Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015219.1 Corchorus olitorius cultivar O-4 contig15252, 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: 60026
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:5303 original size:53 final size:54
Alignment explanation
Indices: 5114--5312 Score: 213
Period size: 54 Copynumber: 3.7 Consensus size: 54
5104 CTTTTAAAGT
* * * * * * * * *
5114 TTTCAAAGATCTAAGTTGA-CGATCAAATGGCCCTATGCGGTATTTCAAAGAAGT
1 TTTCAGAGATCTAAGTTGATC-TTCAGATGACCCTGTGCAGTCTTTCATAGAAGC
* * * *
5168 TTTCAAAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGT
1 TTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCAGTCTTTCATAGAAGC
* * *
5222 TTTCAGAGATCTAAGTTGATTTTAAGATGACCTTGTGCAGTCTTTCATA-AAGC
1 TTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCAGTCTTTCATAGAAGC
*
5275 TTTCAGAGATCTAAGTTGATCTCCAGATGACCCATGTG
1 TTTCAGAGATCTAAGTTGATCTTCAGATGACCC-TGTG
5313 GTCATTCCAA
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 32 0.26
54 92 0.74
55 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
TTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCAGTCTTTCATAGAAGC
Found at i:5382 original size:35 final size:35
Alignment explanation
Indices: 5320--5871 Score: 757
Period size: 35 Copynumber: 15.8 Consensus size: 35
5310 GTGGTCATTC
* * *
5320 CAAGAA-TTTTCCAATGACCAGAGTTGATCTCCTTT
1 CAAGAAGTTTT-CGATGATCAGAGTTGATCTCGTTT
* **
5355 CCAGAAGTTTTCGATGATCAGAGTTGATCTTATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * * *
5390 CAAGAAGTTTTTGAAGATTAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
5425 CAAGAAGTTTTTAATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
5460 CAAGAAGTTTTCCATGATCAGAGTTGATCTTGGTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
5495 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
5530 CAAGAAGTTTTCCATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
**
5565 CAAGAAGTTTTCGATGATCAGAGTTGAAATCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
5600 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATCT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
5635 CAAGAAGTTTTCGATGATCAGAGTTGAAATCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
5670 CAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
5705 CAAAAAGTTTTCGATGATCACAGTTGATCTTGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
5740 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATCT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
5775 CAAGAAGTTTTCAATGATCATAGTTGATCTTGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
**
5810 CAAGAAGTTTTCGATGATCAGAGTTGATCTTATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
5845 TAAGAAG-TTTCGATGATCAGAGTTGAT
1 CAAGAAGTTTTCGATGATCAGAGTTGAT
5872 TCCTAGATGA
Statistics
Matches: 462, Mismatches: 54, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
34 20 0.04
35 438 0.95
36 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
Found at i:5918 original size:54 final size:53
Alignment explanation
Indices: 5846--6121 Score: 290
Period size: 54 Copynumber: 5.2 Consensus size: 53
5836 ATCTTATTTT
* *
5846 AAGAAGTTTCGATGATCAGAGTTGATTCCTAGATGATCCAGTGCAGTCATTCC
1 AAGAAGTTTCCATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTCC
* * *
5899 AAAAAGTTTCCAGTGATCAGAGTTGA-TCCTAGGTGATCCAGTGCGGTCATACC
1 AAGAAGTTTCCA-TGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTCC
* * *
5952 AAGAAATTTTCCATGATCAGAGTTGATCCCTATATGATCCAGTGCGGTCAGTT-C
1 AAG-AAGTTTCCATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCA-TTCC
* * * ** * *
6006 AAGAAGTTATCAATGGTCAGAGTTGA-TCCCAGAACAATCCAGTCCGGTCATTTC
1 AAGAAGTT-TCCATGATCAGAGTTGATTCCTAG-ATGATCCAGTGCGGTCATTCC
* * * * *
6060 AAGAAGTTTTCAATGGTCAGAGTTGATTCCCA-AAGATCCAGTGCGGTCATTCT
1 AAGAAG-TTTCCATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTCC
6113 AAGAAGTTT
1 AAGAAGTTT
6122 TTTATGATAT
Statistics
Matches: 189, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
52 3 0.02
53 80 0.42
54 98 0.52
55 8 0.04
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (53 bp):
AAGAAGTTTCCATGATCAGAGTTGATTCCTAGATGATCCAGTGCGGTCATTCC
Found at i:6099 original size:107 final size:106
Alignment explanation
Indices: 5841--6121 Score: 309
