Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014858.1 Corchorus capsularis cultivar CVL-1 contig14879, 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: 51763
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 11--40 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 ATATTATAAT
11 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 GATTCGTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1472 original size:22 final size:22
Alignment explanation
Indices: 1444--1503 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
1434 GAAGCAGTCA
1444 AAGAGGTTTCATGTTTATGATT
1 AAGAGGTTTCATGTTTATGATT
*
1466 AAGAGGTTTCATGTTTGTGATT
1 AAGAGGTTTCATGTTTATGATT
1488 AAGAGGTTTCATGTTT
1 AAGAGGTTTCATGTTT
1504 TTAAGACTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (22 bp):
AAGAGGTTTCATGTTTATGATT
Found at i:1646 original size:11 final size:13
Alignment explanation
Indices: 1619--1665 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
1609 GTTTTATTAT
1619 TAATA-ATATATA
1 TAATATATATATA
1631 T-ATATA-ATATA
1 TAATATATATATA
*
1642 -AATATATTTAT-
1 TAATATATATATA
1653 TAATATATATATA
1 TAATATATATATA
1666 GTCGATCGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
11 13 0.46
12 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATATATATA
Found at i:2937 original size:23 final size:23
Alignment explanation
Indices: 2911--2958 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2901 CTTTGGTTTC
2911 ATAAAAAGTATACTAACCAAATA
1 ATAAAAAGTATACTAACCAAATA
2934 ATAAAAAGTATACTAACCAAATA
1 ATAAAAAGTATACTAACCAAATA
2957 AT
1 AT
2959 TTAAGTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.04, T:0.23
Consensus pattern (23 bp):
ATAAAAAGTATACTAACCAAATA
Found at i:22704 original size:48 final size:49
Alignment explanation
Indices: 22650--22767 Score: 193
Period size: 48 Copynumber: 2.4 Consensus size: 49
22640 GTATCTAGTA
*
22650 ACAAAAGCCCCAAAACACATACAACACATGGGCAATACATACATAACAC
1 ACAAAAGCCCCAAAACACATACAACACATGGGCAATACATACAAAACAC
* *
22699 A-AAAAGCCCCAAAACACATATAACACATGGGCAATACGTACAAAACAC
1 ACAAAAGCCCCAAAACACATACAACACATGGGCAATACATACAAAACAC
*
22747 ACAAAATCCCCAAAACACATA
1 ACAAAAGCCCCAAAACACATA
22768 TATAACACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 45 0.70
49 19 0.30
ACGTcount: A:0.53, C:0.30, G:0.08, T:0.10
Consensus pattern (49 bp):
ACAAAAGCCCCAAAACACATACAACACATGGGCAATACATACAAAACAC
Found at i:24536 original size:147 final size:148
Alignment explanation
Indices: 24305--24617 Score: 583
Period size: 147 Copynumber: 2.1 Consensus size: 148
24295 ACATTAACGC
* *
24305 CTTCCGTCCGGGAAAGGCGTTTTGGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAG
24370 GGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATA
66 GGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATA
24435 GCAAGTAAAAATAAATGG
131 GCAAGTAAAAATAAATGG
* *
24453 CTTCCGTCTGGGAAGGGTGTTTT-GGGAGATAGGAAGTAAAGATGAATGGCTTCCGTCTGGGAAG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAG
24517 GGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATA
66 GGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATA
24582 GCAAGTAAAAATAAATGG
131 GCAAGTAAAAATAAATGG
24600 CTTCCGTCTGGGAAGGGC
1 CTTCCGTCTGGGAAGGGC
24618 AAATTGGGAA
Statistics
