Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012327.1 Corchorus capsularis cultivar CVL-1 contig12348, 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: 110853
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:3898 original size:45 final size:45
Alignment explanation
Indices: 3831--3922 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
3821 GTTATCTGTT
* *
3831 ATCCCCGGATTTCTGTATGCTCAGTATTTGGTTCTTCTTCTTCTG
1 ATCCCCAGATTTCTGTAAGCTCAGTATTTGGTTCTTCTTCTTCTG
3876 ATCCCCAGATTTCTGTAAGCTCAGTATTTGGTTCTTCTTCTTCTG
1 ATCCCCAGATTTCTGTAAGCTCAGTATTTGGTTCTTCTTCTTCTG
3921 AT
1 AT
3923 ATTTGTCTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (45 bp):
ATCCCCAGATTTCTGTAAGCTCAGTATTTGGTTCTTCTTCTTCTG
Found at i:4129 original size:2 final size:2
Alignment explanation
Indices: 4122--4154 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
4112 CATTGAGGTA
4122 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
4155 TATTTTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4309 original size:11 final size:11
Alignment explanation
Indices: 4293--4325 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
4283 TATAATATAT
4293 CTAATTAATAG
1 CTAATTAATAG
*
4304 CTAATTAATAT
1 CTAATTAATAG
4315 CTAATTAATAG
1 CTAATTAATAG
4326 TTATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:16172 original size:118 final size:119
Alignment explanation
Indices: 16026--16249 Score: 330
Period size: 119 Copynumber: 1.9 Consensus size: 119
16016 CTCTGGAGCT
* *
16026 AAAAAAAATTGCAAAGAGTGTTGCACCTTACAG-TTTAGTTGCATCT-TGGGAAATATTTCCTGA
1 AAAAAAAATTGCAAAGAGTGTTGCACCTTACAGTTTTAGTTGCATCTCAGAG-AATATTTCCTGA
*
16089 GTATTGCACTTTAAACTTGGGTCGCACCT-TAAGAAAATATTATCCTGCAAAAAA
65 GTATTGCACTTTAAACTTGGGTCGCACCTCAAAGAAAATATTATCCTGCAAAAAA
* *
16143 AAAATAAAATTGC-AAGAAGTGTTGCACCTTAGAGTTTTGGTTGCATCTCAGAGAATATTTCCTG
1 AAAA-AAAATTGCAAAG-AGTGTTGCACCTTACAGTTTTAGTTGCATCTCAGAGAATATTTCCTG
* *
16207 AGTGTTGCACTTTAAACTTGGGTTGCACCTCAAAGAAAATATT
64 AGTATTGCACTTTAAACTTGGGTCGCACCTCAAAGAAAATATT
16250 TTCTTCCATC
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
117 7 0.07
118 24 0.25
119 51 0.54
120 13 0.14
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (119 bp):
AAAAAAAATTGCAAAGAGTGTTGCACCTTACAGTTTTAGTTGCATCTCAGAGAATATTTCCTGAG
TATTGCACTTTAAACTTGGGTCGCACCTCAAAGAAAATATTATCCTGCAAAAAA
Found at i:16362 original size:38 final size:38
Alignment explanation
Indices: 16311--16386 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
16301 AAAAAACTGT
*
16311 CACCATGCTTGCTCTCAATGTGGAAGTGGAAGTGAAGA
1 CACCATGCTTGCTCTCAAGGTGGAAGTGGAAGTGAAGA
*
16349 CACCATGCTTGCTCTCAAGGTGGAAGTGGATGTGAAGA
1 CACCATGCTTGCTCTCAAGGTGGAAGTGGAAGTGAAGA
16387 TTGAGCTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (38 bp):
CACCATGCTTGCTCTCAAGGTGGAAGTGGAAGTGAAGA
Found at i:16500 original size:15 final size:15
Alignment explanation
Indices: 16480--16522 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
16470 CTTGTGGCGC
16480 TGGCGCTTCCAACAA
1 TGGCGCTTCCAACAA
*
16495 TGGCGCTTCCAACAG
1 TGGCGCTTCCAACAA
16510 TGGCGCTTCCAAC
1 TGGCGCTTCCAAC
16523 CTTCCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.21
Consensus pattern (15 bp):
TGGCGCTTCCAACAA
Found at i:18246 original size:3 final size:3
Alignment explanation
