Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017722.1 Corchorus olitorius cultivar O-4 contig17755, 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: 48100
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:800 original size:42 final size:42
Alignment explanation
Indices: 738--820 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
728 AAACCGGACT
738 CAAAGCTTTTTCCTTCTGCGGTTTCTCCATTTTTCTGAAAAG
1 CAAAGCTTTTTCCTTCTGCGGTTTCTCCATTTTTCTGAAAAG
*
780 CAAAGCTTTTTCCTTTTGCGGTTTCTCCATTTTTCTGAAAA
1 CAAAGCTTTTTCCTTCTGCGGTTTCTCCATTTTTCTGAAAA
821 AAAAAAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (42 bp):
CAAAGCTTTTTCCTTCTGCGGTTTCTCCATTTTTCTGAAAAG
Found at i:913 original size:44 final size:45
Alignment explanation
Indices: 863--947 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
853 AAAGAAACTT
*
863 TTAGGGTTTGGAAAAATTGAAGGCTAAAAGAAAC-AATGGGACTG
1 TTAGGGTTTGGAAAAATTGAAGGATAAAAGAAACAAATGGGACTG
* * * *
907 TTAGGGTTTTGAAAATTTGAAGTATAAAATAAACAAATGGG
1 TTAGGGTTTGGAAAAATTGAAGGATAAAAGAAACAAATGGG
948 CTATTACCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 29 0.83
45 6 0.17
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.27
Consensus pattern (45 bp):
TTAGGGTTTGGAAAAATTGAAGGATAAAAGAAACAAATGGGACTG
Found at i:1375 original size:6 final size:6
Alignment explanation
Indices: 1364--1397 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1354 TTAGAGAGAA
1364 TATAAG TATAAG TATAA- TATAAG TATAAAG TATA
1 TATAAG TATAAG TATAAG TATAAG TAT-AAG TATA
1398 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (6 bp):
TATAAG
Found at i:1384 original size:17 final size:18
Alignment explanation
Indices: 1362--1397 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1352 AATTAGAGAG
1362 AATATAAGTAT-AAGTAT
1 AATATAAGTATAAAGTAT
1379 AATATAAGTATAAAGTAT
1 AATATAAGTATAAAGTAT
1397 A
1 A
1398 TTTGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (18 bp):
AATATAAGTATAAAGTAT
Found at i:1386 original size:11 final size:12
Alignment explanation
Indices: 1364--1397 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
1354 TTAGAGAGAA
1364 TATAAGTATAAG
1 TATAAGTATAAG
1376 TATAA-TATAAG
1 TATAAGTATAAG
1387 TATAAAGTATA
1 TAT-AAGTATA
1398 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 7 0.35
13 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (12 bp):
TATAAGTATAAG
Found at i:3011 original size:23 final size:23
Alignment explanation
Indices: 2985--3039 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2975 CTAAATTTCT
* *
2985 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAATAATCAACTCTATA
* *
3008 AAGTTTAAACAATTAACTCTATA
1 AAGTTTAAATAATCAACTCTATA
3031 AAG-TTAAAT
1 AAGTTTAAAT
3040 TTCTGAGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
AAGTTTAAATAATCAACTCTATA
Found at i:5880 original size:22 final size:22
Alignment explanation
Indices: 5851--5975 Score: 116
Period size: 22 Copynumber: 5.7 Consensus size: 22
5841 TTGAATATTT
5851 TATGAAATTTTGATAACTAACC
1 TATGAAATTTTGATAACTAACC
* *
5873 TATTAAATTTTGATAAC-CACC
1 TATGAAATTTTGATAACTAACC
* *
5894 ATATGAAATTTTGAT-AGTTACC
1 -TATGAAATTTTGATAACTAACC
*
5916 TATGAAATTGTGATAGACT--CC
1 TATGAAATTTTGATA-ACTAACC
