Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007883.1 Corchorus capsularis cultivar CVL-1 contig07904, 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: 21487
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:4998 original size:15 final size:14
Alignment explanation
Indices: 4978--5030 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
4968 TTATATTTCT
4978 AAATTTAAATTATTA
1 AAATTT-AATTATTA
4993 AAATTT-ATTACTTA
1 AAATTTAATTA-TTA
*
5007 AAAATTAATTA-TA
1 AAATTTAATTATTA
5020 AAATTTCAATT
1 AAATTT-AATT
5031 TAGATCGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 11 0.33
14 12 0.36
15 10 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTAATTATTA
Found at i:5086 original size:121 final size:118
Alignment explanation
Indices: 4928--5166 Score: 336
Period size: 121 Copynumber: 2.0 Consensus size: 118
4918 AGTACGAATA
* * *
4928 ATGGAAAACTTTATGTTTTCCGATTGTATCATTTTTT-CAATTATATTTCTAAATTTAAATTATT
1 ATGGAAAACTTTATGTTTTCCGATTGCACCATTTTTTCCAAATATATTTCTAAATTTAAATTATT
* *
4992 AAAATTTATTACTTAAAAATTAATTATAAAATTTCAATTTAGATCGAATTATAAGTT
66 ---ATTAATTACTTAAAAATTAATTA-AAAATTTCAATTTAGACCGAATTATAAGTT
* * **
5049 ATGGGAAACTTTATGTTTTCCGATTGCACCCTTTTTTCCAAATATATTTCTAAATTTCCATTATT
1 ATGGAAAACTTTATGTTTTCCGATTGCACCATTTTTTCCAAATATATTTCTAAATTTAAATTATT
* *
5114 ATTAATTATTTAAAAATTAATTAAAAATTTTAATTTAGACCGAATTATAAGTT
66 ATTAATTACTTAAAAATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTT
5167 TGTCAAATTG
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
118 28 0.26
119 21 0.20
121 33 0.31
122 24 0.23
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (118 bp):
ATGGAAAACTTTATGTTTTCCGATTGCACCATTTTTTCCAAATATATTTCTAAATTTAAATTATT
ATTAATTACTTAAAAATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTT
Found at i:5490 original size:44 final size:44
Alignment explanation
Indices: 5421--5548 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 44
5411 GTCTCTATGT
* ** * *
5421 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-ATGAA
5465 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGAA
*
5509 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
5549 GAATCAGGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.04
44 73 0.96
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGAA
Found at i:5524 original size:66 final size:66
Alignment explanation
Indices: 5418--5549 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 66
5408 CTTGTCTCTA
* ** * * *
5418 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAG-GAGGTTATCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCAT-AGTGAGGTTACCAAAATTTCAT
5482 AG
65 AG
* *
5484 TGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCATA
5549 G
66 G
5550 AATCAGGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 2 0.04
66 55 0.96
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCATA
G
Found at i:5549 original size:22 final size:22
Alignment explanation
Indices: 5418--5603 Score: 146
Period size: 22 Copynumber: 8.4 Consensus size: 22
5408 CTTGTCTCTA
5418 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
* * *
5441 -ATGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
*
5463 -GAGGTTATCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
*
5484 TGTGGTTACCAAAATTTCATA-
1 TGTGGTTATCAAAATTTCATAG
**
5505 TGAAAGTTATCAAAATTTCATAG
1 TG-TGGTTATCAAAATTTCATAG
*
5528 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
** * * *
5550 AATCAGGTTATTAAAATTTCTTCG
1 --TGTGGTTATCAAAATTTCATAG
**
5574 -GTTGGTTATTGAAATTTCATAG
1 TG-TGGTTATCAAAATTTCATAG
*
5596 GGTGGTTA
1 TGTGGTTA
5604 ATTATCACAA
Statistics
Matches: 129, Mismatches: 27, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.03
22 106 0.82
23 3 0.02
24 16 0.12
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:5664 original size:22 final size:21
Alignment explanation
