Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022815.1 Corchorus olitorius cultivar O-4 contig22848, 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: 85240
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2643 original size:16 final size:15
Alignment explanation
Indices: 2605--2646 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2595 ACAGAGATTG
*
2605 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
2620 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2635 ACTAGAAAACAA
1 AC-AGAAAACAA
2647 AGCAAAGTAA
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:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4637 original size:20 final size:20
Alignment explanation
Indices: 4612--4662 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4602 TACTTATATC
*
4612 ATTTGGGTTTTAGGGTTAGT-
1 ATTTGGGTTTTAGAGTTA-TA
*
4632 ATTTGGGCTTTAGAGTTATA
1 ATTTGGGTTTTAGAGTTATA
*
4652 ACTTGGGTTTT
1 ATTTGGGTTTT
4663 TATTAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.18, C:0.04, G:0.29, T:0.49
Consensus pattern (20 bp):
ATTTGGGTTTTAGAGTTATA
Found at i:12310 original size:145 final size:145
Alignment explanation
Indices: 12117--12520 Score: 522
Period size: 145 Copynumber: 2.7 Consensus size: 145
12107 CCATTTTGGT
**
12117 AAGTTTTTCAA-CAAAGCTGTGTTTAAATTTCAAAATCACAACCTTGCTCAAGGTTAAGTTTGCA
1 AAGTTTTT-AATCAAAGCTGCATTTAAATTTCAAAATCACAACCTTGCTCAAGGTTAAGTTTGCA
* * *
12181 TTTGTAAGACCTCCGGGCACGATTTCGGAAACCTTCAGGTATTAATTCTGATAAATCCTCCGGGT
65 TTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGT
12246 ATCATTTCATTTCATC
130 ATCATTTCATTTCATC
* * ** * *
12262 AAGTTTTTAATCAAAGTTGCATTTAATTTTCAAAAAAAAAACCTTGCTCAAGGTTGAGTTTGCAT
1 AAGTTTTTAATCAAAGCTGCATTTAAATTTCAAAATCACAACCTTGCTCAAGGTTAAGTTTGCAT
* * *
12327 TTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATTAATTTTGATGAATCCTCCGGGTA
66 TTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGTA
12392 TCATTTCATTTCATC
131 TCATTTCATTTCATC
* ** *
12407 AGGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACAACCTTGCTCAAGGTCTCAATTCAGA
1 AAGTTTTTAATCAAAGCTGCATTTAAATTTCAAAATCACAACCTTGCTCAAGG------TT-A-A
* * * *
12472 GTTTACATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGGGTAT
58 GTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCAGGTAT
12521 CATTTCATTT
Statistics
Matches: 224, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
144 2 0.01
145 173 0.77
151 2 0.01
153 47 0.21
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (145 bp):
AAGTTTTTAATCAAAGCTGCATTTAAATTTCAAAATCACAACCTTGCTCAAGGTTAAGTTTGCAT
TTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGTA
TCATTTCATTTCATC
Found at i:12526 original size:128 final size:128
Alignment explanation
Indices: 12382--12646 Score: 503
Period size: 128 Copynumber: 2.1 Consensus size: 128
12372 TTTGATGAAT
*
12382 CCTCCGGGTATCATTTCATTTCATCAGGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACA
*
12447 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATTTCAGAAA
66 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAA
*
12510 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACA
12575 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAA
66 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAA
12638 CCTCCGGGT
1 CCTCCGGGT
12647 GTTAATTCTG
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 134 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (128 bp):
CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACA
ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAA
Found at i:12685 original size:281 final size:273
Alignment explanation
Indices: 12237--12799 Score: 901
Period size: 281 Copynumber: 2.0 Consensus size: 273
12227 TCTGATAAAT
*
12237 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAATTTTCAAAAAAAAA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAAAAAAA
* * *
12302 ACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTA
66 ACCTTGCTCAAGGTTGAGTTTACATTTGTAAGACCTCCGGGCACAATCTCAGAAACCTCCGGGTA
* * *
12367 TTAATTTTGATGAATCCTCCGGGTATCATTTCATTTCATCAGGTTTTTAATCAAAGCTGTGTTTA
131 TTAATTCTGATGAATCCTCCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTA
**
12432 AGTTTCAAAATCACAACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGC
196 AGTTTCAAAATCACAACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGC
*
12497 ACAATTTCAGAAA
261 ACAATCTCAGAAA
** ** *
12510 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAAAAAAA
*
12575 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
66 ACCTTGCTCAAGG------TT--GAGTTTACATTTGTAAGACCTCCGGGCACAATCTCAGAAACC
*
12640 TCCGGGTGTTAATTCTGATGAATCCTCCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGC
123 TCCGGGTATTAATTCTGATGAATCCTCCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGC
12705 TGTGTTTAAGTTTCAAAATCACAACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTC
188 TGTGTTTAAGTTTCAAAATCACAACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTC
12770 CTCCGGGCACAATCTCAGAAA
253 CTCCGGGCACAATCTCAGAAA
12791 CCTCCGGGT
1 CCTCCGGGT
12800 GTTAATTCTG
Statistics
Matches: 265, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
273 72 0.27
279 2 0.01
281 191 0.72
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (273 bp):
CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAAAAAAA
ACCTTGCTCAAGGTTGAGTTTACATTTGTAAGACCTCCGGGCACAATCTCAGAAACCTCCGGGTA
TTAATTCTGATGAATCCTCCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTA
AGTTTCAAAATCACAACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGC
ACAATCTCAGAAA
Found at i:12702 original size:153 final size:153
Alignment explanation
Indices: 12510--12875 Score: 597
Period size: 153 Copynumber: 2.4 Consensus size: 153
12500 ATTTCAGAAA
12510 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
**
12575 ACCTTGCTCAAGGTCTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
66 ACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
* *
12640 TCCGGGTGTTAATTCTGATGAAT
131 TCCGGGTGTTAATTCTGATAAAC
* *
12663 CCTCCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCACA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
12728 ACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
66 ACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
12793 TCCGGGTGTTAATTCTGATAAAC
131 TCCGGGTGTTAATTCTGATAAAC
** ** * * * * *
12816 CCTTTGGGTATCACCTCATTTCATCAAGTTGTTAATCAAAATTGCGTTTAAATTTAAAAA
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAA
12876 AAAAAAAAAA
Statistics
Matches: 196, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 196 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (153 bp):
CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTGTTTAAGTTTCAAAATCACA
ACCTTGCTCAAGCACTCAATTCAGAGTTTACATTTGTAAGTCCTCCGGGCACAATCTCAGAAACC
TCCGGGTGTTAATTCTGATAAAC
Found at i:12877 original size:1 final size:1
Alignment explanation
Indices: 12871--12895 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12861 GTTTAAATTT
12871 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12896 CCTTGCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12971 original size:20 final size:20
Alignment explanation
Indices: 12946--12983 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12936 AATTAATTCA
12946 GACAAGTCCC-CCGGGCATCT
1 GACAAG-CCCTCCGGGCATCT
12966 GACAAGCCCTCCGGGCAT
1 GACAAGCCCTCCGGGCAT
12984 TCCATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GACAAGCCCTCCGGGCATCT
Found at i:13133 original size:37 final size:37
Alignment explanation
Indices: 13023--13521 Score: 300
Period size: 37 Copynumber: 13.7 Consensus size: 37
13013 TTATATGTTT
* * * *
13023 TAATCCTATTCAAGACCATTGCTTTATCAATCATTTC
1 TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
* ** * * **
13060 AGAATCCTGCTCAGGATCATATCTTTATTAGGCAATTC
1 -TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
*
13098 TAATCGTATTCAGGATCATTTCTTTATCAATCAATT-
1 TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
* * * * **
13134 TCAATCCTATTTAGGATCACTGCCTTATGGAT---TTC
1 T-AATCCTATTCAGGATCATTTCTTTATCAATCAATTC
* * *
13169 ---T--T-TT--GAATCATTGCTTTATCAATCATTTC
1 TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
* ** *
13198 AGAATCCTGCTCAGGATCATTTCTTTATTAGA-CAATTC
1 -TAATCCTATTCAGGATCATTTCTTTATCA-ATCAATTC
13236 TAATCCTATTCAGGATCATTTCTTT-TCCAATCAATT-
1 TAATCCTATTCAGGATCATTTCTTTAT-CAATCAATTC
* * * *
13272 TCCATCCTATTCAGGATCGTTGT-TGTATCAATCATTTC
1 T-AATCCTATTCAGGATCATT-TCTTTATCAATCAATTC
* * * **
13310 AGAATCCTGCTT-AGGATCATTTCTTTATTAGCCAATTC
1 -TAATCCT-ATTCAGGATCATTTCTTTATCAATCAATTC
* *
13348 TAATCCTATTCAAGATCATTTCTTTACCAATCAATT-
1 TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
* * * *
13384 TCCATCCTATTCAGGATCGTTGT-TGTATCAATCATTTC
1 T-AATCCTATTCAGGATCATT-TCTTTATCAATCAATTC
* ** * * **
13422 AGAATCCTGCTCAGGATCAATTCTTTATTAGCCAATTC
1 -TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
*
13460 TAATCCAATTCAGGATCATTTCTTTATCAATCAATT-
1 TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
*
13496 TCAATCCTATTCAGGATCATTGCTTT
1 T-AATCCTATTCAGGATCATTTCTTT
13522 CCGAATCCTA
Statistics
Matches: 343, Mismatches: 87, Indels: 63
0.70 0.18 0.13
Matches are distributed among these distances:
26 14 0.04
28 2 0.01
29 4 0.01
31 1 0.00
33 1 0.00
34 2 0.01
35 1 0.00
36 9 0.03
37 211 0.62
38 95 0.28
39 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (37 bp):
TAATCCTATTCAGGATCATTTCTTTATCAATCAATTC
Found at i:13288 original size:138 final size:138
Alignment explanation
Indices: 13039--13289 Score: 441
Period size: 138 Copynumber: 1.8 Consensus size: 138
13029 TATTCAAGAC
* *
13039 CATTGCTTTATCAATCATTTCAGAATCCTGCTCAGGATCATATCTTTATTAGGCAATTCTAATCG