*
5937 ATATGAAACTTTGATAACCTAA-C
1 -TATGAAATTTTGATAA-CTAACC
*
5960 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
5976 ACCTTCAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
21 20 0.24
22 61 0.73
23 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACTAACC
Found at i:5930 original size:43 final size:43
Alignment explanation
Indices: 5851--5968 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
5841 TTGAATATTT
* *
5851 TATGAAATTTTGATAACTAACCTATTAAATTTTGATA-ACCACCA
1 TATGAAATTTTGAT-ACTAACCTATGAAATTGTGATAGA-CACCA
* * *
5895 TATGAAATTTTGATAGTTACCTATGAAATTGTGATAGACTCCA
1 TATGAAATTTTGATACTAACCTATGAAATTGTGATAGACACCA
*
5938 TATGAAACTTTGATAACCTAA-CTATGAAATT
1 TATGAAATTTTGAT-A-CTAACCTATGAAATT
5969 TTAATAAACC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 35 0.56
44 26 0.41
45 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (43 bp):
TATGAAATTTTGATACTAACCTATGAAATTGTGATAGACACCA
Found at i:6045 original size:22 final size:21
Alignment explanation
Indices: 5988--6055 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 21
5978 CTTCAAATGA
*
5988 AATTTT-TTAATCTTCCTATG
1 AATTTTGTTAATCTCCCTATG
* * * *
6008 ATTTTTGATAACCTCCCTGTG
1 AATTTTGTTAATCTCCCTATG
6029 AGATTTTGTTAATCTCCCTAT-
1 A-ATTTTGTTAATCTCCCTATG
6050 AATTTT
1 AATTTT
6056 TTGATACTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.27
21 12 0.32
22 15 0.41
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (21 bp):
AATTTTGTTAATCTCCCTATG
Found at i:7671 original size:22 final size:21
Alignment explanation
Indices: 7639--7849 Score: 117
Period size: 22 Copynumber: 9.7 Consensus size: 21
7629 ACCAAACTGA
*
7639 AAATTTGATAACCTCATTATG
1 AAATTTGATAACCTCACTATG
* *
7660 AAATTTCAATAACCTCCCTATG
1 AAATTT-GATAACCTCACTATG
7682 AAAATTTGATAACCAT-ACTATG
1 -AAATTTGATAACC-TCACTATG
* *
7704 AAATTTTGATAAGCTCAGTATG
1 AAA-TTTGATAACCTCACTATG
*
7726 AAATTTTGATAATCC-CCCTATG
1 AAA-TTTGATAA-CCTCACTATG
*
7748 AAATTTTGATAATCAT-ACTAT-
1 AAA-TTTGATAA-CCTCACTATG
* * ** *
7769 AAAATTGGTAACAACACAATG
1 AAATTTGATAACCTCACTATG
**
7790 AAAATTTTGATAACCTC-CTCAAA
1 -AAA-TTTGATAACCTCACT-ATG
* * *
7813 AAATTATGATAAACACACCATG
1 AAATT-TGATAACCTCACTATG
7835 AAATTTCGATAACCT
1 AAATTT-GATAACCT
7850 TCTTATGAGA
Statistics
Matches: 145, Mismatches: 30, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
19 2 0.01
20 10 0.07
21 16 0.11
22 99 0.68
23 18 0.12
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (21 bp):
AAATTTGATAACCTCACTATG
Found at i:7712 original size:66 final size:66
Alignment explanation
Indices: 7618--7774 Score: 194
Period size: 66 Copynumber: 2.4 Consensus size: 66
7608 TCTAACATAG
* * *
7618 AAATATTGATAACCAAAC--TGAAAATTTGATAACCTCATTATGAAATTTCAATAA-CCTCCCTA
1 AAAT-TTGATAACCATACTATGAAATTTTGATAACCTCAGTATGAAATTTCAATAATCC-CCCTA
7680 TGA
64 TGA
* **
7683 AAATTTGATAACCATACTATGAAATTTTGATAAGCTCAGTATGAAATTTTGATAATCCCCCTATG
1 AAATTTGATAACCATACTATGAAATTTTGATAACCTCAGTATGAAATTTCAATAATCCCCCTATG
7748 A
66 A
* * *
7749 AATTTTGATAATCATACTATAAAATT
1 AAATTTGATAACCATACTATGAAATT
7775 GGTAACAACA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 12 0.15
65 4 0.05
66 62 0.77
67 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.34