Indices: 18240--18264 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18230 GACGACGACG
18240 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
18265 AAACCTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:22105 original size:28 final size:29
Alignment explanation
Indices: 22074--22134 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
22064 ATGTGCAGAG
*
22074 TGCAAGCATACGTT-TTGCGGCTCTTACT
1 TGCAAGCATACGTTCTTGCAGCTCTTACT
22102 TGCAAGCATACGTTCTTGCAGCTCTTACT
1 TGCAAGCATACGTTCTTGCAGCTCTTACT
22131 TGCA
1 TGCA
22135 TTGGGGCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (29 bp):
TGCAAGCATACGTTCTTGCAGCTCTTACT
Found at i:27768 original size:22 final size:20
Alignment explanation
Indices: 27718--27769 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
27708 ATTATTATTC
27718 AATATATTA-TAATTATAAT
1 AATATATTATTAATTATAAT
** *
27737 TTTATCTTATTAATATTATAAT
1 AATATATTATT-A-ATTATAAT
27759 AATATATTATT
1 AATATATTATT
27770 TTTATTTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 1 0.04
22 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATATTATTAATTATAAT
Found at i:27996 original size:43 final size:43
Alignment explanation
Indices: 27944--28025 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
27934 TTTAGGGAAT
*
27944 CCTCAAATAGGTCCATTCTGTCAAAGTGATTTCCACTTTCTCG
1 CCTCAAATAGGTCCATTCTGTCAAACTGATTTCCACTTTCTCG
* *
27987 CCTCAAATAGGTCCATTTTGTCAAACTTATTTCCACTTT
1 CCTCAAATAGGTCCATTCTGTCAAACTGATTTCCACTTT
28026 TCACTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (43 bp):
CCTCAAATAGGTCCATTCTGTCAAACTGATTTCCACTTTCTCG
Found at i:37031 original size:12 final size:14
Alignment explanation
Indices: 37003--37034 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
36993 ACATAAATTT
37003 AATGTTATAACATA
1 AATGTTATAACATA
37017 AATGTTAT-A-ATA
1 AATGTTATAACATA
37029 AATGTT
1 AATGTT
37035 CTAGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Found at i:37804 original size:8 final size:8
Alignment explanation
Indices: 37793--37821 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
37783 GCGTCGGGCG
37793 TTTTTTTA
1 TTTTTTTA
37801 TTTTTTTA
1 TTTTTTTA
37809 TTTTTTTA
1 TTTTTTTA
37817 TTTTT
1 TTTTT
37822 GCTTTCTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:38107 original size:22 final size:22
Alignment explanation
Indices: 38082--38128 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
38072 ATTTATTCAT
38082 TATTAATTAACTATTAACTAGA
1 TATTAATTAACTATTAACTAGA
* *
38104 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAACTAGA
38126 TAT
1 TAT
38129 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAATTAACTATTAACTAGA
Found at i:38124 original size:11 final size:11
Alignment explanation
Indices: 38082--38124 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
38072 ATTTATTCAT
*
38082 TATTAATTAAC
1 TATTAATTAGC
* *
38093 TATTAACTAGA
1 TATTAATTAGC
38104 TATTAATTAGC
1 TATTAATTAGC
38115 TATTAATTAG
1 TATTAATTAG
38125 ATATAGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:39237 original size:155 final size:155
Alignment explanation
Indices: 39016--39580 Score: 613
Period size: 156 Copynumber: 3.6 Consensus size: 155
39006 TAGGTCATCT
* ** *
39016 TGGCCAAGTTTCATCTCAAACAGACTTA-AGATGAAAACCTTATGCAAGTTTTTCAGTTAAGGAC