Indices: 5639--5736 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 21
5629 ATCAAAGTGA
*
5639 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
5661 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
5683 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
5705 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
5727 TTATCAAAAT
1 TTATCAAAAT
5737 GAACTTAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
21 4 0.06
22 52 0.84
23 6 0.10
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:5922 original size:20 final size:20
Alignment explanation
Indices: 5897--5935 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5887 CTTTTATTAA
5897 TAAAAATCAAAGCTTTAAAT
1 TAAAAATCAAAGCTTTAAAT
* *
5917 TAAAAATCCAATCTTTAAA
1 TAAAAATCAAAGCTTTAAA
5936 CAAATTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAAATCAAAGCTTTAAAT
Found at i:6843 original size:14 final size:14
Alignment explanation
Indices: 6824--6850 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6814 TAGGAAAATG
6824 TGAGAGAGAGTGAT
1 TGAGAGAGAGTGAT
6838 TGAGAGAGAGTGA
1 TGAGAGAGAGTGA
6851 GAGAGCCCAG
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:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (14 bp):
TGAGAGAGAGTGAT
Found at i:9334 original size:47 final size:46
Alignment explanation
Indices: 9283--9463 Score: 222
Period size: 47 Copynumber: 3.9 Consensus size: 46
9273 ATTGACCAAC
* * *
9283 TTTGGTCACTAAATTAAAAACTCGCGTGGAAGCGAGAGAAGACCATT
1 TTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAGACCA-T
*
9330 TTTGGTCACTAAATTGAACACCCGCGTGGAAGCGAGAAAAGACCA-
1 TTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAGACCAT
* * *
9375 -TCGGTCACTAAATTTGAAAACTCGCATGGAAGCGAGAAAAGACCAT
1 TTTGGTCACTAAA-TTGAAAACCCGCGTGGAAGCGAGAAAAGACCAT
** * *
9421 CTTTGGTCACCCAATTGAAAACCCGCGTGGAAGCAAGAGAAGA
1 -TTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAGA
9464 TTGCCTGGAT
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
44 11 0.10
45 29 0.25
47 66 0.57
48 9 0.08
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (46 bp):
TTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAGACCAT
Found at i:9398 original size:92 final size:91
Alignment explanation
Indices: 9286--9463 Score: 266
Period size: 92 Copynumber: 1.9 Consensus size: 91
9276 GACCAACTTT
* * * * *
9286 GGTCACTAAATTAAAAACTCGCGTGGAAGCGAGAGAAGACCATTTTTGGTCACTAAATTGAACAC
1 GGTCACTAAATTAAAAACTCGCATGGAAGCGAGAAAAGACCATCTTTGGTCACCAAATTGAAAAC
*
9351 CCGCGTGGAAGCGAGAAAAGACCATC
66 CCGCGTGGAAGCAAGAAAAGACCATC
* *
9377 GGTCACTAAATTTGAAAACTCGCATGGAAGCGAGAAAAGACCATCTTTGGTCACCCAATTGAAAA
1 GGTCACTAAA-TTAAAAACTCGCATGGAAGCGAGAAAAGACCATCTTTGGTCACCAAATTGAAAA
*
9442 CCCGCGTGGAAGCAAGAGAAGA
65 CCCGCGTGGAAGCAAGAAAAGA
9464 TTGCCTGGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 10 0.13
92 67 0.87
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (91 bp):
GGTCACTAAATTAAAAACTCGCATGGAAGCGAGAAAAGACCATCTTTGGTCACCAAATTGAAAAC
CCGCGTGGAAGCAAGAAAAGACCATC
Found at i:9705 original size:69 final size:70
Alignment explanation
Indices: 9573--10074 Score: 540
Period size: 69 Copynumber: 7.2 Consensus size: 70
9563 CTCACTGAAC
* * * **
9573 TTGGCTTATGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTAAAACT-ATCTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAA
*
9637 GCGAGT
65 ACGAGT
* * * ** * * *
9643 TTGGCTTATGGAAAAGTCTCT-CTTG-TCCGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCT-TGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAA
9706 ACGAGT
65 ACGAGT
* * **
9712 TTGGCTTGTGGAAAAACCCCTGAATGCTTGGATGGAACCAAACCTGAAACT-ATCTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAA
*
9776 GCGAGT
65 ACGAGT
* * ** * *
9782 TTGGCTTATGGAAAAGCCTCT-CTTG-TCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCT-TGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAA
