Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016126.1 Corchorus capsularis cultivar CVL-1 contig16147, 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: 65939
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:1653 original size:9 final size:10
Alignment explanation
Indices: 1619--1650 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1609 AGCCGCCCAG
1619 TTTAATTTTT
1 TTTAATTTTT
1629 TTTAATTTTT
1 TTTAATTTTT
1639 TTTAATTTTT
1 TTTAATTTTT
1649 TT
1 TT
1651 AATATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:1734 original size:26 final size:26
Alignment explanation
Indices: 1705--1772 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
1695 TACTTAGTTT
*
1705 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
* *
1731 ATTAGTTTCTGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
1757 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
1773 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:1811 original size:23 final size:25
Alignment explanation
Indices: 1782--1841 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
1772 AAATGAAGGA
*
1782 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
1805 AAATGAAGTTTGAAGAAAGTTGTTAG
1 AAATGAAGTTTGAAG-AAGTTGTTAG
1831 AAATGAAGTTT
1 AAATGAAGTTT
1842 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
26 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:1933 original size:21 final size:21
Alignment explanation
Indices: 1909--1951 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1899 GGGCAAAAGT
*
1909 GTAAAAATGGGGCGGTATTTA
1 GTAAAAAGGGGGCGGTATTTA
* *
1930 GTAAAAGGGGGGCGGTGTTTA
1 GTAAAAAGGGGGCGGTATTTA
1951 G
1 G
1952 CAATCCAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.42, T:0.26
Consensus pattern (21 bp):
GTAAAAAGGGGGCGGTATTTA
Found at i:9101 original size:11 final size:11
Alignment explanation
Indices: 9085--9127 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
9075 TATACTATAT
9085 CTAATTAATAG
1 CTAATTAATAG
*
9096 CTAATTAATAT
1 CTAATTAATAG
9107 CTAATTAATAG
1 CTAATTAATAG
*
9118 TTAATTAATA
1 CTAATTAATA
9128 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:9107 original size:22 final size:22
Alignment explanation
Indices: 9081--9127 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9071 CCATTATACT
9081 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
9103 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
9125 ATA
1 ATA
9128 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:9374 original size:11 final size:11
Alignment explanation
Indices: 9358--9400 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
9348 TATACTATAT
9358 CTAATTAATAG
1 CTAATTAATAG
*
9369 CTAATTAATAT
1 CTAATTAATAG
9380 CTAATTAATAG
1 CTAATTAATAG
* *
9391 TTAACTAATA
1 CTAATTAATA
9401 ATGAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:9380 original size:22 final size:22
Alignment explanation
Indices: 9354--9400 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
9344 CCATTATACT
*
9354 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAACTA
*
9376 ATATCTAATTAATAGTTAACTA
1 ATATCTAATTAATAGCTAACTA
9398 ATA
1 ATA
9401 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAACTA
Found at i:9419 original size:273 final size:273
Alignment explanation
