Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010342.1 Corchorus capsularis cultivar CVL-1 contig10363, 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: 108907
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:486 original size:25 final size:27
Alignment explanation
Indices: 434--486 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
424 TTACTCAACT
**
434 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
461 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
486 A
1 A
487 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:19769 original size:3 final size:3
Alignment explanation
Indices: 19761--19785 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19751 ATTAAGTAAA
19761 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
19786 GAATTAGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22729 original size:13 final size:13
Alignment explanation
Indices: 22711--22737 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22701 TTGAAATTGA
22711 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
22724 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
22737 T
1 T
22738 CCATGGGAAA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:36815 original size:17 final size:17
Alignment explanation
Indices: 36795--37008 Score: 237
Period size: 17 Copynumber: 13.1 Consensus size: 17
36785 ACTCACCCAA
*
36795 TACAAATACCCACCTGG
1 TACAAATACTCACCTGG
* *
36812 TACAAACACTCATCTGG
1 TACAAATACTCACCTGG
*
36829 TACAAATACTTACCTGG
1 TACAAATACTCACCTGG
* *
36846 TACAAATACCCACCTAG
1 TACAAATACTCACCTGG
*
36863 TACAAACACTCACCTGG
1 TACAAATACTCACCTGG
36880 TACAAATACTCACCT-G
1 TACAAATACTCACCTGG
36896 ---AAATACTCACCTGG
1 TACAAATACTCACCTGG
36910 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
*
36927 TACAAACACTCACCTGG
1 TACAAATACTCACCTGG
* *
36944 TGC-AATGCTCACCTGG
1 TACAAATACTCACCTGG
*
36960 TGC-AATACTCACCTGG
1 TACAAATACTCACCTGG
* * **
36976 T-GAGATACTCACCCAG
1 TACAAATACTCACCTGG
36992 TAC-AATACTCACCTGG
1 TACAAATACTCACCTGG
37008 T
1 T
37009 GATGTCACCA
Statistics
Matches: 165, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
13 12 0.07
14 1 0.01
16 50 0.30
17 102 0.62
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.22
Consensus pattern (17 bp):
TACAAATACTCACCTGG
Found at i:36901 original size:13 final size:13
Alignment explanation
Indices: 36883--36908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36873 CACCTGGTAC
36883 AAATACTCACCTG
1 AAATACTCACCTG
36896 AAATACTCACCTG
1 AAATACTCACCTG
36909 GTACAAATAC
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:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
AAATACTCACCTG
Found at i:36912 original size:64 final size:64
Alignment explanation
Indices: 36784--37008 Score: 222
Period size: 64 Copynumber: 3.5 Consensus size: 64
36774 GTTCCTACCC
* * * * * * *
