Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008355.1 Corchorus capsularis cultivar CVL-1 contig08376, 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: 37402
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:6236 original size:44 final size:44
Alignment explanation
Indices: 6183--6292 Score: 157
Period size: 44 Copynumber: 2.5 Consensus size: 44
6173 GGTTTTTTAG
* *
6183 TTTATGATTGAAATTGAGTAATTTTGCGCAGTTGGGTTTTTCGA
1 TTTATGATTGGAATTGAGTAATTTTGCGCAGTCGGGTTTTTCGA
** * * *
6227 TTTATGATTGGAACCGAGTTAGTTTGCGCAGTCGGGTTTTTCGG
1 TTTATGATTGGAATTGAGTAATTTTGCGCAGTCGGGTTTTTCGA
6271 TTTATGATTGGAATTGAGTAAT
1 TTTATGATTGGAATTGAGTAAT
6293 GTCAATTCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (44 bp):
TTTATGATTGGAATTGAGTAATTTTGCGCAGTCGGGTTTTTCGA
Found at i:6637 original size:2 final size:2
Alignment explanation
Indices: 6630--6670 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
6620 AATAGTAAGG
*
6630 TA TA TA TA TA TA TA T- TA TT TA TA TA T- TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
6671 CAAGTATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6670 original size:11 final size:11
Alignment explanation
Indices: 6630--6667 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6620 AATAGTAAGG
6630 TATA-TATATA
1 TATATTATATA
*
6640 TATATTATTTA
1 TATATTATATA
6651 TATATTATATA
1 TATATTATATA
6662 CTATAT
1 -TATAT
6668 ATACAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.17
11 15 0.62
12 5 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTATATA
Found at i:6687 original size:8 final size:8
Alignment explanation
Indices: 6674--6708 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
6664 ATATATACAA
6674 GTATGAAT
1 GTATGAAT
6682 GTATGAAT
1 GTATGAAT
6690 GTATGAAT
1 GTATGAAT
*
6698 GTATTAAT
1 GTATGAAT
6706 GTA
1 GTA
6709 GAGTGTAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (8 bp):
GTATGAAT
Found at i:10309 original size:21 final size:22
Alignment explanation
Indices: 10270--10312 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10260 TTTGGTTTGG
*
10270 AAAAGAGTGTTTGAAAATAAGT
1 AAAAGAGTGTGTGAAAATAAGT
10292 AAAAGAGTGTGT-AAAATAAGT
1 AAAAGAGTGTGTGAAAATAAGT
10313 GATCGAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (22 bp):
AAAAGAGTGTGTGAAAATAAGT
Found at i:10382 original size:21 final size:22
Alignment explanation
Indices: 10358--10403 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
10348 TTTTCCATGC
* *
10358 TTTTTGCCAT-TTTTATATGTA
1 TTTTTACCATATTTTATAAGTA
10379 TTTTTACCATATTTTATAAGTA
1 TTTTTACCATATTTTATAAGTA
10401 TTT
1 TTT
10404 GTGTTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTACCATATTTTATAAGTA
Found at i:19431 original size:19 final size:18
Alignment explanation
Indices: 19394--19433 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19384 TTCTTGAAAT
*
19394 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
19412 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
19431 AAT
1 AAT
19434 CAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:25463 original size:36 final size:36
Alignment explanation
Indices: 25423--25520 Score: 144
Period size: 36 Copynumber: 2.7 Consensus size: 36
25413 TCAATGTTCC
25423 ACTTAATTGCCCTGAATTAAGTTCTTTAGTAA-CTCT
