Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019194.1 Corchorus olitorius cultivar O-4 contig19227, 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: 84836
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5790 original size:28 final size:29
Alignment explanation
Indices: 5744--5807 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
5734 AAAGTAGTGT
*
5744 TAATCCAGCGATGTCAATAACTCGAT-CA
1 TAATCCAGCGATATCAATAACTCGATACA
* * * *
5772 TAATCCAGTGATATTAATAACTTGATATA
1 TAATCCAGCGATATCAATAACTCGATACA
5801 TAATCCA
1 TAATCCA
5808 AGTTCCAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (29 bp):
TAATCCAGCGATATCAATAACTCGATACA
Found at i:10838 original size:224 final size:224
Alignment explanation
Indices: 10448--10895 Score: 887
Period size: 224 Copynumber: 2.0 Consensus size: 224
10438 GCGGATGGTG
10448 GTGTATCATAAGAAATAGAGTGGAGAAGGGGGCATGAGCCTTCAACATTGTCCATATTCCATAGC
1 GTGTATCATAAGAAATAGAGTGGAGAAGGGGGCATGAGCCTTCAACATTGTCCATATTCCATAGC
*
10513 ACAATAAAAGTGCAATGTATTACTGCCAGAAAAAAATGCAGTGTATTAAAGTATATTACTCAAAG
66 ACAATAAAAGTGCAATGTATTACTGCCAAAAAAAAATGCAGTGTATTAAAGTATATTACTCAAAG
10578 TGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATAA
131 TGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATAA
10643 AAATTCCCATTTTATTCAGATGCACCATT
196 AAATTCCCATTTTATTCAGATGCACCATT
10672 GTGTATCATAAGAAATAGAGTGGAGAAGGGGGCATGAGCCTTCAACATTGTCCATATTCCATAGC
1 GTGTATCATAAGAAATAGAGTGGAGAAGGGGGCATGAGCCTTCAACATTGTCCATATTCCATAGC
10737 ACAATAAAAGTGCAATGTATTACTGCCAAAAAAAAATGCAGTGTATTAAAGTATATTACTCAAAG
66 ACAATAAAAGTGCAATGTATTACTGCCAAAAAAAAATGCAGTGTATTAAAGTATATTACTCAAAG
10802 TGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATAA
131 TGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATAA
10867 AAATTCCCATTTTATTCAGATGCACCATT
196 AAATTCCCATTTTATTCAGATGCACCATT
10896 ATACCTTAAT
Statistics
Matches: 223, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 223 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (224 bp):
GTGTATCATAAGAAATAGAGTGGAGAAGGGGGCATGAGCCTTCAACATTGTCCATATTCCATAGC
ACAATAAAAGTGCAATGTATTACTGCCAAAAAAAAATGCAGTGTATTAAAGTATATTACTCAAAG
TGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATAA
AAATTCCCATTTTATTCAGATGCACCATT
Found at i:11585 original size:84 final size:85
Alignment explanation
Indices: 11421--11577 Score: 244
Period size: 84 Copynumber: 1.9 Consensus size: 85
11411 GCACCAACAA
* ** *
11421 TTAAAAGCATAATATGAATTTGAGTCATATGCTTGGCCCGTAAAAATCATAGGGTTTTGAAATTT
1 TTAAAAGCATAATATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTT
11486 CAAAAAAATACTGTCACACT
66 CAAAAAAATACTGTCACACT
* *
11506 TTAAAA-CATAATATGAAATTGGGTCATATGCTCCGCCGGTAAAAATCATAGGGTTTAGAAATTT
1 TTAAAAGCATAATATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTT
*
11570 CAGAAAAA
66 CAAAAAAA
11578 CTTTGTCAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 59 0.91
85 6 0.09
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (85 bp):
TTAAAAGCATAATATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTT
CAAAAAAATACTGTCACACT
Found at i:13232 original size:83 final size:84
Alignment explanation
Indices: 13104--13260 Score: 244
Period size: 83 Copynumber: 1.9 Consensus size: 84
13094 CACTTAAAAG
* ** *
13104 CATAACATGAATTTGAGTCATATGCTTGGCCCGTAAAAATCATAGGGTTTTGAAATTTCA-AAAA
1 CATAACATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTTCAGAAAA
13168 ACTTTGTCACACTTTCAAA
66 ACTTTGTCACACTTTCAAA
* * *
13187 CATAATATGAAATTGGGTCATATGCTCCGCCGGTAAAAATCATAGGGTTTAGAAATTTCAGAAAA
1 CATAACATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTTCAGAAAA
13252 ACTTTGTCA
66 ACTTTGTCA
13261 AAATCAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 53 0.80
84 13 0.20
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (84 bp):
CATAACATGAAATTGAGTCATATGCTCCGCCCGTAAAAATCATAGGGTTTAGAAATTTCAGAAAA
ACTTTGTCACACTTTCAAA
Found at i:13480 original size:15 final size:15
Alignment explanation
Indices: 13460--13490 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13450 CGCGCCCTTG
13460 CCCTTTCTTTCTTTT
1 CCCTTTCTTTCTTTT
13475 CCCTTTCTTTCTTTT
1 CCCTTTCTTTCTTTT
13490 C
1 C
13491 TTTAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
CCCTTTCTTTCTTTT
Found at i:25725 original size:24 final size:24
Alignment explanation
Indices: 25687--25735 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
25677 AATTGATTGC
* *
25687 TCTATTTCAGGTTGGGGAGTCTAA
1 TCTATTGCAGCTTGGGGAGTCTAA
*
25711 TCTATTGCAGCTTGGTGAGTCTAA
1 TCTATTGCAGCTTGGGGAGTCTAA
25735 T
1 T
25736 GTATATCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (24 bp):
TCTATTGCAGCTTGGGGAGTCTAA
Found at i:26334 original size:3 final size:3
Alignment explanation
Indices: 26326--26352 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
26316 CATAAAGTTC