Matches: 160, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
147 140 0.88
148 20 0.12
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (148 bp):
CTTCCGTCTGGGAAGGGCGTTTTGGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAG
GGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATA
GCAAGTAAAAATAAATGG
Found at i:24627 original size:49 final size:49
Alignment explanation
Indices: 24305--24617 Score: 509
Period size: 49 Copynumber: 6.4 Consensus size: 49
24295 ACATTAACGC
* * * * *
24305 CTTCCGTCCGGGAAAGGCGTTTTGGGGAGATAGCAAGTAAAGATGAATGG
1 CTTCCGTCTGGGAAGGGCGCTTT-GGGAAATAGCAAGTAAAAATGAATGG
24355 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
1 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
*
24404 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
* * * * *
24453 CTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGGAAGTAAAGATGAATGG
1 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
24502 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
1 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
*
24551 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
24600 CTTCCGTCTGGGAAGGGC
1 CTTCCGTCTGGGAAGGGC
24618 AAATTGGGAA
Statistics
Matches: 245, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
49 225 0.92
50 20 0.08
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (49 bp):
CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGG
Found at i:29161 original size:15 final size:15
Alignment explanation
Indices: 29143--29195 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
29133 GAATTTACAT
29143 CTACTAAATTCGAAC
1 CTACTAAATTCGAAC
* *
29158 CTACTACATTCGCAC
1 CTACTAAATTCGAAC
* * *
29173 CTGCTGAATTCGTAC
1 CTACTAAATTCGAAC
*
29188 CTGCTAAA
1 CTACTAAA
29196 GCATTAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (15 bp):
CTACTAAATTCGAAC
Found at i:32442 original size:28 final size:29
Alignment explanation
Indices: 32411--32466 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
32401 ATAGGGAAAC
*
32411 GTAA-AATTAGAATTCATGAGGAGAGATA
1 GTAAGAATTAGAATTCATGAAGAGAGATA
**
32439 GTAAGTGGTTAGAATTCATGAAGAGAGA
1 GTAAG-AATTAGAATTCATGAAGAGAGA
32467 GTGGGAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
30 19 0.83
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.25
Consensus pattern (29 bp):
GTAAGAATTAGAATTCATGAAGAGAGATA
Found at i:34915 original size:2 final size:2
Alignment explanation
Indices: 34903--34935 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
34893 GAAAGAGACT
34903 GA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34936 TGGGGTCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
GA
Found at i:36404 original size:15 final size:15
Alignment explanation
Indices: 36379--36415 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
36369 GTTTAGGCCA
36379 ATATA-ATTATTAATT
1 ATATATATTATT-ATT
36394 AT-TATATTATTATT
1 ATATATATTATTATT
36408 ATATATAT
1 ATATATAT
36416 AATAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTATTATT
Found at i:41145 original size:80 final size:79
Alignment explanation
Indices: 41052--41234 Score: 294
Period size: 80 Copynumber: 2.3 Consensus size: 79
41042 AAGGAGTAAG
* *
41052 GAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAGGTAAAGGGATTAATCAGTAAAT