1 ACTTAATTGCCCTGAATTAAGTTCTTTAGTAACCT-T
* * * *
25459 ACTTAATTACCCTGAATTAAGCTCTTTATTGACCTT
1 ACTTAATTGCCCTGAATTAAGTTCTTTAGTAACCTT
25495 ACTTAATTGCCCTGAATTAAGTTCTT
1 ACTTAATTGCCCTGAATTAAGTTCTT
25521 CACTTCACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 53 0.96
37 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (36 bp):
ACTTAATTGCCCTGAATTAAGTTCTTTAGTAACCTT
Found at i:25663 original size:37 final size:36
Alignment explanation
Indices: 25613--26060 Score: 612
Period size: 36 Copynumber: 12.3 Consensus size: 36
25603 AATTACCCGG
*
25613 AATTAAGTATGTGCTTGATTTTACCTAATTTCCTTGA
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGA
* *
25650 AATTAAGTCTGTGCTTAATTTTACCCAATTTCCTTGA
1 AATTAAGTCTGTGCTT-GTTTTACCTAATTTCCTTGA
* *
25687 AACTAAGTCTGTGCTTGTTTTACCTAATTTCGTTGA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
* * * *
25723 AACTAAGTCTTTGCTGGTCTTACCTAATTTCCTTGA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
* *
25759 AATTAAGTCTGTG-TTGATCTTACCTAATTTCCTTGG
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGA
25795 AATTAAGTCTTGTGCTTGTTTTACCTAATTTCCTTGA
1 AATTAAGTC-TGTGCTTGTTTTACCTAATTTCCTTGA
*
25832 AATTAAGTCTGTGCTTGTGTTACCTAATTTCCTTGA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
* * *
25868 AATTAAGTTTGTGCTTAATTTTACTTAATTTCCTTGA
1 AATTAAGTCTGTGCTT-GTTTTACCTAATTTCCTTGA
*
25905 AATTAAGTCTTTGCTTGTTTTACCTAATTTCCTTGA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
*
25941 AATTAA-ACATGTGCTTGTGTTTACCTAATTTCCTTGA
1 AATTAAGTC-TGTGCTTGT-TTTACCTAATTTCCTTGA
* *
25978 AATTAAGTATGTGCTTGATTTTACCTAATTCCCTTGA
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGA
* * *
26015 AATTAAGTCTATGCTTGTGTTACCTAATTTCCATGA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
26051 AATTAAGTCT
1 AATTAAGTCT
26061 TTGACTGGTT
Statistics
Matches: 366, Mismatches: 36, Indels: 19
0.87 0.09 0.05
Matches are distributed among these distances:
35 3 0.01
36 186 0.51
37 173 0.47
38 4 0.01
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (36 bp):
AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGA
Found at i:25672 original size:73 final size:72
Alignment explanation
Indices: 25613--26060 Score: 612
Period size: 73 Copynumber: 6.1 Consensus size: 72
25603 AATTACCCGG
* * *
25613 AATTAAGTATGTGCTTGATTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTAATTTTACCCAA
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTT-GTTTTACCTAA
25678 TTTCCTTGA
64 TTTCCTTGA
* * * * * *
25687 AACTAAGTCTGTGCTTGTTTTACCTAATTTCGTTGAAACTAAGTCTTTGCTGGTCTTACCTAATT
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTTTTACCTAATT
25752 TCCTTGA
66 TCCTTGA
* *
25759 AATTAAGTCTGTG-TTGATCTTACCTAATTTCCTTGGAATTAAGTCTTGTGCTTGTTTTACCTAA
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGAAATTAAGTC-TGTGCTTGTTTTACCTAA
25823 TTTCCTTGA
64 TTTCCTTGA
* * * *
25832 AATTAAGTCTGTGCTTGTGTTACCTAATTTCCTTGAAATTAAGTTTGTGCTTAATTTTACTTAAT
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTT-GTTTTACCTAAT
25897 TTCCTTGA
65 TTCCTTGA
* *
25905 AATTAAGTCTTTGCTTGTTTTACCTAATTTCCTTGAAATTAA-ACATGTGCTTGTGTTTACCTAA
1 AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGAAATTAAGTC-TGTGCTTGT-TTTACCTAA
25969 TTTCCTTGA
64 TTTCCTTGA
* * * *
25978 AATTAAGTATGTGCTTGATTTTACCTAATTCCCTTGAAATTAAGTCTATGCTTGTGTTACCTAAT
