 0.25
22 31 0.24
23 31 0.24
24 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
AATTTTGATAAACACACTATAA
Found at i:13354 original size:22 final size:21
Alignment explanation
Indices: 13254--13881 Score: 235
Period size: 22 Copynumber: 29.5 Consensus size: 21
13244 TCACAGATGG
* *
13254 AATTTTGATAATCTCACTATAA
1 AATTTTGATAACCTC-CTATGA
* * **
13276 AATCTTGATAAACATTCCTACAA
1 AATTTTGAT-AAC-CTCCTATGA
* * *
13299 AATTTTGATAAAGCACACTATAA
1 AATTTTGAT-AACCTC-CTATGA
*
13322 AATTTCGATAACCTCCTTATGA
1 AATTTTGATAACCTCC-TATGA
* *
13344 AGTTTTGATAACCACCTATGA
1 AATTTTGATAACCTCCTATGA
**
13365 TTTTTTGATAACCTCCTATGA
1 AATTTTGATAACCTCCTATGA
***
13386 AATTTTG--AACAAAACTATGA
1 AATTTTGATAAC-CTCCTATGA
*
13406 AATTTTGATAATC-CCTATGA
1 AATTTTGATAACCTCCTATGA
13426 AATTTTGACATTTAA-CT--TATGA
1 AATTTTG--A--TAACCTCCTATGA
**
13448 AATTTCAATAACCTCCTTAT-A
1 AATTTTGATAACCTCC-TATGA
* * *
13469 ACATTTTGGTAACCTTCATAGGA
1 A-ATTTTGATAACC-TCCTATGA
* *
13492 AATTTTGATAA-CTCCACAATAA
1 AATTTTGATAACCT-C-CTATGA
* * *
13514 AATTTTAATAA-C-CCT-CGT
1 AATTTTGATAACCTCCTATGA
* *
13532 AA-TTTGGT-ACCTACACCATGA
1 AATTTTGATAACCT-C-CTATGA
* **
13553 AATTTTGAGAACCTTTATATGA
1 AATTTTGATAACC-TCCTATGA
**
13575 AA---T-ACCACAC-CCTA--A
1 AATTTTGATAAC-CTCCTATGA
* *
13590 AATTTTGATAACCACACTCTGA
1 AATTTTGATAACCTC-CTATGA
13612 AATTTTGATAACCTCCATATGA
1 AATTTTGATAACCTCC-TATGA
*
13634 AAATTTGAT-A-CT-CTATGA
1 AATTTTGATAACCTCCTATGA
* * *
13652 AATTTTGTTAACGTCTCGATGA
1 AATTTTGATAACCTC-CTATGA
* *
13674 AATTTTCATAACCATCCTAAGA
1 AATTTTGATAACC-TCCTATGA
13696 AATTTTG-TAACCTCCATATGA
1 AATTTTGATAACCTCC-TATGA
* * * *
13717 AATTTTGAAAACCACACCATAA
1 AATTTTGATAACCTC-CTATGA
* *
13739 AATTGTGATGACCTCACTATGA
1 AATTTTGATAACCTC-CTATGA
* ***
13761 GATTTTGATAAAAACGCTATGA
1 AATTTTGATAACCTC-CTATGA
* * *
13783 AGTTTTGATAACGTCGCTTTGA
1 AATTTTGATAACCTC-CTATGA
*
13805 AATTTTGATAACCTCCCTATAA
1 AATTTTGATAACCT-CCTATGA
* *
13827 AATTTTGATAA-CTGCACTGTAA
1 AATTTTGATAACCT-C-CTATGA
* *
13849 AATTTTGATAACTTTCTTATGA
1 AATTTTGATAAC-CTCCTATGA
13871 AATTTTGATAA
1 AATTTTGATAA
13882 TTTGATCTCT
Statistics
Matches: 447, Mismatches: 108, Indels: 102
0.68 0.16 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 7 0.02
18 22 0.05
19 15 0.03
20 38 0.09
21 57 0.13
22 253 0.57
23 44 0.10
24 7 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (21 bp):
AATTTTGATAACCTCCTATGA
Found at i:13370 original size:21 final size:21
Alignment explanation
Indices: 13328--13393 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
13318 ATAAAATTTC
13328 GATAACCTCCTTATGAAGTTTT
1 GATAACCTCC-TATGAAGTTTT
* **
13350 GATAACCACCTATGATTTTTT
1 GATAACCTCCTATGAAGTTTT
*
13371 GATAACCTCCTATGAAATTTT
1 GATAACCTCCTATGAAGTTTT
13392 GA
1 GA
13394 ACAAAACTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
21 29 0.76
22 9 0.24
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (21 bp):
GATAACCTCCTATGAAGTTTT
Found at i:13423 original size:20 final size:20
Alignment explanation
Indices: 13316--14100 Score: 135
Period size: 22 Copynumber: 36.9 Consensus size: 20
13306 ATAAAGCACA
* *
13316 CTATAAAATTTCGATAACCTC
1 CTATGAAATTTTGATAACC-C
*
13337 CTTATGAAGTTTTGATAACCAC
1 C-TATGAAATTTTGATAACC-C
**
13359 CTATGATTTTTTGATAACCTC
1 CTATGAAATTTTGATAACC-C
***
13380 CTATGAAATTTTGA-ACAAAA
1 CTATGAAATTTTGATA-ACCC
*
13400 CTATGAAATTTTGATAATCC
1 CTATGAAATTTTGATAACCC
13420 CTATGAAATTTTGACATTTAA--C
1 CTATGAAATTTTG--A--TAACCC
* **
13442 TTATGAAATTTCAATAACCTC
