Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008009.1 Corchorus capsularis cultivar CVL-1 contig08030, 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: 55751
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:747 original size:13 final size:13
Alignment explanation
Indices: 729--753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
719 TTCAATGTTC
729 TAAATATTATTTA
1 TAAATATTATTTA
742 TAAATATTATTT
1 TAAATATTATTT
754 TTGGAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:1337 original size:20 final size:22
Alignment explanation
Indices: 1290--1337 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1280 ATGGTTAAAA
*
1290 TTATAACAATATGGATTTTATT
1 TTATAACAATATGAATTTTATT
**
1312 GAATAA-AATAT-AATTTTATT
1 TTATAACAATATGAATTTTATT
1332 TTATAA
1 TTATAA
1338 TATTCTTAGG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.57
21 5 0.24
22 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
TTATAACAATATGAATTTTATT
Found at i:5645 original size:19 final size:18
Alignment explanation
Indices: 5612--5648 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5602 ATAGTTTTTC
*
5612 TTTGCATTTTTGCATTAT
1 TTTGCATTATTGCATTAT
5630 TTTGCATTCATTGCATTAT
1 TTTGCATT-ATTGCATTAT
5649 CAGGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTGCATTATTGCATTAT
Found at i:5875 original size:13 final size:13
Alignment explanation
Indices: 5857--5881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5847 AAAGGCTGTT
5857 TAACACACCTCTG
1 TAACACACCTCTG
5870 TAACACACCTCT
1 TAACACACCTCT
5882 TGAGATCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.40, G:0.04, T:0.24
Consensus pattern (13 bp):
TAACACACCTCTG
Found at i:6598 original size:20 final size:20
Alignment explanation
Indices: 6573--6610 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6563 TACGGAATTA
6573 ACCCGTTGAAAACCGGTGTG
1 ACCCGTTGAAAACCGGTGTG
*
6593 ACCCGTTGAAACCCGGTG
1 ACCCGTTGAAAACCGGTG
6611 ACCCGGCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (20 bp):
ACCCGTTGAAAACCGGTGTG
Found at i:6613 original size:18 final size:20
Alignment explanation
Indices: 6573--6615 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
6563 TACGGAATTA
*
6573 ACCCGTTGAAAACCGGTGTG
1 ACCCGTTGAAAACCCGTGTG
6593 ACCCGTTG-AAACCCG-GTG
1 ACCCGTTGAAAACCCGTGTG
6611 ACCCG
1 ACCCG
6616 GCCGGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (20 bp):
ACCCGTTGAAAACCCGTGTG
Found at i:10493 original size:4 final size:4
Alignment explanation
Indices: 10484--10513 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
10474 TAAATAGGAT
10484 AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
10514 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:11694 original size:106 final size:105
Alignment explanation
Indices: 11510--11716 Score: 405
Period size: 106 Copynumber: 2.0 Consensus size: 105
11500 GAAGAGAAGA
11510 TATCCATGAAGTACTTAAGATACCACAAGCCTTAAACATCATCTATCTTAACAGTAGCAGTTAAT
1 TATCCATGAAGTACTTAAGATACCACAAGCCTTAAACATCATCTATCTTAACAGTAGCAGTTAAT
11575 CTCGTTCAAAATATTCAATCTATTGAGAGCATTTATCATC
66 CTCGTTCAAAATATTCAATCTATTGAGAGCATTTATCATC
11615 TATCCATGAAGTACTTAAAGATACCACAAGCCTTAAACATCATCTATCTTAACAGTAGCAGTTAA
1 TATCCATGAAGTACTT-AAGATACCACAAGCCTTAAACATCATCTATCTTAACAGTAGCAGTTAA
11680 TCTCGTTCAAAATATTCAATCTATTGAGAGCATTTAT
65 TCTCGTTCAAAATATTCAATCTATTGAGAGCATTTAT
11717 GATGGGATGG
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
105 16 0.16
106 85 0.84
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (105 bp):
TATCCATGAAGTACTTAAGATACCACAAGCCTTAAACATCATCTATCTTAACAGTAGCAGTTAAT
CTCGTTCAAAATATTCAATCTATTGAGAGCATTTATCATC
Found at i:19462 original size:19 final size:19
Alignment explanation
Indices: 19451--19487 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19441 AATTTTTAAG
19451 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
19470 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
19488 ACAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:23728 original size:9 final size:9
Alignment explanation
Indices: 23714--23774 Score: 70
Period size: 9 Copynumber: 6.8 Consensus size: 9
23704 CACAACCCCC
23714 GCCACCACA
1 GCCACCACA
*
23723 GCCACCACC
1 GCCACCACA
23732 GCCACCACA
1 GCCACCACA
*
23741 GCAACCACCA
1 GCCACCA-CA