1 TGGCCAAGTTTCAGCTC-ATTAGACTTAGA-ATGAAAAACTTATGCAAGTTTTTCAGTTAAGGAC
39080 AGTTTGGGGTGAGAAACC-ACTTCACCATGAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCAT
64 AGTTTGGGGTGAGAAACCAACTTCACCATGAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCAT
*
39144 AGTCTTATGGAGATAGTCTAAGTCTCG
129 AGTCTTATGGAGATAATCTAAGTCTCG
* * *
39171 TGGCCAAGTTTCAACTCAATTGGACTTAGCATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACA
1 TGGCCAAGTTTCAGCTC-ATTAGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACA
* * * * *
39236 GTTTGGGGTGTGAAACCAACTTCACTATGATA-GGGTGTTTGGTTTTACTTATAATTTTTTCCAT
65 GTTTGGGGTGAGAAACCAACTTCACCATGA-AGGGGAGTTCGGTTTTACTTAGAATTTTTTCCAT
* * *
39300 AGTTTTACGGAGATAATCTAAGCCTACTGG
129 AGTCTTATGGAGATAATCTAAG--T-CTCG
** * * *
39330 TGG--AA-AATCAGCTTCATTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
1 TGGCCAAGTTTCAGC-TCATTAGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACA
*** ** * * * *
39392 ACCTGGGAAGAGAAACCAAGTTCACCATCAAGGGGAGCTCGATTTTACTTAGAATTTTTTCCATA
65 GTTTGGGGTGAGAAACCAACTTCACCATGAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
* ** * *
39457 GTCTTGTGGAGGGAATCTAAGTCCCT
130 GTCTTATGGAGATAATCTAAGTCTCG
* * * *
39483 TGGCAAAGTTTCAGCTCATTCATACTTAGAATGAAAAACTTATGCTAA-TTTTTCATTTAAGAAC
1 TGGCCAAGTTTCAGCTCATT-AGACTTAGAATGAAAAACTTATGC-AAGTTTTTCAGTTAAGGAC
* * *
39547 AGTTTGGGGTGTGAAACCTAGTTCACCATGAAGG
64 AGTTTGGGGTGAGAAACCAACTTCACCATGAAGG
39581 AGGGCTCGAA
Statistics
Matches: 340, Mismatches: 57, Indels: 25
0.81 0.14 0.06
Matches are distributed among these distances:
153 4 0.01
154 1 0.00
155 82 0.24
156 240 0.71
157 6 0.02
158 1 0.00
159 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (155 bp):
TGGCCAAGTTTCAGCTCATTAGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAG
TTTGGGGTGAGAAACCAACTTCACCATGAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAG
TCTTATGGAGATAATCTAAGTCTCG
Found at i:43159 original size:21 final size:22
Alignment explanation
Indices: 43133--43177 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
43123 ATAATGGGTG
*
43133 TTGCTAAATACCGCCCCA-TTT
1 TTGCTAAACACCGCCCCACTTT
*
43154 TTGCTAAACATCGCCCCACTTT
1 TTGCTAAACACCGCCCCACTTT
43176 TT
1 TT
43178 ACACTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Found at i:43389 original size:33 final size:33
Alignment explanation
Indices: 43351--43427 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
43341 GCGCGTACCG
43351 CCCAGGAGGGCGGCATGCCAGGGCTAAC-GCCGC
1 CCCAGGAGGGCGGCATGCCAGGGCT-ACTGCCGC
* *
43384 CCCAGGAGGGCGGCATGCTATGGCTACTGCCGC
1 CCCAGGAGGGCGGCATGCCAGGGCTACTGCCGC
*
43417 CCCAGTAGGGC
1 CCCAGGAGGGC
43428 AGCACACACA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.05
33 38 0.95
ACGTcount: A:0.17, C:0.35, G:0.38, T:0.10
Consensus pattern (33 bp):
CCCAGGAGGGCGGCATGCCAGGGCTACTGCCGC
Found at i:43504 original size:33 final size:32
Alignment explanation
Indices: 43450--43651 Score: 219
Period size: 33 Copynumber: 6.1 Consensus size: 32
43440 CATCCTACTT
* *
43450 GGGCGGCATCAGCCATAGCATGCCGCCCTCCTG
1 GGGCGGC-TTAGCCATGGCATGCCGCCCTCCTG
* *
43483 GGGCGGTCTTATCCATGGCATGCCACCCTCCTG
1 GGGCGG-CTTAGCCATGGCATGCCGCCCTCCTG
* *
43516 GGGCGGCCCTT-GCCATGGCATGTCGTCCTCCTG
1 GGGCGG--CTTAGCCATGGCATGCCGCCCTCCTG
* *
43549 GGGCGGCACTAGCCATGGCATGCCGCCCACCTG
1 GGGCGGC-TTAGCCATGGCATGCCGCCCTCCTG