1 GAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAAAT
41117 TCATAATTAAAAGAA
66 TCATAATTAAAAG-A
*
41132 GAAGCAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAAAT
1 GAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAAAT
* *
41197 TGATAATTAAGAGA
66 TCATAATTAAAAGA
*
41211 GAAAGTAAAACTAGTAATCAGTAA
1 G-AAGTAAAAGTAGTAATCAGTAA
41235 TTAAGAAAGG
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 2 0.02
80 93 0.98
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (79 bp):
GAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAAAT
TCATAATTAAAAGA
Found at i:41230 original size:40 final size:40
Alignment explanation
Indices: 41053--41234 Score: 183
Period size: 40 Copynumber: 4.5 Consensus size: 40
41043 AGGAGTAAGG
*
41053 AAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCA
1 AAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGACA
* * * * *
41093 AGGTAAAGGGATTAATCAGTAAATTCA-TAATTAAAAGA-A
1 AAGTAAAAGTAGTAATCAGTAAA-TCAGTAATTAAGAGACA
* *
41132 GAAGCAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCA
1 -AAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGACA
* * * *
41173 AAGTAAAGGGA-TAAATCAGTAAAT-TGATAATTAAGAGAGA
1 AAGTAAAAGTAGT-AATCAGTAAATCAG-TAATTAAGAGACA
*
41213 AAGTAAAACTAGTAATCAGTAA
1 AAGTAAAAGTAGTAATCAGTAA
41235 TTAAGAAAGG
Statistics
Matches: 113, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
39 6 0.05
40 102 0.90
41 5 0.04
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.24
Consensus pattern (40 bp):
AAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGACA
Found at i:41495 original size:35 final size:35
Alignment explanation
Indices: 41407--41532 Score: 137
Period size: 35 Copynumber: 3.5 Consensus size: 35
41397 ATTAGTAATT
** *
41407 AAGAGTAAAATGGTAAGGAGTAAAAGAGTAATCAGTA
1 AAGAG-AAAATGGTAAAAAGT-AAAGAATAATCAGTA
* *
41444 AAGAGGAAAATGGTAAAGAGTAGAGAATAATCAGTA
1 AAGA-GAAAATGGTAAAAAGTAAAGAATAATCAGTA
* *
41480 CAGAGAAAA-GAGTAAAAAGTAAAGAGTAATCAGTA
1 AAGAGAAAATG-GTAAAAAGTAAAGAATAATCAGTA
41515 AAGAGAAAAATGGTAAAA
1 AAGAG-AAAATGGTAAAA
41533 TGGTAATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
34 1 0.01
35 30 0.39
36 26 0.34
37 19 0.25
38 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (35 bp):
AAGAGAAAATGGTAAAAAGTAAAGAATAATCAGTA
Found at i:41514 original size:14 final size:14
Alignment explanation
Indices: 41486--41648 Score: 69
Period size: 14 Copynumber: 10.9 Consensus size: 14
41476 AGTACAGAGA
41486 AAAGAGTAAAAAGT
1 AAAGAGTAAAAAGT
**
41500 AAAGAGTAATCAGT
1 AAAGAGTAAAAAGT
41514 AAAGAG-AAAAATGGT
1 AAAGAGTAAAAA--GT
*
41529 AAA-ATGGTAATTAAATT
1 AAAGA--GTAA--AAAGT
41546 CAAGAGAGTAAAAATAGT
1 -AA-AGAGT-AAAA-AGT
** * *
41564 AATTAGTAAAGAGAA
1 AAAGAGTAAAAAG-T
*
41579 AAAGAGTAAAGAGT
1 AAAGAGTAAAAAGT
**
41593 AAAGAGTAATCAGT
1 AAAGAGTAAAAAGT
*
41607 AAAGAGTAAAATGGT
1 AAAGAGTAAAA-AGT
* *
41622 AAAAAGTAAAGAGT
1 AAAGAGTAAAAAGT
**
41636 AATCAGTAAAAAG
1 AAAGAGTAAAAAG
41649 CAAAATGGTA
Statistics
Matches: 111, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
13 3 0.03
14 54 0.49
15 30 0.27
16 4 0.04
17 7 0.06
18 6 0.05
19 6 0.05
20 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.19
Consensus pattern (14 bp):
AAAGAGTAAAAAGT