1 CATTGCTTTATCAATCATTTCAGAATCCTGCTCAGGATCATATCTTTATTAGACAATTCTAATCC
*
13104 TATTCAGGATCATTTCTTTATCAATCAATTTCAATCCTATTTAGGATCACTGCCTTATGGATTTC
66 TATTCAGGATCATTTCTTTATCAATCAATTTCAATCCTATTCAGGATCACTGCCTTATGGATTTC
13169 TTTTGAAT
131 TTTTGAAT
*
13177 CATTGCTTTATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGACAATTCTAATCC
1 CATTGCTTTATCAATCATTTCAGAATCCTGCTCAGGATCATATCTTTATTAGACAATTCTAATCC
*
13242 TATTCAGGATCATTTCTTT-TCCAATCAATTTCCATCCTATTCAGGATC
66 TATTCAGGATCATTTCTTTAT-CAATCAATTTCAATCCTATTCAGGATC
13290 GTTGTTGTAT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
137 1 0.01
138 106 0.99
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (138 bp):
CATTGCTTTATCAATCATTTCAGAATCCTGCTCAGGATCATATCTTTATTAGACAATTCTAATCC
TATTCAGGATCATTTCTTTATCAATCAATTTCAATCCTATTCAGGATCACTGCCTTATGGATTTC
TTTTGAAT
Found at i:13382 original size:112 final size:112
Alignment explanation
Indices: 13185--13513 Score: 586
Period size: 112 Copynumber: 2.9 Consensus size: 112
13175 ATCATTGCTT
*
13185 TATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGACAATTCTAATCCTATTCAGG
1 TATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAATTCTAATCCTATTCAGG
*
13250 ATCATTTCTTTTCCAATCAATTTCCATCCTATTCAGGATCGTTGTTG
66 ATCATTTCTTTACCAATCAATTTCCATCCTATTCAGGATCGTTGTTG
* *
13297 TATCAATCATTTCAGAATCCTGCTTAGGATCATTTCTTTATTAGCCAATTCTAATCCTATTCAAG
1 TATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAATTCTAATCCTATTCAGG
13362 ATCATTTCTTTACCAATCAATTTCCATCCTATTCAGGATCGTTGTTG
66 ATCATTTCTTTACCAATCAATTTCCATCCTATTCAGGATCGTTGTTG
* *
13409 TATCAATCATTTCAGAATCCTGCTCAGGATCAATTCTTTATTAGCCAATTCTAATCCAATTCAGG
1 TATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAATTCTAATCCTATTCAGG
* *
13474 ATCATTTCTTTATCAATCAATTTCAATCCTATTCAGGATC
66 ATCATTTCTTTACCAATCAATTTCCATCCTATTCAGGATC
13514 ATTGCTTTCC
Statistics
Matches: 207, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 207 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (112 bp):
TATCAATCATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAATTCTAATCCTATTCAGG
ATCATTTCTTTACCAATCAATTTCCATCCTATTCAGGATCGTTGTTG
Found at i:13905 original size:20 final size:20
Alignment explanation
Indices: 13880--13920 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13870 TAAATCTATG
13880 TGATAGCTTTCCTCTTCTAA
1 TGATAGCTTTCCTCTTCTAA
13900 TGATAGCTTTCCTCTTCTAA
1 TGATAGCTTTCCTCTTCTAA
13920 T
1 T
13921 TAAGTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (20 bp):
TGATAGCTTTCCTCTTCTAA
Found at i:15465 original size:519 final size:521
Alignment explanation
Indices: 14475--15521 Score: 1976
Period size: 519 Copynumber: 2.0 Consensus size: 521
14465 GCATGAAAGG
14475 TAAGCACAAATTAGATCACCCTCACACGTGCACCATTCCATACATCCACCACACATATATATATA
1 TAAGCACAAATTAGATCACCCTCACACGTGCACCATTCCATACATCCACCACACATATATATATA
14540 TGACCTATATTTGTCACACCCCATTAGTGACACACATACACACATAGTTCATCCCAAGCATGCAT
66 TGACCTATATTTGTCACACCCCATTAGTGACACACATACACACATAGTTCATCCCAAGCATGCAT
14605 TCCACCACAGTCCAGTTCAAGCATTTTACAATTTTTGTCAATCATAGCTTCGTATTTAATTTGCA
131 TCCACCACAGTCCAGTTCAAGCATTTTACAATTTTTGTCAATCATAGCTTCGTATTTAATTTGCA
14670 ACATTACATCGATATTGGTAAAGTCAGATTTCATTCATCAATAGCAAGTATCACCTACGCTTTGC
196 ACATTACATCGATATTGGTAAAGTCAGATTTCATTCATCAATAGCAAGTATCACCTACGCTTTGC
14735 ATTTTGAAGTTTCAAGTTCAATTAAGCAAATACCACTTTGCACACGAATTCTCAAGTTGCAGCAT
261 ----T--AG-TT-AAGTTCAATTAAGCAAATACCACTTTGCACACGAATTCTCAAGTTGCAGCAT
14800 GGTTTTTCATTTACAATTAAGTAATGACATTGTAAAGCGTTCAAAAATTTGCAAAAACAGGGGGG
318 GGTTTTTCATTTACAATTAAGTAATGACATTGTAAAGCGTTCAAAAATTTGCAAAAACAGGGGGG
14865 GTCCATCAATACATTTCAGTCATACTTGGCAAGCATTATCAACATAGGATCGTTCTTAGTTGCAT
383 GTCCATCAATACATTTCAGTCATACTTGGCAAGCATTATCAACATAGGATCGTTCTTAGTTGCAT
14930 TGCATTCTGTTTCGATCAATCAAAAAGAAAGAGCAGTCAACATACAAGCACACATAGCAACACAG
448 TGCATTCTGTTTCGATCAATCAAAAAGAAAGAGCAGTCAACATACAAGCACACATAGCAACACAG
14995 GACATCATC
513 GACATCATC
15004 TAAGCACAAATTAGATCACCCTCACACGTGCACCATTCCATACATCCACCACACATATATATATA
1 TAAGCACAAATTAGATCACCCTCACACGTGCACCATTCCATACATCCACCACAC--ATATATATA
15069 TATGACCTATATTTGTCACACCCCATTAGTGACACACATACACACATAGTTCATCCCAAGCATGC
64 TATGACCTATATTTGTCACACCCCATTAGTGACACACATACACACATAGTTCATCCCAAGCATGC
15134 ATTCCACCACAGTCCAGTTCAAGCATTTTACAATTTTTGTCAATCATAGCTTCGTATTTAATTTG
129 ATTCCACCACAGTCCAGTTCAAGCATTTTACAATTTTTGTCAATCATAGCTTCGTATTTAATTTG
15199 CAACATTACATCGATATTGGTAAAGTCAGATTTCATTCATCAATAGCAAGTATCACCTA-GCTTT
194 CAACATTACATCGATATTGGTAAAGTCAGATTTCATTCATCAATAGCAAGTATCACCTACGCTTT
15263 GC-A-TT-AGTTCAATTAAGCAAATACCACTTTGCACACGAATTCTCAAGTTGCAGCATGGTTTT
259 GCTAGTTAAGTTCAATTAAGCAAATACCACTTTGCACACGAATTCTCAAGTTGCAGCATGGTTTT
15325 TCATTTACAATTAAGTAATGACATTGTAAAGCGTTCAAAAATTTGCAAAAACAGGGGGGGTCCAT
324 TCATTTACAATTAAGTAATGACATTGTAAAGCGTTCAAAAATTTGCAAAAACAGGGGGGGTCCAT
15390 CAATACATTTCAGTCATACTTGGCAAGCATTATCAACATAGGATCGTTCTTAGTTGCATTGCATT