*
43582 GGGCGGCCCTT-GCCATGGCATGCCGTCCTCCTG
1 GGGCGG--CTTAGCCATGGCATGCCGCCCTCCTG
* *
43615 GGGCGGCACTAGCCATGGCATGCCGCCCTCCTA
1 GGGCGGC-TTAGCCATGGCATGCCGCCCTCCTG
43648 GGGC
1 GGGC
43652 AGCACATGCA
Statistics
Matches: 142, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.01
32 2 0.01
33 132 0.93
34 5 0.04
35 1 0.01
ACGTcount: A:0.11, C:0.38, G:0.32, T:0.18
Consensus pattern (32 bp):
GGGCGGCTTAGCCATGGCATGCCGCCCTCCTG
Found at i:43537 original size:66 final size:66
Alignment explanation
Indices: 43461--43651 Score: 294
Period size: 66 Copynumber: 2.9 Consensus size: 66
43451 GGCGGCATCA
* * * * *
43461 GCCATAGCATGCCGCCCTCCTGGGGCGGTC-TTATCCATGGCATGCCACCCTCCTGGGGCGGCCC
1 GCCATGGCATGCCGTCCTCCTGGGGCGG-CACTAGCCATGGCATGCCGCCCTCCTGGGGCGGCCC
43525 TT
65 TT
* *
43527 GCCATGGCATGTCGTCCTCCTGGGGCGGCACTAGCCATGGCATGCCGCCCACCTGGGGCGGCCCT
1 GCCATGGCATGCCGTCCTCCTGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTGGGGCGGCCCT
43592 T
66 T
*
43593 GCCATGGCATGCCGTCCTCCTGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTAGGGC
1 GCCATGGCATGCCGTCCTCCTGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTGGGGC
43652 AGCACATGCA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 1 0.01
66 113 0.99
ACGTcount: A:0.11, C:0.39, G:0.31, T:0.19
Consensus pattern (66 bp):
GCCATGGCATGCCGTCCTCCTGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTGGGGCGGCCCT
T
Found at i:43575 original size:99 final size:100
Alignment explanation
Indices: 43450--43656 Score: 276
Period size: 99 Copynumber: 2.1 Consensus size: 100
43440 CATCCTACTT
* * *
43450 GGGCGGCA-TCAGCCATAGCATGCCGCCCTCCTGGGGCGG-TCTTATCCATGGCATGCCACCCTC
1 GGGCGGCACTCAGCCATAGCATGCCGCCCACCTGGGGCGGCCCTT-GCCATGGCATGCCACCCTC
* * * * *
43513 CTGGGGCGGCCCTTGCCATGGCATGTCGTCCTCCTG
65 CTGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTA
* **
43549 GGGCGGCACT-AGCCATGGCATGCCGCCCACCTGGGGCGGCCCTTGCCATGGCATGCCGTCCTCC
1 GGGCGGCACTCAGCCATAGCATGCCGCCCACCTGGGGCGGCCCTTGCCATGGCATGCCACCCTCC
43613 TGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTA
66 TGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTA
*
43648 GGGCAGCAC
1 GGGCGGCAC
43657 ATGCATTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 90 0.96
100 4 0.04
ACGTcount: A:0.12, C:0.38, G:0.32, T:0.18
Consensus pattern (100 bp):
GGGCGGCACTCAGCCATAGCATGCCGCCCACCTGGGGCGGCCCTTGCCATGGCATGCCACCCTCC
TGGGGCGGCACTAGCCATGGCATGCCGCCCTCCTA
Found at i:46196 original size:27 final size:27
Alignment explanation
Indices: 46152--46286 Score: 182
Period size: 27 Copynumber: 5.0 Consensus size: 27
46142 ATAATCCTCG
*
46152 GCCCCATCATAATAACCCGGCTGAGCA
1 GCCCCATCATAGTAACCCGGCTGAGCA
* *
46179 GCCCCATCATAGTGACCCGGCTGAACA
1 GCCCCATCATAGTAACCCGGCTGAGCA
* * *
46206 GCCACATCATAGTAACCCAGCTGAGCT
1 GCCCCATCATAGTAACCCGGCTGAGCA
*
46233 GCCCCATCATAGTAACCGGGCTGAGC-
1 GCCCCATCATAGTAACCCGGCTGAGCA
*
46259 TCCCTCATCATAGTAACCCGGCTGAGCA
1 GCCC-CATCATAGTAACCCGGCTGAGCA
46287 CACTCGAACT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 3 0.03
27 90 0.97
ACGTcount: A:0.27, C:0.36, G:0.21, T:0.17
Consensus pattern (27 bp):
GCCCCATCATAGTAACCCGGCTGAGCA
Found at i:49895 original size:32 final size:33
Alignment explanation
Indices: 49853--49953 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 33