1 AATTAAGTCTGTGCTTG-TTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTTTTACCTAAT
*
26043 TTCCATGA
65 TTCCTTGA
26051 AATTAAGTCT
1 AATTAAGTCT
26061 TTGACTGGTT
Statistics
Matches: 330, Mismatches: 36, Indels: 17
0.86 0.09 0.04
Matches are distributed among these distances:
71 3 0.01
72 61 0.18
73 215 0.65
74 50 0.15
75 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (72 bp):
AATTAAGTCTGTGCTTGTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTTTTACCTAATT
TCCTTGA
Found at i:26193 original size:36 final size:36
Alignment explanation
Indices: 25997--26225 Score: 209
Period size: 36 Copynumber: 6.2 Consensus size: 36
25987 TGTGCTTGAT
* *
25997 TTTACCTAATT-CCCTTGAAATTAAGTCTATG-CT-TG
1 TTTACTTAATTACCC-TG-AATTAAGTCTTTGACTGTG
* * * *
26032 TGTTACCTAATTTCCATGAAATTAAGTCTTTGACTGGTT
1 T-TTACTTAATTACCCTG-AATTAAGTCTTTGACT-GTG
* * * *
26071 TTTACTTAATTACCCCGATTTAAGTCATTGACTG-C
1 TTTACTTAATTACCCTGAATTAAGTCTTTGACTGTG
*
26106 TTTACTTAATTACCCT-ATATTAAGTCTTTGACTGCTT
1 TTTACTTAATTACCCTGA-ATTAAGTCTTTGACTG-TG
26143 TACTTACTTAATTACCCTGAATTAAGT-TCTTGACTGTG
1 T--TTACTTAATTACCCTGAATTAAGTCT-TTGACTGTG
*
26181 TTTACTTAATTACCCTGAATTAAGACTTTGACTTGTG
1 TTTACTTAATTACCCTGAATTAAGTCTTTGAC-TGTG
26218 TTTACTTA
1 TTTACTTA
26226 TGCATATGAT
Statistics
Matches: 164, Mismatches: 16, Indels: 26
0.80 0.08 0.13
Matches are distributed among these distances:
34 1 0.01
35 30 0.18
36 54 0.33
37 32 0.20
38 15 0.09
39 31 0.19
40 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (36 bp):
TTTACTTAATTACCCTGAATTAAGTCTTTGACTGTG
Found at i:26210 original size:75 final size:71
Alignment explanation
Indices: 26051--26213 Score: 220
Period size: 75 Copynumber: 2.2 Consensus size: 71
26041 ATTTCCATGA
* *
26051 AATTAAGTCTTTGACTGGTTTTTACTTAATTACCCCGATTTAAGTCATTGACTGCTTTACTTAAT
1 AATTAAGTCTTTGACTGCTTTTTACTTAATTACCCCGAATTAAGTCATTGACTGCTTTACTTAAT
26116 TACCCT
66 TACCCT
* *
26122 ATATTAAGTCTTTGACTGCTTTACTTACTTAATTACCCTGAATTAAGTTC-TTGACTGTGTTTAC
1 A-ATTAAGTCTTTGACTGCTTT--TTACTTAATTACCCCGAATTAAG-TCATTGACTG-CTTTAC
26186 TTAATTACCCT
61 TTAATTACCCT
*
26197 GAATTAAGACTTTGACT
1 -AATTAAGTCTTTGACT
26214 TGTGTTTACT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
71 1 0.01
72 19 0.23
74 28 0.35
75 32 0.40
76 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (71 bp):
AATTAAGTCTTTGACTGCTTTTTACTTAATTACCCCGAATTAAGTCATTGACTGCTTTACTTAAT
TACCCT
Found at i:30123 original size:24 final size:23
Alignment explanation
Indices: 30091--30149 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
30081 TCTTTATTAT
*
30091 ATTTTGTTTTCTTTTAT-ATATTG
1 ATTTAGTTTTCTTTTATAATA-TG
* *
30114 ATTTAGGTTTCCTTTATAATATG
1 ATTTAGTTTTCTTTTATAATATG
*
30137 CTTTAGTTTTCTT
1 ATTTAGTTTTCTT
30150 AATTAGTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (23 bp):
ATTTAGTTTTCTTTTATAATATG
Found at i:32438 original size:41 final size:41
Alignment explanation
Indices: 32389--33410 Score: 709
Period size: 41 Copynumber: 24.8 Consensus size: 41
32379 TATTCCCAAA
*
32389 TTGCCCTT-CCCATTCGGAAGGTGTTGTTGT-CTTTTCCCTGT
1 TTGCCCTTCCCCA-CCGGAAGGTGTTGTT-TACTTTTCCCTGT
* *
32430 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACATTTCCCAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
*