23751 -CCACCACA
1 GCCACCACA
* *
23759 GCCACCGCC
1 GCCACCACA
23768 GCCACCA
1 GCCACCA
23775 ACAACGCCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 2 0.05
9 39 0.91
10 2 0.05
ACGTcount: A:0.30, C:0.59, G:0.11, T:0.00
Consensus pattern (9 bp):
GCCACCACA
Found at i:23735 original size:18 final size:18
Alignment explanation
Indices: 23712--23774 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
23702 TCCACAACCC
23712 CCGCCACCACAGCCACCA
1 CCGCCACCACAGCCACCA
*
23730 CCGCCACCACAGCAACCA
1 CCGCCACCACAGCCACCA
* *
23748 CCACCACCACAGCCACCG
1 CCGCCACCACAGCCACCA
23766 CCGCCACCA
1 CCGCCACCA
23775 ACAACGCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.29, C:0.60, G:0.11, T:0.00
Consensus pattern (18 bp):
CCGCCACCACAGCCACCA
Found at i:23755 original size:36 final size:36
Alignment explanation
Indices: 23706--23774 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
23696 CCCTCCTCCA
* *
23706 CAACCCCCGCCACCACAGCCACCACCGCCACCACAG
1 CAACCACCACCACCACAGCCACCACCGCCACCACAG
*
23742 CAACCACCACCACCACAGCCACCGCCGCCACCA
1 CAACCACCACCACCACAGCCACCACCGCCACCA
23775 ACAACGCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.61, G:0.10, T:0.00
Consensus pattern (36 bp):
CAACCACCACCACCACAGCCACCACCGCCACCACAG
Found at i:25043 original size:22 final size:22
Alignment explanation
Indices: 25014--25096 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
25004 AAAATATTCA
*
25014 TATGAAATTATGATAACATCTC
1 TATGAAATTATGATAACAACTC
* * * *
25036 TATTAAATTTTGGTAACCAC-C
1 TATGAAATTATGATAACAACTC
*
25057 TCATGAAATTATAATAAACAACT-
1 T-ATGAAATTATGAT-AACAACTC
*
25080 TATGAAATTTTGATAAC
1 TATGAAATTATGATAAC
25097 CACATAGAGA
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
21 5 0.11
22 35 0.76
23 6 0.13
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (22 bp):
TATGAAATTATGATAACAACTC
Found at i:25064 original size:44 final size:44
Alignment explanation
Indices: 25015--25099 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
25005 AAATATTCAT
* * * *
25015 ATGAAATTATGAT-AACATCTCTATTAAATTTTGGTAACCACCTC
1 ATGAAATTATAATAAACAACT-TATGAAATTTTGATAACCACCTC
25059 ATGAAATTATAATAAACAACTTATGAAATTTTGATAACCAC
1 ATGAAATTATAATAAACAACTTATGAAATTTTGATAACCAC
25100 ATAGAGACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 30 0.83
45 6 0.17
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (44 bp):
ATGAAATTATAATAAACAACTTATGAAATTTTGATAACCACCTC
Found at i:25294 original size:19 final size:20
Alignment explanation
Indices: 25263--25300 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25253 TATTGACATT
25263 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
25282 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
25301 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:25971 original size:30 final size:31
Alignment explanation
Indices: 25937--26000 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
25927 GGCAATTTAG
* * *
25937 AAATATGTTTTTAAAA-AAGGGTATAATTGA
1 AAATATGTTTTAAAAATAAGGGTACAATCGA
25967 AAATATGTTTTAAAAATAAGGGTACAATCGA
1 AAATATGTTTTAAAAATAAGGGTACAATCGA
25998 AAA
1 AAA
26001 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (31 bp):
AAATATGTTTTAAAAATAAGGGTACAATCGA
Found at i:36544 original size:13 final size:13
Alignment explanation
Indices: 36526--36550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36516 ACTTCGTCAT
36526 ATATATGAAGATC
1 ATATATGAAGATC
36539 ATATATGAAGAT
1 ATATATGAAGAT
36551 GATCTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
ATATATGAAGATC
Found at i:37651 original size:12 final size:12
Alignment explanation
Indices: 37634--37670 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
37624 CCATATAATA
37634 ATTTCTAGAATG
1 ATTTCTAGAATG
*
37646 ATTTCTAGAATA
1 ATTTCTAGAATG
37658 ATTTCTAGAATG
1 ATTTCTAGAATG
37670 A
1 A
37671 AAATCTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (12 bp):
ATTTCTAGAATG
Found at i:39285 original size:2 final size:2
Alignment explanation
Indices: 39247--39277 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39237 TTGATGAACA
39247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39278 GTTATATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41283 original size:27 final size:26
Alignment explanation