Found at i:41580 original size:22 final size:23
Alignment explanation
Indices: 41550--41648 Score: 75
Period size: 22 Copynumber: 4.5 Consensus size: 23
41540 TAAATTCAAG
* **
41550 AGAGTAAAAATAGTAATTAGTAA
1 AGAGTAAAAAGAGTAAAGAGTAA
41573 AGAG-AAAAAGAGTAAAGAGTAA
1 AGAGTAAAAAGAGTAAAGAGTAA
**
41595 AGAGT--AATCAGTAAAGAGTAA
1 AGAGTAAAAAGAGTAAAGAGTAA
41616 A-ATGGT-AAAA-AGTAAAGAGTAA
1 AGA--GTAAAAAGAGTAAAGAGTAA
**
41638 TCAGTAAAAAG
1 AGAGTAAAAAG
41649 CAAAATGGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 17 0.27
22 37 0.60
23 7 0.11
ACGTcount: A:0.58, C:0.02, G:0.22, T:0.18
Consensus pattern (23 bp):
AGAGTAAAAAGAGTAAAGAGTAA
Found at i:41589 original size:7 final size:7
Alignment explanation
Indices: 41568--41673 Score: 72
Period size: 7 Copynumber: 14.7 Consensus size: 7
41558 AATAGTAATT
41568 AGTAAAG
1 AGTAAAG
*
41575 AGAAAAAG
1 AG-TAAAG
41583 AGTAAAG
1 AGTAAAG
41590 AGTAAAG
1 AGTAAAG
**
41597 AGTAATC
1 AGTAAAG
41604 AGTAAAG
1 AGTAAAG
41611 AGTAAA-
1 AGTAAAG
*
41617 ATGGTAAAA
1 A--GTAAAG
41626 AGTAAAG
1 AGTAAAG
**
41633 AGTAATC
1 AGTAAAG
*
41640 AGTAAAA
1 AGTAAAG
*
41647 AGCAAA-
1 AGTAAAG
41653 ATGGTAAAG
1 A--GTAAAG
*
41662 AGTAAAT
1 AGTAAAG
41669 AGTAA
1 AGTAA
41674 TTAGTAAAGT
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
6 2 0.03
7 59 0.76
8 15 0.19
9 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:41608 original size:36 final size:36
Alignment explanation
Indices: 41561--41694 Score: 173
Period size: 36 Copynumber: 3.8 Consensus size: 36
41551 GAGTAAAAAT
* *
41561 AGTAATTAGTAAAGAG-AAAAAGAGTAAAGAGTAAAG
1 AGTAATCAGTAAAGAGCAAAATG-GTAAAGAGTAAAG
* *
41597 AGTAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAG
1 AGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAG
* *
41633 AGTAATCAGTAAAAAGCAAAATGGTAAAGAGTAAAT
1 AGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAG
* *
41669 AGTAATTAGTAAAGTG-AAAATGGTAA
1 AGTAATCAGTAAAGAGCAAAATGGTAA
41695 TCAGTAGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 10 0.11
36 72 0.83
37 5 0.06
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (36 bp):
AGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAG
Found at i:41623 original size:29 final size:30
Alignment explanation
Indices: 41486--41666 Score: 90
Period size: 29 Copynumber: 5.8 Consensus size: 30
41476 AGTACAGAGA
41486 AAAGAGTAAAA--AGTAAAGAGTAATCAGT
1 AAAGAGTAAAATGAGTAAAGAGTAATCAGT
* * *
41514 AAAGAGAAAAATG-GTAAA-ATGGTAATTAAATT
1 AAAGAGTAAAATGAGTAAAGA--GTAA-T-CAGT
** ** *
41546 CAAGAGAGTAAAAAT-AGTAATTAGTAAAGAGAA
1 -AA-AGAGT-AAAATGAGTAAAGAGTAATCAG-T
41579 AAAGAGT-AAA-GAGTAAAGAGTAATCAGT
1 AAAGAGTAAAATGAGTAAAGAGTAATCAGT
41607 AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATCAGT
1 AAAGAGTAAAAT-G-----AGTAAAGAGTAATCAGT
* *
41643 AAAAAGCAAAATG-GTAAAGAGTAA
1 AAAGAGTAAAATGAGTAAAGAGTAA
41667 ATAGTAATTA
Statistics
Matches: 116, Mismatches: 16, Indels: 41
0.67 0.09 0.24
Matches are distributed among these distances:
28 18 0.16
29 34 0.29
30 4 0.03
31 7 0.06
32 5 0.04
33 2 0.02
34 8 0.07
35 10 0.09
36 28 0.24
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.19
Consensus pattern (30 bp):
AAAGAGTAAAATGAGTAAAGAGTAATCAGT
Found at i:41678 original size:7 final size:7
