Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024574.1 Corchorus olitorius cultivar O-4 contig24607, 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: 86767
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1761 original size:66 final size:66
Alignment explanation
Indices: 1655--1787 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
1645 ATGCTAATGT
*
1655 ACAACAGAGAGAGTTATTACCTCAGCCAGTTCCCTTGCCAGAAACTCAAATCGCACCACAGCCTG
1 ACAACAGAGAGAGTTATTACCTCAGCCAGTTCCCTTGCCAGAAACTCAAATCGCAACACAGCCTG
1720 C
66 C
1721 ACAACAGAGAGAGTTATTACCTCAGCCAGTTCCCTTGCCAGAAACTCAAATCGCAACACAGCCTG
1 ACAACAGAGAGAGTTATTACCTCAGCCAGTTCCCTTGCCAGAAACTCAAATCGCAACACAGCCTG
1786 C
66 C
1787 A
1 A
1788 TCAATCCCAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.18
Consensus pattern (66 bp):
ACAACAGAGAGAGTTATTACCTCAGCCAGTTCCCTTGCCAGAAACTCAAATCGCAACACAGCCTG
C
Found at i:6256 original size:2 final size:2
Alignment explanation
Indices: 6249--6284 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6239 GACTTGTCTA
6249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6285 CTTTCACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6500 original size:22 final size:21
Alignment explanation
Indices: 6391--6496 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 21
6381 ATTTTTTATT
*
6391 ACCTCCTTATAAAATTTTGATA
1 ACCTTCTTAT-AAATTTTGATA
*
6413 ACCTTCCTATGAAATTTTGATA
1 ACCTTCTTAT-AAATTTTGATA
* * *
6435 ACGATAC-TATAGAATTTTGAGA
1 AC-CTTCTTATA-AATTTTGATA
* * **
6457 ACCTTTTTATAATTTTTTTTA
1 ACCTTCTTATAAATTTTGATA
6478 ACCTTCTTATGAAATTTTG
1 ACCTTCTTAT-AAATTTTG
6497 TTAAACTCCC
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
21 17 0.27
22 45 0.70
23 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (21 bp):
ACCTTCTTATAAATTTTGATA
Found at i:6656 original size:22 final size:22
Alignment explanation
Indices: 6631--6934 Score: 116
Period size: 22 Copynumber: 14.1 Consensus size: 22
6621 GAATTGTTAG
*
6631 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
6653 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
6675 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
6697 TAAGC-CTTCCTATAAAACTTTGA
1 TAATCAC--ACTATGAAATTTTGA
* * *
6720 TAAAC-CTCCTTATAAAATTTTGA
1 TAATCAC-AC-TATGAAATTTTGA
* *
6743 TAA-C-CTC-ATGAAATCTTG-
1 TAATCACACTATGAAATTTTGA
*
6761 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
6778 TAACCTCCCTATGATTTTTTTGA
1 TAATCACACTATGA-AATTTTGA
* * * *
6801 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
6823 TAATCTTC-CTATGAAATTTTGT
1 TAATC-ACACTATGAAATTTTGA
* *
6845 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
6867 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* *
6889 TAA-CCCTCTTATGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
6911 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
6933 TA
1 TA
6935 TCCTCCCTGA
Statistics
Matches: 220, Mismatches: 42, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
16 9 0.04
17 1 0.00
19 10 0.05
21 10 0.05
22 136 0.62
23 53 0.24
24 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:6777 original size:16 final size:18
Alignment explanation
Indices: 6734--6781 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
6724 CCTCCTTATA
*
6734 AAATTTTGATAACCTCATG
1 AAATTTTGATAA-CTCATC
*
6753 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
6769 AAATTTTGATAAC
1 AAATTTTGATAAC
6782 CTCCCTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:6860 original size:44 final size:43
Alignment explanation
Indices: 6661--6951 Score: 151
Period size: 44 Copynumber: 6.8 Consensus size: 43
6651 GATAATCACA
* * * *
6661 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAGCCTTC
1 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGTTAA--CTTC