Indices: 41210--41284 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
41200 GCATTAGGGT
*
41210 CACA-TAAGGGCATTTTGGTCATTTT
1 CACACTAAGGGCATTTTGGTCATTTG
*
41235 CACACTAAGGGCATTCTGGTCATTTG
1 CACACTAAGGGCATTTTGGTCATTTG
* * *
41261 CACATTCAGGGGCATTTTTGTCAT
1 CACACT-AAGGGCATTTTGGTCAT
41285 CTTAAGTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.10
26 24 0.57
27 14 0.33
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (26 bp):
CACACTAAGGGCATTTTGGTCATTTG
Found at i:42328 original size:26 final size:26
Alignment explanation
Indices: 42292--42344 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42282 ACATCTTTGC
42292 ACTGTAAGAGTAATCAAAAATACAAA
1 ACTGTAAGAGTAATCAAAAATACAAA
42318 ACTGTAAGAGTAATCAAAAATACAAA
1 ACTGTAAGAGTAATCAAAAATACAAA
42344 A
1 A
42345 AACAGAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (26 bp):
ACTGTAAGAGTAATCAAAAATACAAA
Found at i:43649 original size:3 final size:3
Alignment explanation
Indices: 43643--43680 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
43633 GCTGATCGAG
43643 GAA GAA GAA GAA GAA GAA GAA GATA GAA G-A GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA
43681 AAAATTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:45177 original size:15 final size:15
Alignment explanation
Indices: 45142--45177 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45132 AAAAAGAAGA
*
45142 AGAAAAGGAAAAATG
1 AGAAAAGGAAAAATC
*
45157 AAAAAAGGAAAAATC
1 AGAAAAGGAAAAATC
45172 AGAAAA
1 AGAAAA
45178 TTAAAAGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (15 bp):
AGAAAAGGAAAAATC
Found at i:47945 original size:10 final size:10
Alignment explanation
Indices: 47930--47958 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
47920 CCATATTAAC
47930 AATTTTATTT
1 AATTTTATTT
47940 AATTTTA-TT
1 AATTTTATTT
47949 AATTTTATTT
1 AATTTTATTT
47959 CCTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Found at i:47964 original size:19 final size:18
Alignment explanation
Indices: 47930--47969 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
47920 CCATATTAAC
47930 AATTTTATTTAATTTTATT
1 AATTTTATTTAATTTT-TT
**
47949 AATTTTATTTCCTTTTTT
1 AATTTTATTTAATTTTTT
47967 AAT
1 AAT
47970 ATTTCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTTATTTAATTTTTT
Found at i:49227 original size:28 final size:28
Alignment explanation
Indices: 49196--49254 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
49186 TTTTGAAGAA
* *
49196 TGAACCGTGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
* *
49224 TGAACCATGAGATGCTGATTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
49252 TGA
1 TGA
49255 TTTTTGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAATTT
Found at i:49368 original size:42 final size:43
Alignment explanation
Indices: 49266--49374 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 43
49256 TTTTGAATAA
* * * * * *
49266 TGAAATTCAAATTTTGAACTTTAATTTTTGAAGAATAGAATGC
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
49309 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAAT-GAAC-C
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
*
49350 GTGAAATGCAGGTTTTGAATTTTGA
1 -TGAAATGCAAGTTTTGAATTTTGA
49375 ACCATGAGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 26 0.45
43 31 0.53
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (43 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
Found at i:49400 original size:148 final size:149
Alignment explanation
Indices: 49169--49442 Score: 505
Period size: 148 Copynumber: 1.8 Consensus size: 149
49159 TTCGGTGTCT
49169 AAGTTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGA
1 AAGTTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGA
*
49234 GATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATTCAAATTTTGAACTTT-AATTTTTGAA
66 GATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTGAATTTTTGAA
49298 GAATAGAATGCTGAAATGC
131 GAATAGAATGCTGAAATGC
49317 AAGTTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGA
1 AAGTTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGA
* **
49382 GTTGCTGATTTTTTATTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTGAATTTT
66 GATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTGAATTTT
49443 GAATTTTGAA
Statistics