Alignment explanation
Indices: 41557--41681 Score: 56
Period size: 7 Copynumber: 17.4 Consensus size: 7
41547 AAGAGAGTAA
41557 AAATAGT
1 AAATAGT
*
41564 AATTAGT
1 AAATAGT
* *
41571 AAAGAGAA
1 AAATAG-T
*
41579 AAAGAGT
1 AAATAGT
*
41586 AAAGAGT
1 AAATAGT
*
41593 AAAGAGT
1 AAATAGT
41600 -AATCAGT
1 AAAT-AGT
*
41607 AAAGAGT
1 AAATAGT
*
41614 AAAATGGT
1 -AAATAGT
*
41622 AAAAAGT
1 AAATAGT
*
41629 AAAGAGT
1 AAATAGT
41636 -AATCAGT
1 AAAT-AGT
* *
41643 AAAAAGCA
1 AAATAG-T
*
41651 AAATGGT
1 AAATAGT
*
41658 AAAGAGT
1 AAATAGT
41665 AAATAGT
1 AAATAGT
*
41672 AATTAGT
1 AAATAGT
41679 AAA
1 AAA
41682 GTGAAAATGG
Statistics
Matches: 88, Mismatches: 23, Indels: 14
0.70 0.18 0.11
Matches are distributed among these distances:
6 4 0.05
7 65 0.74
8 19 0.22
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.20
Consensus pattern (7 bp):
AAATAGT
Found at i:41689 original size:21 final size:21
Alignment explanation
Indices: 41656--41700 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41646 AAGCAAAATG
* *
41656 GTAAAGAGTAAATAGTAATTA
1 GTAAAGAGAAAATAGTAATCA
* *
41677 GTAAAGTGAAAATGGTAATCA
1 GTAAAGAGAAAATAGTAATCA
41698 GTA
1 GTA
41701 GAAAAGAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (21 bp):
GTAAAGAGAAAATAGTAATCA
Found at i:41756 original size:63 final size:63
Alignment explanation
Indices: 41685--41805 Score: 215
Period size: 63 Copynumber: 1.9 Consensus size: 63
41675 TAGTAAAGTG
* * *
41685 AAAATGGTAATCAGTAGAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAAAAACAGTA
1 AAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAACAGTA
41748 AAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAA
1 AAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAA
41806 TGGTATTGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (63 bp):
AAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAACAGTA
Found at i:41799 original size:28 final size:26
Alignment explanation
Indices: 41738--41952 Score: 241
Period size: 26 Copynumber: 8.1 Consensus size: 26
41728 TAAAAAGAGC
* *
41738 AAAAACAGTAAAAATGGTAATCAATA
1 AAAAAGAGTAAAAATGGTATTCAATA
* * *
41764 AAAAAGAGTAGAGATGATATTCAATA
1 AAAAAGAGTAAAAATGGTATTCAATA
* * *
41790 GTAAAAAGAGCAAAAATGGTATTGAGTA
1 --AAAAAGAGTAAAAATGGTATTCAATA
* *
41818 AAAAAGAGTAAAAATGGTAATCAGTA
1 AAAAAGAGTAAAAATGGTATTCAATA
* *
41844 AAAAAGAGTAGAGATGGTATTCAATA
1 AAAAAGAGTAAAAATGGTATTCAATA
* *
41870 GTAAAAAGAGCAAAAATGGTATTCAGTA
1 --AAAAAGAGTAAAAATGGTATTCAATA
* *
41898 AAAAAGAGTAAAAATGGTAATCAGTAA
1 AAAAAGAGTAAAAATGGTATTCAAT-A
41925 AAAAAGAGTAAAAATGGTATTCAATA
1 AAAAAGAGTAAAAATGGTATTCAATA
41951 AA
1 AA
41953 GAAAAAAAAG
Statistics
Matches: 158, Mismatches: 26, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
26 92 0.58
27 24 0.15
28 42 0.27
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (26 bp):
AAAAAGAGTAAAAATGGTATTCAATA
Found at i:41820 original size:54 final size:52
Alignment explanation
Indices: 41738--41952 Score: 241
Period size: 54 Copynumber: 4.0 Consensus size: 52
41728 TAAAAAGAGC
* * * *
41738 AAAAACAGTAAAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATA
1 AAAAAGAGTAAAAATGGTAATCAATAAAAAAGAGTAAAAATGGTATTCAATA
* * * * * *
41790 GTAAAAAGAGCAAAAATGGTATTGAGTAAAAAAGAGTAAAAATGGTAATCAGTA
