Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006974.1 Corchorus capsularis cultivar CVL-1 contig06995, 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: 17712
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1120 original size:24 final size:27
Alignment explanation
Indices: 1093--1145 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1083 TTCTAGTGAT
*
1093 GAGAAT-AAG-GAAGGAAAA-GAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
*
1117 GAGAATCGAGAGAAGGAAAATAAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
1144 GA
1 GA
1146 ATTTCATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 2 0.08
26 9 0.38
27 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.40, T:0.06
Consensus pattern (27 bp):
GAGAATCAAGAGAAGGAAAATAAGGAG
Found at i:2930 original size:19 final size:18
Alignment explanation
Indices: 2906--2941 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2896 TGAAGATTTC
2906 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
2925 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
2942 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:5878 original size:8 final size:8
Alignment explanation
Indices: 5865--5990 Score: 71
Period size: 8 Copynumber: 16.9 Consensus size: 8
5855 ATCGAAAATA
*
5865 AATTGAGG
1 AATTGAAG
5873 AATTGAAG
1 AATTGAAG
5881 AATTG-A-
1 AATTGAAG
*
5887 AAGTGAAG
1 AATTGAAG
*
5895 CATTGAAG
1 AATTGAAG
5903 AATTG-A-
1 AATTGAAG
5909 AATTGAA-
1 AATTGAAG
5916 ATATTGAA-
1 A-ATTGAAG
5924 AA-TG-A-
1 AATTGAAG
5929 AATTG--G
1 AATTGAAG
5935 AATTGAAG
1 AATTGAAG
* *
5943 CATTGTAG
1 AATTGAAG
5951 AATTG-A-
1 AATTGAAG
5957 AATTGAAG
1 AATTGAAG
*
5965 CATTTGAAG
1 -AATTGAAG
5974 AACATTGAAG
1 -A-ATTGAAG
5984 AATTGAA
1 AATTGAA
5991 ATTGTAGAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
5 3 0.03
6 23 0.24
7 8 0.08
8 46 0.48
9 9 0.09
10 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (8 bp):
AATTGAAG
Found at i:5912 original size:6 final size:6
Alignment explanation
Indices: 5903--5963 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
5893 AGCATTGAAG
* *
5903 AATTGA AATTGAA ATATTGA AAATGA AATTGG AATTGA AGCATTGTA GAATTGA
1 AATTGA AATTG-A A-ATTGA AATTGA AATTGA AATTGA A--ATTG-A -AATTGA
5957 AATTGA A
1 AATTGA A
5964 GCATTTGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 26 0.58
7 5 0.11
8 12 0.27
9 1 0.02
10 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (6 bp):
AATTGA
Found at i:5913 original size:14 final size:14
Alignment explanation
Indices: 5873--5999 Score: 68
Period size: 14 Copynumber: 8.7 Consensus size: 14
5863 TAAATTGAGG
5873 AATTGAAGAATTGA
1 AATTGAAGAATTGA
* *
5887 AAGTGAAGCATTGAA
1 AATTGAAGAATTG-A
5902 GAATTG-A-AATTGAA
1 -AATTGAAGAATTG-A
5916 ATATTGAA-AA-TGA
1 A-ATTGAAGAATTGA
5929 AATTG--GAATTGA
1 AATTGAAGAATTGA
*
5941 AGCATTGTAGAATTGA
1 A--ATTGAAGAATTGA
*
5957 AATTGAAGCATTTGAAGA
1 AATTGAAG-AATT---GA
5975 ACATTGAAGAATTGA
1 A-ATTGAAGAATTGA
*
5990 AATTGTAGAA
1 AATTGAAGAA
6000 AGACCACCCT
Statistics