9845 ACGAGT
65 ACGAGT
* **
9851 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACT-ATCTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAA
*
9915 GCGAGT
65 ACGAGT
* * ** *
9921 TTGGCTTATGGAAAAGCCTCT-CTTG-TCTGGATGGAACCAAAGCTAGATA-TGACTCGTGTGGA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCT-TGGATGGAACCAAAGCT-GAAACTGACTCGTGTGGA
9983 AACGAGT
64 AACGAGT
* *
9990 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACC-AAGGTTAAACTGACTCGTGTGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAA
10054 CGAGT
66 CGAGT
10059 TTGGCTTGTGGAAAAG
1 TTGGCTTGTGGAAAAG
10075 TCGGAGCATT
Statistics
Matches: 354, Mismatches: 62, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
68 5 0.01
69 200 0.56
70 146 0.41
71 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (70 bp):
TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAA
CGAGT
Found at i:9823 original size:139 final size:139
Alignment explanation
Indices: 9573--10074 Score: 848
Period size: 139 Copynumber: 3.6 Consensus size: 139
9563 CTCACTGAAC
* *
9573 TTGGCTTATGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTAAAACTATCTCGCATGGAAG
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCATGGAAG
* *
9638 CGAGTTTGGCTTATGGAAAAGTCTCTCTTGTCCGGATGGAACCAAAGCTGGATCTGACTCGTGTG
66 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTGGATCTGACTCGTGTG
9703 GAAACGAGT
131 GAAACGAGT
* *
9712 TTGGCTTGTGGAAAAACCCCTGAATGCTTGGATGGAACCAAACCTGAAACTATCTCGCATGGAAG
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCATGGAAG
9777 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTGGATCTGACTCGTGTG
66 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTGGATCTGACTCGTGTG
9842 GAAACGAGT
131 GAAACGAGT
9851 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCATGGAAG
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCATGGAAG
* *
9916 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTAGATATGACTCGTGTG
66 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTGGATCTGACTCGTGTG
9981 GAAACGAGT
131 GAAACGAGT
* **
9990 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAGGT-T-AAACTGA-CTCGTGTGGA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAA-ATCTGAAACT-ATCTCGCATGGA
* *
10052 AACGAGTTTGGCTTGTGGAAAAG
64 AGCGAGTTTGGCTTATGGAAAAG
10075 TCGGAGCATT
Statistics
Matches: 346, Mismatches: 15, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
138 34 0.10
139 311 0.90
140 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (139 bp):
TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCATGGAAG
CGAGTTTGGCTTATGGAAAAGCCTCTCTTGTCTGGATGGAACCAAAGCTGGATCTGACTCGTGTG
GAAACGAGT
Found at i:10930 original size:14 final size:14
Alignment explanation
Indices: 10902--10952 Score: 61
Period size: 13 Copynumber: 3.7 Consensus size: 14
10892 ACCCTAGAGC
*
10902 CTTTTTCTTCATTCT
1 CTTTTTCTT-TTTCT
10917 CTTTTTCTTTTTCT
1 CTTTTTCTTTTTCT
10931 C-TTTTC-TTTTCT
1 CTTTTTCTTTTTCT
*
10943 CATTTTCTTT
1 CTTTTTCTTT
10953 CACTTAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 7 0.21
13 10 0.30
14 7 0.21
15 9 0.27
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTTTCTTTTTCT
Found at i:11338 original size:16 final size:17
Alignment explanation
Indices: 11317--11351 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11307 TTATTTTTCC
11317 TCCTCTT-TTCTCTTTT
1 TCCTCTTCTTCTCTTTT
*
11333 TCCTCTTCTTCTTTTTT
1 TCCTCTTCTTCTCTTTT
11350 TC
1 TC
11352 ATTTCCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TCCTCTTCTTCTCTTTT
Found at i:11764 original size:45 final size:43
Alignment explanation
Indices: 11689--11827 Score: 179
Period size: 44 Copynumber: 3.1 Consensus size: 43
11679 TACAACTTTG
* * *
11689 GAAAATCCTTTCATCAAAACCCTCTTGAAAACCATGACTATTTTT
1 GAAAAACCTTTTATCAAAA-CCTTTTGAAAACCATGACT-TTTTT
* *
11734 GAAAAAGCCTTTTACCAAAACCTTTTGAAAACCATGACTCTTTT