36784 TACTCACCCAATACAAATACCCACCTGGTACAAACACTCATCTGGTACAAATACTTACCTGGTAC
1 TACTCACCTAGTACAAACACTCACCTGGTACAAATACTCACCT-G---AAATACTCACCTGGTAC
36849 AAA
62 AAA
*
36852 TACCCACCTAGTACAAACACTCACCTGGTACAAATACTCACCTGAAATACTCACCTGGTACAAA
1 TACTCACCTAGTACAAACACTCACCTGGTACAAATACTCACCTGAAATACTCACCTGGTACAAA
* * * * *
36916 TACTCACCTGGTACAAACACTCACCTGGTGC-AATGCTCACCTGGTGCAATACTCACCTGGT-GA
1 TACTCACCTAGTACAAACACTCACCTGGTACAAATACTCACC---TGAAATACTCACCTGGTACA
*
36979 GA
63 AA
* *
36981 TACTCACCCAGTAC-AATACTCACCTGGT
1 TACTCACCTAGTACAAACACTCACCTGGT
37009 GATGTCACCA
Statistics
Matches: 136, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 9 0.07
64 60 0.44
65 14 0.10
66 16 0.12
67 1 0.01
68 36 0.26
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.22
Consensus pattern (64 bp):
TACTCACCTAGTACAAACACTCACCTGGTACAAATACTCACCTGAAATACTCACCTGGTACAAA
Found at i:36925 original size:81 final size:80
Alignment explanation
Indices: 36819--37008 Score: 222
Period size: 81 Copynumber: 2.4 Consensus size: 80
36809 TGGTACAAAC
* * *
36819 ACTCATCTGGTACAAATACTTACCTGGTACAAATACCCACCTAGTACAAACACTCACCTGGTACA
1 ACTCACCTGGTACAAATACTCACCTGGTACAAACACCCACCTAGTAC-AACACTCACCTGGTAC-
36884 AATACTCACC-TGAAAT
64 AATACTCACCGTGAAAT
* * * ** *
36900 ACTCACCTGGTACAAATACTCACCTGGTACAAACACTCACCTGGTGCAATGCTCACCTGGTGCAA
1 ACTCACCTGGTACAAATACTCACCTGGTACAAACACCCACCTAGTACAACACTCACCTGGTACAA
*
36965 TACTCACCTGGTGAGAT
66 TACTCACC--GTGAAAT
**
36982 ACTCACCCAGTAC-AATACTCACCTGGT
1 ACTCACCTGGTACAAATACTCACCTGGT
37009 GATGTCACCA
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
79 10 0.11
80 13 0.14
81 55 0.59
82 16 0.17
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (80 bp):
ACTCACCTGGTACAAATACTCACCTGGTACAAACACCCACCTAGTACAACACTCACCTGGTACAA
TACTCACCGTGAAAT
Found at i:40323 original size:33 final size:33
Alignment explanation
Indices: 40281--40367 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
40271 GTTGTGCGGT
* * *
40281 AGGGGAGACTCCCTTGCTATGCGATACTCTCTC
1 AGGGGAGACTCCCTTGCTACGCGAGACTCCCTC
* *
40314 AGGGGAGACTCCCTTCCTACGCGAGACTCCCTT
1 AGGGGAGACTCCCTTGCTACGCGAGACTCCCTC
*
40347 AGGGGAGACTCTCTTGCTACG
1 AGGGGAGACTCCCTTGCTACG
40368 TGATAGGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.24
Consensus pattern (33 bp):
AGGGGAGACTCCCTTGCTACGCGAGACTCCCTC
Found at i:40712 original size:40 final size:38
Alignment explanation
Indices: 40621--40714 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 38
40611 TAATGGTTGT
*
40621 GCGTTAGGGGAGACTCCCCTGAGGGAGACTCTTGCTTG
1 GCGTTAGAGGAGACTCCCCTGAGGGAGACTCTTGCTTG
* *
40659 GCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGC-TG
1 GCGTTAGAGGAGACTCCCCTGAGGGAGA--CTCTTGCTTG
*
40698 CGCGTTAGAAGAGACTC
1 -GCGTTAGAGGAGACTC
40715 TTGCTTTGCG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 26 0.54
39 2 0.04
40 20 0.42
ACGTcount: A:0.18, C:0.27, G:0.34, T:0.21
Consensus pattern (38 bp):