Matches: 90, Mismatches: 8, Indels: 30
0.70 0.06 0.23
Matches are distributed among these distances:
11 2 0.02
12 8 0.09
13 3 0.03
14 41 0.46
15 11 0.12
16 12 0.13
18 6 0.07
19 7 0.08
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.28
Consensus pattern (14 bp):
AATTGAAGAATTGA
Found at i:5921 original size:22 final size:22
Alignment explanation
Indices: 5874--5959 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
5864 AAATTGAGGA
* **
5874 ATTGAAGAATTGAAAGTGAAGC
1 ATTGAAGAATTGAAATTGAAAT
5896 ATTGAAGAATTGAAATTGAAAT
1 ATTGAAGAATTGAAATTGAAAT
*
5918 ATTGAA-AA-TGAAATTG-GA-
1 ATTGAAGAATTGAAATTGAAAT
*
5936 ATTGAAGCATTGTAGAATTGAAAT
1 ATTGAAGAATTG-A-AATTGAAAT
5960 TGAAGCATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.12
19 2 0.04
20 10 0.19
21 3 0.06
22 30 0.58
23 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (22 bp):
ATTGAAGAATTGAAATTGAAAT
Found at i:5947 original size:26 final size:28
Alignment explanation
Indices: 5903--5963 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
5893 AGCATTGAAG
*
5903 AATTGAAATTGAAATATTG-A-AAATGA
1 AATTGAAATTGAAACATTGTAGAAATGA
* * *
5929 AATTGGAATTGAAGCATTGTAGAATTGA
1 AATTGAAATTGAAACATTGTAGAAATGA
5957 AATTGAA
1 AATTGAA
5964 GCATTTGAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 16 0.57
27 1 0.04
28 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (28 bp):
AATTGAAATTGAAACATTGTAGAAATGA
Found at i:6177 original size:22 final size:22
Alignment explanation
Indices: 6129--6699 Score: 169
Period size: 22 Copynumber: 25.8 Consensus size: 22
6119 AGGATTGAAT
* * * *
6129 TTGAAGAATAGCAATAGAAGCA
1 TTGAAGAATTGAAATTGAAACA
* *
6151 CTGAAGAATTGAAATTGAAACT
1 TTGAAGAATTGAAATTGAAACA
* * *
6173 TTGAAGGACTGAATTTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
6195 TTG-A-AATTGAAGCATTGAAA-A
1 TTGAAGAATTGAA--ATTGAAACA
*
6216 -TG-A-AATTGGAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
*
6235 TTGAAGAATTGCAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
* * *
6257 TCGAAGGATTGAATTTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
* *
6279 TTG-A-AATTGGAGCATTGAAAGA
1 TTGAAGAATT-GA-AATTGAAACA
*
6301 TTGAATTTGGAGAATTGAAATTGAAGCA
1 TTG-A-----AGAATTGAAATTGAAACA
* *
6329 TT-AAAACATCGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAACA
* *
6351 TTGAAGAATTGAATTTGGAGA-A
1 TTGAAGAATTGAAATT-GAAACA
*
6373 TTG-A-AATTGAAGCGTTG-AACTA
1 TTGAAGAATTGAA--ATTGAAAC-A
*
6395 TTG-A-AATTGAAGCATTTGAGGA-A
1 TTGAAGAATTGAA--A-TTGA-AACA
* *
6418 TT-AAAATATTGAAGTATTGAAATA
1 TTGAAGA-ATTGAA--ATTGAAACA
* * * *
6442 TTGAAGCATTGACATTTGGAA-T
1 TTGAAGAATTGA-AATTGAAACA
6464 TTGAAGAATTGAAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
* *
6486 TTGAA-ATATTGAAATCGAAGCA
1 TTGAAGA-ATTGAAATTGAAACA
*
6508 TTGAAGTATTGAAATTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
* *
6530 TTGAA-ATGTTGAAATAGAAACA
1 TTGAAGA-ATTGAAATTGAAACA
* * * * *
6552 TAGAAGGACTGAACTTGTAGA-A
1 TTGAAGAATTGAAATTG-AAACA
* *
6574 TT-AA-AATCGGAGCATTGAAACA
