Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013469.1 Corchorus olitorius cultivar O-4 contig13502, 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: 62681
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:298 original size:18 final size:19
Alignment explanation
Indices: 257--298 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
247 CGCCCTTCCA
257 TGATTTTAGATGTTGTTGGGT
1 TGATTTTAGATGTTGTT--GT
278 TGATTTTAGATGTTGTT-T
1 TGATTTTAGATGTTGTTGT
296 TGA
1 TGA
299 ATGATTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
21 17 0.81
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.55
Consensus pattern (19 bp):
TGATTTTAGATGTTGTTGT
Found at i:3858 original size:21 final size:21
Alignment explanation
Indices: 3833--3888 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3823 CACCATACAT
*
3833 GATTTGGTGTTTGACCATTAA
1 GATTTGGGGTTTGACCATTAA
* *
3854 GATTTGGGGTTTAACCATTAC
1 GATTTGGGGTTTGACCATTAA
*
3875 GCTTTGGGGTTTGA
1 GATTTGGGGTTTGA
3889 TCCCATTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (21 bp):
GATTTGGGGTTTGACCATTAA
Found at i:3892 original size:108 final size:109
Alignment explanation
Indices: 3767--3974 Score: 355
Period size: 109 Copynumber: 1.9 Consensus size: 109
3757 ATTTAGTTTT
3767 GCTTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGC-TTTAAATTTCACCATAC
1 GCTTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTTAAATTTCACCATAC
*
3831 ATGATTTGGTGTTTGACCATTAAGATTTGGGGTTTAACCATTAC
66 ATGATTTGGGGTTTGACCATTAAGATTTGGGGTTTAACCATTAC
* * *
3875 GCTTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTTAAATTTCACTATAG
1 GCTTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTTAAATTTCACCATAC
* *
3940 ATGATTTGGGGTTTGACTATTACGATTTGGGGTTT
66 ATGATTTGGGGTTTGACCATTAAGATTTGGGGTTT
3975 GATCCTATTA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 46 0.49
109 47 0.51
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (109 bp):
GCTTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTTAAATTTCACCATAC
ATGATTTGGGGTTTGACCATTAAGATTTGGGGTTTAACCATTAC
Found at i:3967 original size:21 final size:22
Alignment explanation
Indices: 3942--3985 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3932 CACTATAGAT
3942 GATTTGGGGTTTGA-CTATTAC
1 GATTTGGGGTTTGACCTATTAC
3963 GATTTGGGGTTTGATCCTATTAC
1 GATTTGGGGTTTGA-CCTATTAC
3986 TAGTAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.18, C:0.11, G:0.27, T:0.43
Consensus pattern (22 bp):
GATTTGGGGTTTGACCTATTAC
Found at i:4286 original size:100 final size:99
Alignment explanation
Indices: 4117--4369 Score: 380
Period size: 100 Copynumber: 2.5 Consensus size: 99
4107 CCAAAGTTTG
* * * * *
4117 ATAGTCAAACCCCAATGTTTGATAGTCAACCCCCAAATTTTGATAGTCAACCCCCAAAATTTGAT
1 ATAGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGAT
4182 AGTCAAACCACAAAAAACATTTCACTATACAGAC
66 AGTCAAACCACAAAAAACATTTCACTATACAGAC
* * *
4216 ATAGTCAAACCCCAAAGTTTAATAGTCAAACCTCCAAAGTTTAATATTCAAACCCCAAAGTTTGA
1 ATAGTCAAACCCCAAAGTTTAATAGTCAAACC-CCAAAGTTTGATAGTCAAACCCCAAAATTTGA
* *
4281 TAGTCAAATCACAAAAAACATTTCACTATACAGGC
65 TAGTCAAACCACAAAAAACATTTCACTATACAGAC