Indices: 8944--9475 Score: 1010
Period size: 273 Copynumber: 1.9 Consensus size: 273
8934 CACTTGTACT
*
8944 ATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAACCTGGTGTCAC
1 ATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAACCTGGTGCCAC
** * *
9009 CTTATCGTCCCATTTTGGTAATTTCTCACGTCTAATATATTAATTTAAAGCCCCTCCTTAATCCA
66 CTTATCACCCCATTTTGGTAATTTCTCACATCTAACATATTAATTTAAAGCCCCTCCTTAATCCA
*
9074 TTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGTTAATTAATAATGAATAAATT
131 TTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGTTAACTAATAATGAATAAATT
9139 CAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCTCATTTTTA
196 CAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCTCATTTTTA
9204 GTATATATTTATG
261 GTATATATTTATG
9217 ATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAACCTGGTGCCAC
1 ATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAACCTGGTGCCAC
9282 CTTATCACCCCATTTTGGTAATTTCTCACATCTAACATATTAATTTAAAGCCCCTCCTTAATCCA
66 CTTATCACCCCATTTTGGTAATTTCTCACATCTAACATATTAATTTAAAGCCCCTCCTTAATCCA
9347 TTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGTTAACTAATAATGAATAAATT
131 TTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGTTAACTAATAATGAATAAATT
9412 CAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCTCATTTTT
196 CAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCTCATTTTT
9476 GTGATTACAC
Statistics
Matches: 253, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 253 1.00
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (273 bp):
ATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAACCTGGTGCCAC
CTTATCACCCCATTTTGGTAATTTCTCACATCTAACATATTAATTTAAAGCCCCTCCTTAATCCA
TTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGTTAACTAATAATGAATAAATT
CAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCTCATTTTTA
GTATATATTTATG
Found at i:10231 original size:11 final size:11
Alignment explanation
Indices: 10215--10239 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10205 CATGGAGAAC
10215 AAAAAAAATAA
1 AAAAAAAATAA
10226 AAAAAAAATAA
1 AAAAAAAATAA
10237 AAA
1 AAA
10240 GACACCCGAC
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:10501 original size:15 final size:15
Alignment explanation
Indices: 10469--10519 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
10459 AGGACGTTAG
*
10469 TTTAATTATT-AT-T
1 TTTAATTATTCCTAT
* *
10482 TTTAATTTTTGCTAT
1 TTTAATTATTCCTAT
*
10497 TTTAATTATTCCTAA
1 TTTAATTATTCCTAT
10512 TTTAATTA
1 TTTAATTA
10520 GGATGGAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
15 21 0.68
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTAATTATTCCTAT
Found at i:14384 original size:28 final size:26
Alignment explanation
Indices: 14324--14376 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
14314 TGTTCATGAC
* *
14324 TTAGGGGTTACTAACTCCCTTTTTCT
1 TTAGAGGTTACTAACACCCTTTTTCT
*
14350 TTAGAGGTTACTAACACTC-TTTTCT
1 TTAGAGGTTACTAACACCCTTTTTCT
14375 TT
1 TT
14377 TTCAGAGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (26 bp):
TTAGAGGTTACTAACACCCTTTTTCT
Found at i:18688 original size:14 final size:14
Alignment explanation
Indices: 18669--18695 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18659 ACAACTTGGA
18669 TTGCAACAACAACC
1 TTGCAACAACAACC
18683 TTGCAACAACAAC
1 TTGCAACAACAAC
