Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013533.1 Corchorus olitorius cultivar O-4 contig13566, 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: 56279
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:2818 original size:154 final size:154
Alignment explanation
Indices: 3--2799 Score: 4478
Period size: 154 Copynumber: 18.2 Consensus size: 154
1 AT
* * * *
3 TTTTGATTCGTCTTCGATTTGGGAAACCTCAAAGATTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
68 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
133 GCCTATCGGGGCCCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTGACG
* * * *
157 TATTGAATCGACTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
222 AATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
*
287 GCCTATCAGGGCCCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTGACG
* * *
311 TTTTGAAACGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCTACCTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* * *
376 AATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGT
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* *
441 GCCTTTCGGGGCCCATTAGTGCCG
131 GCCTATCGGGGCCCATTAGTGACG
* * * *
465 TTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCTATTGTTTATGGCCTAAATAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
530 AATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
*
595 GCCTATC-GGGCATCATTAGTGACG
131 GCCTATCGGGGC-CCATTAGTGACG
*
619 TTTTGAATCGTCTTCGATTTGGCAAACCTAAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
684 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* **
749 GCCTATCGGGACCCATTAGTTTCG
131 GCCTATCGGGGCCCATTAGTGACG
773 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
838 AATCATTTCGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
** **
903 AACTATCGGGGATCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTGACG
927 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
** * *
992 AATCATTTTGGTGAGATTAGTCCACTAAGAAGTTCTTAGCACATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* **
1057 GCCTATCGGGACCCATTAGTTCCG
131 GCCTATCGGGGCCCATTAGTGACG
1081 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1146 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* *
1211 GCCTATCGGAGCCCATTAGTGATG
131 GCCTATCGGGGCCCATTAGTGACG
1235 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
1300 AAACATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* *
1365 GACTATCGGGGACCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTGACG
** * * *
1389 TTTTGAATCAACTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCTGACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* *
1454 AATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTTGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
** *
1519 AACTATC-GGGCATCATTAGTGACG
131 GCCTATCGGGGC-CCATTAGTGACG
1543 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* * * *
1608 AATCATTTTGGTGAGATGAGTCCACTATGAAATTTTTAGCACATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* * *
1673 GCATATC-GGGACCATTAGTGTCG
131 GCCTATCGGGGCCCATTAGTGACG
*
1696 TTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC-AC
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-
* **
1760 TAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTAAAACACTTGTTATTTTG
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
*
1825 GGCCTATCGGGGACCATTAGTGACG
130 GGCCTATCGGGGCCCATTAGTGACG
1850 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* *
1915 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTGGCTCATTTGGAACAATTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* **
1980 GCCTATCGGGGACCATTAGTTCCG
131 GCCTATCGGGGCCCATTAGTGACG
2004 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
2069 AATCATTTTGGTGAGATTAGTCCACTGAGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
*
2134 GCCTATCGGGGACCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTGACG
2158 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
*
2223 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAATTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
**
2288 GCCTATCGGGGCCCATTAGTTTCG
131 GCCTATCGGGGCCCATTAGTGACG
* *
2312 TTGTGAATCGTCTTCGATTTGGC-AACCTTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* * *
2376 TAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCA-CTGTGAAAACTTGTTATTTT
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG-GAACACTTGTTATTTT
* * * **
2440 GGGCCTTTCAGGGCCCATAAGTGTTG
129 GGGCCTATCGGGGCCCATTAGTGACG
* * * * *
2466 TTTTGAATCGTCTTCGATTTAGCAAACCACAAAGATTTTCTTTCCATTGTTTATGACC-AACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* * *
2530 AATCATTTTGATGAGATTAGTCCACTATGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
*
2595 GCCTTTCGGGGCCCATTAGTG-CTG
131 GCCTATCGGGGCCCATTAGTGAC-G
** * * *
2619 TTTTGAATCGTCTTCGATTTAACAAACCACAAAGCTTTTCTTTCCATTGTTTATGACCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* * *
2684 AATCATTTTGGTGAGATTAGTCCACTCTGAAGTTTTTAGCTCA-CTGTGAAAACTTGTTATTTTG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG-GAACACTTGTTATTTTG
* **
2748 GGCCTTTCGGGGCCCATTAGTGTTG
130 GGCCTATCGGGGCCCATTAGTGACG
* * *
2773 TTTTGAATCGTTTTTGATTTTGCAAAC
1 TTTTGAATCGTCTTCGATTTGGCAAAC
2800 AATAAAACTT
Statistics
Matches: 2453, Mismatches: 176, Indels: 28
0.92 0.07 0.01
Matches are distributed among these distances:
152 1 0.00
153 289 0.12
154 2155 0.88
155 8 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
GCCTATCGGGGCCCATTAGTGACG
Found at i:3570 original size:21 final size:21
Alignment explanation
Indices: 3546--3592 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3536 TTTAGTTTCC
3546 AGAGATTGTTGAAGTGCTAAT
1 AGAGATTGTTGAAGTGCTAAT
3567 AGAGATTGTTGAAGTGCTAAT
1 AGAGATTGTTGAAGTGCTAAT
*
3588 TGAGA
1 AGAGA
3593 AGCACGCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (21 bp):
AGAGATTGTTGAAGTGCTAAT
Found at i:15742 original size:21 final size:21