Period size: 107 Copynumber: 2.6 Consensus size: 106
5831 AGTTGATCTT
* * * * *
5841 ATTTTAAGAAG-TTTCGATGATCAGAGTTGATTCCTAGATGATCCAGTGCAGTCATTCCAAAAAG
1 ATTTCAAGAAGTTTTCAATGATCAGAGTTGATTCCCAGATGATCCAGTGCGGTCATT-CAAGAAG
* * *** *
5905 TTTCCAGTGATCAGAGTTGATCCTAGGTGATCCAGTGCGGTC
65 TTTCCAATGATCAGAGTTGATCCCAGACAATCCAGTCCGGTC
** * * *
5947 ATACCAAGAAATTTTCCATGATCAGAGTTGA-TCCCTATATGATCCAGTGCGGTCAGTTCAAGAA
1 ATTTCAAGAAGTTTTCAATGATCAGAGTTGATTCCC-AGATGATCCAGTGCGGTCA-TTCAAGAA
*
6011 GTTAT-CAATGGTCAGAGTTGATCCCAGAACAATCCAGTCCGGTC
64 GTT-TCCAATGATCAGAGTTGATCCCAG-ACAATCCAGTCCGGTC
* *
6055 ATTTCAAGAAGTTTTCAATGGTCAGAGTTGATTCCCA-AAGATCCAGTGCGGTCATTCTAAGAAG
1 ATTTCAAGAAGTTTTCAATGATCAGAGTTGATTCCCAGATGATCCAGTGCGGTCATTC-AAGAAG
6119 TTT
65 TTT
6122 TTTATGATAT
Statistics
Matches: 146, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
106 14 0.10
107 86 0.59
108 42 0.29
109 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (106 bp):
ATTTCAAGAAGTTTTCAATGATCAGAGTTGATTCCCAGATGATCCAGTGCGGTCATTCAAGAAGT
TTCCAATGATCAGAGTTGATCCCAGACAATCCAGTCCGGTC
Found at i:6162 original size:33 final size:33
Alignment explanation
Indices: 6099--6162 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
6089 CCAAAGATCC
* * **
6099 AGTGCGGTCATTCTAAGAAGTTTTTTATGATAT
1 AGTGCGATCATTCCAAGAAGTTTTCAATGATAT
6132 AGTGCGATCATTCCAAGAAGTTTTCAATGAT
1 AGTGCGATCATTCCAAGAAGTTTTCAATGAT
6163 CAGAGTTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (33 bp):
AGTGCGATCATTCCAAGAAGTTTTCAATGATAT
Found at i:6200 original size:54 final size:55
Alignment explanation
Indices: 6141--6355 Score: 256
Period size: 54 Copynumber: 4.0 Consensus size: 55
6131 TAGTGCGATC
*
6141 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGA-TGATCCAGTGTGGTA
1 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATTGATCCAGTGTGGTA
** *
6195 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTTTAAA-TGATCCAGTGTGGTC
1 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATTGATCCAGTGTGGTA
* * * * *** *
6249 TTTCCAATAAGTTTCCGATGATCAGAGTTGATCTCC-AATTGATCCAGTACAGTT
1 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATTGATCCAGTGTGGTA
* * ** *
6303 GTTTCAAGAAGTTTTTGATGGTCAGAGTTGATCTCCAAATTGATCCAGTGTGG
1 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATTGATCCAGTGTGG
6356 ACGTTCAAAG
Statistics
Matches: 136, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
53 2 0.01
54 121 0.89
55 13 0.10
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (55 bp):
ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATTGATCCAGTGTGGTA
Found at i:6276 original size:248 final size:248
Alignment explanation
Indices: 5892--6352 Score: 590
Period size: 248 Copynumber: 1.9 Consensus size: 248
5882 TCCAGTGCAG
* * * *
5892 TCATTCCAAAAAGTTTCCAGTGATCAGAGTTGATCCTAGGTGATCCAGTGCGGTCATACCAAGAA
1 TCATTCCAAAAAGTTTCCAATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTAATACCAAGAA
* * *
5957 ATTTTCCATGATCAGAGTTGATCCCTATATGATCCAGTGCGGTCAGTTCAAGAAGTTATCAATGG
66 ATTTTCAATGATCAGAGTTGATCCCTAAATGATCCAGTGCGGTCAGTTCAAGAAGTTATCAATGA
* *
6022 TCAGAGTTGATC-CCAGAACAATCCAGTCCGGTCATTTCAAGAAGTTTTCAATGGTCAGAGTTGA
131 TCAGAGTTGATCTCCA-AACAATCCAGTACAGTCATTTCAAGAAGTTTTCAATGGTCAGAGTTGA
6086 T-TCCCAAA-GATCCAGTGCGGTCATTCTAAGAAGTTTTTTATGATATAGTGCGA
195 TCT-CCAAATGATCCAGTGCGGTCATTCTAAGAAGTTTTTTATGATATAGTGCGA
* * * *
6139 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTAATTCCAAGA
1 TCATTCCAAAAAGTTTCCAATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTAATACCAAGA
* ** * * * *
6204 AGTTTTCAATGATCAGAGTTGATCTTTAAATGATCCAGTGTGGTC-TTTCCAATAAGTT-TCCGA
65 AATTTTCAATGATCAGAGTTGATCCCTAAATGATCCAGTGCGGTCAGTT-CAAGAAGTTAT-CAA
*** ** **
6267 TGATCAGAGTTGATCTCCAATTGATCCAGTACAGTTGTTTCAAGAAGTTTTTGATGGTCAGAGTT
128 TGATCAGAGTTGATCTCCAAACAATCCAGTACAGTCATTTCAAGAAGTTTTCAATGGTCAGAGTT
6332 GATCTCCAAATTGATCCAGTG
193 GATCTCCAAA-TGATCCAGTG
6353 TGGACGTTCA
Statistics
Matches: 180, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
247 35 0.19
248 132 0.73
249 4 0.02
250 9 0.05
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (248 bp):
TCATTCCAAAAAGTTTCCAATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTAATACCAAGAA
ATTTTCAATGATCAGAGTTGATCCCTAAATGATCCAGTGCGGTCAGTTCAAGAAGTTATCAATGA