18696 TATCACAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15
Consensus pattern (14 bp):
TTGCAACAACAACC
Found at i:20364 original size:35 final size:34
Alignment explanation
Indices: 20301--20639 Score: 329
Period size: 35 Copynumber: 9.6 Consensus size: 34
20291 CTTACTAAAT
20301 TTAATTACCCTGAATTAAAGTTGATTACTGACTCAC
1 TTAATTACCCTGAATT-AAGTT-ATTACTGACTCAC
* **
20337 TTAATTACCCTCAATTAAGTTGATTACTGACTTGC
1 TTAATTACCCTGAATTAAGTT-ATTACTGACTCAC
* * *
20372 TTAATTACCCTGAATTAAGTTACTTATTAACTCGC
1 TTAATTACCCTGAATTAAGTTA-TTACTGACTCAC
* * * * *
20407 TTAATTACCTTGAATGAAATTACTTATTACTGATTTAC
1 TTAATTACCCTGAAT----TAAGTTATTACTGACTCAC
* * * *
20445 TTAATTATCCTGAATTAAGTTATCTTCTAATTCAC
1 TTAATTACCCTGAATTAAGTTAT-TACTGACTCAC
* *
20480 TTGATTACCCTGAATTAAGTTACTTATTGAACT-AC
1 TTAATTACCCTGAATTAAGTTA-TTACTG-ACTCAC
* *
20515 TTAATTACCCTGAATTAAGTTACTTATTAACTCAC
1 TTAATTACCCTGAATTAAGTTA-TTACTGACTCAC
20550 TTAATTACCCTGAATTATAGTTGATTACTGACTCAC
1 TTAATTACCCTGAATTA-AGTT-ATTACTGACTCAC
* * **
20586 TTAATTACCCTGACTTAAGTTGATTACCGACTTGC
1 TTAATTACCCTGAATTAAGTT-ATTACTGACTCAC
20621 TTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAG
20640 GTTCTTATTA
Statistics
Matches: 255, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
34 10 0.04
35 171 0.67
36 48 0.19
37 1 0.00
38 20 0.08
39 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (34 bp):
TTAATTACCCTGAATTAAGTTATTACTGACTCAC
Found at i:20490 original size:143 final size:141
Alignment explanation
Indices: 20301--20639 Score: 407
Period size: 143 Copynumber: 2.4 Consensus size: 141
20291 CTTACTAAAT
*
20301 TTAATTACCCTGAATTAAAGTTGATTACTGACTCACTTAATTACCCTCAATTAAGTTGA-TTACT
1 TTAATTACCCTGAATT-AAGTTGATTACTAACTCACTTAATTACCCTCAATTAAGTT-ACTTACT
* * *
20365 G-ACTTGCTTAATTACCCTGAATTAAGTTACTTATTAACTCGCTTAATTACCTTGAATGAAATTA
64 GAAC-TACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAAT--AA-TA
* *
20429 CTT-ATTACTGATTTAC
125 CTTGATTACTGACTCAC
* * * * * *
20445 TTAATTATCCTGAATTAAGTT-ATCTTCTAATTCACTTGATTACCCTGAATTAAGTTACTTATTG
1 TTAATTACCCTGAATTAAGTTGAT-TACTAACTCACTTAATTACCCTCAATTAAGTTACTTACTG
* *
20509 AACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATTATAGTTGA
65 AACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATAATACTTGA
20574 TTACTGACTCAC
130 TTACTGACTCAC
* ** ** *
20586 TTAATTACCCTGACTTAAGTTGATTACCGACTTGCTTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAGTTGATTACTAACTCACTTAATTACCCTCAATTAAG
20640 GTTCTTATTA
Statistics
Matches: 167, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
140 4 0.02
141 54 0.32
142 5 0.03
143 87 0.52
144 17 0.10
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (141 bp):
TTAATTACCCTGAATTAAGTTGATTACTAACTCACTTAATTACCCTCAATTAAGTTACTTACTGA
ACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATAATACTTGAT
TACTGACTCAC
Found at i:23992 original size:34 final size:36
Alignment explanation
Indices: 23954--24023 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
23944 GCCCATTCTC
23954 CCTAAGAAATGC-AATTCCAAGGATCC-AAAGAAAA
1 CCTAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
23988 CCTAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
1 CCTAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
24024 GGAGGAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 12 0.35
35 14 0.41
36 8 0.24