1 CTATGAAATTTTGATAACC-C
*
13463 CTTAT-AACATTTTGGTAACCTTC
1 C-TATGAA-ATTTTGATAACC--C
* *
13486 ATAGGAAATTTTGATAACTCC
1 CTATGAAATTTTGATAAC-CC
* * *
13507 ACAATAAAATTTTAATAA-CC
1 -CTATGAAATTTTGATAACCC
* * *
13527 CT-CGTAA-TTTGGT-ACCTAC
1 CTATGAAATTTTGATAACC--C
* * *
13546 ACCATGAAATTTTGAGAACCTTT
1 -CTATGAAATTTTGATAACC--C
* **
13569 ATATGAAA---T-ACCACACC
1 CTATGAAATTTTGATAAC-CC
13586 CTA--AAATTTTGATAACCAC
1 CTATGAAATTTTGATAACC-C
*
13605 ACTCTGAAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACC-C
* *
13627 CATATGAAAATTTGAT-A-CT
1 C-TATGAAATTTTGATAACCC
* *
13646 CTATGAAATTTTGTTAACGTCT
1 CTATGAAATTTTGATAAC--CC
* *
13668 CGATGAAATTTTCATAACCATC
1 CTATGAAATTTTGATAACC--C
*
13690 CTAAGAAATTTTG-TAACCTC
1 CTATGAAATTTTGATAACC-C
*
13710 CATATGAAATTTTGAAAACCAC
1 C-TATGAAATTTTGATAACC-C
* * * *
13732 ACCATAAAATTGTGATGACCTC
1 -CTATGAAATTTTGATAACC-C
* * *
13754 ACTATGAGATTTTGATAAAAACG
1 -CTATGAAATTTTGAT--AACCC
* *
13777 CTATGAAGTTTTGATAACGTCG
1 CTATGAAATTTTGATAAC--CC
*
13799 CTTTGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAA-C-CC
* *
13821 CTATAAAATTTTGATAACTGCA
1 CTATGAAATTTTGATAAC--CC
* * *
13843 CTGTAAAATTTTGATAACTTTC
1 CTATGAAATTTTGATAAC--CC
* * *
13865 TTATGAAATTTTGATAATTTGATCT
1 CTATGAAATTTTGAT-A----ACCC
13890 CTATGAAATTTTGATAA---
1 CTATGAAATTTTGATAACCC
13907 -TA-G--ATTTTGATAACCTC
1 CTATGAAATTTTGATAACC-C
13924 CTTATGAAATTTTGATAACCAC
1 C-TATGAAATTTTGATAACC-C
* *
13946 ACTATAAAATTATGATAACATCC
1 -CTATGAAATTTTGATAAC--CC
* * *
13969 CTATTAGATATTGATAACATCC
1 CTATGAAATTTTGATAAC--CC
* * * *
13991 TTATAAAATTGAGATTTTTATATCCTTC
1 --CT---A-TGAAATTTTGATAACC--C
* * * *
14019 TTACGATCATTTTG-TAACCA
1 CTATGA-AATTTTGATAACCC
14039 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAA-C-CC
*
14061 CTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACC-C
14082 CTTATGAAATTTTGATAAC
1 C-TATGAAATTTTGATAAC
14101 TATACTACGA
Statistics
Matches: 559, Mismatches: 126, Indels: 157
0.66 0.15 0.19
Matches are distributed among these distances:
13 10 0.02
15 4 0.01
16 3 0.01
17 7 0.01
18 22 0.04
19 18 0.03
20 52 0.09
21 62 0.11
22 323 0.58
23 20 0.04
24 8 0.01
25 14 0.03
26 2 0.00
27 2 0.00
28 12 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (20 bp):
CTATGAAATTTTGATAACCC
Found at i:14114 original size:44 final size:44
Alignment explanation
Indices: 14040--14126 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
14030 TTGTAACCAC
* * *
14040 TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCACTACAAAATTCTGATAACCTCCT
* * *
14084 TATGAAATTTTGATAA-CTATACTACGAAATTCTGATAATCTCC
1 TATGAAATTTTGATAACCT-CACTACAAAATTCTGATAACCTCC
14127 CTATAAAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCACTACAAAATTCTGATAACCTCCT
Found at i:14468 original size:22 final size:22
Alignment explanation
Indices: 14413--14542 Score: 73
Period size: 22 Copynumber: 5.9 Consensus size: 22
14403 TTTCAGGGGG
*
14413 AGGTTATCAAAATTTCATAATA
1 AGGTTATCAAAATTTCATAAGA
* * *
14435 TGATTACCAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAAGA
* * * *
14457 AGGTTATTAAAATTTTAT-TGTG
1 AGGTTATCAAAATTTCATAAG-A
* * * * ** *
14479 GGGGTAGTTAAAATTTCTTTGGG
1 AGGTTA-TCAAAATTTCATAAGA
* * *
14502 AGTTTATCCAAATTTCATATGA
1 AGGTTATCAAAATTTCATAAGA
14524 AGGTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
14543 GGGATCCAAG
Statistics
Matches: 78, Mismatches: 27, Indels: 6
0.70 0.24 0.05
Matches are distributed among these distances:
21 1 0.01