49843 ACTTGTCAAG
49853 TCGAGCTCGAGTAGTTCAATACTCGATTCGAGC
1 TCGAGCTCGAGTAGTTCAATACTCGATTCGAGC
* *
49886 -CGAGCTCGAGCTCGATAATCAAAACTCGA-TCGAGC
1 TCGAGCTCGAG-TAG-T--TCAATACTCGATTCGAGC
* * *
49921 TCGAGCTCAAGTAGCTCACTACTCGATCTCGAG
1 TCGAGCTCGAGTAGTTCAATACTCGAT-TCGAG
49954 TAGCTCACTA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
32 19 0.35
33 2 0.04
34 6 0.11
35 8 0.15
36 19 0.35
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (33 bp):
TCGAGCTCGAGTAGTTCAATACTCGATTCGAGC
Found at i:49926 original size:36 final size:38
Alignment explanation
Indices: 49853--49928 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
49843 ACTTGTCAAG
* *
49853 TCGAGCTCGAGTAGTTCAATACTCGATTCGAGCCGAGC
1 TCGAGCTCGAGTAGATCAAAACTCGATTCGAGCCGAGC
49891 TCGAGCTCGA-TA-ATCAAAACTCGA-TCGAGCTCGAGC
1 TCGAGCTCGAGTAGATCAAAACTCGATTCGAGC-CGAGC
49927 TC
1 TC
49929 AAGTAGCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.17
36 17 0.49
37 2 0.06
38 10 0.29
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (38 bp):
TCGAGCTCGAGTAGATCAAAACTCGATTCGAGCCGAGC
Found at i:49955 original size:22 final size:22
Alignment explanation
Indices: 49920--49965 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
49910 CTCGATCGAG
49920 CTCGAGCTCAAGTAGCTCACTA
1 CTCGAGCTCAAGTAGCTCACTA
* *
49942 CTCGATCTCGAGTAGCTCACTA
1 CTCGAGCTCAAGTAGCTCACTA
49964 CT
1 CT
49966 TGACTCGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (22 bp):
CTCGAGCTCAAGTAGCTCACTA
Found at i:55194 original size:29 final size:29
Alignment explanation
Indices: 55116--55215 Score: 143
Period size: 29 Copynumber: 3.5 Consensus size: 29
55106 ATACCATCAT
*
55116 ATGATAATATTTTTTTCTG--ATCAAATC
1 ATGATAATATTTTTTTCTGACATGAAATC
*
55143 ATGATAATAATTTTTTTTTGACATGAAATC
1 ATGATAAT-ATTTTTTTCTGACATGAAATC
*
55173 ATGAGAATATTTTTTTCTGACATGAAATC
1 ATGATAATATTTTTTTCTGACATGAAATC
55202 ATGATAAT-TTTTTT
1 ATGATAATATTTTTT
55216 AAATCATGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
27 8 0.12
28 16 0.25
29 27 0.42
30 14 0.22
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (29 bp):
ATGATAATATTTTTTTCTGACATGAAATC
Found at i:55235 original size:17 final size:18
Alignment explanation
Indices: 55197--55237 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
55187 TTCTGACATG
*
55197 AAATCATGATAATTTTTTT
1 AAATCATGATAA-TTATTT
55216 AAATCATGATAA-TATTT
1 AAATCATGATAATTATTT
55233 AAATC
1 AAATC
55238 TTAAAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
AAATCATGATAATTATTT
Found at i:58522 original size:27 final size:27
Alignment explanation
Indices: 58492--58545 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
58482 ATAGTAATTG
58492 TTATGAGAAGATTAAACACTTGAAAAT
1 TTATGAGAAGATTAAACACTTGAAAAT
58519 TTATGAGAAGATTAAACACTTGAAAAT
1 TTATGAGAAGATTAAACACTTGAAAAT
58546 GGAAAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (27 bp):
TTATGAGAAGATTAAACACTTGAAAAT
Found at i:64892 original size:28 final size:28
Alignment explanation
Indices: 64841--64894 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
64831 GCCACGTGGC
**
64841 AAGTTTAGGGGCAAAATGTCCAAAATTA
1 AAGTTTAGGGGCAAAACATCCAAAATTA
64869 AAGTTTAGGGGGCAAAACAT-CAAAAT
1 AAGTTTA-GGGGCAAAACATCCAAAAT
64895 CATACAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (28 bp):
AAGTTTAGGGGCAAAACATCCAAAATTA