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.14
Consensus pattern (36 bp):
CCTAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
Found at i:32835 original size:16 final size:15
Alignment explanation
Indices: 32799--32843 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
32789 ATGGAATAAA
*
32799 AAATTTAATTACAGTG
1 AAATTTAATTA-AATG
32815 AAATTTAATTAAATG
1 AAATTTAATTAAATG
32830 ACAATTT-ATTAAAT
1 A-AATTTAATTAAAT
32844 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (15 bp):
AAATTTAATTAAATG
Found at i:32850 original size:15 final size:16
Alignment explanation
Indices: 32797--32856 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
32787 TCATGGAATA
*
32797 AAAAATTTAATTACAGT
1 AAAAATTTAATTA-AAT
*
32814 -GAAATTTAATTAAAT
1 AAAAATTTAATTAAAT
* *
32829 GACAATTT-ATTAAAT
1 AAAAATTTAATTAAAT
*
32844 AAAAATTCAATTA
1 AAAAATTTAATTA
32857 CAATTCAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 14 0.41
16 20 0.59
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (16 bp):
AAAAATTTAATTAAAT
Found at i:35764 original size:35 final size:35
Alignment explanation
Indices: 35725--35851 Score: 130
Period size: 35 Copynumber: 3.6 Consensus size: 35
35715 ATTCTGACTC
*
35725 AAACTAAAGAAAGACCACCCTGGGTAGACTGAAAT
1 AAACTGAAGAAAGACCACCCTGGGTAGACTGAAAT
* * * * ** *
35760 AAACTGAAGAACGATCACCCTCGATCATTCTG-ACT
1 AAACTGAAGAAAGACCACCCTGGGT-AGACTGAAAT
*
35795 CAAACTGAAGAAAGACCGCCCTGGGTAGACTGAAAT
1 -AAACTGAAGAAAGACCACCCTGGGTAGACTGAAAT
* *
35831 AAACTGAAGAACGATCACCCT
1 AAACTGAAGAAAGACCACCCT
35852 CGATCATTCC
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
35 44 0.63
36 26 0.37
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (35 bp):
AAACTGAAGAAAGACCACCCTGGGTAGACTGAAAT
Found at i:35769 original size:71 final size:71
Alignment explanation
Indices: 35692--35860 Score: 293
Period size: 71 Copynumber: 2.4 Consensus size: 71
35682 ACTAAAACTG
* * *
35692 CTGAAGAACAACCATCCTCGATCATTCTGACTCAAACTAAAGAAAGACCACCCTGGGTAGACTGA
1 CTGAAGAACGATCACCCTCGATCATTCTGACTCAAACTAAAGAAAGACCACCCTGGGTAGACTGA
35757 AATAAA
66 AATAAA
* *
35763 CTGAAGAACGATCACCCTCGATCATTCTGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTGA
1 CTGAAGAACGATCACCCTCGATCATTCTGACTCAAACTAAAGAAAGACCACCCTGGGTAGACTGA
35828 AATAAA
66 AATAAA
35834 CTGAAGAACGATCACCCTCGATCATTC
1 CTGAAGAACGATCACCCTCGATCATTC
35861 CGGACTACTG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (71 bp):
CTGAAGAACGATCACCCTCGATCATTCTGACTCAAACTAAAGAAAGACCACCCTGGGTAGACTGA
AATAAA
Found at i:35888 original size:105 final size:105
Alignment explanation
Indices: 35762--35991 Score: 370
Period size: 105 Copynumber: 2.2 Consensus size: 105
35752 ACTGAAATAA
* * *
35762 ACTGAAGAACGATCACCCTCGATCATTCTGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTG
1 ACTGAAGAACAACCACCCTCGATCATTCCGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTG
*
35827 AAATAAACTGAAGAACGATCACCCTCGATCATTCCGGACT
66 AAATAAACTGAAGAACGATCACCCTCGATCATTCCAGACT
*
35867 ACTGAAGAACAACCATCCTCGATCATTCCGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTG
1 ACTGAAGAACAACCACCCTCGATCATTCCGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTG
*
35932 AAATAAACTGAAGAATGATCACCCTCGATCATTCCAGACT
66 AAATAAACTGAAGAACGATCACCCTCGATCATTCCAGACT
* *
35972 GAACTCAAGAAAAACCACCC