22 62 0.79
23 14 0.18
24 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAGA
Found at i:15326 original size:22 final size:22
Alignment explanation
Indices: 15299--15357 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
15289 AATTCACAAG
15299 GAGGTTATCAAAATTTCCTAGT
1 GAGGTTATCAAAATTTCCTAGT
* *
15321 GTGGTTATCAAAATTTCTTAGT
1 GAGGTTATCAAAATTTCCTAGT
*
15343 GAGGTTTTCAAAATT
1 GAGGTTATCAAAATT
15358 CCATAGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCCTAGT
Found at i:15484 original size:22 final size:22
Alignment explanation
Indices: 15459--15517 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
15449 TCATAGTGTT
*
15459 GTTATTAAAATTTTATACAA-AG
1 GTTATCAAAATTTTATA-AATAG
*
15481 GTTATCAAAATTTCATAAATAG
1 GTTATCAAAATTTTATAAATAG
*
15503 GTTATCATAATTTTA
1 GTTATCAAAATTTTA
15518 GAATGTGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (22 bp):
GTTATCAAAATTTTATAAATAG
Found at i:18085 original size:30 final size:30
Alignment explanation
Indices: 18049--18110 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
18039 TCTTCAAGGG
18049 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
18079 GGAGGGAATGATGCGCCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCAAGGACTTATCAT
18109 GG
1 GG
18111 TCTTGAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Found at i:22343 original size:12 final size:13
Alignment explanation
Indices: 22328--22372 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
22318 AATCTAAATC
22328 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
22340 TAAAGCAAATTAA
1 TAAAGCAGATTAA
22353 TAAAGCAGATTAA
1 TAAAGCAGATTAA
22366 TAAAGCA
1 TAAAGCA
22373 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:22379 original size:25 final size:25
Alignment explanation
Indices: 22328--22380 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
22318 AATCTAAATC
*
22328 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
22353 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
22378 TAA
1 TAA
22381 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:24298 original size:18 final size:18
Alignment explanation
Indices: 24275--24311 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24265 TAGGGTTAGA
24275 TATATATATATATAATAT
1 TATATATATATATAATAT
* *
24293 TATATATGTATATTATAT
1 TATATATATATATAATAT
24311 T
1 T
24312 TTGGGGCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATATATATAATAT
Found at i:28156 original size:71 final size:71
Alignment explanation
Indices: 28073--28208 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
28063 ACTCTCCAAC
* *
28073 ACTAATTAAATTTTCAACCAACTTAATTAACACTAAACAACCTAAATTAAATACTCAAATGGCTG
1 ACTAATTAAATTTTCAACCAACCTAATTAACACTAAACAACCTAAATTAAACACTCAAATGGCTG
28138 ACAAAG
66 ACAAAG
* *
28144 ACTAATTAAATTTTCAACCACCCTAATTAACACTAAGCAACCTAAATTAAACACTCAAATGGCTG
1 ACTAATTAAATTTTCAACCAACCTAATTAACACTAAACAACCTAAATTAAACACTCAAATGGCTG
28209 GAAAAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (71 bp):
ACTAATTAAATTTTCAACCAACCTAATTAACACTAAACAACCTAAATTAAACACTCAAATGGCTG
ACAAAG
Found at i:32268 original size:17 final size:17
Alignment explanation
Indices: 32239--32280 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
32229 CTTTTTATTA
*
32239 CATTTTTT-AATTTTCT
1 CATTTTTTCCATTTTCT
* *
32255 GATTTTTTCCATTTTTT
1 CATTTTTTCCATTTTCT
32272 CATTTTTTC
1 CATTTTTTC
32281 TTTTCCTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (17 bp):
CATTTTTTCCATTTTCT
Done.