Found at i:84387 original size:2 final size:2
Alignment explanation
Indices: 84380--84413 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
84370 AATATAAAGA
84380 AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
84414 TTGGATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:87129 original size:15 final size:15
Alignment explanation
Indices: 87111--87163 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
87101 ATTTTCTCTT
87111 AATTAATTTCTTCCA
1 AATTAATTTCTTCCA
87126 AATT--TTCTCTT---
1 AATTAATT-TCTTCCA
87137 AATTAATTTCTTCCA
1 AATTAATTTCTTCCA
*
87152 ATTTAATTTCTT
1 AATTAATTTCTT
87164 AATGAGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
11 4 0.13
12 4 0.13
13 4 0.13
14 4 0.13
15 15 0.48
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTAATTTCTTCCA
Found at i:87130 original size:26 final size:26
Alignment explanation
Indices: 87101--87152 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
87091 CTATGTAGAC
87101 ATTTTCTCTTAATTAATTTCTTCCAA
1 ATTTTCTCTTAATTAATTTCTTCCAA
87127 ATTTTCTCTTAATTAATTTCTTCCAA
1 ATTTTCTCTTAATTAATTTCTTCCAA
87153 TTTAATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTCTCTTAATTAATTTCTTCCAA
Found at i:98873 original size:23 final size:23
Alignment explanation
Indices: 98843--98900 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
98833 TCTCAAAAAC
98843 GTTTAGGCTCAATTTGGTTCACA
1 GTTTAGGCTCAATTTGGTTCACA
*
98866 GTTTAGGCTCAATTTGGTTCATA
1 GTTTAGGCTCAATTTGGTTCACA
*
98889 GTTTAGACTCAA
1 GTTTAGGCTCAA
98901 ATTGAGCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (23 bp):
GTTTAGGCTCAATTTGGTTCACA
Found at i:99037 original size:22 final size:22
Alignment explanation
Indices: 99020--99077 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
99010 TATAAATGTG
99020 ACTCGA-TTTAATTTTAAATTA
1 ACTCGAGTTTAATTTTAAATTA
*
99041 AGTCGATGTTTAATTTTAAATTA
1 ACTCGA-GTTTAATTTTAAATTA
*
99064 AGTCGATGTTTAAT
1 ACTCGA-GTTTAAT
99078 GTAATACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 5 0.15
23 29 0.85
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (22 bp):
ACTCGAGTTTAATTTTAAATTA
Found at i:99053 original size:23 final size:23
Alignment explanation
Indices: 99026--99077 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
99016 TGTGACTCGA
99026 TTTAATTTTAAATTAAGTCGATG
1 TTTAATTTTAAATTAAGTCGATG
99049 TTTAATTTTAAATTAAGTCGATG
1 TTTAATTTTAAATTAAGTCGATG
99072 TTTAAT
1 TTTAAT
99078 GTAATACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (23 bp):
TTTAATTTTAAATTAAGTCGATG
Found at i:101627 original size:6 final size:6
Alignment explanation
Indices: 101616--101645 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
101606 TTGTTTTCGC
101616 TTCTAG TTCTAG TTCTAG TTCTAG TTCTAG
1 TTCTAG TTCTAG TTCTAG TTCTAG TTCTAG
101646 GTAAGGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TTCTAG
Found at i:107914 original size:30 final size:30
Alignment explanation
Indices: 107878--107937 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
107868 AGGGCAAGAT
*
107878 GTGCATTGTGCACCTTTGGACTCCTAAGGC
1 GTGCATTGTGCACCTTTGGACTACTAAGGC
*
107908 GTGCATTGTGCACCTTTTGACTACTAAGGC
1 GTGCATTGTGCACCTTTGGACTACTAAGGC
107938 AAGTGCTGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (30 bp):
GTGCATTGTGCACCTTTGGACTACTAAGGC
Done.