* *
4316 ATAGTCAAACCCCCAAAATTTAATAGTTAAACCCCAAAGTTTGATAGTCAAACC
1 ATAGTCAAA-CCCCAAAGTTTAATAGTCAAACCCCAAAGTTTGATAGTCAAACC
4370 ACGTTAAACC
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
99 29 0.21
100 88 0.64
101 21 0.15
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (99 bp):
ATAGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGAT
AGTCAAACCACAAAAAACATTTCACTATACAGAC
Found at i:4295 original size:21 final size:21
Alignment explanation
Indices: 4055--4288 Score: 169
Period size: 21 Copynumber: 11.3 Consensus size: 21
4045 TACAGGCATG
*
4055 GTCAAACCCTCAAATTTTAATA
1 GTCAAACCC-CAAAGTTTAATA
*
4077 GTCAAACACCCAAAATTTAATA
1 GTCAAAC-CCCAAAGTTTAATA
* *
4099 GTTAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTAATA
* *
4120 GTCAAACCCCAATGTTTGATA
1 GTCAAACCCCAAAGTTTAATA
* * *
4141 GTCAACCCCCAAATTTTGATA
1 GTCAAACCCCAAAGTTTAATA
* * *
4162 GTCAACCCCCAAAATTTGATA
1 GTCAAACCCCAAAGTTTAATA
* * *
4183 GTCAAACCACAAA---AAACA
1 GTCAAACCCCAAAGTTTAATA
* *** *
4201 TTTC--ACTATACAG---ACATA
1 -GTCAAACCCCAAAGTTTA-ATA
4219 GTCAAACCCCAAAGTTTAATA
1 GTCAAACCCCAAAGTTTAATA
4240 GTCAAACCTCCAAAGTTTAATA
1 GTCAAACC-CCAAAGTTTAATA
* *
4262 TTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTAATA
4283 GTCAAA
1 GTCAAA
4289 TCACAAAAAA
Statistics
Matches: 174, Mismatches: 28, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
17 8 0.05
18 4 0.02
19 7 0.04
21 108 0.62
22 45 0.26
23 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTAATA
Found at i:4347 original size:22 final size:22
Alignment explanation
Indices: 4316--4369 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
4306 CTATACAGGC
4316 ATAGTCAAACCCCCAAAATTTA
1 ATAGTCAAACCCCCAAAATTTA
* * *
4338 ATAGTTAAA-CCCCAAAGTTTG
1 ATAGTCAAACCCCCAAAATTTA
4359 ATAGTCAAACC
1 ATAGTCAAACC
4370 ACGTTAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (22 bp):
ATAGTCAAACCCCCAAAATTTA
Found at i:4749 original size:22 final size:21
Alignment explanation
Indices: 4694--4762 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
4684 AAAATGCATG
**
4694 GTCAAACCCCAAAAGATGATA
1 GTCAAACCCCAAAATTTGATA
4715 GTCAAACCCCAAAATTTGATA
1 GTCAAACCCCAAAATTTGATA
*
4736 GTCAAACCCCCAAAGTTTGATA
1 GTCAAA-CCCCAAAATTTGATA
4758 GTCAA
1 GTCAA
4763 TCCCAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 25 0.57
22 19 0.43
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.20
Consensus pattern (21 bp):
GTCAAACCCCAAAATTTGATA
Found at i:7186 original size:3 final size:3
Alignment explanation
Indices: 7178--7228 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
7168 TACTTATAGA
7178 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7226 TAT
1 TAT
7229 ACTATAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:7753 original size:21 final size:22
Alignment explanation
Indices: 7729--7777 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
7719 CATTTAGAGT
* *
7729 CATTTTCT-AATTCACTTTTGG
1 CATTTACTAAATTCAATTTTGG
*
7750 CATTTAGTAAATTCAATTTTGG
1 CATTTACTAAATTCAATTTTGG
7772 CATTTA
1 CATTTA
7778 GCATAGCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (22 bp):