26326 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
26353 TTTTATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33240 original size:18 final size:18
Alignment explanation
Indices: 33217--33264 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
33207 AATCTTATGG
33217 GTGTCTTTTTTTGAATTT
1 GTGTCTTTTTTTGAATTT
33235 GTGTCTTTTTTTGAATTT
1 GTGTCTTTTTTTGAATTT
33253 GTGTCTTTTTTT
1 GTGTCTTTTTTT
33265 CTTCAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (18 bp):
GTGTCTTTTTTTGAATTT
Found at i:34695 original size:7 final size:7
Alignment explanation
Indices: 34683--34708 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34673 TTAAAATGGG
34683 TTGGGAC
1 TTGGGAC
34690 TTGGGAC
1 TTGGGAC
34697 TTGGGAC
1 TTGGGAC
34704 TTGGG
1 TTGGG
34709 GAGTTGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.46, T:0.31
Consensus pattern (7 bp):
TTGGGAC
Found at i:34959 original size:27 final size:27
Alignment explanation
Indices: 34921--34976 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
34911 GTTGCCAAAA
* *
34921 TCGTTTCATTTGCCCATGTTTCTCTTT
1 TCGTTTCATTTGCCCATGTCTCCCTTT
34948 TCGTTTCATTTGCCCATGTCTCCCTTT
1 TCGTTTCATTTGCCCATGTCTCCCTTT
34975 TC
1 TC
34977 TTTATACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (27 bp):
TCGTTTCATTTGCCCATGTCTCCCTTT
Found at i:35417 original size:115 final size:115
Alignment explanation
Indices: 35277--35508 Score: 342
Period size: 115 Copynumber: 2.0 Consensus size: 115
35267 TTTTTCTTTT
* * *
35277 GGAAAATAAGCTTATCAAGGTGAAACCTTTTGGTGAAAATGTGGTTCCTTTTTTTCCTTCATTTT
1 GGAAAAAAAGCTTATCAAGGTGAAACCTTTTGGTGAAAATGTGGTTCC-TTTATACCTTCATTTT
*
35342 GATTTTATGTTTCA-C-AGAAGCTAATCTGTGATCTTAATCGGACTTTTGG
65 GATTTTATGTTTCATCAAGAAGCTAATCTGTGATCATAATCGGACTTTTGG
*
35391 GGAAAAAAAGGCTTATCAAGGTGAAACCTTTTGGTGAAAATGTTGTTCCTTTATACCTTCATTTT
1 GGAAAAAAA-GCTTATCAAGGTGAAACCTTTTGGTGAAAATGTGGTTCCTTTATACCTTCATTTT
*
35456 GATTTTATGTTTCAGTTTCAGAGAAGCTAATCTGTTATCATAATCGGACTTTT
65 GATTTTATGTTTCA---TCA-AGAAGCTAATCTGTGATCATAATCGGACTTTT
35509 ACACTTGTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
114 36 0.34
115 38 0.36
118 1 0.01
120 30 0.29
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (115 bp):
GGAAAAAAAGCTTATCAAGGTGAAACCTTTTGGTGAAAATGTGGTTCCTTTATACCTTCATTTTG
ATTTTATGTTTCATCAAGAAGCTAATCTGTGATCATAATCGGACTTTTGG
Found at i:36902 original size:31 final size:29
Alignment explanation
Indices: 36850--36923 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 29
36840 GCTATATTCC
* * *
36850 ATCACTCTTAATTTTTCTTTTGGCCTAAT
1 ATCACTCTTAATTGTTCTTTTGGCCGAAA
36879 ATCACTCTCTAATCTGTTCTTTTGGCCGAAA
1 ATCACTCT-TAAT-TGTTCTTTTGGCCGAAA
36910 ATCACTCTTTAATT
1 ATCACTC-TTAATT
36924 CAGTGTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.21
30 5 0.13
31 25 0.64
32 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (29 bp):
ATCACTCTTAATTGTTCTTTTGGCCGAAA
Found at i:37537 original size:204 final size:204
Alignment explanation
Indices: 37166--37584 Score: 447
Period size: 204 Copynumber: 2.1 Consensus size: 204
37156 GCTCTTGGGG
* * * * *
37166 TGGATGAAAGTGTTGATCAGCTTACTGGTTATCCAGAGAGAAAAGCTTCAGAGAAAGAAGGGGAG
1 TGGATAAAAGTATTGATCAGCTTACTGGCTATCCAGAGAGAAAAGCATCAAAGAAAGAAGGGGAG
* * * * * ** *
37231 ATGGTCTTCAATATTGATGTTGGGTCAGCTAAGAACACATACATCGACATCGATGACAATAGGAT
66 ATGGTCCTCAATATTGATGTTAGATCAGCTAAGAACAAATACATCCACATCGATGACAATACAAG
* * * * *
37296 GATTAAGGAAGAGAATAATCAGGATGATATGGCTGATGACATGGGAAGAAAAG-CTTCTGAAGTT
131 GATTAAAGAAGAGAATAATCAGGATCATATGGCTGATGACATGAGAAG-AAAGCCCTCTGAAATT
* *
37360 CATTTTGAGA
195 CATATTGAAA
* * * *
37370 TGGATAAAAGTATTGATCAGGTTACTGGCTGTTCAGAGAGAAAAGCATCAAAGAAAGAAGTGGAG
1 TGGATAAAAGTATTGATCAGCTTACTGGCTATCCAGAGAGAAAAGCATCAAAGAAAGAAGGGGAG
* *
37435 ACT-GTCC-CTGATATTGATGTTAGATCAGCTAAGGAA-AAATACAGTGCCAC-T-GATGATAAT
66 A-TGGTCCTC-AATATTGATGTTAGATCAGCTAA-GAACAAATACA-T-CCACATCGATGACAAT
* * * *
37495 ACAAGGATTAAAGAAGATAATGATCA-GACTCATATTGCTGATGACATGAGAAGCAAGCCCTCTG
126 ACAAGGATTAAAGAAGAGAATAATCAGGA-TCATATGGCTGATGACATGAGAAGAAAGCCCTCTG
*
37559 AAATTGATATTGAAA
190 AAATTCATATTGAAA
37574 TGGATAAAAGT
1 TGGATAAAAGT
37585 TCTGATGATG
Statistics
Matches: 177, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
203 6 0.03
204 162 0.92
205 6 0.03
206 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (204 bp):
TGGATAAAAGTATTGATCAGCTTACTGGCTATCCAGAGAGAAAAGCATCAAAGAAAGAAGGGGAG
ATGGTCCTCAATATTGATGTTAGATCAGCTAAGAACAAATACATCCACATCGATGACAATACAAG
GATTAAAGAAGAGAATAATCAGGATCATATGGCTGATGACATGAGAAGAAAGCCCTCTGAAATTC
ATATTGAAA
Found at i:50654 original size:30 final size:26
Alignment explanation
Indices: 50611--50693 Score: 103
Period size: 26 Copynumber: 3.0 Consensus size: 26
50601 TATTTAACTC
50611 TGCTCGATAAGTTCAGATCCTTTATT
1 TGCTCGATAAGTTCAGATCCTTTATT
** *
50637 TGATCTTTTATGAAGTTCAGATCCTTTATC