1 --ACTGAAGAACAACCACCC
35992 CGGGTCATTA
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 99 0.87
107 15 0.13
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (105 bp):
ACTGAAGAACAACCACCCTCGATCATTCCGACTCAAACTGAAGAAAGACCGCCCTGGGTAGACTG
AAATAAACTGAAGAACGATCACCCTCGATCATTCCAGACT
Found at i:36052 original size:24 final size:24
Alignment explanation
Indices: 36007--36052 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
35997 CATTAAAGTA
* * *
36007 TTGAATAGTTGAAGGATTGAAGCC
1 TTGAATAATTGAAGAATCGAAGCC
*
36031 TTGAATAATTGGAGAATCGAAG
1 TTGAATAATTGAAGAATCGAAG
36053 AAAGACCACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (24 bp):
TTGAATAATTGAAGAATCGAAGCC
Found at i:36143 original size:35 final size:36
Alignment explanation
Indices: 36061--36143 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
36051 AGAAAGACCA
* * *
36061 CCCTAGATC-ATTGAAGTAAATTGAAGAAATGATCG
1 CCCTGGATCAATTGAAGTAAACTGAAGAAATAATCG
*
36096 CCCTGGACCAATTGAAAGT-AACTGAAGAAA-AATCG
1 CCCTGGATCAATTG-AAGTAAACTGAAGAAATAATCG
36131 CCCTGGATCAATT
1 CCCTGGATCAATT
36144 AACTTAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 23 0.56
36 14 0.34
37 4 0.10
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (36 bp):
CCCTGGATCAATTGAAGTAAACTGAAGAAATAATCG
Found at i:42782 original size:35 final size:35
Alignment explanation
Indices: 42719--43060 Score: 352
Period size: 35 Copynumber: 9.6 Consensus size: 35
42709 CTTACTAAAT
42719 TTAATTACCCTGAATTAAAGTTGATTACTAACTCAC
1 TTAATTACCCTGAATT-AAGTTGATTACTAACTCAC
* **
42755 TTAATTACCCTGAATTAAGTTGATTACTGACTTGC
1 TTAATTACCCTGAATTAAGTTGATTACTAACTCAC
* *
42790 TTAATTACCCTGAATTAAGTT-ACTTATTAACTCGC
1 TTAATTACCCTGAATTAAGTTGA-TTACTAACTCAC
* * * * * * *
42825 TTAATTACCTTGAATGAAATTACTTATTACTGATTTAC
1 TTAATTACCCTGAAT-TAAGT--TGATTACTAACTCAC
** *
42863 TTAATTACCCTGAATTAAGTT-ATCTTTTAATTCAC
1 TTAATTACCCTGAATTAAGTTGAT-TACTAACTCAC
* *
42898 TTGATTACCCTGAATTAAGTT-ACTTATTGAACT-AC
1 TTAATTACCCTGAATTAAGTTGA-TTACT-AACTCAC
*
42933 TTAATTACCCTGAATTAAGTT-ACTTATTAACTCAC
1 TTAATTACCCTGAATTAAGTTGA-TTACTAACTCAC
*
42968 TTAATTACCCTGAATTAAAGTTGATTACTGACTCAC
1 TTAATTACCCTGAATT-AAGTTGATTACTAACTCAC
** **
43004 TTAATTACCCTGAATTAAGTTGATTACCGACTTGC
1 TTAATTACCCTGAATTAAGTTGATTACTAACTCAC
43039 TTAATTACCCTGAATTAAGTTG
1 TTAATTACCCTGAATTAAGTTG
43061 CTTATTACTG
Statistics
Matches: 265, Mismatches: 30, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
34 7 0.03
35 177 0.67
36 54 0.20
37 4 0.02
38 22 0.08
39 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (35 bp):
TTAATTACCCTGAATTAAGTTGATTACTAACTCAC
Found at i:42907 original size:143 final size:141
Alignment explanation
Indices: 42719--43064 Score: 455
Period size: 143 Copynumber: 2.4 Consensus size: 141
42709 CTTACTAAAT
42719 TTAATTACCCTGAATTAAAGTTGATTACTAACTCACTTAATTACCCTGAATTAAGTTGA-TTACT
1 TTAATTACCCTGAATT-AAGTTGATTACTAACTCACTTAATTACCCTGAATTAAGTT-ACTTACT
* * * *
42783 G-ACTTGCTTAATTACCCTGAATTAAGTTACTTATTAACTCGCTTAATTACCTTGAATGAAATTA
64 GAAC-TACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATGAAAGT-
* * *
42847 CTTATTACTGATTTAC
127 -TGATTACTGACTCAC
** * * *
42863 TTAATTACCCTGAATTAAGTT-ATCTTTTAATTCACTTGATTACCCTGAATTAAGTTACTTATTG
1 TTAATTACCCTGAATTAAGTTGAT-TACTAACTCACTTAATTACCCTGAATTAAGTTACTTACTG
*