CATTTACTAAATTCAATTTTGG
Found at i:7763 original size:22 final size:22
Alignment explanation
Indices: 7737--7778 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7727 GTCATTTTCT
*
7737 AATTCACTTTTGGCATTTAGTA
1 AATTCAATTTTGGCATTTAGTA
7759 AATTCAATTTTGGCATTTAG
1 AATTCAATTTTGGCATTTAG
7779 CATAGCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (22 bp):
AATTCAATTTTGGCATTTAGTA
Found at i:7871 original size:61 final size:61
Alignment explanation
Indices: 7803--7925 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
7793 GATTGCATTC
7803 GAAATGCAAGAGCCCAACAATTTTTTTATTTCACTTCTTTTGCATAGTCTATATACAACTA
1 GAAATGCAAGAGCCCAACAATTTTTTTATTTCACTTCTTTTGCATAGTCTATATACAACTA
7864 GAAATGCAAGAGCCCAACAATTTTTTTATTTCACTTCTTTTGCATAGTCTATATACAACTA
1 GAAATGCAAGAGCCCAACAATTTTTTTATTTCACTTCTTTTGCATAGTCTATATACAACTA
7925 G
1 G
7926 TCATCTTGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (61 bp):
GAAATGCAAGAGCCCAACAATTTTTTTATTTCACTTCTTTTGCATAGTCTATATACAACTA
Found at i:9336 original size:17 final size:17
Alignment explanation
Indices: 9314--9347 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9304 ACAATGCAGC
9314 AATGATTCAATTTCAGT
1 AATGATTCAATTTCAGT
9331 AATGATTCAATTTCAGT
1 AATGATTCAATTTCAGT
9348 CTCAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
AATGATTCAATTTCAGT
Found at i:9630 original size:18 final size:18
Alignment explanation
Indices: 9593--9645 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
9583 AAACAAAAGG
* *
9593 GGACAAA-AATGAGCCAA
1 GGACAAACAAAGAGACAA
*
9610 GGACAAACAGAGAGACAA
1 GGACAAACAAAGAGACAA
9628 GGACAAACAAAGAGACAA
1 GGACAAACAAAGAGACAA
9646 AGAGCTTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.57, C:0.17, G:0.25, T:0.02
Consensus pattern (18 bp):
GGACAAACAAAGAGACAA
Found at i:11811 original size:67 final size:66
Alignment explanation
Indices: 11738--12105 Score: 365
Period size: 67 Copynumber: 5.5 Consensus size: 66
11728 TTCTTTTTTC
*
11738 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAATTTAGTATTTTCAAA
1 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTCAAATTTAGTATTTTC--A
11802 TTT
64 TTT
11805 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTCAACA--TAGTATTTTCA
1 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCA-TTCAA-ATTTAGTATTTTCA
*
11867 TTC
64 TTT
* * *
11870 CCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTT-GTCTTTTTGCATTCAAGTTTAGTTTTTTTT
1 CC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTTGCATTCAAATTTAG--TATTTT
*
11934 CGTTT
62 CATTT
* * * * *
11939 CCAGAAATACCCTTTCGGTCAAAGGGTCGGTCTT-GTCTTTTTGCATTCAAGTTTAGTATTTTCG
1 CCA-AAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTCTTTTTGCATTCAAATTTAGTATTTTCA
12003 TTT
64 TTT
* * * * **
12006 CCAGAGATACTCTTTCGGTTGAAGGGTCAATTTCGTCTTTTTGCATTCAGTTTTAGT-TTTACTC
1 CCA-AAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTCAAATTTAGTATTT--TC
*
12070 -TTA
63 ATTT
** * *
12073 AAAAAATACCCTTCCGGTCGAAGGGTCAGTTTC
1 CCAAAATACCCTTTCGGTCGAAGGGTCATTTTC
12106 ACCAGGTTGT
Statistics
Matches: 260, Mismatches: 27, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