1 TG--C-TCGAT-AAGTTCAGATCCTTTATT
50667 TGCTCGATAAGTTCAGATCCTTTATT
1 TGCTCGATAAGTTCAGATCCTTTATT
50693 T
1 T
50694 AAGTTCGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 20 0.43
27 3 0.06
28 2 0.04
29 3 0.06
30 19 0.40
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (26 bp):
TGCTCGATAAGTTCAGATCCTTTATT
Found at i:53362 original size:29 final size:29
Alignment explanation
Indices: 53330--53392 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
53320 CCTAACGTCT
53330 CAAAATTGAAAATT-ATGGGACAAAATATC
1 CAAAATT-AAAATTCATGGGACAAAATATC
* *
53359 CAAAATTAAAATTCATGGGATAAAATGTC
1 CAAAATTAAAATTCATGGGACAAAATATC
53388 CAAAA
1 CAAAA
53393 ACTACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (29 bp):
CAAAATTAAAATTCATGGGACAAAATATC
Found at i:56376 original size:7 final size:7
Alignment explanation
Indices: 56366--56396 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
56356 TATTCTGTAT
56366 ATATAGC
1 ATATAGC
56373 ATATAGC
1 ATATAGC
56380 ATATAGC
1 ATATAGC
56387 ATATAGC
1 ATATAGC
56394 ATA
1 ATA
56397 CATAAGAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (7 bp):
ATATAGC
Found at i:66467 original size:5 final size:5
Alignment explanation
Indices: 66450--66479 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
66440 TCTCTCAAAG
66450 TTTTC TCTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC T-TTTC TTTTC TTTTC TTTTC TTTT
66480 TGCTGGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:79722 original size:323 final size:321
Alignment explanation
Indices: 78536--80529 Score: 2456
Period size: 323 Copynumber: 6.2 Consensus size: 321
78526 TTTTGTAAAA
* *
78536 TTTTAGCCGAAATCGTATACTAACCATCAC-GATTTTTGGCTAAAAACGCGTTCCGGAGCCCGA-
1 TTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
* * * * *
78599 CTCAATTTTGCACGATTTTTGGCATAAAGAATCCTT-ACAATATCTATATTCATCGAACCAAATC
65 TTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGA-AATATCTATATTCATTGGACCAAATC
* ** * *
78663 TCAGACACATTGGAATTAAGAATTTTAGTTTTAACGAGAATCTGAATCTTGTTTCGATTTAATTA
129 TCAGCCACATTAAAATTAAGGA-TTT-GTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTA
* * * * * *
78728 TAAATTAATTCGGAAAACAATGGAAAAACAATATTAGAAGCGTGAACAGCTCGACAATATTTTTG
192 GAAATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTG
*
78793 GCATTGAATTATATATTTTTCAGAGTATTGTGGC-AAAAATTGAG-AAAAAAATCTTCGGGTCAG
257 GCATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAT-TTCGGGTCAG
78856 T
321 T
* * *
78857 TTTTAGCCGAAATCGTGTACTAACAATCACAGTTTTTTTTGGCTAAAAACACGTTCTGGAGCCCC
1 TTTTAGCCGAAATCGTGTACTAACCATCACAG---TTTTTGGCTAAAAACGCGTTCCGGAGCCCC
* * *
78922 -GAATCAATTTTGCAGGAGTTTTTGGCATAAAGACTCCTTGAAATATCTAGATTCATT-GACCCA
63 AG-TTCAATTTTGCATGA-TTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGA-CCA
* * *
78985 AATCTTAGCCACATTAAAATTAAGGATTTGTTTTTCCGATAATCTGAATCTTGTTTCGATTTAAT
125 AATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAAT
** * *
79050 TAGAAATTAATTTTGAAAAAAATTGGGAAAACGATATTAAAAGCGTGAAAAGCTCGTCAAT-GTT
190 TAGAAATTAATTCGGAAAAAAA-TGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTT
* *
79114 TTGGCATTGAATTATATATATTTTTTGGGTATTGTGGCAAAAAAATTGAGAAAAAAAATTTCGGG
254 TTGGCATTGAATTATATAT-TTTTCTGAGTATTGTGGC-AAAAAATTGAGAAAAAAAATTTCGGG
**
79179 TCAAA
317 TCAGT
* *
79184 TTTTAGTCGAAATCGTGTA-TAAACCATCA-AGGTTTTTTTTTGGCTAAAAACGCGTTCCAGAGC
1 TTTTAGCCGAAATCGTGTACT-AACCATCACA-G----TTTTTGGCTAAAAACGCGTTCCGGAGC
* *
79247 CCCAGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTTATT-GACCC
60 CCCAGTTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGA-CC
* ** * * *
79311 AAATCTCTGTAATATTAAAATTAAGGATTTATTTTTACGAGAATCTGAATCTTGTATCGATTTAA
124 AAATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA
* * *
79376 TTAGAAATTAATTCGGAAAAAAAAT-AGAAATATGATATTAGAAGCGTGAAAAGCTTGTCAATAT
189 TTAGAAATTAATTCGG-AAAAAAATGGGAAA-ACGATATTAGAAGCGTGAAAAGCTCGTCAATAT
* * * *
79440 TTTTGGCATTAAATTATATATTTTTTCCGAGTATTGCGGCAAAAAAATGAGAAAAAAAATTTCGG
252 TTTTGGCATTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGG
79505 GTCAGT
316 GTCAGT
*
79511 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCATTCCGGAGCCCCAGT
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGT
* * * * *
79576 TCAATTTTGCATTATTATTGGCGTAAACACTCCTTGAAATATCTATATTCATTGGATCAAATCTC
66 TCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCTC
* *
79641 AGCCATATTAAAATTAAGGATTTGCTTTTTACGAGAATCTGAATCTTGTATCGATTTAATTAGAA
131 AGCCACATTAAAATTAAGGATTTG-TTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAA
* * *
79706 ATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGCA
195 ATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTGGCA
* * * *
79771 TTGAATTATATATTTCTCTAAGTATTATGGCAAAGAATTGAG-AAAAAAATTTCGGGTCAGT
260 TTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGT
79832 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGT
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGT
* ** *
79897 TCAATTTTGCATGATTATTGGTGTAAACACTCCTTGAAATATCTATATTCATTGGACCAAATCTC
66 TCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCTC
* *
79962 AGCCATATTAAAATTAAGGATTTGCTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAAA
131 AGCCACATTAAAATTAAGGATTTG-TTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAA
* * * *
80027 ATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAACTCATCAATCTTTTTGGCA
195 ATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTGGCA
* * * * * *
80092 TTGAATTAAATATTTTTCTAAGTATTATGGCAAAGAATTGAGAAAAAAATTTTTAGGGTCAGT
260 TTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAA-ATTTCGGGTCAGT
* ** * * *
80155 TTTTAGCCGAAATCGTGTACTAACTATCATGGTTTTTGGCTAAAAACACGTTTCGG-GACCCA-T
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGT
* ** * * *
80218 TCAGTTTTGCATGATTTTTTTTTCTAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
66 TCAATTTTGCATGA--TTTTTGGC-ATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAAT
**** * * * * **
80283 CTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCACCCAAATCTTGTTTCGATTTAATTAG
128 CTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAG
* * * * * * * *
80348 AAATTAATTCGGAAAAAAATGGAAAAATGAAATTAGAAGCGCGGCAAATC-CTTCAATTTTTTTG
193 AAATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCG-TGAAAAGCTCGTCAATATTTTTG
** * * * *
80412 GTGTTGAATTATATATTTTTCCT-ATGTATTGTGGCAAAGAATTGAGAAAAAAATTTTAGGATCA
257 GCATTGAATTATATATTTTT-CTGA-GTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCA
80476 GT
320 GT
* * * *
80478 TTTTAGCCGAAATCTTGTACTAATCATCACGGTTTTGGGCTAAAAACGCGTT
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTT
80530 TTGGGGCCAT
Statistics
Matches: 1484, Mismatches: 155, Indels: 66
0.87 0.09 0.04
Matches are distributed among these distances:
321 354 0.24
322 35 0.02
323 386 0.26
324 243 0.16
325 65 0.04
326 64 0.04
327 242 0.16
328 93 0.06
329 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (321 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGT
TCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCTC
AGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAA
TTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTGGCAT
TGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGT
Found at i:80059 original size:644 final size:640
Alignment explanation
Indices: 78536--80594 Score: 2491
Period size: 644 Copynumber: 3.2 Consensus size: 640
78526 TTTTGTAAAA
* * *
78536 TTTTAGCCGAAATCGTATACTAACCATCAC-GATTTTTGGCTAAAAACGCGTTCCGGAGCCCGA-
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
* * * *
78599 CTCAATTTTGCACGATTTTTGGCATAAAGAATCCTT-ACAATATCTATATTCATCGAACCAAATC
66 CTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGA-AATATCTATATTCATTGGACCAAATC
* ** * *
78663 TCAGACACATTGGAATTAAGAATTTTAGTTTTAACGAGAATCTGAATCTTGTTTCGATTTAATTA
130 TCAGACATATTAAAATTAAGGA-TTT-GTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTA
* * * * * *
78728 TAAATTAATTCGGAAAACAATGGAAAAACAATATTAGAAGCGTGAACAGCTCGACAATATTTTTG
193 AAAATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTG
78793 GCATTGAATTATATATTTTTCAGAGTATTGTGGC-AAAAATTGAG-AAAAAAATCTTCGGGTCAG
258 GCATTGAATTATATATTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAAAT-TTCGGGTCAG
*
78856 TTTTTAGCCGAAATCGTGTACTAACAATCACAGTTTTTTTTGGCTAAAAACACGTTCTGGAGCCC
322 TTTTTAGCCGAAATCGTGTACTAACAATCACAG---TTTTTGGCTAAAAACACGTTCCGGAGCCC
* ** *
78921 C-GAATCAATTTTGCAGGAGTTTTTGGCATAAAGACTCCTTGAAATATCTAGATTCATT-GACCC
384 CAG-TTCAATTTTGCATTA-TTTTTGGC-TAAAGACTCCTTGAAATATCTATATTCATTGGA-CC
* * *
78984 AAATCTTAGCCACATTAAAATTAAGGATTTGTTTTTCCGATAATCTGAATCTTGTTTCGATTTAA
445 AAATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA
** * * *
79049 TTAGAAATTAATTTTGAAAAAAATTGGGAAAACGATATTAAAAGCGTGAAAAGCTCGTCAATGTT
510 TTAGAAATTAATTCAGAAAAAAA-TGGGAAAACGATATTAGAAGCGTGAAAAGCTCATCAATTTT
* ** *
79114 TTGGCATTGAATTATATATATTTTTTGGGTATTGTGGCAAAAAAATTGAGAAAAAAAATTTCGGG
574 TTGGCATTGAATTATATAT-TTTTCTAAGTATTGTGGC-AAAGAATTGAG-AAAAAAATTTCGGG
**
79179 TCAAA
636 TCAGT
* *
79184 TTTTAGTCGAAATCGTGTA-TAAACCATCA-AGGTTTTTTTTTGGCTAAAAACGCGTTCCAGAGC
1 TTTTAGCCGAAATCGTGTACT-AACCATCACA-G---TTTTTTGGCTAAAAACGCGTTCCGGAGC
*
79247 CCCAGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTTATT-GACCC
61 CCCAGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGA-CC
* * *
79311 AAATCTCTGTA-ATATTAAAATTAAGGATTTATTTTTACGAGAATCTGAATCTTGTATCGATTTA
125 AAATCTCAG-ACATATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTA
* * * *
79375 ATTAGAAATTAATTCGGAAAAAAAAT-AGAAATATGATATTAGAAGCGTGAAAAGCTTGTCAATA
189 ATTAAAAATTAATTCGG-AAAAAAATGGGAAA-ACGATATTAGAAGCGTGAAAAGCTCGTCAATA
* * * *