1 --AAAAAGAGTAAAAATGGTAATCAATAAAAAAGAGTAAAAATGGTATTCAATA
* * * * *
41844 AAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAAAAATGGTATTCAGTA
1 AAAAAGAGTAAAAATGGTAATCAATA--AAAAAGAGTAAAAATGGTATTCAATA
*
41898 AAAAAGAGTAAAAATGGTAATCAGTAAAAAAAGAGTAAAAATGGTATTCAATA
1 AAAAAGAGTAAAAATGGTAATCAAT-AAAAAAGAGTAAAAATGGTATTCAATA
41951 AA
1 AA
41953 GAAAAAAAAG
Statistics
Matches: 135, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
52 21 0.16
53 26 0.19
54 87 0.64
55 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (52 bp):
AAAAAGAGTAAAAATGGTAATCAATAAAAAAGAGTAAAAATGGTATTCAATA
Found at i:41831 original size:63 final size:63
Alignment explanation
Indices: 41697--41831 Score: 150
Period size: 63 Copynumber: 2.1 Consensus size: 63
41687 AATGGTAATC
* **
41697 AGTAGAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAAAAACAGTAAAAATGGTAATCAA
1 AGTA-AAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAACAGT--AAATGGTAAAAAA
*
41762 T
63 G
** *
41763 A--AAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAATGGT-ATTGAGTAAAAAAG
1 AGTAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAACAGTAAATG-GTAAAAAAG
41824 AGTAAAAA
1 AGTAAAAA
41832 TGGTAATCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
60 3 0.05
61 7 0.12
63 47 0.80
64 1 0.02
66 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (63 bp):
AGTAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAAAAACAGTAAATGGTAAAAAAG
Found at i:41870 original size:80 final size:80
Alignment explanation
Indices: 41738--41950 Score: 363
Period size: 80 Copynumber: 2.6 Consensus size: 80
41728 TAAAAAGAGC
* * *
41738 AAAAACAGTAAAAATGGTAATCAATAAAAAAGAGTAGAGATGATATTCAATAGTAAAAAGAGCAA
1 AAAAAGAGTAAAAATGGTAATCAGTAAAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAA
*
41803 AAATGGTATTGAGTA
66 AAATGGTATTCAGTA
41818 AAAAAGAGTAAAAATGGTAATCAGTAAAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAA
1 AAAAAGAGTAAAAATGGTAATCAGTAAAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAA
41883 AAATGGTATTCAGTA
66 AAATGGTATTCAGTA
* *
41898 AAAAAGAGTAAAAATGGTAATCAGTAAAAAAAGAGTAAAAATGGTATTCAATA
1 AAAAAGAGTAAAAATGGTAATCAGT-AAAAAAGAGTAGAGATGGTATTCAATA
41951 AAGAAAAAAA
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
80 101 0.80
81 25 0.20
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (80 bp):
AAAAAGAGTAAAAATGGTAATCAGTAAAAAAGAGTAGAGATGGTATTCAATAGTAAAAAGAGCAA
AAATGGTATTCAGTA
Found at i:41962 original size:32 final size:33
Alignment explanation
Indices: 41923--41985 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 33
41913 GGTAATCAGT
41923 AAAAAAAGAGT-AAAAATGGTATTCAA-TAAAGA
1 AAAAAAAGAGTAAAAAATGGTA-TCAAGTAAAGA
41955 AAAAAAAGAGTAAAAAATGGTATCAAGTAAA
1 AAAAAAAGAGTAAAAAATGGTATCAAGTAAA
41986 AAAGGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.17
Consensus pattern (33 bp):
AAAAAAAGAGTAAAAAATGGTATCAAGTAAAGA
Found at i:42017 original size:30 final size:30
Alignment explanation
Indices: 41983--42045 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
41973 GGTATCAAGT
*
41983 AAAAAAGGAAAAGAAAAGGGTAATAAGTAAA
1 AAAAAAGGAAAA-AAAAGAGTAATAAGTAAA
* * *
42014 AAAAAAGTAAAAAAAATAGTAATCAGTAAA
1 AAAAAAGGAAAAAAAAGAGTAATAAGTAAA
42044 AA
1 AA