389 CAATACATTTCAGTCATACTTGGCAAGCATTATCAACATAGGATCGTTCTTAGTTGCATTGCATT
15455 CTGTTTCGATCAATCAAAAAGAAAGAGCAGTCAACATACAAGCACACATAGCAACACAGGACATC
454 CTGTTTCGATCAATCAAAAAGAAAGAGCAGTCAACATACAAGCACACATAGCAACACAGGACATC
15520 AT
519 AT
15522 GCATGCACGA
Statistics
Matches: 516, Mismatches: 0, Indels: 14
0.97 0.00 0.03
Matches are distributed among these distances:
519 254 0.49
521 2 0.00
523 1 0.00
529 54 0.10
530 7 0.01
531 198 0.38
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (521 bp):
TAAGCACAAATTAGATCACCCTCACACGTGCACCATTCCATACATCCACCACACATATATATATA
TGACCTATATTTGTCACACCCCATTAGTGACACACATACACACATAGTTCATCCCAAGCATGCAT
TCCACCACAGTCCAGTTCAAGCATTTTACAATTTTTGTCAATCATAGCTTCGTATTTAATTTGCA
ACATTACATCGATATTGGTAAAGTCAGATTTCATTCATCAATAGCAAGTATCACCTACGCTTTGC
TAGTTAAGTTCAATTAAGCAAATACCACTTTGCACACGAATTCTCAAGTTGCAGCATGGTTTTTC
ATTTACAATTAAGTAATGACATTGTAAAGCGTTCAAAAATTTGCAAAAACAGGGGGGGTCCATCA
ATACATTTCAGTCATACTTGGCAAGCATTATCAACATAGGATCGTTCTTAGTTGCATTGCATTCT
GTTTCGATCAATCAAAAAGAAAGAGCAGTCAACATACAAGCACACATAGCAACACAGGACATCAT
C
Found at i:17294 original size:2 final size:2
Alignment explanation
Indices: 17287--17316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17277 TTATTGTTAT
17287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17317 AGTAATCCTT
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):
TA
Found at i:17601 original size:20 final size:20
Alignment explanation
Indices: 17576--17626 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17566 TACTTATATC
*
17576 ATTTGGGTTTTAGGGTTAGT-
1 ATTTGGGTTTTAGAGTTA-TA
*
17596 ATTTGGGCTTTAGAGTTATA
1 ATTTGGGTTTTAGAGTTATA
*
17616 ACTTGGGTTTT
1 ATTTGGGTTTT
17627 TATTAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.18, C:0.04, G:0.29, T:0.49
Consensus pattern (20 bp):
ATTTGGGTTTTAGAGTTATA
Found at i:20125 original size:21 final size:21
Alignment explanation
Indices: 20092--20131 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20082 AACAGACCAC
* *
20092 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTAGGCAGGACTTGTCAA
*
20113 GTCCTAGGTAGGACTTGTC
1 GTCCTAGGCAGGACTTGTC
20132 CTATTTTTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (21 bp):
GTCCTAGGCAGGACTTGTCAA
Found at i:24368 original size:23 final size:21
Alignment explanation
Indices: 24341--24397 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
24331 AAAAATCCCC
*
24341 AATTTCCAACAATCAAGAACCCT
1 AATTT-CAA-AATCAAGAAACCT
*
24364 AATTTCAAACTCAAGAAACCT
1 AATTTCAAAATCAAGAAACCT
*
24385 AATTT-AAATTCAA
1 AATTTCAAAATCAA
24398 TGAGCTCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 16 0.52
22 3 0.10
23 5 0.16
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (21 bp):
AATTTCAAAATCAAGAAACCT
Found at i:24379 original size:21 final size:20
Alignment explanation
Indices: 24353--24397 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
24343 TTTCCAACAA
*
24353 TCAAGAACCCTAATTTCAAAC
1 TCAAGAAACCTAATTT-AAAC
*
24374 TCAAGAAACCTAATTTAAAT
1 TCAAGAAACCTAATTTAAAC
24394 TCAA
1 TCAA
24398 TGAGCTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (20 bp):
TCAAGAAACCTAATTTAAAC
Found at i:31052 original size:2 final size:2
Alignment explanation
Indices: 31045--31078 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31035 TTGAGTTTTA
31045 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
31079 TTTATATCAA
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:36579 original size:3 final size:3
Alignment explanation
Indices: 36571--36611 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
36561 ACAAAATATC
36571 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36612 CTTCAATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36687 original size:44 final size:44
Alignment explanation
Indices: 36620--36713 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
36610 AACTTCAATC
* *
36620 CAAATACTACACTATACAGAATCCAAACTCTAATCACCATTTAT
1 CAAATACTACACTATACAGAATCCAAACTCTAATCACCACTCAT
* *
36664 CAAATACTAGACTATGCCA-AATCCAAACTCTAATCACCACTCAT
1 CAAATACTACACTAT-ACAGAATCCAAACTCTAATCACCACTCAT
36708 CAAATA
1 CAAATA
36714 GACCAGCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (44 bp):
CAAATACTACACTATACAGAATCCAAACTCTAATCACCACTCAT
Found at i:38396 original size:63 final size:63
Alignment explanation
Indices: 38329--38463 Score: 252
Period size: 63 Copynumber: 2.1 Consensus size: 63
38319 TCGCAACAAT
*
38329 CAACAACCCAGAAATCCCAGAAATTATTTTCGAATTATAAAACGAAATTCAAAAGGAAAATCG
1 CAACAACCAAGAAATCCCAGAAATTATTTTCGAATTATAAAACGAAATTCAAAAGGAAAATCG
*
38392 CAACAACCAAGAAATCCCAGAAATTATTTTCGAATTATAAAATGAAATTCAAAAGGAAAATCG
1 CAACAACCAAGAAATCCCAGAAATTATTTTCGAATTATAAAACGAAATTCAAAAGGAAAATCG
38455 CAACAACCA
1 CAACAACCA
38464 TCAAATTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.20