1 GAAAAA-CCTTTTATCAAAACCTTTTGAAAACCATGACTTTTTT
*
11778 GAAAAACCATTTTATCAAAACCTTTTGAAAATCATGACCTTTTTT
1 GAAAAACC-TTTTATCAAAACCTTTTGAAAACCATGA-CTTTTTT
11823 GAAAA
1 GAAAA
11828 CCATCGTTGC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
43 2 0.02
44 36 0.43
45 34 0.41
46 11 0.13
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (43 bp):
GAAAAACCTTTTATCAAAACCTTTTGAAAACCATGACTTTTTT
Found at i:11877 original size:11 final size:11
Alignment explanation
Indices: 11837--11916 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 11
11827 ACCATCGTTG
11837 CTTCTTCTCTTT
1 CTTCTT-TCTTT
11849 CCTTCCTTTTCTTT
1 -CTT-C-TTTCTTT
11863 -TTCTTT-TTT
1 CTTCTTTCTTT
11872 CATTCTTTCTTT
1 C-TTCTTTCTTT
11884 CTTCTTCTTCTTTT
1 CTTC-T-TTC-TTT
11898 CTTCTCTT-TTT
1 CTTCT-TTCTTT
11909 -TTCTTTCT
1 CTTCTTTCT
11917 ATTTTTTCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
9 5 0.09
10 8 0.14
11 13 0.22
12 7 0.12
13 10 0.17
14 13 0.22
15 2 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (11 bp):
CTTCTTTCTTT
Found at i:11884 original size:25 final size:26
Alignment explanation
Indices: 11856--11924 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
11846 TTTCCTTCCT
11856 TTTCTTTTTCTTTTTTCAT-TCTTTC
1 TTTCTTTTTCTTTTTTCATCTCTTTC
* * *
11881 TTTCTTCTTCTTCTTTTCTTCTCTTTT
1 TTTCTTTTTCTT-TTTTCATCTCTTTC
* *
11908 TTTCTTTCTATTTTTTC
1 TTTCTTTTTCTTTTTTC
11925 TAGGAAACTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 11 0.31
26 11 0.31
27 14 0.39
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTCTTTTTCTTTTTTCATCTCTTTC
Found at i:11900 original size:18 final size:18
Alignment explanation
Indices: 11838--11914 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 18
11828 CCATCGTTGC
*
11838 TTCTTCTCTTTCCTTCCTT
1 TTCTTCTCTTTTCTT-CTT
*
11857 TTCTTTTTCTTTT-TTCATTCT
1 TTC-TTCTCTTTTCTTC--T-T
11878 TTCTT-TCTTCTTCTTCTT
1 TTCTTCTCTT-TTCTTCTT
*
11896 TTCTTCTCTTTTTTTCTT
1 TTCTTCTCTTTTCTTCTT
11914 T
1 T
11915 CTATTTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
18 15 0.31
19 14 0.29
20 12 0.25
21 7 0.15
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (18 bp):
TTCTTCTCTTTTCTTCTT
Found at i:11922 original size:13 final size:12
Alignment explanation
Indices: 11855--11925 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 12
11845 CTTTCCTTCC
*
11855 TTTTCTTTTTCTT
1 TTTTCTTTCT-TT
*
11868 TTTTCATTCTTT
1 TTTTCTTTCTTT
* *
11880 CTTTCTTCTTCTTC
1 TTTTC-T-TTCTTT
11894 TTTTCTTCTCTTT
1 TTTTCTT-TCTTT
11907 TTTTCTTTCTATT
1 TTTTCTTTCT-TT
11920 TTTTCT
1 TTTTCT
11926 AGGAAACTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 10 0.21
13 28 0.60
14 9 0.19
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:12388 original size:74 final size:76
Alignment explanation
Indices: 12301--12450 Score: 178
Period size: 74 Copynumber: 2.0 Consensus size: 76
12291 ATTTTAGTCC
* * * * *
12301 CCTTGAAATCATTGCCTTGACTAAAACTGATTTTGAAA-CATCTTTTGATTAAAA-TCATTATTC
1 CCTTGAAACCATTGCCTTGACTAAAACTGATCTTGAAACCATCTTTTAATTAAAACCCATCATTC
*
12364 TTTTGCTCACA
66 CTTTGCTCACA
* * * * * *
12375 CCTTGAAACCATTGCTTTGCCTGAAACTTATCTTGAAACCTTGTTTTAATTAAAACCCATCATTC
1 CCTTGAAACCATTGCCTTGACTAAAACTGATCTTGAAACCATCTTTTAATTAAAACCCATCATTC
12440 CTTTGCTCACA
66 CTTTGCTCACA
12451 GTCTAGATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
74 32 0.52
75 13 0.21
76 17 0.27
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (76 bp):
CCTTGAAACCATTGCCTTGACTAAAACTGATCTTGAAACCATCTTTTAATTAAAACCCATCATTC
CTTTGCTCACA
Found at i:18530 original size:20 final size:20
Alignment explanation
Indices: 18505--18543 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18495 CTTTTATTAA
18505 TAAAAATCAAAGCTTTAAAT
1 TAAAAATCAAAGCTTTAAAT
* *
18525 TAAAAATCCAATCTTTAAA
1 TAAAAATCAAAGCTTTAAA
18544 CAAATTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAAATCAAAGCTTTAAAT
Done.