42927 AACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATTAAAGTTGA
65 AACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATGAAAGTTGA
42992 TTACTGACTCAC
130 TTACTGACTCAC
** ** *
43004 TTAATTACCCTGAATTAAGTTGATTACCGACTTGCTTAATTACCCTGAATTAAGTTGCTTA
1 TTAATTACCCTGAATTAAGTTGATTACTAACTCACTTAATTACCCTGAATTAAGTTACTTA
43065 TTACTGATTC
Statistics
Matches: 176, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
141 61 0.35
142 5 0.03
143 92 0.52
144 18 0.10
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (141 bp):
TTAATTACCCTGAATTAAGTTGATTACTAACTCACTTAATTACCCTGAATTAAGTTACTTACTGA
ACTACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATGAAAGTTGAT
TACTGACTCAC
Found at i:46147 original size:20 final size:20
Alignment explanation
Indices: 46122--46161 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46112 AATAAAAATC
46122 TTCTTCTCTTTTTTTCTTTT
1 TTCTTCTCTTTTTTTCTTTT
* *
46142 TTCTTCTTTTTTTTTGTTTT
1 TTCTTCTCTTTTTTTCTTTT
46162 GTAATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (20 bp):
TTCTTCTCTTTTTTTCTTTT
Found at i:46161 original size:18 final size:20
Alignment explanation
Indices: 46122--46161 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
46112 AATAAAAATC
*
46122 TTCTTCTCTTTTTTTCTTTT
1 TTCTTCTCTTTTTTTCTGTT
46142 TTCTTCT-TTTTTTT-TGTT
1 TTCTTCTCTTTTTTTCTGTT
46160 TT
1 TT
46162 GTAATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (20 bp):
TTCTTCTCTTTTTTTCTGTT
Found at i:46421 original size:34 final size:36
Alignment explanation
Indices: 46383--46450 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
46373 CCATTCTCCG
46383 TAAGAAATGC-AATTCCAAGGATCC-AAAGAAAACC
1 TAAGAAATGCAAATTCCAAGGATCCAAAAGAAAACC
46417 TAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
1 TAAGAAATGCAAATTCCAAGGATCCAAAAGAAAA
46451 GTAGGAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 10 0.31
35 14 0.44
36 8 0.25
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (36 bp):
TAAGAAATGCAAATTCCAAGGATCCAAAAGAAAACC
Found at i:47810 original size:23 final size:24
Alignment explanation
Indices: 47757--47811 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
47747 GTTAAAGAAT
* **
47757 TTGCATTTTTTTGGTTTGCATATT
1 TTGCATTTTTTTGATTTGCATACA
* *
47781 TTTCATTTTTTT-ATTTGCATGCA
1 TTGCATTTTTTTGATTTGCATACA
47804 TTGCATTT
1 TTGCATTT
47812 GCATTAAGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.62
Consensus pattern (24 bp):
TTGCATTTTTTTGATTTGCATACA
Found at i:49880 original size:29 final size:27
Alignment explanation
Indices: 49848--49910 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 27
49838 GAGTTATTTA
49848 TTTATTTATTTTATAAATAGTTTATGTT
1 TTTATTTATTTTAT-AATAGTTTATGTT
49876 CTTTATTTATTTTATAATAGTTTATGTT
1 -TTTATTTATTTTATAATAGTTTATGTT
49904 TTTATTT
1 TTTATTT
49911 TCATGAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 7 0.21
28 13 0.38
29 14 0.41
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (27 bp):
TTTATTTATTTTATAATAGTTTATGTT
Found at i:61830 original size:30 final size:30
Alignment explanation
Indices: 61790--61848 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
61780 TAAGGGGGAG
61790 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
61820 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
61849 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Done.