Consensus pattern (63 bp):
CAACAACCAAGAAATCCCAGAAATTATTTTCGAATTATAAAACGAAATTCAAAAGGAAAATCG
Found at i:40702 original size:19 final size:20
Alignment explanation
Indices: 40678--40725 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
40668 TTAGGAGTGG
40678 AAACAAGTATACACATGCA-
1 AAACAAGTATACACATGCAT
*
40697 AAACAA--ATA-ACATGTAT
1 AAACAAGTATACACATGCAT
40714 AAACAAGTATAC
1 AAACAAGTATAC
40726 CCACATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (20 bp):
AAACAAGTATACACATGCAT
Found at i:42800 original size:17 final size:16
Alignment explanation
Indices: 42778--42833 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
42768 AAGATTACCA
*
42778 GTGATCTTGCATCACTG
1 GTGATCTAG-ATCACTG
* *
42795 GTGATCTAAAATTACTG
1 GTGATCT-AGATCACTG
42812 GTGATCTAAGATCACTG
1 GTGATCT-AGATCACTG
42829 GTGAT
1 GTGAT
42834 GTGATATGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (16 bp):
GTGATCTAGATCACTG
Found at i:43421 original size:16 final size:16
Alignment explanation
Indices: 43400--43431 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43390 ATTAAGTTGC
43400 ATCTTGCATGTTTCTT
1 ATCTTGCATGTTTCTT
43416 ATCTTGCATGTTTCTT
1 ATCTTGCATGTTTCTT
43432 TAGCTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (16 bp):
ATCTTGCATGTTTCTT
Found at i:44882 original size:16 final size:16
Alignment explanation
Indices: 44861--44893 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44851 CAAAACAACC
44861 ACCCATATTGCAATCT
1 ACCCATATTGCAATCT
44877 ACCCATATTGCAATCT
1 ACCCATATTGCAATCT
44893 A
1 A
44894 TTGGCATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (16 bp):
ACCCATATTGCAATCT
Found at i:47206 original size:35 final size:36
Alignment explanation
Indices: 47156--47228 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
47146 TTTCATCAGG
*
47156 TTTAAGTTTTTAAATTGGGAAAGTTCCCA-CCAGTT
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTT
*
47191 TTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTT
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTT
47227 TT
1 TT
47229 CAAAGCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 28 0.80
36 7 0.20
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTT
Found at i:47306 original size:37 final size:35
Alignment explanation
Indices: 47253--47388 Score: 134
Period size: 37 Copynumber: 3.7 Consensus size: 35
47243 TATCTCTCTT
*
47253 TTTTCAAATTGCGAAAGTTCCCATCCAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCAT-CAGTTTTC-AAG
47290 TTTTCAAATTGGGAAAGTTCCCATCAGGTTTTC-A-
1 TTTTCAAATTGGGAAAGTTCCCATCA-GTTTTCAAG
* *
47324 TTTTCAATTTAGGGAAAGTTCCCGTCA-TTTTCAGTTTTAG
1 TTTTCAAATT-GGGAAAGTTCCCATCAGTTTTCA-----AG
*
47364 TTTTCAAAATGGGAAAGTTCCCATC
1 TTTTCAAATTGGGAAAGTTCCCATC
47389 CAAAGCATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
33 5 0.06
34 9 0.11
35 16 0.19
36 2 0.02
37 29 0.35
39 15 0.18
40 8 0.10
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
Found at i:49819 original size:5 final size:5
Alignment explanation
Indices: 49809--49865 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
49799 CCCACTCCTA
* *
49809 TTTCT TTTCT TTT-T TTT-T TTT-T TTT-T TTT-T TTTCTT TTTCC TTTCC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT
49855 TTTCT TTTCT T
1 TTTCT TTTCT T
49866 CTCCTTTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 20 0.42
5 23 0.48
6 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:49824 original size:1 final size:1
Alignment explanation
Indices: 49813--49847 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
49803 CTCCTATTTC
* *
49813 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49848 CCTTTCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:53119 original size:121 final size:121
Alignment explanation
Indices: 52873--53342 Score: 626
Period size: 121 Copynumber: 3.9 Consensus size: 121
52863 TTCTTGTAGT
* * * *
52873 GATTAACTT-AATCTTAAAAGAATTAT-ACAAGTTTCCAAAAGTTTATTAACTAAAGGTTTTAAT
1 GATTCACTTAAATCTTAAATGAATTATGA-AAATTACC-AAAGTTTATTAACTAAAGGTTTTAAT
*
52936 CACTTAATTAAACCTTAAGTTTT-AGGTCACTTAACCTTAATTTCAAATTCAATTAAA
64 CACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAATTTCAAATTCAATTAAA
* * * * *
52993 GATTCACTTAAATCTTTAATGAATTATGGAAATTACCAAAGTTTATTAACTAAAGGTTGTGATTA
1 GATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTATTAACTAAAGGTTTTAATCA
** * * *
53058 CTTAATTAAACCTAAAGTTTTAAGGTCACTTAAATTTGAGTTCAAATTTAATTAAA
66 CTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAATTTCAAATTCAATTAAA
* *
53114 CATTCACTTAAATCTTAAATGAACTATGAAAATTACCAAAGTTTATTAACTAAAGGTTTTAATCA
1 GATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTATTAACTAAAGGTTTTAATCA
* * *
53179 CTTAATTAAATCTAAAGTTTTAAGGTAACGTAACCTTAATTTCAAATTCAATTAAA
66 CTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAATTTCAAATTCAATTAAA
*