Consensus pattern (66 bp):
AAATTTGATAACCATACTATGAAATTTTGATAACCTCAGTATGAAATTTCAATAATCCCCCTATG
A
Found at i:7900 original size:22 final size:22
Alignment explanation
Indices: 7869--8119 Score: 122
Period size: 22 Copynumber: 11.3 Consensus size: 22
7859 AATAAAACTG
* *
7869 TGATATCCTCTCTATGTAATTT
1 TGATAACCTCTCTATGAAATTT
* *
7891 TGATAACCTCTCCATAAAATTT
1 TGATAACCTCTCTATGAAATTT
*
7913 TCATAACCTC-CATATGAAATTT
1 TGATAACCTCTC-TATGAAATTT
* *
7935 TGTTAATTAACATCCCTATGAAATTT
1 TG---A-TAACCTCTCTATGAAATTT
* *
7961 TGATAA----GC-A-CAAATTT
1 TGATAACCTCTCTATGAAATTT
*
7977 TGATGACCTCACTTCCTATGAAATTT
1 TGATAACCT--C-T-CTATGAAATTT
* * *
8003 TGATAACCACACTATAAAATTT
1 TGATAACCTCTCTATGAAATTT
** * *
8025 CAATAACAT-TCGTATGAGATTT
1 TGATAACCTCTC-TATGAAATTT
* * * *
8047 TGTTAACATCCCTAAGAAATTT
1 TGATAACCTCTCTATGAAATTT
** * *
8069 TGATAAAGTTTTTATGAAATTT
1 TGATAACCTCTCTATGAAATTT
*
8091 TGATAACCTCTGTATGAAATTT
1 TGATAACCTCTCTATGAAATTT
8113 TGATAAC
1 TGATAAC
8120 TACACAATGA
Statistics
Matches: 169, Mismatches: 42, Indels: 36
0.68 0.17 0.15
Matches are distributed among these distances:
16 11 0.07
17 1 0.01
18 1 0.01
21 2 0.01
22 116 0.69
23 2 0.01
24 2 0.01
25 2 0.01
26 31 0.18
27 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGATAACCTCTCTATGAAATTT
Found at i:7977 original size:42 final size:42
Alignment explanation
Indices: 7929--8013 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
7919 CCTCCATATG
* * *
7929 AAATTTTG-TTAATTAACATCCCTATGAAATTTTGATAAGCAC
1 AAATTTTGATGAACTAAC-TCCCTATGAAATTTTGATAACCAC
* * *
7971 AAATTTTGATGACCTCACTTCCTATGAAATTTTGATAACCAC
1 AAATTTTGATGAACTAACTCCCTATGAAATTTTGATAACCAC
8013 A
1 A
8014 CTATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (42 bp):
AAATTTTGATGAACTAACTCCCTATGAAATTTTGATAACCAC
Found at i:8129 original size:22 final size:22
Alignment explanation
Indices: 8082--8159 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
8072 TAAAGTTTTT
***
8082 ATGAAATTTTGATAACCTCTGT
1 ATGAAATTTTGATAACCTCACA
8104 ATGAAATTTTGATAA-CTACACA
1 ATGAAATTTTGATAACCT-CACA
* * *
8126 ATGAAGTGTTGAAAACCTC-CA
1 ATGAAATTTTGATAACCTCACA
8147 TATGAAAATTTTG
1 -ATG-AAATTTTG
8160 TAGCTATACT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
21 4 0.09
22 32 0.73
23 8 0.18
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACA
Found at i:8130 original size:44 final size:44
Alignment explanation
Indices: 8082--8187 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 44
8072 TAAAGTTTTT
**
8082 ATGAAATTTTGATAACCTCTGTATG-AAATTTTGATAACTACACA
1 ATGAAATTTTGATAACCTCCATATGAAAATTTTG-TAACTACACA
* * * * * *
8126 ATGAAGTGTTGAAAACCTCCATATGAAAATTTTGTAGCTATACT
1 ATGAAATTTTGATAACCTCCATATGAAAATTTTGTAACTACACA
* *
8170 ATAAAATTTTAATAACCT
1 ATGAAATTTTGATAACCT
8188 TCCTATGTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
44 40 0.83
45 8 0.17
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (44 bp):
ATGAAATTTTGATAACCTCCATATGAAAATTTTGTAACTACACA
Found at i:9290 original size:3 final size:3
Alignment explanation
Indices: 9282--9307 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9272 GTCCTTTAAA
9282 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