TCAGAGTTGATCTCCAAACAATCCAGTACAGTCATTTCAAGAAGTTTTCAATGGTCAGAGTTGAT
CTCCAAATGATCCAGTGCGGTCATTCTAAGAAGTTTTTTATGATATAGTGCGA
Found at i:15754 original size:87 final size:85
Alignment explanation
Indices: 15548--16152 Score: 545
Period size: 87 Copynumber: 6.9 Consensus size: 85
15538 AATTGTTTTC
* * * **
15548 TTTT-ATTCCAAAAATACCCATTCCTGGTTGGAAGGTCTCCGTTTT-ATTCCAAAAATGCCCCTT
1 TTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTTTTTTCATTCCAAAAATGCCCCTT
** *
15611 CCCAG-CGGAAGGTCACAGTTTT
66 CCTGGTCGGAAGGTCAC---TGT
* *
15633 TTTTCATTCCGAAAATGCCCCTTCCTAGTTGGAAGGTC-CTTATTTTCATTTCCAAAAAAATGCC
1 TTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTT-TTTTCA-TTCC--AAAAATGCC
* *
15697 CCTTCCTGGTTGGAAGGTCTCTGT
62 CCTTCCTGGTCGGAAGGTCACTGT
** * *
15721 TTTT-ATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAACTTTCTTTCTTTCCAAAAATGCC
1 TTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGT--C-ACTTT-TTTCATTCCAAAAATGCC
* *
15785 CATTCCTGGTCGGAAGGTC-TTCG-
62 CCTTCCTGGTCGGAAGGTCACT-GT
* * * *
15808 TTTT-ATTCCAGAAATGCCCCTTCCTGATCGGAAGGTCACAGATTTCTTTCATTCCATAAATGCC
1 TTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCAC---TTT-TTTCATTCCAAAAATGCC
*
15872 CCTTCCTGGTTGGAAGGTC-CT-T
62 CCTTCCTGGTCGGAAGGTCACTGT
*
15894 GTTTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTT-ATTCCAAAAATGCC
1 -TTTTCA-TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCACT-TTTTTCATTCCAAAAATGCC
* *
15958 TCTTCCCGGTCGGAAGGTCACAACT-T
62 CCTTCCTGGTCGGAAGGT--C-ACTGT
* * ** *
15984 TCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCCGTTTT-ATTCCAAAAATGCTCCT
1 T-TTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTTTTTTCATTCCAAAAATGCCCCT
* *
16048 TCCCGGTCGGAAGGTCACAGTTT
65 TCCTGGTCGGAAGGTCAC--TGT
16071 TCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-CTTCTTTTCATTTCCAAAAATGCCC
1 T-TTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTT-TTTTCA-TTCCAAAAATGCCC
*
16135 CTTCCTGGTTGGAAGGTC
63 CTTCCTGGTCGGAAGGTC
16153 CCTATTTTCA
Statistics
Matches: 441, Mismatches: 46, Indels: 62
0.80 0.08 0.11
Matches are distributed among these distances:
84 4 0.01
85 7 0.02
86 63 0.14
87 186 0.42
88 72 0.16
89 39 0.09
90 54 0.12
91 16 0.04
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (85 bp):
TTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTTTTTTCATTCCAAAAATGCCCCTT
CCTGGTCGGAAGGTCACTGT
Found at i:15797 original size:46 final size:43
Alignment explanation
Indices: 15544--16164 Score: 519
Period size: 46 Copynumber: 14.3 Consensus size: 43
15534 CGAAAATTGT
* * *
15544 TTTCTTTTATTCCAAAAATACCCATTCCTGGTTGGAAGGTCTCC
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-CC
* ** * *
15588 -GT-TTT-ATTCCAAAAATGCCCCTTCCCAG-CGGAAGGTCACAGT
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--C
* * *
15630 TTTTTTTCATTCCGAAAATGCCCCTTCCTAGTTGGAAGGT-CC
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
*
15672 TTAT-TTTCATTTCCAAAAAAATGCCCCTTCCTGGTTGGAAGGTCTC
1 TT-TCTTTCA-TTCC--AAAAATGCCCCTTCCTGGTTGGAAGGTCCC
** *
15718 TGTT-TTT-ATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAAC
1 T-TTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--C
* * *
15763 TTTCTTTCTTTCCAAAAATGCCCATTCCTGGTCGGAAGGT--C
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
* * * * *
15804 -TTCGTTTTATTCCAGAAATGCCCCTTCCTGATCGGAAGGTCACAGA
1 TTTC-TTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--C
*
15850 TTTCTTTCATTCCATAAATGCCCCTTCCTGGTTGGAAGGT-CC
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
*
15892 TTGT-TTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCTC
1 TT-TCTTTCA-TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCC
* * *
15937 TGTT-TTT-ATTCCAAAAATGCCTCTTCCCGGTCGGAAGGTCACAAC
1 T-TTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--C
*
15982 TTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCC
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-CC
* * * * *
16026 -GT-TTT-ATTCCAAAAATGCTCCTTCCCGGTCGGAAGGTCACAGT
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--C
16069 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGT-CC
1 TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
16111 -TTCTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