65 5 0.02
66 63 0.24
67 125 0.48
68 7 0.03
69 60 0.23
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (66 bp):
CCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTCAAATTTAGTATTTTCATT
T
Found at i:12031 original size:136 final size:133
Alignment explanation
Indices: 11735--12065 Score: 375
Period size: 136 Copynumber: 2.5 Consensus size: 133
11725 TAGTTCTTTT
* * *
11735 TTCCC-AAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAATTTAGTATTTT
1 TTCCCAAAAATACCCTTTCGGTCGAAGGGTCATTTT-GTCTTTTTGCATTCAAGTTTAGTTTTTT
* *
11798 CAAATTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTCAACATAGTATT
65 CAAATTTCCAAAATACCCTTTCGGTCAAAGGGTCATCTTCGTCTTTTGCATTTCAACATAGTATT
11863 TTCA
130 TTCA
*
11867 TTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTTTTTT
1 TTCCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTTGTCTTTTTGCATTCAAGTTTAGTTTTTT
**** * **
11932 TTCGTTTCCAGAAATACCCTTTCGGTCAAAGGGTCGGTCTT-GTCTTTTTGCA-TTCAAGTTTAG
65 CAAATTTCCA-AAATACCCTTTCGGTCAAAGGGTC-ATCTTCGTC-TTTTGCATTTCAA-CATAG
*
11995 TATTTTCG
126 TATTTTCA
* * * * * *
12003 TTTCCAGAGATACTCTTTCGGTTGAAGGGTCAATTTCGTCTTTTTGCATTC-AGTTTTAGTTTT
1 TTCCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTGTCTTTTTGCATTCAAG-TTTAGTTTT
12066 ACTCTTAAAA
Statistics
Matches: 169, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
132 5 0.03
133 28 0.17
134 31 0.18
135 33 0.20
136 71 0.42
137 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (133 bp):
TTCCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTGTCTTTTTGCATTCAAGTTTAGTTTTTTC
AAATTTCCAAAATACCCTTTCGGTCAAAGGGTCATCTTCGTCTTTTGCATTTCAACATAGTATTT
TCA
Found at i:12099 original size:202 final size:201
Alignment explanation
Indices: 11741--12104 Score: 461
Period size: 202 Copynumber: 1.8 Consensus size: 201
11731 TTTTTTCCCA
* * *
11741 AAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAATTTAGTATTTTCAAATTTC
1 AAATACCCTTTCGGTCAAAGGGTCATCTTCGTCTTTTGCATTCAAATTTAGTATTTTC-AATTTC
* *
11806 CAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTCAACATAGTATTTTCATTCC
65 CAAAATACCCTTTCGGTCGAAGGGTCAATTTCGTCTTTTGCATTTCAACATAGTATTTTCATTCA
* *
11871 CAAAAATACCCTTTCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTTTTTTTTCG
130 AAAAAATACCCTTCCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTTTTTTTTCG
11936 TTTCCAG
195 TTTCCAG
* * *
11943 AAATACCCTTTCGGTCAAAGGGTCGGTCTT-GTCTTTTTGCATTCAAGTTTAGTATTTTC-GTTT
1 AAATACCCTTTCGGTCAAAGGGTC-ATCTTCGTC-TTTTGCATTCAAATTTAGTATTTTCAATTT
* * * ***
12006 CCAGAGATACTCTTTCGGTTGAAGGGTCAATTTCGTCTTTTTGCA-TTCAGTTTTAGT-TTTACT
64 CCA-AAATACCCTTTCGGTCGAAGGGTCAATTTCGTC-TTTTGCATTTCA-ACATAGTATTT--T
*
12069 C-TT-AAAAAAATACCCTTCCGGTCGAAGGGTCAGTTT
124 CATTCAAAAAAATACCCTTCCGGTCAAAGGGTCAGTTT
12105 CACCAGGTTG
Statistics
Matches: 138, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
201 6 0.04
202 91 0.66
203 39 0.28
204 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (201 bp):
AAATACCCTTTCGGTCAAAGGGTCATCTTCGTCTTTTGCATTCAAATTTAGTATTTTCAATTTCC
AAAATACCCTTTCGGTCGAAGGGTCAATTTCGTCTTTTGCATTTCAACATAGTATTTTCATTCAA
AAAAATACCCTTCCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTTTTTTTTCGT
TTCCAG
Found at i:12246 original size:66 final size:65
Alignment explanation
Indices: 12136--12297 Score: 159
Period size: 66 Copynumber: 2.5 Consensus size: 65
12126 TCTAGTCTTT
* * * *
12136 CTTTCCAAAGAATACCCTTTCGATCAAAGGGTCAATTCTGTCA-TTCTTACACTTGAGTTTACTT
1 CTTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAATTCTATCATTTC-CACACTTCAGTTTA-TT
*
12200 TTGA
63 CT-A
* ** * *
12204 -TTTCCAAAAATACCCTTTCGGTGAAAGGGTCTGTT-TCATCATTTCCGCATTTCAGTTTATTCT
1 CTTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCT-ATCATTTCCACACTTCAGTTTATTCT
12267 A
65 A
*
12268 CTTTCCAAAAATGCCCTTTCGGTCAAAGGG
1 CTTTCCAAAAATACCCTTTCGGTCAAAGGG
12298 AGAACTTTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
64 1 0.01
65 31 0.39
66 36 0.46
67 11 0.14
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (65 bp):
CTTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCTATCATTTCCACACTTCAGTTTATTCTA
Found at i:14990 original size:383 final size:389
Alignment explanation
Indices: 14249--15035 Score: 1239
Period size: 383 Copynumber: 2.0 Consensus size: 389
14239 TTCGAATCCC
*
14249 ATGGACAACGAAAATGTTTTTTCCAAAAATTTTTCCCATTAAAATCATATCAATCCGGTCTAATT
1 ATGGACAACGAAAATGCTTTTTCCAAAAATTTTTCCCATTAAAATCATATCAATCCGGTC-AA--
* * *
14314 CGGTCCCGATCCGGGTCAACCGTCAGTCAAATCGATTGTTAACCGAGTCTTGACCGGACCAAACT
63 ------C-ATCCGGGTCAACCGCCAGTCAAACCGATTGTTAACCGAGTCTTGACCGGACCAAACC
* *
14379 CCTCCCGATTAACCCCATCTCCGGACCGGATAGGCTTCCGCGTCCCGATTGAACCGGTCCGACTA
121 CCTCCCGATTAACCCCATCTCCGGACCGGATAGGCTTCCGCGTCCCAATTGAACCGATCCGACTA
*
14444 GTCGATCCGATCCGATCCGGGTTTGAAAACACTAGTGCAAACAGGGATGTAAAGGTTTTGGAAGA
186 G-CGA-CCAATCCGATCCGGGTTTGAAAACACTAGTGCAAACAGGGATGTAAAGGTTTTGGAAGA
* *
14509 ATTATTAAGACTAAAATAATGACTTCATTTAATTTTTGCAGTGGAACCTAGAAAAGTCAAATAAT
249 ATTATTAAGACTAAAATAATGACTTCATTTAATTTTTACAATGGAACCTAGAAAAGTCAAATAAT
14574 CAAATTCATTATACCTATAGTAATTTTGATCTATCTGATTTCATGAAAAGAG-AAAAAAAATTGT
314 CAAATTCATTATACCTATAGTAATTTTGATCTATCTGATTTCATGAAAAGAGAAAAAAAAATTGT
14638 CTCAAATATTG
379 CTCAAATATTG
14649 ATGGACAACGAAAATGCTTTTTCC-AAAATTTTTCCTCATTAAAATCATATCAATCCGGTC-A-A
1 ATGGACAACGAAAATGCTTTTTCCAAAAATTTTTCC-CATTAAAATCATATCAATCCGGTCAACA
* * *
14711 TCCGGGTCAACTGCCAGTCAAACCGGTTGTTGACCGAGTCTTGACCGGACCAAACCCCTCCCGAT
65 TCCGGGTCAACCGCCAGTCAAACCGATTGTTAACCGAGTCTTGACCGGACCAAACCCCTCCCGAT
*
14776 TAACCCCATCTCCGGACCGGATAGGTTTCCAG-GTCCCAATTGAACCGATCCGACT-G-G-CCAA
130 TAACCCCATCTCCGGACCGGATAGGCTTCC-GCGTCCCAATTGAACCGATCCGACTAGCGACCAA
* * *
14837 TCCGATCCGGGTTTGAAAACACTGGTGCAAATAGGGATGTAATGGTTTTGGAAGAATTATTAAGA
194 TCCGATCCGGGTTTGAAAACACTAGTGCAAACAGGGATGTAAAGGTTTTGGAAGAATTATTAAGA
14902 CTAAAATAATGACTTCATTTAATTTTTACAATGGAACCTAGAAAAGTCAAATAATCAAATTCATT
259 CTAAAATAATGACTTCATTTAATTTTTACAATGGAACCTAGAAAAGTCAAATAATCAAATTCATT
*
14967 ATACCTATAGTAATTTTGATCTATCTGATTTCATGAAAAGAGAAAAAAAAATTGTCTTAAATATT
324 ATACCTATAGTAATTTTGATCTATCTGATTTCATGAAAAGAGAAAAAAAAATTGTCTCAAATATT
15032 G
389 G
15033 ATG
1 ATG
15036 TGCATTTTGC
Statistics
Matches: 367, Mismatches: 17, Indels: 22
0.90 0.04 0.05
Matches are distributed among these distances:
383 170 0.46
384 25 0.07
385 1 0.00
387 1 0.00
388 110 0.30
389 1 0.00
398 1 0.00
399 11 0.03
400 47 0.13
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (389 bp):
ATGGACAACGAAAATGCTTTTTCCAAAAATTTTTCCCATTAAAATCATATCAATCCGGTCAACAT
CCGGGTCAACCGCCAGTCAAACCGATTGTTAACCGAGTCTTGACCGGACCAAACCCCTCCCGATT
AACCCCATCTCCGGACCGGATAGGCTTCCGCGTCCCAATTGAACCGATCCGACTAGCGACCAATC
CGATCCGGGTTTGAAAACACTAGTGCAAACAGGGATGTAAAGGTTTTGGAAGAATTATTAAGACT
AAAATAATGACTTCATTTAATTTTTACAATGGAACCTAGAAAAGTCAAATAATCAAATTCATTAT
ACCTATAGTAATTTTGATCTATCTGATTTCATGAAAAGAGAAAAAAAAATTGTCTCAAATATTG
Found at i:15249 original size:41 final size:42
Alignment explanation
Indices: 15194--15279 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 42
15184 CCAACAAATC
*
15194 ATCTAACAAACCCTTTTTCTTACTTGATGCCAAAAAAA-AAA
1 ATCTAACAAACCCTTTTTCTCACTTGATGCCAAAAAAAGAAA
*
15235 ATCTAACAAACCCTTTTTCTCACTTGGTGCCAAAAAAAGAAA
1 ATCTAACAAACCCTTTTTCTCACTTGATGCCAAAAAAAGAAA
15277 ATC
1 ATC
15280 ATCTAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 36 0.86
42 6 0.14
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (42 bp):
ATCTAACAAACCCTTTTTCTCACTTGATGCCAAAAAAAGAAA
Found at i:15580 original size:34 final size:35
Alignment explanation
Indices: 15520--15593 Score: 132
Period size: 34 Copynumber: 2.1 Consensus size: 35
15510 AGTTCGTTTA
*
15520 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTAGTTTATTGTTCATTTAAG
15555 TGTTCACGAAC-GGCTAGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTAGTTTATTGTTCATTTAAG
15589 TGTTC
1 TGTTC
15594 GTTTATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (35 bp):
TGTTCACGAACAGGCTAGTTTATTGTTCATTTAAG
Found at i:15656 original size:16 final size:16
Alignment explanation
Indices: 15635--15666 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15625 TATGATTATT
15635 TATATATTAATAATAA
1 TATATATTAATAATAA
*
15651 TATATATTATTAATAA
1 TATATATTAATAATAA
15667 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:15742 original size:15 final size:14
Alignment explanation
Indices: 15715--15756 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
15705 ACTTAAAATT
15715 TAATTAT-TATATA
1 TAATTATATATATA
15728 TAATATATATATATA
1 TAAT-TATATATATA
15743 TAATTATATA-ATA
1 TAATTATATATATA
15756 T
1 T
15757 TTTGTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 9 0.33
15 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:18694 original size:36 final size:36
Alignment explanation
Indices: 18647--18720 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
18637 GTTCTCTGAT
*
18647 TTAGTGTGGGAGTGAGTGAATCTAAGACACATTTTA
1 TTAGTGTGGGAGTGAGTGAATCCAAGACACATTTTA
18683 TTAGTGTGGGAGTGAGTGAATCCAAGACACATTTTA
1 TTAGTGTGGGAGTGAGTGAATCCAAGACACATTTTA
18719 TT
1 TT
18721 CACGATATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (36 bp):
TTAGTGTGGGAGTGAGTGAATCCAAGACACATTTTA
Found at i:31005 original size:21 final size:21
Alignment explanation
Indices: 30967--31007 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30957 AAGCTAATAG
*
30967 CTTTCTTTGTTTTTACAGTAA
1 CTTTCTTTGTTTTCACAGTAA