32471 TTGCCCTTCCCCATCGGAAGGTGTTGTTTACTTTTCCCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* *** * * *
32512 TTTCCCTTCCCGGTCGGAAGGTGTTGTTTTCATTTCACTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* *
32553 TTGCCCTTCCCCACCTGAAGGTGTTGTTTACTTTTCCCTAT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* *
32594 TTGCCCTTCCCCACCGGAAGGTTTTGTTGA-TGTTTCCCTGTT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACT-TTTCCCTG-T
** *
32636 TTGCCCTT-CCCACTAGAAGGTATTGTTTACATTTT-CCTAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAC-TTTTCCCT-GT
* *
32677 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACATTTCCCAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
*** **** * * *** **
32718 TTGCCCTTTTACATTTTCATA-GT-TTGCCCTTCCCAGTCGGAAGATGTTGT
1 TTGCCCTTCCCCA-CCGGA-AGGTGTTG--TTTACTTTTC-------CCTGT
* ** * ******* * ** ** *
32768 TTACTTTTCCCTATTTGCCCTTCCCCGCTG-GAAGGTGT---TGT
1 TTGCCCTTCCCCA----CCGGAAGGTGTTGTTTACTTTTCCCTGT
* * * *** ***
32809 TT-ACATTTCCCA---GTTTGCCCT-TTTACATTTT-CCTAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAC-TTTTCCCT-GT
* * * *
32846 TTGCCCTT-CCCAGTCGGAAGATGTTGTTTACATTTCCCAGT
1 TTGCCCTTCCCCA-CCGGAAGGTGTTGTTTACTTTTCCCTGT
* *
32887 CTGCCCTTCCCCACCGGAAGGTGTTGTTTA-TCTTTCTCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACT-TTTCCCTGT
* * *
32928 TTGTCTTTCCCCACCGGAAGGTGTTGTTTACCTTTCCCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * * * *
32969 TTGTCCTTCCCCACCGGAAGGTTTTGTTTTCTTTTGCATGTT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTG-T
* *** * * *
33011 TTGCCCTTACCGGTCGGAAGGTGTTGTTTACATTTCCCAGG
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
*
33052 TTGCCCTTCCCCACCGGAACGTGTTGTTTACTTTTCCCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * * *
33093 TTGCCCTTCCCCACCGGAAAGTATTGTTTACCTTTCCTTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * *
33134 TTACCCTTCCCCACCGGAAGGTGTTATTTACTTTTCCATGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * *
33175 TTGTCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTTAT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
*
33216 TTGCCCTTCCCCACCGAAAGGTGTTGTTTACTTTTCCCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * *
33257 TTGCCCTTCCCCACCGAAAGGTGTTTTTTGCTTTTCCCTGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
* * * *
33298 TTTCCCTT-CCTACCGGAAGGTGTTGTTTACATTTCCCAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
** *
33338 TTGCCCTTCCCCACCGGAAGGTGTTGTTTA-AATTCCCAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
** *
33378 TTGCCCTTCCCGGCTGGAAGGTGTTGTTTACTT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
33411 GTTTTTGTTG
Statistics
Matches: 767, Mismatches: 171, Indels: 86
0.75 0.17 0.08
Matches are distributed among these distances:
33 5 0.01
34 2 0.00
36 1 0.00
37 8 0.01
38 3 0.00
40 76 0.10
41 571 0.74
42 82 0.11
43 7 0.01
50 8 0.01
51 2 0.00
54 2 0.00
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (41 bp):
TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCTGT
Found at i:32731 original size:22 final size:23
Alignment explanation
Indices: 32703--32748 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
32693 GAAGGTGTTG
*
32703 TTTACA-TTTCCCAGTTTGCCCT
1 TTTACATTTTCACAGTTTGCCCT
*
32725 TTTACATTTTCATAGTTTGCCCT