1 TTTC-TTTCA-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
*
16155 TAT-TTTCATT
1 TTTCTTTCATT
16165 TTCATTTTCA
Statistics
Matches: 475, Mismatches: 59, Indels: 88
0.76 0.09 0.14
Matches are distributed among these distances:
40 12 0.03
41 84 0.18
42 77 0.16
43 53 0.11
44 45 0.09
45 67 0.14
46 133 0.28
47 4 0.01
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (43 bp):
TTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
Found at i:15923 original size:219 final size:217
Alignment explanation
Indices: 15544--16152 Score: 997
Period size: 219 Copynumber: 2.8 Consensus size: 217
15534 CGAAAATTGT
*
15544 TTTCTTT-TATTCCAAAAATACCCATTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCCC
1 TTTCTTTCT-TTCCAAAAATGCCCATTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCCC
* * * *
15608 CTTCCCAGCGGAAGGTCACAGTTTTTTTTCATTCCGAAAATGCCCCTTCCTAGTTGGAAGGTCCT
65 CTTCCGATCGGAAGGTCACAGTTTTCTTTCATTCC-AAAATGCCCCTTCCTGGTTGGAAGGTCCT
15673 TATTTTCATTTCCAAAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTATTCCAAAAATGC
129 TATTTTCATTTCC-AAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTATTCCAAAAATGC
15738 CCCTTCCCAGTCGGAAGGTCACAAC
193 CCCTTCCCAGTCGGAAGGTCACAAC
* * *
15763 TTTCTTTCTTTCCAAAAATGCCCATTCCTGGTCGGAAGGTCTTCGTTTTATTCCAGAAATGCCCC
1 TTTCTTTCTTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCCCC
*
15828 TTCCTGATCGGAAGGTCACAGATTTCTTTCATTCCATAAATGCCCCTTCCTGGTTGGAAGGTCCT
66 TTCC-GATCGGAAGGTCACAGTTTTCTTTCATTCCA-AAATGCCCCTTCCTGGTTGGAAGGTCCT
*
15893 TGTTTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTATTCCAAAAATGCC
129 TATTTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTATTCCAAAAATGCC
* *
15958 TCTTCCCGGTCGGAAGGTCACAAC
194 CCTTCCCAGTCGGAAGGTCACAAC
* *
15982 TTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCTCC
1 TTTCTTTCTTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCCCC
*
16047 TTCCCGGTCGGAAGGTCACAGTTTTCTTTCATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCT
66 TT-CCGATCGGAAGGTCACAGTTTTCTTTCATTCC-AAAATGCCCCTTCCTGGTTGGAAGGTCCT
*
16112 TCTTTTCATTTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTC
129 TATTTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTC
16153 CCTATTTTCA
Statistics
Matches: 365, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
218 28 0.08
219 268 0.73
220 69 0.19
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.35
Consensus pattern (217 bp):
TTTCTTTCTTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCTCCGTTTTATTCCAAAAATGCCCC
TTCCGATCGGAAGGTCACAGTTTTCTTTCATTCCAAAATGCCCCTTCCTGGTTGGAAGGTCCTTA
TTTTCATTTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTATTCCAAAAATGCCCC
TTCCCAGTCGGAAGGTCACAAC
Found at i:16295 original size:40 final size:40
Alignment explanation
Indices: 16231--16422 Score: 203
Period size: 40 Copynumber: 4.8 Consensus size: 40
16221 TATATTCCAA
* * * *
16231 AGTTTGCACTTCCTCGTCGGAAGGTGTTG-TTAGCATCCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-AATTCCC
*
16271 AGTTTGCCCTTCCTCATCGAAAGGTGTTGTTTAAATTCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
*
16311 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCTC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
* * * * *
16351 AGTTTGCCCTTCCCCACCGGAAGGTTTTGATTT-CATT-AC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATTCCC
* *
16390 TGTTTTGCCCTTCC-CGGTCGGAAGGTGTTGTTT
1 AG-TTTGCCCTTCCTC-ATCGGAAGGTGTTGTTT
16423 TCGATGTTTT
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
39 6 0.05
40 120 0.91
41 6 0.05
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (40 bp):
AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
Found at i:16375 original size:80 final size:80
Alignment explanation
Indices: 16231--16595 Score: 260
Period size: 88 Copynumber: 4.4 Consensus size: 80
16221 TATATTCCAA
* ** * * * *
16231 AGTTTGCACTTCCTCGTCGGAAGGTGTTG-TTAGCATCCCCAGTTTGCCCTTCCTCATCGAAAGG
1 AGTTTGCCCTTCCTCGTCGGAAGGTGTTGTTTATAAT-TCCAGTTTGCCCTTCCCCACCGGAAGG
*
16295 TGTTG-TTTAAATTCCC
65 TGTTGATTT-CATTCCC
*
16311 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-AATTCTCAGTTTGCCCTTCCCCACCGGAAGG
1 AGTTTGCCCTTCCTCGTCGGAAGGTGTTGTTTATAATTC-CAGTTTGCCCTTCCCCACCGGAAGG
* *
16375 TTTTGATTTCATT-AC
65 TGTTGATTTCATTCCC
* * *