53235 GATTCACTTAAATCTTAAATGAATATTTATCAAAATTACCAAA-TTTAATT-ACTAAAGGTTTTA
1 GATTCACTTAAATCTTAAATG-A-A-TTATGAAAATTACCAAAGTTT-ATTAACTAAAGGTTTTA
* * * *
53298 ATCACTTAATTAATCCTTAAGTGTTAAGGTCACTTAACCTGAATT
62 ATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAATT
53343 GTAAATCTAT
Statistics
Matches: 303, Mismatches: 40, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
120 53 0.17
121 176 0.58
122 1 0.00
123 55 0.18
124 18 0.06
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (121 bp):
GATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTATTAACTAAAGGTTTTAATCA
CTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAATTTCAAATTCAATTAAA
Found at i:57074 original size:96 final size:96
Alignment explanation
Indices: 56967--57396 Score: 567
Period size: 96 Copynumber: 4.5 Consensus size: 96
56957 AGCTACTGGT
* * * * *
56967 ATGCCCGTTTGTGAGCCACCAAGAAA-CTGCTGAACTGAAAACTGTTGGCATGTCCCC-TTATAA
1 ATGCCCCTTTGTGAGCCGCCAAGAAACCT-CCGAACTGAAAACTGTTGGCATG-CCCCTTTGTGA
* * *
57030 GCCGCCAAGGCCACTGAATTGAAGATTGCTAGG
64 GCCGCCATGACCACTGAACTGAAGATTGCTAGG
* *
57063 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTATTAGCATGCCCCTTTGTGAGC
1 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTGTTGGCATGCCCCTTTGTGAGC
* * *
57128 TGCCACGACCATTGAACTGAAGATTGCTAGG
66 CGCCATGACCACTGAACTGAAGATTGCTAGG
* * *
57159 ATGCCCCTTTGTGAACCGCCAAGAAACCTCCGAGCTGAAAACTGTTGGCATGCCCTTTTGTGAGC
1 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTGTTGGCATGCCCCTTTGTGAGC
* *
57224 CGCCATGACCATTGAACAGAAGATTGCTAGG
66 CGCCATGACCACTGAACTGAAGATTGCTAGG
* ** * * * * * *
57255 ATGCCCCTTTATGAGCCGCTTAGAAACCTCCGGATTGAAAATTATTTGCATGCCCCTTTGTCAGC
1 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTGTTGGCATGCCCCTTTGTGAGC
*
57320 CGCCATGACCACTGAACTGGAGATTGCTAGG
66 CGCCATGACCACTGAACTGAAGATTGCTAGG
*
57351 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCTGAACTGAAAACTGTT
1 ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTGTT
57397 ACAATCCCGA
Statistics
Matches: 289, Mismatches: 43, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
95 4 0.01
96 283 0.98
97 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (96 bp):
ATGCCCCTTTGTGAGCCGCCAAGAAACCTCCGAACTGAAAACTGTTGGCATGCCCCTTTGTGAGC
CGCCATGACCACTGAACTGAAGATTGCTAGG
Found at i:57080 original size:47 final size:47
Alignment explanation
Indices: 57029--57389 Score: 283
Period size: 49 Copynumber: 7.5 Consensus size: 47
57019 TCCCCTTATA
* *
57029 AGCCGCCAAGGCCACTGAATTGAAGATTGCTAGGATGCCCCTTTGTG
1 AGCCGCCAAGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
* * * * ** *
57076 AGCCGCCAAGAAACCTCCGAACTGAAAACTATTAGCATGCCCCTTTGTG
1 AGCCGCCAAG--ACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
* * *
57125 AGCTGCCACGACCATTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
1 AGCCGCCAAGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
* * * * * * * *
57172 AACCGCCAAGAAACCTCCGAGCTGAAAACTG-TTGGCATGCCCTTTTGTG
1 AGCCGCCAAG--ACCACTGAACTGAAGATTGCTAGG-ATGCCCCTTTGTG
* * * *
57221 AGCCGCCATGACCATTGAACAGAAGATTGCTAGGATGCCCCTTTATG
1 AGCCGCCAAGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
* * * * * * * ** * * *
57268 AGCCGCTTAGAAACCTCCGGATTGAAAATTATTTGCATGCCCCTTTGTC
1 AGCCGC-CA-AGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
* *
57317 AGCCGCCATGACCACTGAACTGGAGATTGCTAGGATGCCCCTTTGTG
1 AGCCGCCAAGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
*
57364 AGCCGCCAAGAAACCTCTGAACTGAA
1 AGCCGCCAAG--ACCACTGAACTGAA
57390 AACTGTTACA
Statistics
Matches: 229, Mismatches: 75, Indels: 18
0.71 0.23 0.06
Matches are distributed among these distances:
47 110 0.48
48 8 0.03
49 111 0.48
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (47 bp):
AGCCGCCAAGACCACTGAACTGAAGATTGCTAGGATGCCCCTTTGTG
Found at i:57432 original size:26 final size:26
Alignment explanation
Indices: 57403--57499 Score: 104
Period size: 26 Copynumber: 3.7 Consensus size: 26
57393 TGTTACAATC
* * **
57403 CCGAGCTAGGGGTGACTGCTAAGATG
1 CCGAGCGAGGGGCGACCACTAAGATG
*
57429 CCGAGCGAGGGGCGACCACTGAGATG
1 CCGAGCGAGGGGCGACCACTAAGATG
* * *
57455 CCGAGTGAGGGGCGATCACTGAGATG
1 CCGAGCGAGGGGCGACCACTAAGATG
*
57481 TCGAGCGAGGGGGCGACCA
1 CCGAGCGA-GGGGCGACCA
57500 TTGAAGACTC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 51 0.85
27 9 0.15
ACGTcount: A:0.23, C:0.23, G:0.42, T:0.12
Consensus pattern (26 bp):
CCGAGCGAGGGGCGACCACTAAGATG
Found at i:66701 original size:19 final size:19
Alignment explanation
Indices: 66663--66701 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
66653 GAAGCTTGAA
*
66663 GGGGACTTTAAAATTGAAT
1 GGGGACTTTAAAATTAAAT
*
66682 GGGGACTTTAAGATTAAAT
1 GGGGACTTTAAAATTAAAT
66701 G
1 G
66702 CAAAGAAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (19 bp):
GGGGACTTTAAAATTAAAT
Found at i:71696 original size:2 final size:2