1 TTGAAGAAT-TGA-AATTGAAACA
*
6596 TTGAA-ATACTGAAATTGAAGA-A
1 TTGAAGA-ATTGAAATTGAA-ACA
* *
6618 TTGAA-ATATTGAAACTGAAGCA
1 TTGAAGA-ATTGAAATTGAAACA
* * *
6640 TTAAAGAACTGAAA--GAATCA
1 TTGAAGAATTGAAATTGAAACA
*
6660 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAACA
* *
6682 TTGAAGATTTGTAATTGA
1 TTGAAGAATTGAAATTGA
6700 GGCACTGAAT
Statistics
Matches: 411, Mismatches: 85, Indels: 106
0.68 0.14 0.18
Matches are distributed among these distances:
18 7 0.02
19 1 0.00
20 45 0.11
21 26 0.06
22 259 0.63
23 30 0.07
24 14 0.03
25 12 0.03
26 1 0.00
28 9 0.02
29 3 0.01
30 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.28
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAACA
Found at i:6329 original size:36 final size:36
Alignment explanation
Indices: 6091--6512 Score: 161
Period size: 36 Copynumber: 11.4 Consensus size: 36
6081 AAATTGAAGT
* * *
6091 ATTTGAATAATTGAAATTGGAA-CATCGAAGGATTGA
1 ATTTGAAGAATTGAAATT-GAAGCATTGAAAGATTGA
* * * *
6127 ATTTGAAGAATAGCAATAGAAGCACTG-AAGAATTGA
1 ATTTGAAGAATTGAAATTGAAGCATTGAAAG-ATTGA
* * * *
6163 AATTGAA-ACTTTGAAGGACTGAA--TTTG-AAGAATTGA
1 ATTTGAAGA-ATTGAA--ATTGAAGCATTGAAAG-ATTGA
* * * *
6199 AATTGAAGCATTGAAAATGAA--ATTG-GA-ATTGAA
1 ATTTGAAGAATTGAAATTGAAGCATTGAAAGATTG-A
* * * * *
6232 ACATTGAAGAATTGCAATTGAAACATCGAAGGATTGA
1 A-TTTGAAGAATTGAAATTGAAGCATTGAAAGATTGA
*
6269 ATTTGAAGAATTGAAATTGGAGCATTGAAAGATTGA
1 ATTTGAAGAATTGAAATTGAAGCATTGAAAGATTGA
* *
6305 ATTTGGAGAATTGAAATTGAAGCATTAAAACATCGAAATTGAA
1 ATTTGAAGAATTGAAATTGAAGCATT-GAA-A--G--ATTG-A
* * * *
6348 ACATTGAAGAATTGAATTTGGAGAATTG-AA-ATTGA
1 A-TTTGAAGAATTGAAATTGAAGCATTGAAAGATTGA
* ** * *
6383 AGCGTTGAACTATTGAAATTGAAGCATTTG-AGGAATTAAA
1 A--TTTGAAGAATTGAAATTGAAGCA-TTGAAAG-ATT-GA
* * *
6423 ATATTGAAGTATTGAAATATTGAAGCATTGACA-TTTGGA
1 AT-TTGAAGAATTG-AA-ATTGAAGCATTGAAAGATT-GA
* *
6462 ATTTGAAGAATTGAAATTGAAACATTGAAATATTGA
1 ATTTGAAGAATTGAAATTGAAGCATTGAAAGATTGA
* * *
6498 AATCGAAGCATTGAA
1 ATTTGAAGAATTGAA
6513 GTATTGAAAT
Statistics
Matches: 293, Mismatches: 63, Indels: 60
0.70 0.15 0.14
Matches are distributed among these distances:
32 4 0.01
33 2 0.01
34 26 0.09
35 8 0.03
36 159 0.54
37 12 0.04
38 19 0.06
39 18 0.06
40 8 0.03
41 10 0.03
42 5 0.02
43 2 0.01
44 20 0.07
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (36 bp):
ATTTGAAGAATTGAAATTGAAGCATTGAAAGATTGA
Found at i:6401 original size:58 final size:58
Alignment explanation
Indices: 6077--6534 Score: 269
Period size: 58 Copynumber: 7.7 Consensus size: 58
6067 GCGTTGCAAT
* * * * *
6077 ATTGAAATTGAAGTATTTGAA-TAATTGAAATTGGAACATCGAAGGATTGAATTTGAAGA
1 ATTGAAATTGAAGCA-TTGAACT-ATTGAAATTGAAACATTGAAGAATTGAATTTGGAGA
* * * * ** * * * *
6136 ATAGCAATAGAAGCACTGAAGAATTGAAATTGAAACTTTGAAGGACTGAATTTGAAGA
1 ATTGAAATTGAAGCATTGAACTATTGAAATTGAAACATTGAAGAATTGAATTTGGAGA
* * *
6194 ATTGAAATTGAAGCATTGAAAATGAAATTGGAATTGAAACATTGAAGAATTGCAA-TT-GAAA
1 ATTGAAATTGAAGCATTG-AACT---ATTGAAATTGAAACATTGAAGAATTG-AATTTGGAGA
* * ** * *
6255 CATCGAAGGATTGAA--TTTGAAGAATTGAAATTGGAGCATTGAA-AGATTGAATTTGGAGA