GCGTTAGAGGAGACTCCCCTGAGGGAGACTCTTGCTTG
Found at i:40775 original size:63 final size:62
Alignment explanation
Indices: 40642--40759 Score: 200
Period size: 63 Copynumber: 1.9 Consensus size: 62
40632 GACTCCCCTG
*
40642 AGGGAGACTCTTGCTTGGCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGCTGCGCGTT
1 AGGGAGACTCTTGCTTGGCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGCTGCACGTT
* *
40704 AGAAGAGACTCTTGCTTTGCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGCT
1 AG-GGAGACTCTTGCTTGGCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGCT
40760 CAACTCTACG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
62 2 0.04
63 51 0.96
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (62 bp):
AGGGAGACTCTTGCTTGGCGCTAGCGGAGACTCCCCTGAGGGAGACTCTCTTGCTGCACGTT
Found at i:41676 original size:17 final size:17
Alignment explanation
Indices: 41656--41868 Score: 237
Period size: 17 Copynumber: 13.1 Consensus size: 17
41646 ACTCACCCAA
*
41656 TACAAATACTTACCTGG
1 TACAAATACTCACCTGG
* *
41673 TACAAACACTCATCTGG
1 TACAAATACTCACCTGG
41690 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
41707 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
41724 TACAAATACTCACCT-G
1 TACAAATACTCACCTGG
*
41740 ---AAACACTCACCTGG
1 TACAAATACTCACCTGG
41754 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
* *
41771 TACAAACACTCACATGG
1 TACAAATACTCACCTGG
* *
41788 TGC-AATGCTCACCTGG
1 TACAAATACTCACCTGG
*
41804 TGC-AATACTCACCTGG
1 TACAAATACTCACCTGG
*
41820 TGC-AATACTCACCTGG
1 TACAAATACTCACCTGG
* * **
41836 T-GAGATACTCACCCAG
1 TACAAATACTCACCTGG
41852 TAC-AATACTCACCTGG
1 TACAAATACTCACCTGG
41868 T
1 T
41869 GATGTCACCA
Statistics
Matches: 168, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.07
14 1 0.01
16 65 0.39
17 91 0.54
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.23
Consensus pattern (17 bp):
TACAAATACTCACCTGG
Found at i:41867 original size:64 final size:67
Alignment explanation
Indices: 41645--41869 Score: 239
Period size: 64 Copynumber: 3.4 Consensus size: 67
41635 GTTCCTACCC
* * * *
41645 TACTCACCCAATACAAATACTTACCTGGTACAAACACTCATCTGGTACAAATACTCACCTGGTAC
1 TACTCACCCAGTACAAATACTCACCTGGTGC-AACACTCACCTGGTACAAATACTCACCTGGTAC
41710 AAA
65 AAA
** *
41713 TACTCACCTGGTACAAATACTCACC---TGAAACACTCACCTGGTACAAATACTCACCTGGTACA
1 TACTCACCCAGTACAAATACTCACCTGGTGCAACACTCACCTGGTACAAATACTCACCTGGTACA
41775 AA
66 AA
* *** * * * * *
41777 CACTCACATGGTGC-AATGCTCACCTGGTGCAATACTCACCTGGTGC-AATACTCACCTGGT-GA
1 TACTCACCCAGTACAAATACTCACCTGGTGCAACACTCACCTGGTACAAATACTCACCTGGTACA
*
41839 GA
66 AA
41841 TACTCACCCAGTAC-AATACTCACCTGGTG
1 TACTCACCCAGTACAAATACTCACCTGGTG
41870 ATGTCACCAA
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
63 9 0.07
64 71 0.54
65 15 0.11
66 16 0.12
68 21 0.16
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (67 bp):
TACTCACCCAGTACAAATACTCACCTGGTGCAACACTCACCTGGTACAAATACTCACCTGGTACA