Alignment explanation
Indices: 15703--15742 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15693 AGGAGTTGCC
* *
15703 AAAGATGTCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
15724 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
15743 ATGACAAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:28841 original size:10 final size:9
Alignment explanation
Indices: 28814--28852 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
28804 CTTGTAGTTT
28814 AATCTAAAAA
1 AATC-AAAAA
*
28824 TATCAAAAA
1 AATCAAAAA
28833 AATCAAAAA
1 AATCAAAAA
28842 AAT-AAAAA
1 AATCAAAAA
28850 AAT
1 AAT
28853 ATTTCGACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 8 0.30
9 16 0.59
10 3 0.11
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (9 bp):
AATCAAAAA
Found at i:29191 original size:21 final size:21
Alignment explanation
Indices: 29165--29205 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29155 TTTAAACCCT
29165 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
29186 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
29206 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:29679 original size:15 final size:15
Alignment explanation
Indices: 29659--29687 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29649 CCTTGGAGAT
29659 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
29674 TCAAAATCAACAAG
1 TCAAAATCAACAAG
29688 TTACACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:29894 original size:21 final size:21
Alignment explanation
Indices: 29868--29959 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
29858 TGCTAGGAGT
29868 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
*
29889 TCATTGGAGCATGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
29910 TCATTGGAG-AAGGTTCCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
* * *
29931 CCATTGGAGAAAGTTTCAAGC
1 TCATTGGAGCAAGTTCCAAGC
29952 TCATTGGA
1 TCATTGGA
29960 ATTGCCTAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.95
22 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:30865 original size:25 final size:24
Alignment explanation
Indices: 30829--30875 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
30819 TCCTTCTATT
30829 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
30852 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
30876 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:32259 original size:21 final size:21
Alignment explanation
Indices: 32235--32275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32225 AAAGATCAAA
32235 CTAAAGTGAGA-GATGAATTTG
1 CTAAAGTG-GATGATGAATTTG
*
32256 CTAAATTGGATGATGAATTT
1 CTAAAGTGGATGATGAATTT
32276 AGGGCTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (21 bp):
CTAAAGTGGATGATGAATTTG
Found at i:32454 original size:33 final size:33
Alignment explanation
Indices: 32353--32490 Score: 97
Period size: 33 Copynumber: 4.2 Consensus size: 33
32343 TTGCAAAGAG
* * * * *
32353 TGTTTTAGATGTTGTTTGCGATGATACTAAAGC
1 TGTTTTAGGTGTTGTTTGTGATAAAACTAAATC
** *
32386 TAATTT-GAGTGTTGTTTGTGATAACACTAAATC
1 TGTTTTAG-GTGTTGTTTGTGATAAAACTAAATC
32419 TGTTTTAGGTGTTGTTTGTGA-AGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATA-AAACTAAA-TC
* **
32452 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTAGG-TGTTGTTTGTGAT-AAAACTAAATC
32485 TGTTTT
1 TGTTTT
32491 GGTTGATCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
32 7 0.08
33 69 0.81
34 8 0.09
35 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.43
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATAAAACTAAATC
Found at i:41913 original size:6 final size:6
Alignment explanation
Indices: 41902--41940 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
41892 TCTTTGCATA
*
41902 TTTAAT TTTAAT TTTAAT TTT-AT TATTAAT TTTGAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT T-TTAAT TTTAAT TTT
41941 TACACCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:42180 original size:14 final size:13
Alignment explanation
Indices: 42161--42190 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
42151 CAGCGCACCA
42161 AGCAGCACCAGCGC
1 AGCAGCACCAG-GC
42175 AGCAGCACCAGGC
1 AGCAGCACCAGGC
42188 AGC
1 AGC
42191 TCGACCAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.30, C:0.40, G:0.30, T:0.00
Consensus pattern (13 bp):
AGCAGCACCAGGC
Found at i:42774 original size:20 final size:20
Alignment explanation
Indices: 42749--42787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42739 GATCAAAGTC
42749 GATAAGAAAAAGCAAGTGTT
1 GATAAGAAAAAGCAAGTGTT
**
42769 GATAAGAGGAAGCAAGTGT
1 GATAAGAAAAAGCAAGTGT
42788 CGACTAAGGG
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:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (20 bp):
GATAAGAAAAAGCAAGTGTT
Found at i:42838 original size:21 final size:21
Alignment explanation
Indices: 42786--42836 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
42776 GGAAGCAAGT
* *
42786 GTCGACTAAGGGAGCAAAATT
1 GTCGACAAAGGGAGCAAAATC
* *
42807 ATCAACAAAGGGAAGCAAAATC
1 GTCGACAAAGGG-AGCAAAATC
42829 GTCGACAA
1 GTCGACAA
42837 GGAGTTAAGC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (21 bp):
GTCGACAAAGGGAGCAAAATC
Found at i:48610 original size:21 final size:21
Alignment explanation
Indices: 48584--48623 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48574 TTTAAACCCT
48584 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
48605 ATTGGATCTAAGTGGTACT
1 ATTGGAACTAAGTGGTACT
48624 TTGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:52212 original size:21 final size:22
Alignment explanation
Indices: 52186--52226 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52176 ACAAAGAGGG
* *
52186 AGATGCTTCCTTCCT-CCTAAA
1 AGATGCCTCCCTCCTACCTAAA
52207 AGATGCCTCCCTCCTACCTA
1 AGATGCCTCCCTCCTACCTA
52227 TCAGGAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.39, G:0.10, T:0.29
Consensus pattern (22 bp):
AGATGCCTCCCTCCTACCTAAA
Done.