30988 CTTTCTTT-TTCTTCACAGTA
1 CTTTCTTTGTT-TTCACAGTA
31008 TTGTTGTTTT
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:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (21 bp):
CTTTCTTTGTTTTCACAGTAA
Found at i:31216 original size:2 final size:2
Alignment explanation
Indices: 31211--31247 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
31201 ATATATATAA
*
31211 AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
31248 TCCTATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:31441 original size:12 final size:12
Alignment explanation
Indices: 31424--31462 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31414 CCAAAATATA
*
31424 TAAATTTAAATT
1 TAAATTTAATTT
*
31436 TAAATTTATTTT
1 TAAATTTAATTT
*
31448 TAATTTTAATTT
1 TAAATTTAATTT
31460 TAA
1 TAA
31463 TTAGAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTAATTT
Found at i:33166 original size:2 final size:2
Alignment explanation
Indices: 33159--33193 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
33149 TAACTATAAT
*
33159 TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
33194 AAAGTACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33419 original size:93 final size:93
Alignment explanation
Indices: 33314--33492 Score: 295
Period size: 93 Copynumber: 1.9 Consensus size: 93
33304 AAATTTTTAC
* *
33314 AGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTAT
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCCTTATAACTATTTTAT
* *
33379 TTTTACCATTTTACTATTTTACTATTAT
66 TTTTACCATATTACTAATTTACTATTAT
* *
33407 AGTTTTACTCAACTAAAAACTCTATTTTTATTCAGTTAAATCTAATATCCTTATACCTATTTTAT
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCCTTATAACTATTTTAT
*
33472 TTTTACGATATTACTAATTTA
66 TTTTACCATATTACTAATTTA
33493 ATTAAATAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.50
Consensus pattern (93 bp):
AGTTTTACTCAACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCCTTATAACTATTTTAT
TTTTACCATATTACTAATTTACTATTAT
Found at i:34845 original size:17 final size:17
Alignment explanation
Indices: 34820--34857 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
34810 CCTAATTAAA
34820 TTCTACTCCTATTTTCTT
1 TTCTACTCC-ATTTTCTT
*
34838 TTCT-CTCCCTTTTCTT
1 TTCTACTCCATTTTCTT
34854 TTCT
1 TTCT
34858 TCTTTTCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (17 bp):
TTCTACTCCATTTTCTT
Found at i:38310 original size:19 final size:18
Alignment explanation
Indices: 38275--38336 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
38265 AGTAAATTTA
38275 ATAAAATTATAAT-AATAAT
1 ATAAAATT-T-ATGAATAAT
38294 ATAAAATTTATTGAATAA-
1 ATAAAATTTA-TGAATAAT
*
38312 ATGATAATTTA-GAATAAT
1 AT-AAAATTTATGAATAAT
38330 -TAAAATT
1 ATAAAATT
38337 ATAACAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 4 0.11
19 20 0.54
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
ATAAAATTTATGAATAAT
Found at i:39660 original size:21 final size:22
Alignment explanation
Indices: 39636--39676 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39626 GTTTATAATA
*
39636 TTCTTGGGTCA-TCGGGTTATT
1 TTCTCGGGTCATTCGGGTTATT
*
39657 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