* * * * * * *
6706 CTATAAAACTTTGATAAACCTCCTTATAAAATTTTGATAACCT-
1 CTATGAAATTTTGAT-AATCTCCCTATGAAATTTTGTTAACTTC
* * * *
6749 C-ATGAAATCTTGATAA-----CTA-CAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGTTAA-CTTC
** * **
6786 CTATGATTTTTTTGATAACCTCATTATGAAATTTTGTTAATCTTC
1 CTATGA-AATTTTGATAATCTCCCTATGAAATTTTGTTAA-CTTC
* * *
6831 CTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCT-ACATA
1 CTATGAAATTTTGATAATCTCCCTATGAAATTTTG-T-TAACTTC
*
6875 CTATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAATCTCC-C-TATGAAATTTTGTTAA-CTTC
*
6919 ATATGAAATTTTGAT-ATCCTCCC--TGAAATTTTG
1 CTATGAAATTTTGATAAT-CTCCCTATGAAATTTTG
6952 ATTACTCCAT
Statistics
Matches: 191, Mismatches: 35, Indels: 43
0.71 0.13 0.16
Matches are distributed among these distances:
35 12 0.06
36 3 0.02
37 1 0.01
38 4 0.02
39 8 0.04
41 2 0.01
42 23 0.12
43 5 0.03
44 73 0.38
45 36 0.19
46 24 0.13
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCTCCCTATGAAATTTTGTTAACTTC
Found at i:6886 original size:66 final size:66
Alignment explanation
Indices: 6683--6933 Score: 189
Period size: 66 Copynumber: 3.9 Consensus size: 66
6673 GATAACCTCG
* * * * * *
6683 CTATGAAATTTTGATAAGCCTTCCTATAAAACTTTGATAAACCTCCTTATAAAATTTTGAT-AAC
1 CTATGAAATTTTGATAA-CCCTCCTATGAAATTTTGAT-AACCTCCATATGAAATTTTGATCTAC
*
6747 CT-
64 ATA
* * * ** * *
6749 C-ATGAAATCTTGATAA-----CTA-CAAATTTTGATAACCTCCCTATGATTTTTTTGAT-AACC
1 CTATGAAATTTTGATAACCCTCCTATGAAATTTTGATAACCTCCATATGA-AATTTTGATCTACA
6806 TCA
65 T-A
* * * * * * *
6809 TTATGAAATTTTGTTAATCTTCCTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT
1 CTATGAAATTTTGATAACCCTCCTATGAAATTTTGATAACCTCCATATGAAATTTTGATCTACAT
6874 A
66 A
* *
6875 CTATGAAATTTTGATAACCCTCTTATGAAATTTTGATAACCTTCATATGAAATTTTGAT
1 CTATGAAATTTTGATAACCCTCCTATGAAATTTTGATAACCTCCATATGAAATTTTGAT
6934 ATCCTCCCTG
Statistics
Matches: 148, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
57 11 0.07
58 21 0.14
59 3 0.02
61 13 0.09
65 14 0.09
66 62 0.42
67 24 0.16
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCCTCCTATGAAATTTTGATAACCTCCATATGAAATTTTGATCTACAT
A
Found at i:7090 original size:22 final size:21
Alignment explanation
Indices: 7061--7116 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
7051 TCACATTTTG
7061 AAAATTTGATAACCTC-TCTAT
1 AAAATTTGATAACC-CGTCTAT
* *
7082 AAAAGTTTGTTGACCCGTCTAT
1 AAAA-TTTGATAACCCGTCTAT
*
7104 GAAATTTTGATAA
1 -AAAATTTGATAA
7117 TCACATTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
AAAATTTGATAACCCGTCTAT
Found at i:7126 original size:22 final size:22
Alignment explanation
Indices: 7101--7161 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
7091 TTGACCCGTC
7101 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAATCACAT
* * * *
7123 TATGTAATTTTGATAACCTCGT
1 TATGAAATTTTGATAATCACAT
*
7145 TTTGAAATTTTGATAAT
1 TATGAAATTTTGATAAT
7162 TTTCCCATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:7230 original size:21 final size:22
Alignment explanation
Indices: 7190--7244 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
7180 CATCCAAAAT
7190 CTCTATGAAATTTCGATAATCA
1 CTCTATGAAATTTCGATAATCA
*
7212 CTCTATGAGATTT-GATAATC-
1 CTCTATGAAATTTCGATAATCA
* *
7232 TTCTATCAAATTT
1 CTCTATGAAATTT
7245 TTGTACTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 12 0.41
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
CTCTATGAAATTTCGATAATCA
Found at i:7244 original size:20 final size:20
Alignment explanation
Indices: 7187--7244 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
7177 GATCATCCAA
7187 AATCTCTATGAAATTTCGAT
1 AATCTCTATGAAATTTCGAT
*
7207 AATCACTCTATGAGATTT-GAT
1 AAT--CTCTATGAAATTTCGAT
*
7228 AATCTTCTATCAAATTT
1 AATC-TCTATGAAATTT
7245 TTGTACTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 6 0.19