Matches: 121, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
148 115 0.95
149 6 0.05
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (149 bp):
AAGTTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATGCAGGTTTTGAATTTTGAACCATGA
GATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTGAATTTTTGAA
GAATAGAATGCTGAAATGC
Found at i:49436 original size:7 final size:7
Alignment explanation
Indices: 49423--49459 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
49413 ATGAAATGCA
49423 AATTTTG
1 AATTTTG
*
49430 AACTTTG
1 AATTTTG
49437 AATTTTG
1 AATTTTG
49444 AATTTTG
1 AATTTTG
49451 AATTTTG
1 AATTTTG
49458 AA
1 AA
49460 GACTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (7 bp):
AATTTTG
Found at i:49629 original size:37 final size:37
Alignment explanation
Indices: 49587--50060 Score: 489
Period size: 37 Copynumber: 12.8 Consensus size: 37
49577 GTTTTCGAAC
* * *
49587 ACCTAAACAGGGATCATAAACAAGATTTTGATGAGAT
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
* *
49624 ACCTAAACAAGGA-CTTTAAATAAGGA-TTTGATAAGAA
1 ACCTAAACAGGGATC-TTAAACAA-GATTTTGATAAGAA
* * * * * *
49661 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGACAC
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
** * *
49698 ACCTAAACAGATACCTTAAATAAGGATTTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAA-GATTTTGATAAGAA
* * * * *
49736 ACCTAAACATGAATCTTGAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
* *
49773 ACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAGAA
1 ACCTAAACAGGGATCTTAAACAA-GATTTTGATAAGAA
* * *
49810 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
*
49847 A-C-AAACAGGGA-CTTTAAACAAGGA-TTTCATAAGAA
1 ACCTAAACAGGGATC-TTAAACAA-GATTTTGATAAGAA
* * *
49882 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
* *
49919 ACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAGAA
1 ACCTAAACAGGGATCTTAAACAA-GATTTTGATAAGAA
* * *
49956 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
*
49993 ACCTAAACAGGGACCTTAAACAAAGA-TTTGATAAGAA
1 ACCTAAACAGGGATCTTAAAC-AAGATTTTGATAAGAA
*
50030 ACCTAAACAGGAATCTTAAACAAGATTTTGA
1 ACCTAAACAGGGATCTTAAACAAGATTTTGA
50061 CAGGGACCTT
Statistics
Matches: 354, Mismatches: 66, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.00
35 25 0.07
36 16 0.05
37 273 0.77
38 39 0.11
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (37 bp):
ACCTAAACAGGGATCTTAAACAAGATTTTGATAAGAA
Found at i:49930 original size:146 final size:148
Alignment explanation
Indices: 49587--50060 Score: 754
Period size: 146 Copynumber: 3.2 Consensus size: 148
49577 GTTTTCGAAC
* * * * * *
49587 ACCTAAACAGGGATCATAAACAAGATTTTGATGAGATACCTAAACAAGGACTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
* * * * * **
49652 TGATAAGAAACCTAAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAGATACCTTAA
66 TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
*
49717 ATAAGGATTTTGATAAGAA
131 ACAAGGA-TTTGATAAGAA
* *
49736 ACCTAAACATGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
49801 TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACA-C-AAACAGGGACTTTAA
66 TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
*
49864 ACAAGGATTTCATAAGAA
131 ACAAGGATTTGATAAGAA
49882 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
49947 TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
66 TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
*
50012 ACAAAGATTTGATAAGAA
131 ACAAGGATTTGATAAGAA
50030 ACCTAAACAGGAATCTTAAACAAGATTTTGA
1 ACCTAAACAGGAATCTTAAACAAGATTTTGA
50061 CAGGGACCTT
Statistics
Matches: 300, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
146 120 0.40
147 19 0.06
148 62 0.21
149 99 0.33
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (148 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
TAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
ACAAGGATTTGATAAGAA
Found at i:50063 original size:24 final size:25
Alignment explanation
Indices: 50036--50082 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
50026 AGAAACCTAA
*
50036 ACAGGAATCTTAAACAA-GATTTTG
1 ACAGGAACCTTAAACAAGGATTTTG
*
50060 ACAGGGACCTTAAACAAGGATTT
1 ACAGGAACCTTAAACAAGGATTT
50083 GACGAGACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (25 bp):
ACAGGAACCTTAAACAAGGATTTTG