16390 TGTTTTGCCCTTCC-CGGTCGGAAGGTGTTGTTTTCGATGTTTTATTCCCGTTTTGCCCTTCCCC
1 AG-TTTGCCCTTCCTC-GTCGGAAGGTGTTG-TTT--A----TAATTCCAG-TTTGCCCTTCCCC
*
16454 ACCGGAAGGTGTTGATTTCATTCCT
56 ACCGGAAGGTGTTGATTTCATTCCC
* * * * * *
16479 ATTTTGCCCTTCCTGGTTGGAAGGTGTTGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCTAC
1 AGTTTGCCCTTCCTCGTCGGAAGGTGTTG-TTT--A----TAATTCCAG-TTTGCCCTTCCCCAC
16544 CGGAAGGTGTTGATTTCATT-CC
58 CGGAAGGTGTTGATTTCATTCCC
*
16566 TGTTTTGCCCTTCC-C-TACCGGAAGGTGTTG
1 AG-TTTGCCCTTCCTCGT--CGGAAGGTGTTG
16596 ATTTCAATTC
Statistics
Matches: 238, Mismatches: 28, Indels: 30
0.80 0.09 0.10
Matches are distributed among these distances:
79 4 0.02
80 82 0.34
81 9 0.04
83 1 0.00
86 1 0.00
87 3 0.01
88 138 0.58
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (80 bp):
AGTTTGCCCTTCCTCGTCGGAAGGTGTTGTTTATAATTCCAGTTTGCCCTTCCCCACCGGAAGGT
GTTGATTTCATTCCC
Found at i:16447 original size:48 final size:48
Alignment explanation
Indices: 16391--16560 Score: 167
Period size: 48 Copynumber: 3.7 Consensus size: 48
16381 TTTCATTACT
**
16391 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGATGTTTTATTCCC
1 GTTTTGCCCTTCCCGACCGGAAGGTGTTGTTTTCGATGTTTTATTCCC
* * *
16439 GTTTTGCCCTTCCCCACCGGAA-G-G-TG--TT-GA--TTTCATTCCT
1 GTTTTGCCCTTCCCGACCGGAAGGTGTTGTTTTCGATGTTTTATTCCC
* * *** *
16479 ATTTTGCCCTTCCTGGTTGGAAGGTGTTGTTTTCAATGTTTTATTCCC
1 GTTTTGCCCTTCCCGACCGGAAGGTGTTGTTTTCGATGTTTTATTCCC
* *
16527 GTTTTGCCCTTCCCTACCGGAAGGTGTTGATTTC
1 GTTTTGCCCTTCCCGACCGGAAGGTGTTGTTTTC
16561 ATTCCTGTTT
Statistics
Matches: 93, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
40 24 0.26
41 1 0.01
42 3 0.03
43 4 0.04
45 4 0.04
46 2 0.02
47 1 0.01
48 54 0.58
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (48 bp):
GTTTTGCCCTTCCCGACCGGAAGGTGTTGTTTTCGATGTTTTATTCCC
Found at i:16502 original size:88 final size:88
Alignment explanation
Indices: 16353--16603 Score: 403
Period size: 88 Copynumber: 2.9 Consensus size: 88
16343 AAATTCTCAG
* *
16353 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTACTGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
*
16418 TGTTTTCGATGTTTTATTCCCGT
66 TGTTTTCAATGTTTTATTCCCGT
* * *
16441 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCTATTTTGCCCTTCCTGGTTGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
16506 TGTTTTCAATGTTTTATTCCCGT
66 TGTTTTCAATGTTTTATTCCCGT
* ***
16529 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCTACCGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
*
16594 TGATTTCAAT
66 TGTTTTCAAT
16604 TCACTTGAAG
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 149 1.00
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (88 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
TGTTTTCAATGTTTTATTCCCGT
Found at i:16561 original size:48 final size:43
Alignment explanation
Indices: 16273--16603 Score: 198
Period size: 40 Copynumber: 7.8 Consensus size: 43
16263 GCATCCCCAG
* *
16273 TTTGCCCTT-CCTCATCGAAAGGTGTTG-TTT-AA-ATTCCCAG-
1 TTTGCCCTTCCCT-ACCGGAAGGTGTTGATTTCAATATTCCC-GT
* *
16313 TTTGCCCTT-CCTCATCGGAAGGTGTTG-TTT-AA-ATTCTCAG-
1 TTTGCCCTTCCCT-ACCGGAAGGTGTTGATTTCAATATTC-CCGT
* * * *
16353 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTC---ATTACTGT
1 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAATATTCCCGT
*** * *
16393 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGATGTTTTATTCCCGT
1 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTC-A----ATATTCCCGT
* **
16441 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTC---ATTCCTAT
1 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAATATTCCCGT
*** *
16481 TTTGCCCTT-CCTGGTTGGAAGGTGTTGTTTTCAATGTTTTATTCCCGT
1 TTTGCCCTTCCCT-ACCGGAAGGTGTTGATTTCAA-----TATTCCCGT
*
16529 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTC---ATTCCTGT
1 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAATATTCCCGT
16569 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAAT
1 TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAAT
16604 TCACTTGAAG
Statistics
Matches: 233, Mismatches: 32, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
39 4 0.02
40 156 0.67
41 6 0.03
48 64 0.27
49 3 0.01
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (43 bp):
TTTGCCCTTCCCTACCGGAAGGTGTTGATTTCAATATTCCCGT