22 12 0.38
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (20 bp):
AATCTCTATGAAATTTCGAT
Found at i:7298 original size:22 final size:22
Alignment explanation
Indices: 7283--7430 Score: 122
Period size: 22 Copynumber: 6.7 Consensus size: 22
7273 ATAACCTTCA
*
7283 TATGAAATTTTGATAACGACAC
1 TATGAAATTTTGATAACCACAC
**
7305 TAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *** *
7327 TATAAAATTTTGATAATGTCCC
1 TATGAAATTTTGATAACCACAC
* * *
7349 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
7370 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
*
7393 TATGAAATTCTT-ATAACCTCAC
1 TATGAAATT-TTGATAACCACAC
*
7415 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
7431 TCTCTTTGAT
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.04
22 93 0.93
23 3 0.03
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:7546 original size:68 final size:66
Alignment explanation
Indices: 7449--7625 Score: 196
Period size: 68 Copynumber: 2.7 Consensus size: 66
7439 ATAACCTTTC
* *
7449 TATAAAAT-TGTGATAACCACACTATGAAATTTCAATAACCTTCCTAACAAATTTTAATAACCTG
1 TATAAAATAT-TGGTAACCACACTATGAAATTTCAATAACCTTCCCAACAAATTTTAAT-ACCT-
7513 ATCC-
63 -TCCA
* ** ** * *
7517 TATGAAATATTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATATCTTCC
1 TATAAAATATTGGTAACCACACTATGAAATTTCAATAACCTTCCCAACAAATTTTAATACCTTCC
7582 A
66 A
* * *
7583 TATAAAATTTTGGTAACCACACTATAAAATTCCAATAACCTTC
1 TATAAAATATTGGTAACCACACTATGAAATTTCAATAACCTTC
7626 TCATGAAATT
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
65 3 0.03
66 37 0.40
67 3 0.03
68 48 0.52
69 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (66 bp):
TATAAAATATTGGTAACCACACTATGAAATTTCAATAACCTTCCCAACAAATTTTAATACCTTCC
A
Found at i:7571 original size:22 final size:22
Alignment explanation
Indices: 7435--7666 Score: 132
Period size: 22 Copynumber: 10.5 Consensus size: 22
7425 TGATAATCTC
* *
7435 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
7457 TGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
** **
7479 TTCAATAACCTTCCTAACAAAT
1 TTTGATAACCTTCCTATGAAAT
*
7501 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* * *
7525 ATTGGTAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
*
7547 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
7569 TTTGAT-ATCTTCCATATAAAAT
1 TTTGATAACCTTCC-TATGAAAT
* * *
7591 TTTGGTAACC-ACACTATAAAAT
1 TTTGATAACCTTC-CTATGAAAT
***
7613 TCCAATAACCTT-CTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * * *
7635 TATAATAAGCATCTTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
7657 TTTGATAACC
1 TTTGATAACC
7667 ACACAGAGAC
Statistics
Matches: 157, Mismatches: 41, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
21 9 0.06
22 126 0.80
23 6 0.04
24 16 0.10
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:7657 original size:66 final size:65
Alignment explanation
Indices: 7453--7670 Score: 213
Period size: 66 Copynumber: 3.3 Consensus size: 65
7443 CCTTTCTATA
* ** *
7453 AAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAACAAATTTTAATAACCTGATCCT
1 AAATTTTGATAACCACACTATGAAATTTCAATAACCTTCC-ATGAAATTTTAATAACC--ATCAT
7518 ATG
63 ATG
* * ** * * *
7521 AAATATTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGAT-ATCTTCCATA
1 AAATTTTGATAACCACACTATGAAATTTCAATAACCTT-CCATGAAATTTTAATAACCAT-CATA
*
7585 TA
64 TG
* * * * * *
7587 AAATTTTGGTAACCACACTATAAAATTCCAATAACCTTCTCATGAAATTATAATAAGCATCTTAT
1 AAATTTTGATAACCACACTATGAAATTTCAATAACCTTC-CATGAAATTTTAATAACCATCATAT
7652 G
65 G
7653 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
7671 AGAGACAAGA
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
65 2 0.02
66 70 0.57
67 5 0.04
68 43 0.35
69 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (65 bp):