Alignment explanation
Indices: 71689--71713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71679 TTGACTATCT
71689 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
71714 CTCGCTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76224 original size:39 final size:39
Alignment explanation
Indices: 76170--76466 Score: 305
Period size: 39 Copynumber: 7.7 Consensus size: 39
76160 GGTTTTTATC
*
76170 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCTGTT
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
76209 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
* * *
76248 TAAATAAACTTGTTTAGGTCTATGTTTAGAATTTCCGTT
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
*
76287 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTT-CATT
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
* * * ** * *
76325 TAAGTAAACCTGCTTATGTCTCTATTTAGAGCTTCCATG
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
* * * * * * ** * *
76364 CAAGTGAATCTACTTATGTCTCTACTTAGAGTGT-CGTT
1 TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
* * *
76402 TAA-TCAAACCTACTTAGGTCCT-TGTTTTGAATTCCCGTT
1 TAAGT-AAACCTGCTTAGGT-CTATGTTTAGAATTTCCGTT
* *
76441 TAAGCAAACCTGCTTAGGTCTCTGTT
1 TAAGTAAACCTGCTTAGGTCTATGTT
76467 CCGTTCAAAT
Statistics
Matches: 217, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
37 1 0.00
38 55 0.25
39 161 0.74
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (39 bp):
TAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCGTT
Found at i:76303 original size:78 final size:77
Alignment explanation
Indices: 76174--76625 Score: 322
Period size: 77 Copynumber: 5.9 Consensus size: 77
76164 TTTATCTAAG
**
76174 TAAACCTGCTTAGGTCTATGTTTAGAATTTCTGTTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
1 TAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
76239 ATTTCCGTTTAAA
66 ATTT-CGTTTAAA
* * *
76252 TAAACTTGTTTAGGTCTATGTTTAGAATTTCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
1 TAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
* *
76317 ATTTCATTTAAG
66 ATTTCGTTTAAA
* * * ** ** * * * * * **
76329 TAAACCTGCTTATGTCTCTATTTAGAGCTTCCATGCAAGTGAATCTACTTATGTCTCTACTTAGA
1 TAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
* *
76394 GTGTCGTTT-AA
66 ATTTCGTTTAAA
* * * * * *
76405 TCAAACCTACTTAGGTCCT-TGTTTTGAATTCCCGTTTAAGCAAACCTGCTTAGGTC----TCT-
1 T-AAACCTGCTTAGGT-CTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTA
* *
76464 G--TTCCGTTCAAA
64 GAATTTCGTTTAAA
* * * ** *
76476 TAAACTTGTTTAGGACTTCTAT-TTT-G-AGTT-CATTCGAGTAAACCTGCTTAGGT-TTTCGTT
1 TAAACCTGCTTAGG---TCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTAT-GTT
76536 TAGAAGTTTCGTTTAAA
62 TAGAA-TTTCGTTTAAA
* * * * * *
76553 CAAACCCGCTTAGGTTCT-TGTTTAGAATTCCCACTTGAGTGAACCTGCTTAGGTCTATGTTTAG
1 TAAACCTGCTTAGG-TCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAG
*
76617 AGTTTCGTT
65 AATTTCGTT
76626 CAATCAAACC
Statistics
Matches: 284, Mismatches: 69, Indels: 43
0.72 0.17 0.11
Matches are distributed among these distances:
69 19 0.07
70 17 0.06
71 4 0.01
72 6 0.02
73 5 0.02
74 2 0.01
75 7 0.02
76 3 0.01
77 124 0.44
78 95 0.33
79 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (77 bp):
TAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGA
ATTTCGTTTAAA
Found at i:82706 original size:13 final size:13
Alignment explanation
Indices: 82671--83023 Score: 127
Period size: 13 Copynumber: 24.2 Consensus size: 13
82661 AATAGGTCAT
* *
82671 AAATTATAATGAG
1 AAATTATATTTAG
*
82684 AAAATAATATTTAG
1 -AAATTATATTTAG
*
82698 AAATGATATATGTAATG
1 AAAT--TATAT-TTA-G
*
82715 AAATTATAATTAG
1 AAATTATATTTAG
* *
82728 GAATTATATTTAT
1 AAATTATATTTAG
82741 AAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
82758 AAA-TATTATTTAG
1 AAATTA-TATTTAG
*
82771 AAAATGATATTTAG
1 -AAATTATATTTAG
*
82785 AAACTATATATGTGAAG
1 AAA-T-TATAT-T-TAG
*
82802 AAATTATAATTAG
1 AAATTATATTTAG
* *
82815 GAATTATA-TTAT
1 AAATTATATTTAG
82827 AAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
82844 AAA-TATTATTTAG
1 AAATTA-TATTTAG
82857 AAATTATATATGTATTG
1 AAATTATAT-T-TA--G
*
82874 AAATTATAATTAG
1 AAATTATATTTAG
*
82887 AAAATAATATTTAG
1 -AAATTATATTTAG
* *
82901 AAATTAAAAATTTTTTAA
1 AAATT----A-TATTTAG
82919 AAATTATATTTAG
1 AAATTATATTTAG
* *
82932 AAAATAATAATTAG
1 -AAATTATATTTAG
*
82946 CAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
*
82963 AAATTATAATTAG
1 AAATTATATTTAG
*
82976 AAAATAATATTTAG
1 -AAATTATATTTAG
82990 AAATTTTAAAATATTTAG
1 AAA--TT---ATATTTAG
83008 AAATTATATTTAG
1 AAATTATATTTAG
83021 AAA
1 AAA
83024 ATAAAATTTG
Statistics
Matches: 257, Mismatches: 39, Indels: 87
0.67 0.10 0.23
Matches are distributed among these distances:
12 10 0.04
13 74 0.29
14 67 0.26
15 28 0.11
16 17 0.07
17 40 0.16
18 21 0.08
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (13 bp):