39677 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATT
Found at i:41234 original size:38 final size:38
Alignment explanation
Indices: 41192--41282 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
41182 ATTATTATCT
41192 CTTAAATTTAATTAGCAGATTTTGTGACTAATAAATCA
1 CTTAAATTTAATTAGCAGATTTTGTGACTAATAAATCA
* * * *
41230 CTTAAATTTAATTAGCAGATTTTGTGGCTAGTAATTCT
1 CTTAAATTTAATTAGCAGATTTTGTGACTAATAAATCA
*
41268 CTTAAATTTAGTTAG
1 CTTAAATTTAATTAG
41283 TCTGTTGACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (38 bp):
CTTAAATTTAATTAGCAGATTTTGTGACTAATAAATCA
Found at i:42143 original size:3 final size:3
Alignment explanation
Indices: 42135--42184 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
42125 AGGTAATGGT
*
42135 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
42183 TT
1 TT
42185 ATTTCCTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:45902 original size:2 final size:2
Alignment explanation
Indices: 45895--45932 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
45885 CGTTTTGACA
45895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45933 AATAATCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50264 original size:3 final size:3
Alignment explanation
Indices: 50258--50309 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
50248 TTATTTCAAG
* *
50258 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50306 AAT A
1 AAT A
50310 TGAGAACCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:51113 original size:6 final size:6
Alignment explanation
Indices: 51102--51132 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
51092 CTCCAATGAT
*
51102 GAAACC GAAACC GAAATC GAAACC GAAACC G
1 GAAACC GAAACC GAAACC GAAACC GAAACC G
51133 TGGTCAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.29, G:0.19, T:0.03
Consensus pattern (6 bp):
GAAACC
Found at i:57118 original size:11 final size:11
Alignment explanation
Indices: 57104--57134 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
57094 AGGAAAAAAT
57104 TAGGAAGGAGC
1 TAGGAAGGAGC
57115 TAGGAAGGAGC
1 TAGGAAGGAGC
57126 TAGGAAGGA
1 TAGGAAGGA
57135 CCCTACTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.45, T:0.10
Consensus pattern (11 bp):
TAGGAAGGAGC
Found at i:60889 original size:15 final size:15
Alignment explanation
Indices: 60859--60900 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
60849 TTACTTTGCT
60859 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
60875 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
60890 TTGCTTTCTGT
1 TTGTTTTCTGT
60901 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:61276 original size:24 final size:22
Alignment explanation
Indices: 61249--61297 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
61239 TTGTTTTGTG
61249 TTTTGCGTAAAAAAAAGAAATAGT
1 TTTTGCGTAAAAAAAA-AAATA-T
* *
61273 TTTTGCGTTATAAAAAAAATAT
1 TTTTGCGTAAAAAAAAAAATAT
61295 TTT
1 TTT
61298 CTTTATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 5 0.22
24 14 0.61
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTTGCGTAAAAAAAAAAATAT
Done.