AAATTTTGATAACCACACTATGAAATTTCAATAACCTTCCATGAAATTTTAATAACCATCATATG
Found at i:7871 original size:20 final size:20
Alignment explanation
Indices: 7833--7871 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7823 TATTGACATT
7833 TAAAAAATTCAAATTAAAAG
1 TAAAAAATTCAAATTAAAAG
*
7853 TAAAATATT-AAATTCAAAA
1 TAAAAAATTCAAATT-AAAA
7872 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAAATTCAAATTAAAAG
Found at i:12234 original size:13 final size:13
Alignment explanation
Indices: 12216--12241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12206 AAGGTAGCAA
12216 CAAAAATCATCAC
1 CAAAAATCATCAC
12229 CAAAAATCATCAC
1 CAAAAATCATCAC
12242 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:22509 original size:21 final size:21
Alignment explanation
Indices: 22483--22532 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
22473 TGCTAGGAGA
22483 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
22504 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
22525 TCATTGGA
1 TCATTGGA
22533 ATTGCCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:23422 original size:25 final size:24
Alignment explanation
Indices: 23386--23432 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
23376 TCCTTCTATT
23386 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
23409 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
23433 AATTTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:26683 original size:21 final size:21
Alignment explanation
Indices: 26659--26725 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
26649 AGGAGATCAC
26659 TGGAGAAGGTTCCAAGCTCAT
1 TGGAGAAGGTTCCAAGCTCAT
26680 TGGAGAAGGTTCCAAGCTCAT
1 TGGAGAAGGTTCCAAGCTCAT
* *
26701 TAGAGAAGGTTTCAAGCTCAT
1 TGGAGAAGGTTCCAAGCTCAT
26722 TGGA
1 TGGA
26726 ATTGCCTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (21 bp):
TGGAGAAGGTTCCAAGCTCAT
Found at i:36098 original size:41 final size:41
Alignment explanation
Indices: 36047--36141 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
36037 AGAAAAATAA
* *
36047 GGACCAAATTGAATCAAATAGTGACTAGAATCCTAAATCAG
1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
* * * *
36088 GGACTAAATTGTATCAAATATTAAATAGAATCCTAAATTAG
1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
*
36129 GGACCATATTGAA
1 GGACCAAATTGAA
36142 CATGGAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (41 bp):
GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
Found at i:38474 original size:22 final size:22
Alignment explanation
Indices: 38449--38498 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
38439 AAAAGGATGG
38449 ATGCAAAAGATACCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
*
38471 ATGCAAAAGATGCCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
38493 ATGCAA
1 ATGCAA
38499 CTATTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (22 bp):
ATGCAAAAGATACCATGCAAAA
Found at i:38949 original size:28 final size:26
Alignment explanation
Indices: 38881--38961 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 26
38871 TGAACATGCG
* *
38881 AATGACCAAAATGCCCCTAA-TGTAAA
1 AATGACC-AAATGCCCCTAATTTTGAA
*
38907 AATGACCAACGTGCCCCTGAATTTTGAA
1 AATGACCAA-ATGCCCCT-AATTTTGAA
38935 AATGACCGAAATGCCCCTAGATTTTGA
1 AATGACC-AAATGCCCCTA-ATTTTGA
38962 TCCTAATGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.04
26 14 0.30
27 3 0.07
28 25 0.54
29 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (26 bp):
AATGACCAAATGCCCCTAATTTTGAA
Found at i:44722 original size:26 final size:27
Alignment explanation
Indices: 44667--44737 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 27
44657 GGTCACCTAT
*
44667 GGGGCATTTTGGTCATTTTAACACTAA
1 GGGGCATTTTGGTCATTTGAACACTAA
* * *
44694 -GGGCATTTTGGTCATTTGCATACTTA
1 GGGGCATTTTGGTCATTTGAACACTAA
**
44720 GGGGCACGTTGGTCATTT