AAATTATATTTAG
Found at i:82768 original size:30 final size:30
Alignment explanation
Indices: 82734--82966 Score: 125
Period size: 30 Copynumber: 7.9 Consensus size: 30
82724 TTAGGAATTA
*
82734 TATTTATAAATTATATATGTAATGAAATAT
1 TATTTAGAAATTATATATGTAATGAAATAT
*
82764 TATTTAGAAA--ATGATAT-TTA-GAAACTAT
1 TATTTAGAAATTAT-ATATGTAATGAAA-TAT
* * *
82792 ATATGTGAAGAAATTATA-AT-T-AGGAATTA-
1 -TAT-T-TAGAAATTATATATGTAATGAAATAT
*
82821 TA-TTATAAATTATATATGTAATGAAATAT
1 TATTTAGAAATTATATATGTAATGAAATAT
*
82850 TATTTAGAAATTATATATGTATTGAAAT-T
1 TATTTAGAAATTATATATGTAATGAAATAT
* * * * * *
82879 ATAATTAGAAAATAATATTTAGAAATTAAAAAT
1 -TATTTAG-AAATTATATAT-GTAATGAAATAT
* * *
82912 TTTTTAAAAATTATAT-T-T-A-GAAAATAA
1 TATTTAGAAATTATATATGTAATG-AAATAT
* *
82939 TAATTAGCAATTATATATGTAATGAAAT
1 TATTTAGAAATTATATATGTAATGAAAT
82967 TATAATTAGA
Statistics
Matches: 152, Mismatches: 29, Indels: 44
0.68 0.13 0.20
Matches are distributed among these distances:
25 9 0.06
26 3 0.02
27 22 0.14
28 16 0.11
29 11 0.07
30 48 0.32
31 29 0.19
32 11 0.07
33 3 0.02
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (30 bp):
TATTTAGAAATTATATATGTAATGAAATAT
Found at i:82797 original size:87 final size:86
Alignment explanation
Indices: 82682--82859 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 86
82672 AATTATAATG
82682 AGAAAATAATATTTAGAAATGATATATGT-AATGAAATTATAATTAGGAATTATATTTATAAATT
1 AGAAAATAATATTTAGAAATGATATATGTGAA-GAAATTATAATTAGGAATTATA-TTATAAATT
82746 ATATATGTAATGAAATATTATTT
64 ATATATGTAATGAAATATTATTT
*
82769 AGAAAATGATATTTAGAAACT-ATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTA
1 AGAAAATAATATTTAGAAA-TGATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTA
82833 TATATGTAATGAAATATTATTT
65 TATATGTAATGAAATATTATTT
82855 AGAAA
1 AGAAA
82860 TTATATATGT
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
86 37 0.42
87 48 0.55
88 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (86 bp):
AGAAAATAATATTTAGAAATGATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTAT
ATATGTAATGAAATATTATTT
Found at i:82878 original size:17 final size:17
Alignment explanation
Indices: 82827--82881 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
82817 ATTATATTAT
*
82827 AAATTATATATGTAATG
1 AAATTATATATGTATTG
*
82844 AAA-TAT-TAT-T-TAG
1 AAATTATATATGTATTG
82857 AAATTATATATGTATTG
1 AAATTATATATGTATTG
82874 AAATTATA
1 AAATTATA
82882 ATTAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 6 0.19
16 4 0.13
17 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTATATATGTATTG
Found at i:82936 original size:45 final size:45
Alignment explanation
Indices: 82844--83032 Score: 186
Period size: 45 Copynumber: 4.2 Consensus size: 45
82834 ATATGTAATG
* * * * *
82844 AAATATTATTTAGAAATTATATATGTATT-GAAATTATAATTAGA
1 AAATAATATTTAGAAATTAAAAATTTTTTAGAAATTATAATTAGA
* *
82888 AAATAATATTTAGAAATTAAAAATTTTTTAAAAATTATATTTAGA
1 AAATAATATTTAGAAATTAAAAATTTTTTAGAAATTATAATTAGA
* * * * * **
82933 AAATAATAATTAGCAATTATATATGTAAT-GAAATTATAATTAGA
1 AAATAATATTTAGAAATTAAAAATTTTTTAGAAATTATAATTAGA
* * *
82977 AAATAATATTTAGAAATTTTAAAA-TATTTAGAAATTATATTTAGA
1 AAATAATATTTAGAAA-TTAAAAATTTTTTAGAAATTATAATTAGA
*
83022 AAATAAAATTT
1 AAATAATATTT
83033 GAATTTAGCG
Statistics
Matches: 115, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
44 52 0.45
45 63 0.55
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.41
Consensus pattern (45 bp):
AAATAATATTTAGAAATTAAAAATTTTTTAGAAATTATAATTAGA
Found at i:82954 original size:89 final size:89
Alignment explanation
Indices: 82844--83031 Score: 290
Period size: 89 Copynumber: 2.1 Consensus size: 89
82834 ATATGTAATG
* * *
82844 AAATATTATTTAGAAATTATATATGTATTGAAATTATAATTAGAAAATAATATTTAGAAA-TTAA
1 AAATAATAATTAGAAATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTAA
*
82908 AAATTTTTTAAAAATTATATTTAGA
66 AAA-TATTTAAAAATTATATTTAGA
* *
82933 AAATAATAATTAGCAATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTTA
1 AAATAATAATTAGAAATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTAA
*
82998 AAATATTTAGAAATTATATTTAGA
66 AAATATTTAAAAATTATATTTAGA
83022 AAATAA-AATT
1 AAATAATAATT
83032 TGAATTTAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 4 0.04
89 81 0.89
90 6 0.07
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (89 bp):
AAATAATAATTAGAAATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTAA
AAATATTTAAAAATTATATTTAGA
Found at i:84056 original size:16 final size:17
Alignment explanation
Indices: 84035--84071 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
84025 AAGGGCAAGT
*
84035 AAAAAGAGGG-GATTGA
1 AAAAAGAGGGAGATTCA
84051 AAAAAGAGGGAGATTCA
1 AAAAAGAGGGAGATTCA
84068 AAAA
1 AAAA
84072 GGAAGGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.57, C:0.03, G:0.30, T:0.11
Consensus pattern (17 bp):
AAAAAGAGGGAGATTCA
Done.