1 TTTACATTTTCACAGTTTGCCCT
32748 T
1 T
32749 CCCAGTCGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.15, C:0.26, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTACATTTTCACAGTTTGCCCT
Found at i:32741 original size:64 final size:64
Alignment explanation
Indices: 32661--32789 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 64
32651 GAAGGTATTG
* *
32661 TTTACATTTTCCTAGTTTGCCCTTCCCCA-CCGGAAGGTGTTGTTTACATTTCCC-AGTTTGCCC
1 TTTACATTTTCATAGTTTGCCCTT-CCCAGCCGGAAGATGTTGTTTACATTTCCCTA-TTTGCCC
32724 T
64 T
* *
32725 TTTACATTTTCATAGTTTGCCCTTCCCAGTCGGAAGATGTTGTTTACTTTTCCCTATTTGCCCT
1 TTTACATTTTCATAGTTTGCCCTTCCCAGCCGGAAGATGTTGTTTACATTTCCCTATTTGCCCT
32789 T
1 T
32790 CCCCGCTGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 4 0.07
64 54 0.92
65 1 0.02
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.43
Consensus pattern (64 bp):
TTTACATTTTCATAGTTTGCCCTTCCCAGCCGGAAGATGTTGTTTACATTTCCCTATTTGCCCT
Found at i:32817 original size:105 final size:106
Alignment explanation
Indices: 32635--32916 Score: 446
Period size: 105 Copynumber: 2.7 Consensus size: 106
32625 GTTTCCCTGT
* * * *
32635 TTTGCCCTTCCCACT-AGAAGGTATTGTTTACATTTT-CCTAGTTTGCCCTTCCCCACCGGAAGG
1 TTTGCCCTTCCCAGTCGGAAGATGTTGTTTAC-TTTTCCCTAGTTTGCCCTTCCCCACCGGAAGG
32698 TGTTGTTTACATTTCCCAGTTTGCCCTTTTACATTTTCATAG
65 TGTTGTTTACATTTCCCAGTTTGCCCTTTTACATTTTCATAG
* *
32740 TTTGCCCTTCCCAGTCGGAAGATGTTGTTTACTTTTCCCTA-TTTGCCCTTCCCCGCTGGAAGGT
1 TTTGCCCTTCCCAGTCGGAAGATGTTGTTTACTTTTCCCTAGTTTGCCCTTCCCCACCGGAAGGT
*
32804 GTTGTTTACATTTCCCAGTTTGCCCTTTTACATTTTCCTAG
66 GTTGTTTACATTTCCCAGTTTGCCCTTTTACATTTTCATAG
* *
32845 TTTGCCCTTCCCAGTCGGAAGATGTTGTTTACATTTCCC-AGTCTGCCCTTCCCCACCGGAAGGT
1 TTTGCCCTTCCCAGTCGGAAGATGTTGTTTACTTTTCCCTAGTTTGCCCTTCCCCACCGGAAGGT
32909 GTTGTTTA
66 GTTGTTTA
32917 TCTTTCTCTG
Statistics
Matches: 163, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
104 1 0.01
105 145 0.89
106 17 0.10
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (106 bp):
TTTGCCCTTCCCAGTCGGAAGATGTTGTTTACTTTTCCCTAGTTTGCCCTTCCCCACCGGAAGGT
GTTGTTTACATTTCCCAGTTTGCCCTTTTACATTTTCATAG
Found at i:32836 original size:22 final size:23
Alignment explanation
Indices: 32808--32853 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
32798 GAAGGTGTTG
32808 TTTACA-TTTCCCAGTTTGCCCT
1 TTTACATTTTCCCAGTTTGCCCT
*
32830 TTTACATTTTCCTAGTTTGCCCT
1 TTTACATTTTCCCAGTTTGCCCT
32853 T
1 T
32854 CCCAGTCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.13, C:0.28, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTACATTTTCCCAGTTTGCCCT
Found at i:32840 original size:64 final size:63
Alignment explanation
Indices: 32767--32894 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 63
32757 GAAGATGTTG
* * *
32767 TTTACTTTTCCCTA-TTTGCCCTTCCCCG-CTGGAAGGTGTTGTTTACATTTCCCAGTTTGCCCT
1 TTTACTTTT-CCTAGTTTGCCCTTCCCAGTC-GGAAGATGTTGTTTACATTTCCCAGTCTGCCCT
32830 TTTACATTTTCCTAGTTTGCCCTTCCCAGTCGGAAGATGTTGTTTACATTTCCCAGTCTGCCCT
1 TTTAC-TTTTCCTAGTTTGCCCTTCCCAGTCGGAAGATGTTGTTTACATTTCCCAGTCTGCCCT
32894 T
1 T
32895 CCCCACCGGA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
63 9 0.15
64 49 0.83
65 1 0.02
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (63 bp):
TTTACTTTTCCTAGTTTGCCCTTCCCAGTCGGAAGATGTTGTTTACATTTCCCAGTCTGCCCT
Done.