42046 GAGTAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.13
Consensus pattern (30 bp):
AAAAAAGGAAAAAAAAGAGTAATAAGTAAA
Found at i:42018 original size:60 final size:59
Alignment explanation
Indices: 41897--42045 Score: 148
Period size: 60 Copynumber: 2.5 Consensus size: 59
41887 GGTATTCAGT
** * *
41897 AAAAAAGAGTAAAAATGGTAATCAGTAAAAAAAGAGTAAAAATGGTATTCAATAAAGAA
1 AAAAAAGAGTAAAAATGGTAATCAGTAAAAAAAGAAAAAAAAGGGTAATCAATAAAGAA
*
41956 AAAAAAGAGTAAAAAATGGT-ATCAAGTAAAAAAGGAAAAGAAAAGGGTAAT-AAGTAAA-AA
1 AAAAAAGAGT-AAAAATGGTAATC-AGTAAAAAAAGAAAA-AAAAGGGTAATCAA-TAAAGAA
*
42016 AAAAGTAA-A--AAAAATAGTAATCAGTAAAAA
1 AAAA--AAGAGTAAAAATGGTAATCAGTAAAAA
42046 GAGTAAGAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
58 16 0.21
59 16 0.21
60 29 0.38
61 14 0.18
62 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.17, T:0.16
Consensus pattern (59 bp):
AAAAAAGAGTAAAAATGGTAATCAGTAAAAAAAGAAAAAAAAGGGTAATCAATAAAGAA
Found at i:42026 original size:27 final size:28
Alignment explanation
Indices: 41897--42026 Score: 74
Period size: 28 Copynumber: 4.5 Consensus size: 28
41887 GGTATTCAGT
* * *
41897 AAAAAAGAGTAAAAATGGTAAT-CAGTA
1 AAAAAAAAGTAAAAAGGGTAATAAAGTA
* *
41924 AAAAAAGAGTAAAAATGGTATTCAATAAAG-A
1 AAAAAAAAGTAAAAA-GG--GT-AATAAAGTA
* *
41955 AAAAAAAGAGTAAAAAATGGT-ATCAAGTA
1 AAAAAAA-AGT-AAAAAGGGTAATAAAGTA
41984 AAAAAGGAAA--AGAAAAGGGTAAT-AAGTA
1 AAAAA--AAAGTA-AAAAGGGTAATAAAGTA
42012 AAAAAAAAGTAAAAA
1 AAAAAAAAGTAAAAA
42027 AAATAGTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
26 3 0.04
27 20 0.25
28 24 0.30
29 8 0.10
30 3 0.04
31 12 0.15
32 6 0.07
33 5 0.06
ACGTcount: A:0.65, C:0.02, G:0.18, T:0.15
Consensus pattern (28 bp):
AAAAAAAAGTAAAAAGGGTAATAAAGTA
Found at i:42076 original size:57 final size:57
Alignment explanation
Indices: 41907--42083 Score: 143
Period size: 58 Copynumber: 3.0 Consensus size: 57
41897 AAAAAAGAGT
* * *
41907 AAAAATGGTAATCAGTAAAAAAAGAGTAA-AAATGGT-ATTCAATAAAGAAAAAAAAG-AGTA
1 AAAAATGGTAATCAGT--AAAAAGAGTAAGAAAGGGTAATT-AGT-AA-AAAAAAAAGTA-AA
* *
41967 AAAAATGGT-ATCAAGTAAAAA-AGGAAAAGAAAAGGGTAATAAGT-AAAAAAAAAGTAAA
1 AAAAATGGTAATC-AGTAAAAAGA-G-TAAG-AAAGGGTAATTAGTAAAAAAAAAAGTAAA
* *
42025 AAAAATAGTAATCAGTAAAAAGAGTAAGAAA-GGTAATTAGTAAAAGAAAAAAGTGAA
1 AAAAATGGTAATCAGTAAAAAGAGTAAGAAAGGGTAATTAGTAAAA-AAAAAAGTAAA
42082 AA
1 AA
42084 TGGTAAAAAG
Statistics
Matches: 97, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
55 9 0.09
56 6 0.06
57 16 0.16
58 33 0.34
59 11 0.11
60 12 0.12
61 8 0.08
62 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.18, T:0.16
Consensus pattern (57 bp):
AAAAATGGTAATCAGTAAAAAGAGTAAGAAAGGGTAATTAGTAAAAAAAAAAGTAAA
Found at i:50398 original size:18 final size:20
Alignment explanation
Indices: 50361--50399 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
50351 TCAAGTTAAT
50361 GGTGGAACTGTTGCTGACAA
1 GGTGGAACTGTTGCTGACAA
*
50381 GGTGG-ACT-TTGCTTACAA
1 GGTGGAACTGTTGCTGACAA
50399 G
1 G
50400 TTCTTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (20 bp):
GGTGGAACTGTTGCTGACAA
Found at i:51739 original size:1 final size:1
Alignment explanation
Indices: 51733--51763 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
51723 ATTGCAAATC
51733 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.