9308 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10132 original size:15 final size:15
Alignment explanation
Indices: 10114--10148 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10104 AAATTGAGGC
10114 TAATTAAATTAGATT
1 TAATTAAATTAGATT
* *
10129 TAATTAAATTGGTTT
1 TAATTAAATTAGATT
10144 TAATT
1 TAATT
10149 TTTGGGCTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (15 bp):
TAATTAAATTAGATT
Found at i:11638 original size:2 final size:2
Alignment explanation
Indices: 11631--11655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11621 GTATAGATAG
11631 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11656 GATTTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25272 original size:115 final size:116
Alignment explanation
Indices: 25078--25291 Score: 252
Period size: 115 Copynumber: 1.9 Consensus size: 116
25068 ACAAAAAGGG
* ** * * * *
25078 CATGTGGCATGCCACATGTTAGGAATACCGTGTGTCACGTGTCTTTTTTGTCCATGTAGCATGCC
1 CATGTGGCATGCCACATGTTAGAAATACCACGTGCCACATGTCTTTTTAGTCCACGTAGCATGCC
* * * *
25143 GCGTCGGACGCCGTGACGGATCCGT-TTGTCCTAACAGGCCAAAAAAATGA
66 ACGTCAGACGCCGTGACGGAGCCGTCATGTCCTAACAGGCCAAAAAAATGA
* * * *
25193 CATGTGGCATGCCACGTGTTA-AAATGCCACGTGCCACATGTCATTTTTAGTGCACGTGGCATGC
1 CATGTGGCATGCCACATGTTAGAAATACCACGTGCCACATGTC-TTTTTAGTCCACGTAGCATGC
* *
25257 CACGTCAGCCGCCGTGATGGAGCCGTCATGTCCTA
65 CACGTCAGACGCCGTGACGGAGCCGTCATGTCCTA
25292 CTGTGATGGA
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
114 15 0.19
115 58 0.73
116 7 0.09
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (116 bp):
CATGTGGCATGCCACATGTTAGAAATACCACGTGCCACATGTCTTTTTAGTCCACGTAGCATGCC
ACGTCAGACGCCGTGACGGAGCCGTCATGTCCTAACAGGCCAAAAAAATGA
Found at i:32888 original size:20 final size:20
Alignment explanation
Indices: 32853--32900 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
32843 AAGTGTCGTC
32853 GGCGCGTGGGGGTGCGTG-T
1 GGCGCGTGGGGGTGCGTGAT
*
32872 GGCGTGTGGGCGGTGCGTGAT
1 GGCGCGTGGG-GGTGCGTGAT
32893 GGCGCGTG
1 GGCGCGTG
32901 CGGCGTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.02, C:0.17, G:0.60, T:0.21
Consensus pattern (20 bp):
GGCGCGTGGGGGTGCGTGAT
Found at i:34661 original size:18 final size:18
Alignment explanation
Indices: 34638--34672 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34628 GATGTCCAGT
*
34638 ATAGAAAATTTGTTGGCC
1 ATAGAAAATCTGTTGGCC
34656 ATAGAAAATCTGTTGGC
1 ATAGAAAATCTGTTGGC
34673 AAACAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (18 bp):
ATAGAAAATCTGTTGGCC
Found at i:36454 original size:3 final size:3
Alignment explanation
Indices: 36448--36480 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
36438 ACAACACAAT
36448 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
36481 GAATTATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:36512 original size:24 final size:24
Alignment explanation
Indices: 36485--36563 Score: 56
Period size: 24 Copynumber: 3.2 Consensus size: 24
36475 ATAATAGAAT
36485 TATTCAATAGTTCATTGCATTTTG
1 TATTCAATAGTTCATTGCATTTTG
* * *
36509 TATT-ATTTAGTAT-GTGTGC-TTTTAA
1 TATTCA-ATAGT-TCAT-TGCATTTT-G
36534 TAGGTTCAATAGTTCATTGCATTTTG
1 TA--TTCAATAGTTCATTGCATTTTG
36560 TATT
1 TATT
36564 ATTTGGTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