79439 TTTTTGGCATTAAATTATATATTTTTTCCGAGTATTGCGGCAAAAAAATGAGAAAAAAAATTTCG
252 TTTTTGGCATTGAATTATATA-TTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCG
* * *
79504 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCATTCCGGAG
316 GGTCAGTTTTTAGCCGAAATCGTGTACTAACAATCACAGTTTTTGGCTAAAAACACGTTCCGGAG
* * *
79569 CCCCAGTTCAATTTTGCATTATTATTGGCGTAAACACTCCTTGAAATATCTATATTCATTGGATC
381 CCCCAGTTCAATTTTGCATTATTTTTGGC-TAAAGACTCCTTGAAATATCTATATTCATTGGACC
* *
79634 AAATCTCAGCCATATTAAAATTAAGGATTTGCTTTTTACGAGAATCTGAATCTTGTATCGATTTA
445 AAATCTCAGCCACATTAAAATTAAGGATTTG-TTTTTACGAGAATCTGAATCTTGTTTCGATTTA
79699 ATTAGAAATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCATCAATCTT
509 ATTAGAAATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCATCAAT-TT
* *
79764 TTTGGCATTGAATTATATATTTCTCTAAGTATTATGGCAAAGAATTGAGAAAAAAATTTCGGGTC
573 TTTGGCATTGAATTATATATTTTTCTAAGTATTGTGGCAAAGAATTGAGAAAAAAATTTCGGGTC
79829 AGT
638 AGT
79832 TTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
* * ** *
79896 TTCAATTTTGCATGATTATTGGTGTAAACACTCCTTGAAATATCTATATTCATTGGACCAAATCT
66 CTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCT
*
79961 CAGCCATATTAAAATTAAGGATTTGCTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAA
131 CAGACATATTAAAATTAAGGATTTG-TTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAA
* * * *
80026 AATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAACTCATCAATCTTTTTGGC
195 AATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTGGC
* * * * *
80091 ATTGAATTAAATATTTTTCTA-AGTATTATGGCAAAGAATTGAGAAAAAAATTTTTAGGGTCAGT
260 ATTGAATTATATATTTTTC-AGAGTATTGTGGCAAAAAATTGAGAAAAAAA-ATTTCGGGTCAGT
* ** * *
80155 TTTTAGCCGAAATCGTGTACTAACTATCATGGTTTTTGGCTAAAAACACGTTTCGG-GACCCA-T
323 TTTTAGCCGAAATCGTGTACTAACAATCACAGTTTTTGGCTAAAAACACGTTCCGGAGCCCCAGT
* * ** * *
80218 TCAGTTTTGCATGATTTTTTTTTCTAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
388 TCAATTTTGCAT--TATTTTTGGCT--AAAGACTCCTTGAAATATCTATATTCATTGGACCAAAT
**** * * * * **
80283 CTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCACCCAAATCTTGTTTCGATTTAATTAG
449 CTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAG
* * * * * * * *
80348 AAATTAATTCGGAAAAAAATGGAAAAATGAAATTAGAAGCGCGGCAAATC-CTTCAATTTTTTTG
514 AAATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCG-TGAAAAGCTCATCAA-TTTTTTG
** * * *
80412 GTGTTGAATTATATATTTTTCCTATGTATTGTGGCAAAGAATTGAGAAAAAAATTTTAGGATCAG
577 GCATTGAATTATATATTTTT-CTAAGTATTGTGGCAAAGAATTGAGAAAAAAA-TTTCGGGTCAG
80477 T
640 T
* * * * ** * ***
80478 TTTTAGCCGAAATCTTGTACTAATCATCAC-GGTTTTGGGCTAAAAACGCGTTTTGGGGCCATGG
1 TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
** * * * *
80542 CTCTGTTTTGCATGATTTTTGTACAGAGAGACTCCTTGAAA-ATCTTTATTCAT
66 CTCAATTTTGCATGATTTTTG-GCATAAAGACTCCTTGAAATATCTATATTCAT
80595 CAAGCACCTG
Statistics
Matches: 1221, Mismatches: 153, Indels: 76
0.84 0.11 0.05
Matches are distributed among these distances:
642 12 0.01
643 37 0.03
644 327 0.27
645 144 0.12
646 91 0.07
647 14 0.01
648 69 0.06
649 13 0.01
650 114 0.09
651 164 0.13
652 88 0.07
653 87 0.07
654 53 0.04
655 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (640 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG
CTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCT
CAGACATATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAAA
ATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCGTCAATATTTTTGGCA
TTGAATTATATATTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTT
TAGCCGAAATCGTGTACTAACAATCACAGTTTTTGGCTAAAAACACGTTCCGGAGCCCCAGTTCA
ATTTTGCATTATTTTTGGCTAAAGACTCCTTGAAATATCTATATTCATTGGACCAAATCTCAGCC
ACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGCTCATCAATTTTTTGGCATTGAAT
TATATATTTTTCTAAGTATTGTGGCAAAGAATTGAGAAAAAAATTTCGGGTCAGT
Found at i:81297 original size:322 final size:320
Alignment explanation
Indices: 80602--81766 Score: 1398
Period size: 322 Copynumber: 3.6 Consensus size: 320
80592 CATCAAGCAC
* * * * *
80602 CTGAATCTTGTTTCGATTTAATT---AATTAATTCAGAAAAAAATGGAAAAACGTTAATGGATGC
1 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
* * * * * *
80664 GTTAAAAG-TCCTTCGATCTTTTTGGCGTTGAATTATATATTTTATATGAGTATTGTGGC-ACAA
66 GTGAAAAGCT-CTTCAATCTTTTTGGCGTTGAATTATATATTTT-TCTAAGTATTATGGCAAAAA
* * * *
80727 AATG-GAGAAAAATTCTTTGGGTCAGTTTTTAGTCGAGATTGTGTACTAACCATCACGGTTTTTG
129 AATGAGA-AAAAATT-TTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * ** * *
80791 GCTAAAAACGTGTTTCGGAGCCCCGGCTCAATTTTGCATGATTTTTTGTGTAAATTCTCATTAAA
192 GCTAAAAACGCGTTTCGGAGCCCCAGTTCAATTTTGCATGATTTTTTGCGTAAACACTCCTTGAA
* * *
80856 ATACCTATATTCATCGAACCAAATCTCAGCCACATTGGAATTAAGGATTTGTTTTTACGAGAAT
257 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGAAATTAAGGATTTATTTTTACGAGAAT
* * *
80920 CTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATTGAAAAAACGATATTAGAAG
1 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AAATGGAAAAACGATATTAGAAG
* * *
80985 CGTGAAAAGCTCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAA
65 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTAAGTATTATGGCAAAAA
* * * *
81050 AATGAGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGAGTACTAACCATCACTGTTTTTGGC
129 AATGAGAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* * ** *
81115 TAAAAACGCGTTCCGGAGCCCCAGTTCAATTTTGCATTATTACTGGCGTAAACACTCCTTGAAAT
194 TAAAAACGCGTTTCGGAGCCCCAGTTCAATTTTGCATGATTTTTTGCGTAAACACTCCTTGAAAT
* * * *
81180 ATCTATATTCATTGGACCAAATCTCAGCCATATTAAAATTAAGGATTTATTTTTTACGAGAAT
259 ATCTATATTCATCGAACCAAATCTCAGCCACATTGAAATTAAGGATTTA-TTTTTACGAGAAT
* * *
81243 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGC
1 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
* * * *
81308 GTGAAAAGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGCAAAGAAT
66 GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCTAAGTATTATGGCAAAAAAA
* * *
81373 TGAGAAAAATTTTTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCATGGTTTTTTGG
131 TGAGAAAAA--ATTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGG
* * * *
81438 ATAAAAACGCGTTTCGG-GACCCCA-TTCAGTTTTGCATGATTTTTTTTC-TAGAAAGACTCCTT
193 CTAAAAACGCGTTTCGGAG-CCCCAGTTCAATTTTGCATGA-TTTTTTGCGT--AAACACTCCTT
*** * * *
81500 GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTGTTTAAGCATTTACTTTTACGAGC
254 GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGAAATTAAGGATTTATTTTTACGAGA
*
81565 AC
319 AT
* *
81567 CCGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGAAATTAGAAGC
1 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
* * * * * * *
81632 GCGGCAAATC-CTTCAAT-TTTTTGGTGTTGAATTATATATTTTTCCAATGTATTGTGGCAAAGA
66 G-TGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCTAA-GTATTATGGCAAAAA
* * * *
81695 ATTGAGAGAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTGGGC
129 AATGAGAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
81760 TAAAAAC
194 TAAAAAC
81767 AAGTTTCAGG
Statistics
Matches: 728, Mismatches: 101, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
318 22 0.03
321 59 0.08
322 301 0.41
323 151 0.21
324 134 0.18
325 61 0.08
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (320 bp):
CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCTAAGTATTATGGCAAAAAAA
TGAGAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
AAAACGCGTTTCGGAGCCCCAGTTCAATTTTGCATGATTTTTTGCGTAAACACTCCTTGAAATAT
CTATATTCATCGAACCAAATCTCAGCCACATTGAAATTAAGGATTTATTTTTACGAGAAT
Found at i:81894 original size:920 final size:916
Alignment explanation
Indices: 80923--84824 Score: 4735
Period size: 920 Copynumber: 4.2 Consensus size: 916
80913 CGAGAATCTA
* * * * * * *
80923 AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATTGAAAAAACGATATTAGAAGCGT
1 AATCTTTTTTCGATTTAATT---AATTAATTCAGAAAA-AAATGGAAAAACGATACTGGATGCGT
* * * * *
80988 GAAAAG-CTCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAAA
62 TAAAAGTC-CTTCAATATTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
* * * * * *
81052 TGAGAAAAAAAT-TTCGGGTCAGTTTTTAGCCGAAATCGAGTACTAACCATCACTGTTTTTGGCT
126 TGAG-AAAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTACTAACCATCACGGTTTTTGGCT
* * * * * *
81116 AAAAACGCGTTCCGGAGCCCCAGTTCAATTTTGCATTATTACTGGCGTAAACACTCCTTGAAATA
190 AAAAACGTGTTTCGGAGCCCCAGTTCAATTTTGCATGATTATTGGCGTAAACACTCATTAAAATA
* * * *
81181 TCTATATTCATTGGACCAAATCTCAGCCATATTAAAATTAAGGATTTATTTTTTACGAGAATCTG
255 TCTATATTCATCGAACCAAATCTCAGCCACATTAAAATTAAGGATTT-GTTTTTACGAGAATCTG
81246 AATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGCGTG
319 AATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGCGTG
81311 AAAAGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGCAAAGAATTGA
384 AAAAGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGCAAAGAATTGA
*** *
81376 GAAAAATTTTTTTAGGGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCATGGTTTTTTGGATA
449 GAAAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTG--CT-ACTATCATGG-TTTTTGGCTA
81441 AAAACGCGTTTCGGGACCCCATTCAGTTTTGCATGATTTTTTTTCTAGAAAGACTCCTTGAAATA
510 AAAACGCGTTTCGGGACCCCATTCAGTTTTGCATGATTTTTTTTCTAGAAAGACTCCTTGAAATA
*
81506 TCTATATTCATCGAACCAAATCTCAGCCACATTGTGTTTAAGCATTTACTTTTACGAGCACCCGA
575 TCTATATTCATCGAACCAAATCTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCACCCGA
81571 ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGAAATTAGAAGCGCGG
640 ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGAAATTAGAAGCGCGG
*
81636 CAAATCCTTCAATTTTTTGGTGTTGAATTATATATTTTTCCAATGTATTGTGGCAAAGAATTGAG
705 CAAATCCTTCAATTTTTTGGTGTTGAATTATATATTTTTCCTATGTATTGTGGCAAAGAATTGAG
*
81701 -AGAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTGGGCTAAAA
770 AAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTGGGCTAAAA
* *
81765 ACAAGTTTCAGGGCCATGGCTCTGTTTTGCATGATTTTTGTACAGAGAGAGTCCTTGAAAATCTT
835 ACGAGTTTCAGGGCCATGGCTCTGTTTTGCATGATTTTTGTACAGAGAGACTCCTTGAAAATCTT
81830 TATTCATCAAGCACCTG
900 TATTCATCAAGCACCTG
81847 AATCTTTTTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
1 AATCTTTTTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
* *
81912 AGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
66 AGTCCTTCAATATTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
*
81977 AAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTACTAACCTTCACGGTTTTTGGCTAAAAAC
131 AAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* * * **
82042 GTGTTTCGGAGCCCCGGCTCAATTTTGCATGACTT-TTGGTGTAAATTCTCATTAAAATATCTAT
196 GTGTTTCGGAGCCCCAGTTCAATTTTGCATGA-TTATTGGCGTAAACACTCATTAAAATATCTAT
* **
82106 ATTCATCGAACCAAATCTCAGTCACATTGGAATTAAGGATTTGTTTTTACGAGAATCTGAATCTT
260 ATTCATCGAACCAAATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTT
* * *
82171 GTTTCGATTCAATTAGAAATTAATTCAGAAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGC
325 GTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGCGTGAAAAGC
*
82236 TCATCAATCTTTTTGGCATTGAATTATATATTTTTGTAAGTATTATGGCAAAGAATTGAGAAAAA
390 TCATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGCAAAGAATTGAGAAAAA
82301 AAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGTGCTAACTATCATGGTTTTTGGCTAAAAACGC
455 AAATTTTAGGGTCAGTTTTTAGCCGAAATC--GTGCT-ACTATCATGGTTTTTGGCTAAAAACGC
*
82366 GTTTCGGGACCCCATTCAGTTTTGCATGA-TTTTTTTCTAGAAAGACTCCTTGAAATATATATAT
517 GTTTCGGGACCCCATTCAGTTTTGCATGATTTTTTTTCTAGAAAGACTCCTTGAAATATCTATAT
* * *
82430 TCATCGAACCAAATCTCAGCCACATTTTGTTTAAGCATTTATTTTTATGAGTACCCCGAATCTTG
582 TCATCGAACCAAATCTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCA-CCCGAATCTTG
* *
82495 TTTCGATTTAATTAGAAATTAATTCGGAAAAAAGATGGAAAAATGAAATTAGAAGCGTGGCAAAT
646 TTTCGATTTAATTAGAAATTAATTCGGAAAAAA-ATGGAAAAACGAAATTAGAAGCGCGGCAAAT
* *
82560 CCTTCAATTTTTTTGGTCTTGAATTATATATTTTTTCTATGTATTGTGGCAAAGAATTGAGAAAA
710 CCTTCAA-TTTTTTGGTGTTGAATTATATATTTTTCCTATGTATTGTGGCAAAGAATTGAGAAAA
* *
82625 AAATTTTAGGGTCAGTTTTTAGACGAAATCTTGTACTAATCATCACGGTTTTGGGCTAAAAACGA
774 AAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTGGGCTAAAAACGA
* * *
82690 GTTTCGGGGCCATGGCTCTGTTTTGCATGATTTTTGTATAGAGAGACTCCTTGAAAATCATTATT
839 GTTTCAGGGCCATGGCTCTGTTTTGCATGATTTTTGTACAGAGAGACTCCTTGAAAATCTTTATT
82755 CATCAAGCACCTG
904 CATCAAGCACCTG
* *
82768 AATC-TTGTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGTTACTGGATGCGTTAAA
1 AATCTTTTTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
* * * *
82832 AGTCCTTTAATCTTTTTGGCATTGAATTATATATTTTATATGAGTATTGTGGCAAAAAATTGAGA
66 AGTCCTTCAATATTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
*
82897 AAAATTCTTTGTGTCAGTTTTTAGCCGAGATTGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
131 AAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* * * * * * **
82962 GTGTTTTGGAGCTCCGGATCAATTTTGCATGATTTTTGGTGTAAATTCTCATTAAAATATCTATA
196 GTGTTTCGGAGCCCCAGTTCAATTTTGCATGATTATTGGCGTAAACACTCATTAAAATATCTATA
** *
83027 TTCATCGAACCAAATCTCAGCCACATTGGAATTAAGGATTTGTTTTTACGAGAATCTAAATCTTG
261 TTCATCGAACCAAATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTG
* ** * *
83092 TTTTCGATTTAATTAGAAATTAATTC-GGAAAAAATGTAAAAACGATATTATAAGCGAGAACAGC
326 -TTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGCGTGAAAAGC
* * * * *
83156 TCGA-CAATATTTTTGGCATTAAATTATATATTTTTCTGAGTATTGTTGCGAAA-AATTGAGAAA
390 TC-ATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGC-AAAGAATTGAGAAA
* * * **
83219 AAAAAATTTCGGTTCAGTTTTTAGCCG-AATC---CT-C-A-C--GGTTTTTGGCTAAAAACATG
453 AAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGCTACTATCATGGTTTTTGGCTAAAAACGCG
** * * * * * ** *
83275 -CACTGGAGCCCCGAATCAATTTTGCTTGAGTTTTTGGC-ATAAAGACTCCTTGAAATATCTATA
518 TTTCGGGA-CCCC-ATTCAGTTTTGCATGATTTTTTTTCTAGAAAGACTCCTTGAAATATCTATA
* * **** * * * ** * **
83338 TTCATTG-ACGCAAATCTTAGCCACATTAAAATTAAGGATTT-GTTTTACTATAATCTAAATCTT
581 TTCATCGAAC-CAAATCTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCACCCGAATCTT
* * * *
83401 GTTTCGATTTAATTAGAAATTAAATCGGAAAAAAATTGGGAAAACGATATT---A--GC-GAAAA
645 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA-TGGAAAAACGAAATTAGAAGCGCGGCAAA
* * ** * * *
83460 GCTCGTCAATCTTTTTGGCATTGAATTATATATATTTT-TTGA-GTATTGTGCGAAAAAAATTGA
709 TC-CTTCAAT-TTTTTGGTGTTGAATTATATAT-TTTTCCT-ATGTATTGTG-GCAAAGAATTGA
* * * * * * * * * *
83523 GAAAAAAAATTTCGGATCAATTTTTAGTCAAAATCGTGTACTAACCATGAAGGTTTTTTTGGCTA
769 GAAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGG--TTTTGGGCTA
* * * * * * * *
83588 AAAACGCA--TTCGAAAGACC-CGGCTCAAG-TTTGCATGATTCTTG-GCATAAAGACTCCTTGA
832 AAAACG-AGTTTC--AGGGCCATGGCTC-TGTTTTGCATGATTTTTGTACAGAGAGACTCCTTGA