Found at i:50075 original size:74 final size:74
Alignment explanation
Indices: 49587--50060 Score: 745
Period size: 74 Copynumber: 6.4 Consensus size: 74
49577 GTTTTCGAAC
* * * * * *
49587 ACCTAAACAGGGATCATAAACAAGATTTTGATGAGATACCTAAACAAGGACTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
49652 TGATAAGAA
66 TGATAAGAA
* * * * ** *
49661 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAGATACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-T
49726 TTGATAAGAA
65 TTGATAAGAA
* *
49736 ACCTAAACATGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
49801 TAATAAGAA
66 TGATAAGAA
*
49810 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACA-C-AAACAGGGACTTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
49873 TCATAAGAA
66 TGATAAGAA
49882 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
49947 TAATAAGAA
66 TGATAAGAA
*
49956 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAAGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
50021 TGATAAGAA
66 TGATAAGAA
50030 ACCTAAACAGGAATCTTAAACAAGATTTTGA
1 ACCTAAACAGGAATCTTAAACAAGATTTTGA
50061 CAGGGACCTT
Statistics
Matches: 371, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
72 69 0.19
73 2 0.01
74 233 0.63
75 67 0.18
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
TGATAAGAA
Found at i:50984 original size:87 final size:87
Alignment explanation
Indices: 50833--51000 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
50823 TGATTGATGC
* * * *
50833 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGTTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
50898 CTTCTCACCTCAAGAATTATTT
66 CTTCTCACCTCAAGAATTATTT
* *
50920 CCCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGTATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
* * *
50985 TTTCTCATCTTAAGAA
66 CTTCTCACCTCAAGAA
51001 ACTTTCAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
CTTCTCACCTCAAGAATTATTT
Found at i:51842 original size:15 final size:14
Alignment explanation
Indices: 51824--51861 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
51814 TGAAAATTCA
51824 TTTTTGAAAGTCATT
1 TTTTTGAAAG-CATT
51839 TTTTTGAAAGCATT
1 TTTTTGAAAGCATT
*
51853 TTCTTGAAA
1 TTTTTGAAA
51862 ATCTTTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTTTGAAAGCATT
Found at i:51962 original size:18 final size:18
Alignment explanation
Indices: 51930--51964 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51920 TGTCACAATT
**
51930 CTTTTTTTTTCTTTTTTC
1 CTTTTTTTTGATTTTTTC
51948 CTTTTTTTTGATTTTTT
1 CTTTTTTTTGATTTTTT
51965 TTTTTGGCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (18 bp):
CTTTTTTTTGATTTTTTC
Found at i:55563 original size:10 final size:10
Alignment explanation
Indices: 55548--55576 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
55538 CCATATTAAC
55548 AATTTTATTT
1 AATTTTATTT
55558 AATTTTA-TT
1 AATTTTATTT
55567 AATTTTATTT
1 AATTTTATTT
55577 CCTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Found at i:55582 original size:19 final size:18
Alignment explanation
Indices: 55548--55587 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
55538 CCATATTAAC
55548 AATTTTATTTAATTTTATT
1 AATTTTATTTAATTTT-TT
**
55567 AATTTTATTTCCTTTTTT
1 AATTTTATTTAATTTTTT
55585 AAT
1 AAT
55588 ATTTCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTTATTTAATTTTTT
Found at i:55655 original size:85 final size:86
Alignment explanation
Indices: 55552--55717 Score: 223
Period size: 86 Copynumber: 1.9 Consensus size: 86
55542 ATTAACAATT
* * * * *
55552 TTATTTAATTTTATTAATTTTATTTCCTTT-TT-TAATAT-TTCTAAATCTCCCACAATTTGGCA
1 TTATTCAATTTTATTAA-TTTATTT-ATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCA
55614 AGATTTAGAAAATATTCTCATTA
64 AGATTTAGAAAATATTCTCATTA
*
55637 TTATTCAATCTTTA-TAATTTATTTATTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGCAA
1 TTATTCAAT-TTTATTAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAA
55701 GATTTAGAAAATATTCT
65 GATTTAGAAAATATTCT
55718 ATTTTCAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
83 3 0.04
84 9 0.13
85 16 0.23
86 43 0.61
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (86 bp):
TTATTCAATTTTATTAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAG
ATTTAGAAAATATTCTCATTA
Done.