Found at i:17947 original size:15 final size:16
Alignment explanation
Indices: 17924--17956 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17914 AAGGAACCTC
*
17924 GGATGAATA-AAAAAA
1 GGATCAATATAAAAAA
17939 GGATCAATATAAAAAA
1 GGATCAATATAAAAAA
17955 GG
1 GG
17957 GAGTTGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.15
Consensus pattern (16 bp):
GGATCAATATAAAAAA
Found at i:20050 original size:19 final size:18
Alignment explanation
Indices: 20017--20052 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20007 TTGAGATAAT
20017 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
20035 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
20053 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:27762 original size:15 final size:16
Alignment explanation
Indices: 27732--27771 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
27722 TTACTTTGCT
27732 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
27748 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
27763 TTGCTTTCT
1 TTGTTTTCT
27772 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:32697 original size:13 final size:13
Alignment explanation
Indices: 32679--32705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32669 CTTTTCTTTT
32679 CTTTTCCTTTACC
1 CTTTTCCTTTACC
32692 CTTTTCCTTTACC
1 CTTTTCCTTTACC
32705 C
1 C
32706 AGGCGCGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTTCCTTTACC
Found at i:34166 original size:53 final size:53
Alignment explanation
Indices: 34086--34624 Score: 835
Period size: 53 Copynumber: 10.2 Consensus size: 53
34076 TAAGTTAAAA
*
34086 AAAAAGTAAAAAGATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
*
34139 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAAAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
*
34192 AAAAAGTAAAGAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
*
34245 TAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
** *
34298 AAAAAGTAAGGAAATGGTAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
* * * * *
34351 AAAAAATAAAAAGATGGTAATTAGTAGTTAGTTTAATTCAGAGTGATTAAGTT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
* * * *
34404 AAAAAATAGAAAGATGGTAATCAGTAGTTAGTTTAATTCAAAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
* ** * *
34457 AAAAATTAAGGAAATGGTAATCAGTAATTAGTTCAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
* *
34510 AAAGAGTAAAAAGATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
* * *
34563 AAAGAGTAAAAAGATGGTAATTAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
1 AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
*
34616 AAGAAGTAA
1 AAAAAGTAA
34625 GGAAATGATA
Statistics
Matches: 445, Mismatches: 41, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 445 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (53 bp):
AAAAAGTAAAAAAATGGTAATCAGTAGTTAGTTTAATTCAGAGTAATTAAGCT
Found at i:34898 original size:19 final size:18
Alignment explanation
Indices: 34874--34909 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34864 TGAAGACTTA
34874 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
34893 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
34910 ATCATCTCAA
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:36444 original size:26 final size:26
Alignment explanation
Indices: 36415--36466 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
36405 ATCAGTATTT
*
36415 AGTTTAATTCGGAGTAATTAAGCTAA
1 AGTTTAATTCAGAGTAATTAAGCTAA
36441 AGTTTAATTCAGAGTAATTAAGCTAA
1 AGTTTAATTCAGAGTAATTAAGCTAA
36467 GAAGTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
AGTTTAATTCAGAGTAATTAAGCTAA
Found at i:44306 original size:21 final size:21
Alignment explanation
Indices: 44259--44542 Score: 269
Period size: 21 Copynumber: 13.4 Consensus size: 21
44249 ATCAAGTAGT
44259 AAAGAGTAAAGAGTAATCAAG-A
1 AAAGAGT-AAGAGTAATC-AGTA
*
44281 AATG-GTAAGAGTAATCAGTA
1 AAAGAGTAAGAGTAATCAGTA
* * *
44301 AGATG-GTAATAATAATCAGTA
1 A-AAGAGTAAGAGTAATCAGTA
*
44322 AAATG-GTAATAGTAATCAGTA
1 AAA-GAGTAAGAGTAATCAGTA
44343 AAAGAGTAAAGAGTAATCAGTA
1 AAAGAGT-AAGAGTAATCAGTA
* *
44365 AAAGAGTAATAGTAATCATTA
1 AAAGAGTAAGAGTAATCAGTA
*
44386 AGAGAGTAAAGAGTAATCAGTA
1 AAAGAGT-AAGAGTAATCAGTA
*
44408 AAAGAGTAATAGTAATCAGT-