* *
83648 AATATCTATATTTATTGACGCAAATCTCAGCCACATTAG
893 AA-ATC----TTTATT----C--ATC-AAG-CAC-CT-G
* ** * * *
83687 AATTAAGGATTTATTTTTAAGAGAATCAGAATCTTGTTTCGATTTAATT-AGAAATTAATTCGGA
1 -----A--A--TCTTTTT-------TC-G-AT-TTAATT--AATTAATTCAGAAA-AAAAT-GG-
* * *** * * * * *** * * *
83751 AAAAATTGAAAAAACGAT--ATTAGAAG--CGTGAA-AAGCTCGTCAAT--A-T-TATATTTTTT
42 AAAAA-CG-ATACTGGATGCGTTAAAAGTCCTTCAATATTTTTGGCATTGAATTATATATTTTTT
* * * *
83807 CTGAGTATTGTGGTCAAAAAAAATGAGAAAAAAATT-TCT-GGTCAGTTTTTAGCCGAAAATCGT
105 CTGAGTATTGTGG-C-AAAAAATTGAG--AAAAATTCTTTGGGTCAGTTTTTAGCCG-AGATTGT
* * * * * *
83870 GTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCAGTTCAATTTTGCATTATT
165 GTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGAGCCCCAGTTCAATTTTGCATGATT
* * * * * *
83935 ATTGGCGTAAACACTCCTTGAAATATATATATTCATTGGACCAAATCTCAGCCATATTAAAATTA
230 ATTGGCGTAAACACTCATTAAAATATCTATATTCATCGAACCAAATCTCAGCCACATTAAAATTA
*
84000 AGGATTTATTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAA
295 AGGATTT-GTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAA
*
84065 ATGGGAAAATGATATTATAAGCGTGAAAAGCTCATCAATCTTTTTGGCATTGAATTATATATTTT
359 ATGGGAAAACGATATTATAAGCGTGAAAAGCTCATCAATCTTTTTGGCATTGAATTATATATTTT
* ** * *
84130 TCTAAGTATTATGGCAAAGAATTGAGAAAAGATTTTTTAGGGTAAGTTTTTAGCCGAAATAGTG-
424 TCTAAGTATTATGGCAAAGAATTGAGAAAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCGTGC
*
84194 TACTATCATGCTTTTTGGCTAAAAACGCGTTTCGGGA-CCCATTCAGTTTTGCATGATTTTTTTT
489 TACTATCATGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCATTCAGTTTTGCATGA-TTTTTTT
* *
84258 TCTAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGTGTTTAAAC
553 TCTAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTGTTTAAGC
* *
84323 ATTTATTTTTACGAGCACCCGAATCTTGTTTCGATTTAATTATAAATTAATTCGGGAAAAAATGG
618 ATTTATTTTTACGAGCACCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGG
*
84388 AAAAATGAAATTAGAAGCGCGGCAAATCCTTCAATTTTTTGGTGTTGAATTATATATTTTTCCTA
683 AAAAACGAAATTAGAAGCGCGGCAAATCCTTCAATTTTTTGGTGTTGAATTATATATTTTTCCTA
84453 TGTATTGTGGCAAAGAATTGAG-AAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAA
748 TGTATTGTGGCAAAGAATTGAGAAAAAAATTTTAGGGTCAGTTTTTAGCCGAAATCTTGTACTAA
* *
84517 CCATCACGGTTTTGGGCTAAAAACGCGTTTCGGGGCCATGGCTCTGTTTTGCATGATTTTTGTAC
813 CCATCACGGTTTTGGGCTAAAAACGAGTTTCAGGGCCATGGCTCTGTTTTGCATGATTTTTGTAC
84582 AGAGAGACTCCTTGAAAATCTTTA-TCATCAAGCACCTG
878 AGAGAGACTCCTTGAAAATCTTTATTCATCAAGCACCTG
* *
84620 AATC-TTGTTCGTTTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
1 AATCTTTTTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
* * * *
84684 AGTCCTTCAATCA-TTTTGACATTGAATTATATATTTTATATGAGTAGTGTGGCAAAAAATTGAG
66 AGTCCTTCAAT-ATTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* *
84748 AAAAATTCTTTGGGTCTGTTTTTAGCCGAGATTGTGTACGTTA-CATCACGGTTTTTGGCTAAAA
130 AAAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTAC-TAACCATCACGGTTTTTGGCTAAAA
84812 ACGTGTTTCGGAG
194 ACGTGTTTCGGAG
84825 ACCCGGCTCA
Statistics
Matches: 2526, Mismatches: 331, Indels: 253
0.81 0.11 0.08
Matches are distributed among these distances:
901 6 0.00
902 35 0.01
903 58 0.02
904 19 0.01
905 37 0.01
906 6 0.00
907 61 0.02
908 32 0.01
909 83 0.03
910 9 0.00
911 15 0.01
912 18 0.01
913 46 0.02
914 31 0.01
915 6 0.00
916 24 0.01
917 86 0.03
918 90 0.04
919 237 0.09
920 681 0.27
921 190 0.08
923 3 0.00
924 21 0.01
926 2 0.00
928 2 0.00
929 3 0.00
933 1 0.00
934 1 0.00
935 3 0.00
936 25 0.01
937 6 0.00
938 28 0.01
939 156 0.06
940 143 0.06
941 17 0.01
942 2 0.00
943 13 0.01
944 6 0.00
945 5 0.00
946 14 0.01
947 13 0.01
948 119 0.05
949 72 0.03
950 42 0.02
951 17 0.01
952 29 0.01
953 8 0.00
954 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (916 bp):
AATCTTTTTTCGATTTAATTAATTAATTCAGAAAAAAATGGAAAAACGATACTGGATGCGTTAAA
AGTCCTTCAATATTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
AAAATTCTTTGGGTCAGTTTTTAGCCGAGATTGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
GTGTTTCGGAGCCCCAGTTCAATTTTGCATGATTATTGGCGTAAACACTCATTAAAATATCTATA
TTCATCGAACCAAATCTCAGCCACATTAAAATTAAGGATTTGTTTTTACGAGAATCTGAATCTTG
TTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGGAAAACGATATTATAAGCGTGAAAAGCT
CATCAATCTTTTTGGCATTGAATTATATATTTTTCTAAGTATTATGGCAAAGAATTGAGAAAAAA
AATTTTAGGGTCAGTTTTTAGCCGAAATCGTGCTACTATCATGGTTTTTGGCTAAAAACGCGTTT
CGGGACCCCATTCAGTTTTGCATGATTTTTTTTCTAGAAAGACTCCTTGAAATATCTATATTCAT
CGAACCAAATCTCAGCCACATTGTGTTTAAGCATTTATTTTTACGAGCACCCGAATCTTGTTTCG
ATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGAAATTAGAAGCGCGGCAAATCCTTCA
ATTTTTTGGTGTTGAATTATATATTTTTCCTATGTATTGTGGCAAAGAATTGAGAAAAAAATTTT
AGGGTCAGTTTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTGGGCTAAAAACGAGTTTCAG
GGCCATGGCTCTGTTTTGCATGATTTTTGTACAGAGAGACTCCTTGAAAATCTTTATTCATCAAG
CACCTG
Done.