AA
Found at i:42525 original size:70 final size:69
Alignment explanation
Indices: 42364--42563 Score: 247
Period size: 70 Copynumber: 2.8 Consensus size: 69
42354 AACCAAAGCA
* * *
42364 CGTCTGCTCTCCATGATTGCAAATTGCAAAGTAGCTGGCTAAGTGAAGAAAATTTAAAACCAAAA
1 CGTCTCCTCTCCATGCTTGCAAATTGCAAAGTA---GGCTAAGTGAGGAAAATTTAAAACCAAAA
42429 CGAAACT
63 CGAAACT
* * * * *
42436 CGTCTCCTCTCCATGCTTGCAAATTGCGAAGTAGGCCAAGTGAGGGAAATTTAGAGCCAAAAACG
1 CGTCTCCTCTCCATGCTTGCAAATTGCAAAGTAGGCTAAGTGAGGAAAATTTAAAACC-AAAACG
42501 AAACT
65 AAACT
* *
42506 CGTCTCGTCTCCATTCTTGCAAATTGCAAAGGTAGGCTATAAGTGAGGAAAATTTAAA
1 CGTCTCCTCTCCATGCTTGCAAATTGCAAA-GTAGGC--TAAGTGAGGAAAATTTAAA
42564 GCAACTTCGA
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
69 20 0.18
70 38 0.35
71 6 0.05
72 30 0.27
73 16 0.15
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (69 bp):
CGTCTCCTCTCCATGCTTGCAAATTGCAAAGTAGGCTAAGTGAGGAAAATTTAAAACCAAAACGA
AACT
Found at i:50406 original size:30 final size:30
Alignment explanation
Indices: 50352--50416 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
50342 GTGATGATGT
*
50352 TCATGGCCATGGCCGTGACCATGACCATGA
1 TCATGGCCATGGCCATGACCATGACCATGA
*** *
50382 TCATGGCCATGGCCATGGTGATGACCGTGA
1 TCATGGCCATGGCCATGACCATGACCATGA
50412 TCATG
1 TCATG
50417 ACCCAACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (30 bp):
TCATGGCCATGGCCATGACCATGACCATGA
Found at i:56343 original size:558 final size:547
Alignment explanation
Indices: 55247--56359 Score: 1465
Period size: 558 Copynumber: 2.0 Consensus size: 547
55237 TAAACCAATT
* * *
55247 AAAATGAACCATGTTTGCATGACTTACCACTTATAAATTGTAATCTAATCATAAGTTTACTGACT
1 AAAACGAACCATGTTTGCATGACTTACAACTTATAAATTGTAATCGAATCATAAGTTTACTGACT
* *
55312 GTATATGGGCCAAAATGAGGATACTTCCATTGACAAGGAAAGGATTAACAATGTTGACAAAGTCC
66 G-ATATGGACCAAAATGAGGATACTTCCATTGACAAGGAAAGGATTAACAATGTTAACAAAGTCC
* * *
55377 ATGTTCAAAGAACCACTGCAATTATCAAAAACTATTTTCACTTTCTTGAAGCAGAACTTACCTCA
130 ATGTTCAAAGAACCAATGCAATTATCAAAAACTATTTTCACATTCTTCAAGCAGAA--TA-CTCA
* * *
55442 ATAGAAGTTTTAAGGCTCTATTTGGAATGAAAACAAAAGAAGACCAATTCCTAAGTTTGCATTTA
192 ATAGAAGTTGTAAGACTCTATTTGGAATCAAAACAAAAGAAGACCAATTCCTAAGTTTGCATTTA
* * *
55507 TTTTTGGCATGATCCAAGAATGTATTTATTACCAATTAGAACAATTAACACTAAGCTGACAAGTG
257 TTTTTGACATGATCCAAGAATGCATTTATTACCAATTAGAACAAATAACACTAAGCTGACAAGTG
* ** * *
55572 CAAATAAATGTGCTACGTCAAATGGAATAATGTTTACTTTGAGGGAGAAGACTGGTGGTATATAC
322 CAAATAAATGTACTACGAAAAAGGGAATAATGTTTACTTTGAGAGAGAAGACTGGTGGTATATAC
** * * *
55637 ATGAGTCATTATCTCAGAGCATCATCAACAATGTCAAAAATCCTTATAGAATCTGTCACCTCTCA
387 ACAAGGCATAATCTCAAAGCATCATCAACAATGTCAAAAATCCTTATAGAATCTGTCACCTCTCA
* * * *
55702 CTCAGCACAACTAGGCCAGCAGAGGGCGCAATATATAATTGACTCCCAGGTTCAAAGAACTCTCA
452 CTCAGCACAAATAGCCCAGCAAAGGGCACAATATATAATTGACTCCCAGGTTCAAAGAACTCTCA
* ** *
55767 ACTAATCTAGTTGAGCATGAATCTAAGATAC
517 ACTAACCTAGCAGAGCATGAATCTAACATAC