1 AAAGAGTAAGAGTAATCAGTA
*
44428 AAAGAGTAAAGATTAATCAGTA
1 AAAGAGT-AAGAGTAATCAGTA
**
44450 AAAGAGTAAAGAGTAAAGAGTA
1 AAAGAGT-AAGAGTAATCAGTA
* *
44472 AAAGAGTAATAATAATCAGT-
1 AAAGAGTAAGAGTAATCAGTA
44492 AAAGAGTAAAGAGTAATCA--A
1 AAAGAGT-AAGAGTAATCAGTA
* *
44512 AGAAGAGTCATAGTAATCAGTA
1 A-AAGAGTAAGAGTAATCAGTA
*
44534 AAGGAGTAA
1 AAAGAGTAA
44543 ACAGTGAGCA
Statistics
Matches: 221, Mismatches: 28, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.01
20 38 0.17
21 112 0.51
22 69 0.31
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAGAGTAAGAGTAATCAGTA
Found at i:44353 original size:7 final size:7
Alignment explanation
Indices: 44343--44507 Score: 104
Period size: 7 Copynumber: 23.3 Consensus size: 7
44333 GTAATCAGTA
44343 AAAGAGT
1 AAAGAGT
44350 AAAGAGT
1 AAAGAGT
**
44357 AATCAGT
1 AAAGAGT
44364 AAAAGAGT
1 -AAAGAGT
*
44372 -AATAGT
1 AAAGAGT
** *
44378 AATCATT
1 AAAGAGT
44385 AAGAGAGT
1 AA-AGAGT
44393 AAAGAGT
1 AAAGAGT
**
44400 AATCAGT
1 AAAGAGT
44407 AAAAGAGT
1 -AAAGAGT
*
44415 -AATAGT
1 AAAGAGT
**
44421 AATCAGT
1 AAAGAGT
44428 AAAGAGT
1 AAAGAGT
*
44435 AAAGATT
1 AAAGAGT
**
44442 AATCAGT
1 AAAGAGT
44449 AAAAGAGT
1 -AAAGAGT
44457 AAAGAGT
1 AAAGAGT
44464 AAAGAGT
1 AAAGAGT
44471 AAAAGAGT
1 -AAAGAGT
44479 AATA-A-T
1 AA-AGAGT
**
44485 AATCAGT
1 AAAGAGT
44492 AAAGAGT
1 AAAGAGT
44499 AAAGAGT
1 AAAGAGT
44506 AA
1 AA
44508 TCAAAGAAGA
Statistics
Matches: 119, Mismatches: 29, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
6 14 0.12
7 78 0.66
8 27 0.23
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.21
Consensus pattern (7 bp):
AAAGAGT
Found at i:44364 original size:64 final size:64
Alignment explanation
Indices: 44259--44585 Score: 281
Period size: 64 Copynumber: 5.2 Consensus size: 64
44249 ATCAAGTAGT
*
44259 AAAGAGTAAAGAGTAATCAAG-AAATG-GT-AAGAGTAATCAGT-AAGATGGTAATAATAATCAG
1 AAAGAGTAAAGAGTAATC-AGTAAAAGAGTAAAGAGTAATCAGTAAAGA--GTAATAATAATCAG
44320 TA
63 TA
* * *
44322 AAATG-GT-AATAGTAATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCATT
1 AAA-GAGTAAAGAGTAATCAGTAAAAGAGTAAAGAGTAATCAGT-AAAGAGTAATAATAATCAGT
44385 A
64 A
* *
44386 AGAGAGTAAAGAGTAATCAGTAAAAGAGT-AATAGTAATCAGTAAAGAGTAA-AGATTAATCAGT
1 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAAAGAGTAATCAGTAAAGAGTAATA-A-TAATCAGT
44449 A
64 A
**
44450 AAAGAGTAAAGAGTAAAGAGTAAAAGAGTAATA-A-TAATCAGTAAAGAGTAA-AGAGTAATCA-
1 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAA-AGAGTAATCAGTAAAGAGTAATA-A-TAATCAG
44511 -A
63 TA
* * * * * * * *
44512 AGAAGAGT-CATAGTAATCAGTAAAGGAGTAAACAGTGAGCAGTCTAATGA-TAATAGTAATCAG
1 A-AAGAGTAAAGAGTAATCAGTAAAAGAGTAAAGAGTAATCAG--TAAAGAGTAATAATAATCAG
44575 T-
63 TA
44576 AAAGAGTAAA
1 AAAGAGTAAA
44586 TGGTAGTGAG
Statistics
Matches: 220, Mismatches: 23, Indels: 41
0.77 0.08 0.14
Matches are distributed among these distances:
61 3 0.01
62 35 0.16
63 40 0.18
64 109 0.50
65 28 0.13
66 5 0.02
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (64 bp):
AAAGAGTAAAGAGTAATCAGTAAAAGAGTAAAGAGTAATCAGTAAAGAGTAATAATAATCAGTA
Found at i:44374 original size:43 final size:43
Alignment explanation
Indices: 44259--44542 Score: 288
Period size: 43 Copynumber: 6.7 Consensus size: 43
44249 ATCAAGTAGT
*
44259 AAAGAGTAAAGAGTAATCAAG-AAATG-GTAAGAGTAATCAGTA
1 AAAGAGTAAAGAGTAATC-AGTAAAAGAGTAAGAGTAATCAGTA
* *
44301 AGATG-GTAATA-A-TAATCAGTAAAATG-GTAATAGTAATCAGTA
1 A-AAGAGTAA-AGAGTAATCAGTAAAA-GAGTAAGAGTAATCAGTA
* *
44343 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCATTA
1 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAAGAGTAATCAGTA
* *
44386 AGAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGTAATCAGT-
1 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAAGAGTAATCAGTA
* **
44428 AAAGAGTAAAGATTAATCAGTAAAAGAGTAAAGAGTAAAGAGTA
1 AAAGAGTAAAGAGTAATCAGTAAAAGAGT-AAGAGTAATCAGTA
44472 AAAGAGTAATA-A-TAATCAGT-AAAGAGTAAAGAGTAATCA--A
1 AAAGAGTAA-AGAGTAATCAGTAAAAGAGT-AAGAGTAATCAGTA
* * *
44512 AGAAGAGT-CATAGTAATCAGTAAAGGAGTAA
1 A-AAGAGTAAAGAGTAATCAGTAAAAGAGTAA
44543 ACAGTGAGCA
Statistics
Matches: 211, Mismatches: 16, Indels: 31
0.82 0.06 0.12
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 27 0.13
42 79 0.37
43 88 0.42
44 10 0.05
45 1 0.00