23 1 0.03
24 15 0.38
25 6 0.15
26 6 0.15
27 11 0.28
28 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
TATTCAATAGTTCATTGCATTTTG
Found at i:36556 original size:51 final size:53
Alignment explanation
Indices: 36487--36596 Score: 188
Period size: 51 Copynumber: 2.1 Consensus size: 53
36477 AATAGAATTA
*
36487 TTCAATAGTTCATTGCATTTTGTATTATTTAGTATGTGTGC-T-TTTAATAGG
1 TTCAATAGTTCATTGCATTTTGTATTATTTAGTATATGTGCTTATTTAATAGG
*
36538 TTCAATAGTTCATTGCATTTTGTATTATTTGGTATATGTGCTTATTTAATAGG
1 TTCAATAGTTCATTGCATTTTGTATTATTTAGTATATGTGCTTATTTAATAGG
36591 TTCAAT
1 TTCAAT
36597 TGAATAAACA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
51 39 0.71
52 1 0.02
53 15 0.27
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (53 bp):
TTCAATAGTTCATTGCATTTTGTATTATTTAGTATATGTGCTTATTTAATAGG
Found at i:38212 original size:42 final size:42
Alignment explanation
Indices: 38165--38257 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
38155 CTCGATGAAA
* *
38165 TGGATTTGAGAGGAATGACCGAAGGCTTGTTATTCCTTGTTG
1 TGGATTTGAGAGAAATGACCGAAGGCTTGTTATTCCTCGTTG
38207 TGGATTTGAGAGAAATGACCGAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGACCGAAGGCTTGTTATTCCTCGTTG
38249 TCGGATTTG
1 T-GGATTTG
38258 CTAGATTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 41 0.85
43 7 0.15
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (42 bp):
TGGATTTGAGAGAAATGACCGAAGGCTTGTTATTCCTCGTTG
Found at i:42510 original size:2 final size:2
Alignment explanation
Indices: 42503--42529 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42493 AACCATATGG
42503 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42530 GTATTTTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42943 original size:22 final size:22
Alignment explanation
Indices: 42918--43150 Score: 138
Period size: 22 Copynumber: 10.6 Consensus size: 22
42908 ACAATCAAAC
*
42918 CAAAATTACATAGGATGGTTAT
1 CAAAATTTCATAGGATGGTTAT
**
42940 CAAAATTTCATAGTG-TGGTTGC
1 CAAAATTTCATAG-GATGGTTAT
* * *
42962 CAAAATTTCATATGAAGATTAT
1 CAAAATTTCATAGGATGGTTAT
* * **
42984 CAAAACTACATAGTG-TACTTAT
1 CAAAATTTCATAG-GATGGTTAT
* *
43006 CAAAATTTCATACAGAT-GTTAC
1 CAAAATTTCATA-GGATGGTTAT
* *
43028 CAAAATTTCATTA-AAAGGTTAT
1 CAAAATTTCA-TAGGATGGTTAT
* * *
43050 CAGAATTTCTTAGGGA-GGTTAA
1 CAAAATTTCATA-GGATGGTTAT
* **
43072 CAAAATTTCATATGAAAGTTAT
1 CAAAATTTCATAGGATGGTTAT
43094 CAAAAATTT-ATAGTG-TGGTTAT
1 C-AAAATTTCATAG-GATGGTTAT
* * * *
43116 CAAAAATTCATAAGAAGGTTAA
1 CAAAATTTCATAGGATGGTTAT
43138 CAAAATTTCATAG
1 CAAAATTTCATAG
43151 TGACTGAATT
Statistics
Matches: 157, Mismatches: 40, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
21 13 0.08
22 130 0.83
23 14 0.09
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGATGGTTAT
Found at i:43208 original size:22 final size:22
Alignment explanation
Indices: 43182--43252 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
43172 GTGCTTATCC
*
43182 AAATTTTCTAGGGACGTTAACA
1 AAATTTTATAGGGACGTTAACA
* * *
43204 AAATTTAATAGGGAGGTTAAGA
1 AAATTTTATAGGGACGTTAACA
* *
43226 AAATTTTAT-GGAGAGGTTATCA
1 AAATTTTATAGG-GACGTTAACA
43248 AAATT
1 AAATT
43253 ACATATAGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (22 bp):