*
55798 AAAACGAACCATGTTTGCATGACTTACAACTTCTAAATTGTAATCGAATCATAAGTTTACTGACT
1 AAAACGAACCATGTTTGCATGACTTACAACTTATAAATTGTAATCGAATCATAAGTTTACTGACT
* * *
55863 G-TATGGACCAAAATGAGGATAGTTCCATTGACAAGGAAAGGATTAGCAATGTTAACAAGGTCCA
66 GATATGGACCAAAATGAGGATACTTCCATTGACAAGGAAAGGATTAACAATGTTAACAAAGTCCA
55927 TGTTCAAAGAACCAATGCATATCAATATC-AAAACTATTTTCACATTCTTCAAGCAG-A-A-TCA
131 TGTTCAAAGAACCAATGCA-AT---TATCAAAAACTATTTTCACATTCTTCAAGCAGAATACTCA
* * * * *
55988 ATAGAAG-TGTGAGATTCTGTTTGGAATCAAAACAAAATAAGACCAATTTCTAAGTTTGCATTTA
192 ATAGAAGTTGTAAGACTCTATTTGGAATCAAAACAAAAGAAGACCAATTCCTAAGTTTGCATTTA
* *
56052 -TTTTGACATGATCCATG-ATGCATTTATTACCAATTAGAACAAATGACACTAAGCTGACAAGTG
257 TTTTTGACATGATCCAAGAATGCATTTATTACCAATTAGAACAAATAACACTAAGCTGACAA--G
* *
56115 TGTTTCTGATAGTGTAAATGAATATTGAACGAAAAAGGGAATAATGTTTACTTTGAGAGAGAAGA
320 TG---C--A-A--ATAAATG--TACT--ACGAAAAAGGGAATAATGTTTACTTTGAGAGAGAAGA
* * * *
56180 GTGGTGGTATATACACAAGGCATAATCTTAAAGCATCATCAACAATGTGAAAAATCTTTATA-AT
373 CTGGTGGTATATACACAAGGCATAATCTCAAAGCATCATCAACAATGTCAAAAATCCTTATAGA-
*
56244 ATCTGTCCACCTCTCACTCAGCA-AGAATAGCCCAGCAAAGGGCACAATATATGATTGACTCCCA
437 ATCTGT-CACCTCTCACTCAGCACA-AATAGCCCAGCAAAGGGCACAATATATAATTGACTCCCA
56308 GGTTCAAAGAACTCT-ATACTAACCTAGCAGAGCATGAATCTAACATAC
500 GGTTCAAAGAACTCTCA-ACTAACCTAGCAGAGCATGAATCTAACATAC
56356 AAAA
1 AAAA
56360 TAGGACTGAT
Statistics
Matches: 490, Mismatches: 50, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
543 40 0.08
544 15 0.03
545 52 0.11
546 10 0.02
548 2 0.00
549 76 0.16
550 3 0.01
551 64 0.13
552 25 0.05
553 10 0.02
555 2 0.00
556 1 0.00
557 94 0.19
558 96 0.20
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (547 bp):
AAAACGAACCATGTTTGCATGACTTACAACTTATAAATTGTAATCGAATCATAAGTTTACTGACT
GATATGGACCAAAATGAGGATACTTCCATTGACAAGGAAAGGATTAACAATGTTAACAAAGTCCA
TGTTCAAAGAACCAATGCAATTATCAAAAACTATTTTCACATTCTTCAAGCAGAATACTCAATAG
AAGTTGTAAGACTCTATTTGGAATCAAAACAAAAGAAGACCAATTCCTAAGTTTGCATTTATTTT
TGACATGATCCAAGAATGCATTTATTACCAATTAGAACAAATAACACTAAGCTGACAAGTGCAAA
TAAATGTACTACGAAAAAGGGAATAATGTTTACTTTGAGAGAGAAGACTGGTGGTATATACACAA
GGCATAATCTCAAAGCATCATCAACAATGTCAAAAATCCTTATAGAATCTGTCACCTCTCACTCA
GCACAAATAGCCCAGCAAAGGGCACAATATATAATTGACTCCCAGGTTCAAAGAACTCTCAACTA
ACCTAGCAGAGCATGAATCTAACATAC
Found at i:64179 original size:35 final size:36
Alignment explanation
Indices: 64120--64194 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
64110 GGTAAAAACT
64120 AAAACGTTATCATCAAAAAAAAAAAAAAATCATGGC
1 AAAACGTTATCATCAAAAAAAAAAAAAAATCATGGC
* *
64156 AAAACGTTATC-TCAAAAAGAAAAAAAAATCATGGT
1 AAAACGTTATCATCAAAAAAAAAAAAAAATCATGGC
64191 AAAA
1 AAAA
64195 AGTTTGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 26 0.70
36 11 0.30
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.17
Consensus pattern (36 bp):
AAAACGTTATCATCAAAAAAAAAAAAAAATCATGGC
Found at i:65044 original size:5 final size:5