1 GGGGCATTTTGGTCATTT
44738 TAAGTCCACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 22 0.59
27 15 0.41
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGAACACTAA
Found at i:48209 original size:38 final size:39
Alignment explanation
Indices: 48153--48259 Score: 148
Period size: 39 Copynumber: 2.8 Consensus size: 39
48143 ATGTTTTTAA
48153 TTAAG-TAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
1 TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
*
48191 TT-AGCTAATTCCAAAAGAAGATTTTGGACAAATAAAAGT
1 TTAAGATAATTCCAAAAGAAGATTTTGGA-AAATAAAAGT
* * *
48230 TTAAGAT-ATCCCAAATGAAGATTTCGGAAA
1 TTAAGATAATTCCAAAAGAAGATTTTGGAAA
48260 TTAATAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
37 2 0.03
38 27 0.44
39 30 0.48
40 3 0.05
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (39 bp):
TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
Found at i:53173 original size:41 final size:41
Alignment explanation
Indices: 53040--53233 Score: 111
Period size: 41 Copynumber: 4.6 Consensus size: 41
53030 ATGTGTTTAG
* ** * *
53040 GGACTTAGATATAAATGCCTTTATGTTATAAATGTGCTTGA
1 GGACTTTGATATGGATGCCTCTGTGTTATAAATGTGCTTGA
* * * ** *
53081 GGACTTTGAGAGAGAGAGATGCC-CATGTGTTATAATTGTATTTGG
1 GGACTTT--GATA-TG-GATGCCTC-TGTGTTATAAATGTGCTTGA
*
53126 GGACTTTGATATGGATGCCTCTGTGTTGTAAATGTGCTTGA
1 GGACTTTGATATGGATGCCTCTGTGTTATAAATGTGCTTGA
* * * * * * * * *
53167 GGACTTTTAGGAAGAATTGCCCCTGTATTATAATTGTGTTTGG
1 GGACTTTGA-TATGGA-TGCCTCTGTGTTATAAATGTGCTTGA
* *
53210 GGACTTTGATATAGATGCCGCTGT
1 GGACTTTGATATGGATGCCTCTGT
53234 ATCATTGGGC
Statistics
Matches: 111, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
41 43 0.39
42 7 0.06
43 34 0.31
45 27 0.24
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (41 bp):
GGACTTTGATATGGATGCCTCTGTGTTATAAATGTGCTTGA
Found at i:53220 original size:84 final size:86
Alignment explanation
Indices: 53031--53233 Score: 268
Period size: 86 Copynumber: 2.4 Consensus size: 86
53021 TTGTGTTACA
* * * * *
53031 TGTGTTTAGGGACTTAGATATAAATGCCTTTATGTTATAAATGTGCTTGAGGACTTTGAGAGAGA
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGA
*
53096 GAGATGCCCATGTGTTATAAT
66 GAGATGCCCATGTATTATAAT
* * * *
53117 TGTATTTGGGGACTTTGATATGGATGCCTCTGTGTTGTAAATGTGCTTGAGGACTTTTAG-GA-A
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGA
*
53180 GA-ATTGCCCCTGTATTATAAT
66 GAGA-TGCCCATGTATTATAAT
*
53201 TGTGTTTGGGGACTTTGATATAGATGCCGCTGT
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGT
53234 ATCATTGGGC
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
83 1 0.01
84 48 0.47
85 2 0.02
86 51 0.50
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (86 bp):
TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGA
GAGATGCCCATGTATTATAAT
Found at i:58992 original size:6 final size:6
Alignment explanation
Indices: 58952--58985 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
58942 ATTATTTAAC
*
58952 TATATA TATAGA TATAGA TATAGA TATAGA TATA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATA
58986 TAGATATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (6 bp):
TATAGA
Found at i:59967 original size:2 final size:2
Alignment explanation
Indices: 59962--59990 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59952 TGTGATGATG
59962 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
59991 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:63001 original size:42 final size:38
Alignment explanation
Indices: 62954--63033 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 38
62944 GCTGTTATTA
* *
62954 ACTATTTTGCATAGAAGTGAAGTAAGTCATAACTTCTAAATC
1 ACTATTGTGCAAAGAAGTGAAGT---TC-TAACTTCTAAATC
62996 ACTATTGTGCAAAGAAGTGAAGTTCTAACTTCTAAATC
1 ACTATTGTGCAAAGAAGTGAAGTTCTAACTTCTAAATC