1 -ATTGAA--ATTGAAGCATTGAACTATTGAAATTGAAACATTGAAGA-ATTGAATTTGGAGA
* *
6314 ATTGAAATTGAAGCATTAAAAC-ATCGAAATTGAAACATTGAAGAATTGAATTTGGAGA
1 ATTGAAATTGAAGCATT-GAACTATTGAAATTGAAACATTGAAGAATTGAATTTGGAGA
* * * * * *
6372 ATTGAAATTGAAGCGTTGAACTATTGAAATTGAAGCATTTGAGGAATTAAAATATTGAAGT
1 ATTGAAATTGAAGCATTGAACTATTGAAATTGAAACA-TTGAAGAATT-GAAT-TTGGAGA
* * *
6433 ATTGAAATATTGAAGCATTG-AC-ATTTGGAATTTGAAGA-ATTG-A-AATTGAAACATT-GAAA
1 ATTG-AA-ATTGAAGCATTGAACTA-TT-GAAATTGAA-ACATTGAAGAATTG-AA-TTTGGAGA
* *
6492 TATTGAAATCGAAGCATTGAAGTATTGAAATTGAAGA-ATTGAA
1 -ATTGAAATTGAAGCATTGAACTATTGAAATTGAA-ACATTGAA
6535 ATGTTGAAAT
Statistics
Matches: 311, Mismatches: 57, Indels: 62
0.72 0.13 0.14
Matches are distributed among these distances:
56 6 0.02
57 6 0.02
58 165 0.53
59 35 0.11
60 16 0.05
61 14 0.05
62 41 0.13
63 22 0.07
64 6 0.02
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (58 bp):
ATTGAAATTGAAGCATTGAACTATTGAAATTGAAACATTGAAGAATTGAATTTGGAGA
Found at i:6481 original size:14 final size:14
Alignment explanation
Indices: 6464--6536 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
6454 CATTTGGAAT
6464 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
6478 TTGAA-ACATTGAAATA
1 TTGAAGA-ATTG-AA-A
*
6494 TTG-A-AATCGAAGCA
1 TTGAAGAATTGAA--A
*
6508 TTGAAGTATTGAAA
1 TTGAAGAATTGAAA
6522 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
6536 T
1 T
6537 GTTGAAATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
13 3 0.06
14 31 0.65
15 5 0.10
16 9 0.19
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:6708 original size:22 final size:22
Alignment explanation
Indices: 6605--6713 Score: 71
Period size: 22 Copynumber: 5.0 Consensus size: 22
6595 ATTGAAATAC
* *
6605 TGAAATTGAAGAATTGAA-ATAT
1 TGAAATTGAAGCACTGAAGA-AT
* * * *
6627 TGAAACTGAAGCATTAAAGAAC
1 TGAAATTGAAGCACTGAAGAAT
* *
6649 TGAAA--GAATCATTGAAGAAT
1 TGAAATTGAAGCACTGAAGAAT
* *
6669 TGAAATTGAAGCATTGAAGATT
1 TGAAATTGAAGCACTGAAGAAT
* * *
6691 TGTAATTGAGGCACTGAATAAT
1 TGAAATTGAAGCACTGAAGAAT
6713 T
1 T
6714 AAGGAACGGA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
20 17 0.24
22 52 0.74
23 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (22 bp):
TGAAATTGAAGCACTGAAGAAT
Found at i:6817 original size:58 final size:58
Alignment explanation
Indices: 6694--6824 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
6684 GAAGATTTGT
* * * *
6694 AATTGAGGCACTGAATAATTAAGGAACGGAAGAAAGACCACCATGTATCATTTAAGCA
1 AATTGAAGCATTGAATAATTAAGAAACGGAAGAAAGACCACCATGTATCATTGAAGCA
* * * **
6752 AACTGAAGCATTGAATAATTGAATAAAC-GAAGAAAGACCACCCTG-AGTCATTGAAGTG
1 AATTGAAGCATTGAATAATT-AAGAAACGGAAGAAAGACCACCATGTA-TCATTGAAGCA
*
6810 AATTGAAGAATTGAA
1 AATTGAAGCATTGAA
6825 GCATTGAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 1 0.02
58 54 0.90
59 5 0.08
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (58 bp):
AATTGAAGCATTGAATAATTAAGAAACGGAAGAAAGACCACCATGTATCATTGAAGCA
Found at i:6822 original size:8 final size:8
Alignment explanation