Alignment explanation
Indices: 65034--65060 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
65024 ACTAAATGTC
65034 TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TA
65061 TAATGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:77059 original size:29 final size:29
Alignment explanation
Indices: 76992--77085 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 29
76982 GAGAAAGGGT
76992 AAAACGTCCAAAATTGAGAGATT-AGGAGG-C
1 AAAACGTCCAAAATTGA-AG-TTCAGG-GGAC
* *
77022 AAAATGTCCAAAACTGAAGTTCAGGGGAC
1 AAAACGTCCAAAATTGAAGTTCAGGGGAC
* *
77051 AAAACGTCCAAATGTTACAAGTTCAGGGGAC
1 AAAACGTCCAAA-ATT-GAAGTTCAGGGGAC
77082 AAAA
1 AAAA
77086 AGGGTATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 4 0.07
29 17 0.31
30 16 0.30
31 17 0.31
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (29 bp):
AAAACGTCCAAAATTGAAGTTCAGGGGAC
Found at i:87483 original size:25 final size:25
Alignment explanation
Indices: 87455--87507 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
87445 GATACTAATA
87455 TATACAAGATAATAATTATGATGTG
1 TATACAAGATAATAATTATGATGTG
87480 TATACAAGATAATAATTATGATGTG
1 TATACAAGATAATAATTATGATGTG
87505 TAT
1 TAT
87508 GAGATAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (25 bp):
TATACAAGATAATAATTATGATGTG
Found at i:95372 original size:2 final size:2
Alignment explanation
Indices: 95365--95390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
95355 GTTAACAACT
95365 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
95391 CTAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104128 original size:19 final size:20
Alignment explanation
Indices: 104082--104129 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
104072 TGTGGCACGC
*
104082 CACATGTACCAAAAAGTCGTGT
1 CACATGTACCAAAAA--CGTGA
104104 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
104123 CACATGT
1 CACATGT
104130 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:104189 original size:31 final size:31
Alignment explanation
Indices: 104104--104196 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
104094 AAAGTCGTGT
* * * * *
104104 CACATGTACCAAAAAGTGACACATGTCACGC
1 CACATGTATCAAAAAATGACACGTGGCATGC
* *
104135 CACGTGTATCAAAAAGTGACACGTGGCATGC
1 CACATGTATCAAAAAATGACACGTGGCATGC
* *
104166 CACATGTTTCAAAAAATGGCACGTGGCATGC
1 CACATGTATCAAAAAATGACACGTGGCATGC
104197 AACGTGCACA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (31 bp):
CACATGTATCAAAAAATGACACGTGGCATGC
Found at i:107986 original size:21 final size:21
Alignment explanation
Indices: 107940--107986 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
107930 TGACAATCTT
* *
107940 ATTTAATTTATGTACGTTCCA
1 ATTTGATTTACGTACGTTCCA
107961 ATTTGATTTACGTACGTTCCA
1 ATTTGATTTACGTACGTTCCA
107982 ATTTG
1 ATTTG
107987 TATATAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.47
Consensus pattern (21 bp):
ATTTGATTTACGTACGTTCCA
Done.