63034 GGCTTAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 13 0.36
39 2 0.06
42 21 0.58
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (38 bp):
ACTATTGTGCAAAGAAGTGAAGTTCTAACTTCTAAATC
Found at i:68624 original size:7 final size:7
Alignment explanation
Indices: 68612--68642 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
68602 ATTATTATTA
68612 TATATAC
1 TATATAC
68619 TATATAC
1 TATATAC
68626 TATATAC
1 TATATAC
68633 T-TATAC
1 TATATAC
68639 TATA
1 TATA
68643 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (7 bp):
TATATAC
Found at i:70028 original size:24 final size:24
Alignment explanation
Indices: 70001--70049 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
69991 GAGTCCATAT
70001 ACTATCTTACTTGTCCTATGAGTA
1 ACTATCTTACTTGTCCTATGAGTA
70025 ACTATCTTACTTGTCCTATGAGTA
1 ACTATCTTACTTGTCCTATGAGTA
70049 A
1 A
70050 TTTGTCTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (24 bp):
ACTATCTTACTTGTCCTATGAGTA
Found at i:73697 original size:28 final size:28
Alignment explanation
Indices: 73659--73715 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
73649 CTCTCTTTTC
73659 TTTTTCCTCTCTGCATAGTTTTAAGTTT
1 TTTTTCCTCTCTGCATAGTTTTAAGTTT
*
73687 TTTTTCTTCTCTGCATAGTTTTAAGTTT
1 TTTTTCCTCTCTGCATAGTTTTAAGTTT
73715 T
1 T
73716 CAAAGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.60
Consensus pattern (28 bp):
TTTTTCCTCTCTGCATAGTTTTAAGTTT
Found at i:74783 original size:147 final size:146
Alignment explanation
Indices: 74509--74801 Score: 543
Period size: 147 Copynumber: 2.0 Consensus size: 146
74499 ATCTAAATAC
*
74509 AATAGTTGATCAATTATTATTAATTTATATTCCCATTTTTTCTAGCTTTAGGCTGCTCTTTCTTT
1 AATAGTTGATCAATTATTATTAATTTATATTCCCATTTTTTCCAGCTTTAGGCTGCTCTTTCTTT
*
74574 CTCTGTTCTTCAAATTTAAAGATTAACAGAGCTCTGTATATATATACTACTTATAGAAATATATA
66 CTCTGTTCTTCAAATTTAAAGATTAACAGAGCTATG-ATATATATACTACTTATAGAAATATATA
74639 GCAAAATTGATTCTTGA
130 GCAAAATTGATTCTTGA
74656 AATAGTTGATCAATTATTATTAATTTATATTCCCATTTTTTCCAGCTTTAGGCTGCTCTTTCTTT
1 AATAGTTGATCAATTATTATTAATTTATATTCCCATTTTTTCCAGCTTTAGGCTGCTCTTTCTTT
*
74721 CTCTGTTCTTCAAATTTAAAGATTAACATAGCTATG-TATATATACTACTTATAGAAATATATAG
66 CTCTGTTCTTCAAATTTAAAGATTAACAGAGCTATGATATATATACTACTTATAGAAATATATAG
74785 CAAAATTGATTCTTGA
131 CAAAATTGATTCTTGA
74801 A
1 A
74802 TTCAGTTAAA
Statistics
Matches: 143, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
145 45 0.31
147 98 0.69
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (146 bp):
AATAGTTGATCAATTATTATTAATTTATATTCCCATTTTTTCCAGCTTTAGGCTGCTCTTTCTTT
CTCTGTTCTTCAAATTTAAAGATTAACAGAGCTATGATATATATACTACTTATAGAAATATATAG
CAAAATTGATTCTTGA
Found at i:80724 original size:2 final size:2
Alignment explanation
Indices: 80717--80796 Score: 60
Period size: 2 Copynumber: 42.0 Consensus size: 2
80707 AAATATTTGG
* **
80717 AT AT AT AT AT AT AT A- AT AT A- AT AT GT GG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * **
80757 A- AT TT AA AT AT TT GG AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80797 GTCTTACAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
1 4 0.07
2 57 0.93
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:80774 original size:55 final size:56
Alignment explanation
Indices: 80692--80798 Score: 198
Period size: 55 Copynumber: 1.9 Consensus size: 56
80682 TTTTTGCTTC
*
80692 ATATATTTATAATTTAAATATTTGGATATATATATATATA-ATATAATATGTGGAT
1 ATATATATATAATTTAAATATTTGGATATATATATATATATATATAATATGTGGAT
80747 ATATATATATAATTTAAATATTTGGATATATATATATATATATATAATATGT
1 ATATATATATAATTTAAATATTTGGATATATATATATATATATATAATATGT
80799 CTTACAACGT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 39 0.78
56 11 0.22
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (56 bp):
ATATATATATAATTTAAATATTTGGATATATATATATATATATATAATATGTGGAT
Done.