Indices: 6809--6997 Score: 117
Period size: 8 Copynumber: 24.4 Consensus size: 8
6799 TCATTGAAGT
6809 GAATTGAA
1 GAATTGAA
6817 GAATTGAA
1 GAATTGAA
*
6825 GCATTG-A
1 GAATTGAA
6832 GTAATTGAA
1 G-AATTGAA
6841 GAATTGAA
1 GAATTGAA
*
6849 GCAA-TAAA
1 G-AATTGAA
*
6857 TAATTGAA
1 GAATTGAA
6865 GAATTGAA
1 GAATTGAA
*
6873 GAAAT--A
1 GAATTGAA
6879 -AATTGAA
1 GAATTGAA
*
6886 GTATTGAA
1 GAATTGAA
6894 GAATTGAA
1 GAATTGAA
*
6902 TAATTGAA
1 GAATTGAA
* *
6910 TAATTAAA
1 GAATTGAA
* *
6918 GAGTCGAA
1 GAATTGAA
6926 G-A--GATA
1 GAATTGA-A
6932 -AATTGAA
1 GAATTGAA
* *
6939 AAACTGAA
1 GAATTGAA
*
6947 GTATTGAA
1 GAATTGAA
6955 GAATTGAA
1 GAATTGAA
* *
6963 TAATGGAA
1 GAATTGAA
*
6971 GATTTGAA
1 GAATTGAA
*
6979 GCATTGAA
1 GAATTGAA
* *
6987 TAGTTGAA
1 GAATTGAA
6995 GAA
1 GAA
6998 AGAGATTATT
Statistics
Matches: 135, Mismatches: 34, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
5 5 0.04
6 3 0.02
7 6 0.04
8 117 0.87
9 4 0.03
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.27
Consensus pattern (8 bp):
GAATTGAA
Found at i:6898 original size:53 final size:53
Alignment explanation
Indices: 6809--6979 Score: 166
Period size: 53 Copynumber: 3.2 Consensus size: 53
6799 TCATTGAAGT
* *
6809 GAATTGAAGAATTGAAGCATTG-AGTAATTGAAGAATTGAAGCAA-TAAATAATTGAA
1 GAATTGAAGAAAT-AA--ATTGAAGT-ATTGAAGAATTGAAG-AATTGAATAATTGAA
* *
6865 GAATTGAAGAAATAAATTGAAGTATTGAAGAATTGAATAATTGAATAATTAAA
1 GAATTGAAGAAATAAATTGAAGTATTGAAGAATTGAAGAATTGAATAATTGAA
* * * ** * * *
6918 GAGTCGAAGAGATAAATTGAAAAACTGAAGTATTGAAGAATTGAATAATGGAA
1 GAATTGAAGAAATAAATTGAAGTATTGAAGAATTGAAGAATTGAATAATTGAA
*
6971 GATTTGAAG
1 GAATTGAAG
6980 CATTGAATAG
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 78 0.80
54 3 0.03
55 2 0.02
56 12 0.12
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (53 bp):
GAATTGAAGAAATAAATTGAAGTATTGAAGAATTGAAGAATTGAATAATTGAA
Found at i:6904 original size:45 final size:45
Alignment explanation
Indices: 6834--6919 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
6824 AGCATTGAGT
*
6834 AATTGAAGAATTGAAGCAATAAATAATTGAAGAATTGAAGAAATA
1 AATTGAAGAATTGAAGCAATAAATAATTGAAGAATTAAAGAAATA
* * *
6879 AATTGAAGTATTGAAG-AATTGAATAATTGAATAATTAAAGA
1 AATTGAAGAATTGAAGCAA-TAAATAATTGAAGAATTAAAGA
6920 GTCGAAGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.53, C:0.01, G:0.17, T:0.28
Consensus pattern (45 bp):
AATTGAAGAATTGAAGCAATAAATAATTGAAGAATTAAAGAAATA
Found at i:6927 original size:61 final size:60
Alignment explanation
Indices: 6813--6971 Score: 146
Period size: 61 Copynumber: 2.6 Consensus size: 60
6803 TGAAGTGAAT
* * * * * *
6813 TGAAGAATTGAAGCATTG-AGTAATTGAAGAATTGAAGCAATAAATAATTGAAGA-ATTGAA
1 TGAAAAATTGAAGTATTGAAG-AATTGAATAATTGAAGCAATAAAGAATCGAAGAGA-TAAA
* *
6873 -GAAATAAATTGAAGTATTGAAGAATTGAATAATTGAA-TAATTAAAGAGTCGAAGAGATAAA
1 TG-AA-AAATTGAAGTATTGAAGAATTGAATAATTGAAGCAA-TAAAGAATCGAAGAGATAAA
* *
6934 TTGAAAAACTGAAGTATTGAAGAATTGAATAATGGAAG
1 -TGAAAAATTGAAGTATTGAAGAATTGAATAATTGAAG
6972 ATTTGAAGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