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (43 bp):
AAAGAGTAAAGAGTAATCAGTAAAAGAGTAAGAGTAATCAGTA
Found at i:44706 original size:26 final size:26
Alignment explanation
Indices: 44608--44717 Score: 96
Period size: 27 Copynumber: 4.0 Consensus size: 26
44598 ATTAAAGTTC
* *
44608 AAAGAGTAAAAGTGGTAAAAAGTGAAA
1 AAAGAGTAAAAATGGTAATAAGT-AAA
* **
44635 AAAGAGTAAAAATGGAAACCAGTAAAA
1 AAAGAGTAAAAATGGTAATAAGT-AAA
*
44662 AAAAAGGTAAGAAAATGGTAATAAGT-AA
1 AAAGA-GT-A-AAAATGGTAATAAGTAAA
*
44690 AAAGAGTAAAAATTGGTAATCAGTAAA
1 AAAGAGTAAAAA-TGGTAATAAGTAAA
44717 A
1 A
44718 TGAGTAAGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
25 4 0.06
26 11 0.16
27 31 0.46
28 8 0.12
29 1 0.01
30 12 0.18
ACGTcount: A:0.60, C:0.03, G:0.21, T:0.16
Consensus pattern (26 bp):
AAAGAGTAAAAATGGTAATAAGTAAA
Found at i:45484 original size:13 final size:14
Alignment explanation
Indices: 45452--45484 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45442 GCTAAGTGTA
*
45452 AAAATTAATAAATG
1 AAAATAAATAAATG
45466 AAAATAAATAAAT-
1 AAAATAAATAAATG
45479 AAAATA
1 AAAATA
45485 GAAAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAATAAATAAATG
Found at i:50908 original size:42 final size:38
Alignment explanation
Indices: 50875--50947 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
50865 ATTAGTTTTA
* *
50875 CTTTGATGAATTATCTAGAGATGGAGTAGAATATTA-T
1 CTTTAATGAATTACCTAGAGATGGAGTAGAATATTAGT
50912 CTTTAATGAATTACCTAGAGATGGAGTAGAAT-TTAG
1 CTTTAATGAATTACCTAGAGATGGAGTAGAATATTAG
50948 GTAATGCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 3 0.09
37 30 0.91
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (38 bp):
CTTTAATGAATTACCTAGAGATGGAGTAGAATATTAGT
Found at i:51846 original size:19 final size:20
Alignment explanation
Indices: 51822--51863 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
51812 TTAGATATAT
*
51822 ATAATTCTT-TTCTGTCTGG
1 ATAATTCTTCATCTGTCTGG
*
51841 ATAATTCTTCATGTGTCTGG
1 ATAATTCTTCATCTGTCTGG
51861 ATA
1 ATA
51864 TATAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (20 bp):
ATAATTCTTCATCTGTCTGG
Found at i:52128 original size:2 final size:2
Alignment explanation
Indices: 52121--52150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52111 TAATAAGTAA
52121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52151 TACTTTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56251 original size:2 final size:2
Alignment explanation
Indices: 56244--56277 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56234 TATCATGTTA
56244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56278 TCCTTTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56469 original size:128 final size:128
Alignment explanation
Indices: 56318--56570 Score: 452
Period size: 128 Copynumber: 2.0 Consensus size: 128
56308 TTATTTGTTA
* * *
56318 CAAAATGAAGTTCCATTTTGAAAGTTAAAAAGTAATCCTACTTTCCTATTATATCCTTTAATTAA
1 CAAAATGAAGTCCCATTTCGAAAGTTAAAAAGTAATCCTACTTTCCTATTATATCCCTTAATTAA
*
56383 ATATACTACTTTCTTTTATCGCAATAAAATTTTTATGGATAATTTTGTAAAAAGACTTAATTC
66 ATATACTACTTTCTTTTATCGCAATAAAATTTTTAAGGATAATTTTGTAAAAAGACTTAATTC
56446 CAAAATGAAGTCCCATTTCGAAAGTTAAAAAGTAATCCTACTTTCCTATTATATCCCTTAATTAA
1 CAAAATGAAGTCCCATTTCGAAAGTTAAAAAGTAATCCTACTTTCCTATTATATCCCTTAATTAA
* *
56511 ATATACTACTTTCTTTTATGGCAATAAAATTTTTAAGGATAATTTTGTAGAAAGACTTAA
66 ATATACTACTTTCTTTTATCGCAATAAAATTTTTAAGGATAATTTTGTAAAAAGACTTAA
56571 AATATCTACT
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 119 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (128 bp):
CAAAATGAAGTCCCATTTCGAAAGTTAAAAAGTAATCCTACTTTCCTATTATATCCCTTAATTAA
ATATACTACTTTCTTTTATCGCAATAAAATTTTTAAGGATAATTTTGTAAAAAGACTTAATTC
Found at i:59546 original size:28 final size:27
Alignment explanation
Indices: 59514--59593 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 27
59504 GCACTTAGGT
59514 CATTTAGGGGCATTTTGGTCATTTTTC
1 CATTTAGGGGCATTTTGGTCATTTTTC
*
59541 ACATTTAGGGGCATTTTGGT--TATTTC
1 -CATTTAGGGGCATTTTGGTCATTTTTC
59567 CATGTTCAGGGGCATTTTGGTCATTTT
1 CAT-TT-AGGGGCATTTTGGTCATTTT
59594 AGGTTCATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
25 3 0.07
26 7 0.15
27 14 0.30
28 19 0.41
29 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (27 bp):
CATTTAGGGGCATTTTGGTCATTTTTC
Done.