AAATTTTATAGGGACGTTAACA
Found at i:43323 original size:22 final size:22
Alignment explanation
Indices: 43298--43459 Score: 116
Period size: 22 Copynumber: 7.4 Consensus size: 22
43288 GACCAATTTT
* *
43298 AATTTTATAGTGTGATTATCAA
1 AATTTCATAGTGAGATTATCAA
*
43320 AATTTCATAGGGAGATTATCAA
1 AATTTCATAGTGAGATTATCAA
* * *
43342 AATTTCACACTGAGGTTATCAA
1 AATTTCATAGTGAGATTATCAA
* * *
43364 AATGTCATAGTGTGGTTATCAA
1 AATTTCATAGTGAGATTATCAA
*
43386 AATTTCAACAGTGTA-ATTAT--A
1 AATTTC-ATAGTG-AGATTATCAA
* * **
43407 ATTTTCATAGGGA-AGTTATTGA
1 AATTTCATAGTGAGA-TTATCAA
* *
43429 AATTTCATAATGAGGTTATCAA
1 AATTTCATAGTGAGATTATCAA
*
43451 ATTTTCATA
1 AATTTCATA
43460 CTTTGGTTAT
Statistics
Matches: 109, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 6 0.06
22 84 0.77
23 9 0.08
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
AATTTCATAGTGAGATTATCAA
Found at i:43361 original size:44 final size:43
Alignment explanation
Indices: 43313--43459 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 43
43303 TATAGTGTGA
43313 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCA-ACTGAGG
* * * *
43357 TTATCAAAATGTCATAGTGTGGTTATCAAAATTTCAAC--AGTG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCAACTGAG-G
* * * ** *
43399 TAATTATAATTTTCATAGGGA-AGTTATTGAAATTTCATAATGAGG
1 TTATCA-AAATTTCATAGGGAGA-TTATCAAAATTTCA-ACTGAGG
*
43444 TTATCAAATTTTCATA
1 TTATCAAAATTTCATA
43460 CTTTGGTTAT
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.02
42 5 0.06
43 24 0.30
44 43 0.53
45 5 0.06
46 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGGAGATTATCAAAATTTCAACTGAGG
Found at i:43478 original size:22 final size:21
Alignment explanation
Indices: 43442--43486 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
43432 TTCATAATGA
*
43442 GGTTATCAAATTTTCATACTTT
1 GGTTATCAAATTTTC-TACGTT
43464 GGTTATC-AATATTTCTACGTT
1 GGTTATCAAAT-TTTCTACGTT
43485 GG
1 GG
43487 AGCAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (21 bp):
GGTTATCAAATTTTCTACGTT
Found at i:46645 original size:16 final size:15
Alignment explanation
Indices: 46624--46656 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
46614 GAATTATGTG
46624 AACAATAAAATAAATA
1 AACAATAAAAT-AATA
46640 AACAATAAAATAATA
1 AACAATAAAATAATA
46655 AA
1 AA
46657 ATTAAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AACAATAAAATAATA
Found at i:46679 original size:21 final size:21
Alignment explanation
Indices: 46631--46679 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
46621 GTGAACAATA
46631 AAATAAA-TAAACAATAAAAT
1 AAATAAATTAAACAATAAAAT
* *
46651 -AATAAAATTAAGCAATAAGAT
1 AAAT-AAATTAAACAATAAAAT
46672 AAATAAAT
1 AAATAAAT
46680 AGTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
AAATAAATTAAACAATAAAAT
Found at i:47277 original size:21 final size:19
Alignment explanation
Indices: 47252--47294 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
47242 GATGAAGACC
47252 GAGAACAAGAAAAGTAGAAGA
1 GAGAACAAGAAAAG-AGAA-A
* *
47273 GAGAAGAATAAAAGAGAAA
1 GAGAACAAGAAAAGAGAAA
47292 GAG
1 GAG
47295 TGTGTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.63, C:0.02, G:0.30, T:0.05
Consensus pattern (19 bp):
GAGAACAAGAAAAGAGAAA
Done.