59 1 0.01
60 4 0.05
61 70 0.86
62 5 0.06
63 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (60 bp):
TGAAAAATTGAAGTATTGAAGAATTGAATAATTGAAGCAATAAAGAATCGAAGAGATAAA
Found at i:7965 original size:22 final size:22
Alignment explanation
Indices: 7937--7978 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
7927 CTAGAGCTTT
7937 TTCTTCT-TCTTTTTCTTTTTTC
1 TTCTTCTCTCTTTTT-TTTTTTC
7959 TTCTTCTCTCTTTTTTTTTT
1 TTCTTCTCTCTTTTTTTTTT
7979 GGCACTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTCTTCTCTCTTTTTTTTTTTC
Found at i:7974 original size:19 final size:19
Alignment explanation
Indices: 7934--7976 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
7924 ACCCTAGAGC
*
7934 TTTTTCTTCTTCTTTTTCT
1 TTTTTCTTCTTCTTCTTCT
7953 TTTTTCTTCTTCTCTCTT-T
1 TTTTTCTTCTTCT-TCTTCT
7972 TTTTT
1 TTTTT
7977 TTGGCACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTCTTCTTCTTCT
Found at i:8300 original size:16 final size:17
Alignment explanation
Indices: 8269--8313 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
8259 ATCTTATACC
*
8269 TTTCAACTTCTTTTTTCTT
1 TTTCAA-TT-TTTTTTCAT
8288 TTTC-ATTTTTTTTCAT
1 TTTCAATTTTTTTTCAT
8304 TTTCAATTTT
1 TTTCAATTTT
8314 CACTTTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.50
17 7 0.29
18 1 0.04
19 4 0.17
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCAATTTTTTTTCAT
Found at i:8756 original size:8 final size:8
Alignment explanation
Indices: 8743--8780 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
8733 CCAAGTGCTA
8743 TTTTTTCT
1 TTTTTTCT
8751 TTTTTTCT
1 TTTTTTCT
8759 TTTTTTCT
1 TTTTTTCT
8767 TTTTGTT-T
1 TTTT-TTCT
8775 TTTTTT
1 TTTTTT
8781 GTTGAATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 2 0.07
8 25 0.86
9 2 0.07
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:14763 original size:19 final size:19
Alignment explanation
Indices: 14707--14763 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
14697 CCAAATTCTT
* *
14707 AAGCCCAACAGAAAAT-TAA
1 AAGCCCAAAAGAAAGTCT-A
*
14726 AAGCCCAAAAGATAG-CTA
1 AAGCCCAAAAGAAAGTCTA
*
14744 AAGCCCAAGAGAAAGTCTA
1 AAGCCCAAAAGAAAGTCTA
14763 A
1 A
14764 GACCACAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (19 bp):
AAGCCCAAAAGAAAGTCTA
Found at i:17191 original size:33 final size:33
Alignment explanation
Indices: 17131--17260 Score: 154
Period size: 33 Copynumber: 3.9 Consensus size: 33
17121 AAGGATCATG
** * **
17131 TGGCCGGGCATGGCCGAGTCGTTTGGCCGGTTG-
1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGG-TGA
* **
17164 TGGCCGGGCATGTCCTTGTCGCGTGGCCGGTGA
1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA
*
17197 TGGTCGGGCATCTCCAAGTCGCGTGGCCGGTGA
1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA
*
17230 TGGTCGGGCATCTCCAAGTCGCGTGGCCGGT
1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGT
17261 CACAAGTGCT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 2 0.02
33 85 0.98
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA
Done.