Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002610.1 Hibiscus syriacus cultivar Beakdansim tig00005276_pilon, 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: 86985
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:7829 original size:20 final size:22
Alignment explanation
Indices: 7776--7840 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
7766 ATTTGAAATT
*
7776 TAAT-ATGAAAAAT-ATTTTGA
1 TAATAATGAAATATGATTTTGA
*
7796 TAATATTGAAATATGATTTTG-
1 TAATAATGAAATATGATTTTGA
* *
7817 TAATAAT-AAATATTATTTTAA
1 TAATAATGAAATATGATTTTGA
7838 TAA
1 TAA
7841 AGTTTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.41
21 16 0.43
22 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.45
Consensus pattern (22 bp):
TAATAATGAAATATGATTTTGA
Found at i:11191 original size:29 final size:30
Alignment explanation
Indices: 11132--11199 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
11122 TTCCCATTTA
* * *
11132 GGTCCTTAAACTTTCCCAAATTTATACTTT
1 GGTCATTAAACTTTCCAAAATTTACACTTT
*
11162 -GTCTATTAAACTTT-CAAAATTTACATTTT
1 GGTC-ATTAAACTTTCCAAAATTTACACTTT
11191 GGTCATTAA
1 GGTCATTAA
11200 CAAAAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (30 bp):
GGTCATTAAACTTTCCAAAATTTACACTTT
Found at i:12499 original size:25 final size:25
Alignment explanation
Indices: 12465--12514 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12455 CCACCTGGAT
12465 GTATAATCAATG-ATCTGTAGTATGC
1 GTATAATCAATGAAT-TGTAGTATGC
*
12490 GTATAGTCAATGAATTGTAGTATGC
1 GTATAATCAATGAATTGTAGTATGC
12515 CTTAGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (25 bp):
GTATAATCAATGAATTGTAGTATGC
Found at i:22496 original size:486 final size:486
Alignment explanation
Indices: 21585--22558 Score: 1666
Period size: 486 Copynumber: 2.0 Consensus size: 486
21575 TTTACCATTA
* *
21585 ACGAAACTTGATAATTACATCCATTCCAAGCCACTTGTTAATTATCATATTCCTAAATTCAAAGA
1 ACGAAACTTGATAATTACATCCATTCCAAGCCACTTGCTAATTATCATATTCCTAAAGTCAAAGA
*
21650 TGAACAAATTAATTTGTCCTTTACAACTTTACCATCCACTTTTCTAAAAATTTCATTATTGCCAT
66 TGAACAAATTAATTTGTCCTTTACAACTTTACCATCAACTTTTCTAAAAATTTCATTATTGCCAT
21715 TTTCATCCAATAATTCAAATTGAACATGGAAATAAATTCTCAAATTCAATGATCCATATTATTTT
131 TTTCATCCAATAATTCAAATTGAACATGGAAATAAATTCTCAAATTCAATGATCCATATTATTTT
*
21780 CCATAATTTTAAAATGTGGAAATAATATTTCTAGGCTTAATTAAATATCATTTAAATTTTCTCAA
196 CCATAATTTTAAAATGTGGAAATAATATTTCTAGGCTTAATTAAATATCATTCAAATTTTCTCAA
21845 AATTTATAACCGATCCAATTACCAATTTTTTTTCAAACTTTAACATGTTATAGTTTTTAACACAA
261 AATTTATAACCGATCCAATTACCAATTTTTTTTCAAACTTTAACATGTTATAGTTTTTAACACAA
*
21910 ATTCCGAATCAAAAATCCGATTATCAAAAGAATGTCATTCTTGGGGGTAAAATATTCATTTATGG
326 ATTCCGAATCAAAAATCCGATTATCAAAAGAATGTCATTCTTGGAGGTAAAATATTCATTTATGG
*
21975 AATAAAATTTCTTTTTAATAAAATTACCACTTAGGTCCCTAAACATTTCCTAAA-TTTATACTTT
391 AATAAAATTTCTTTTTAACAAAATTACCACTTAGGTCCCTAAACATTTCCTAAACTTT-TACTTT
22039 TACAACTAAACTTTAAAATGTATGTTTTGGTC
455 TACAACTAAACTTTAAAATGTATGTTTTGGTC
22071 ACGAAACTTGATAATTACATCCATTCCAAGCCACTTGCTAATTATCATATTCCTAAAGTCAAAGA
1 ACGAAACTTGATAATTACATCCATTCCAAGCCACTTGCTAATTATCATATTCCTAAAGTCAAAGA
*
22136 TGAACAAATTAATTTGTCCTTTACAACTTTACCATCAACTTTTCTAAAAATTTTATTATTGCCAT
66 TGAACAAATTAATTTGTCCTTTACAACTTTACCATCAACTTTTCTAAAAATTTCATTATTGCCAT
* * *
22201 TTTCATCCACCT-GTTCAAATTGAACATGGAAATAAATTCTCAAATTCAATGATCCTTATTATTT
131 TTTCATCCA-ATAATTCAAATTGAACATGGAAATAAATTCTCAAATTCAATGATCCATATTATTT
** *
22265 TTGATCATTTTAAAATGTGGAAATAATATTTCTAGGCTTAATTAAATATCATTCAAATTTTCTCA
195 TCCATAATTTTAAAATGTGGAAATAATATTTCTAGGCTTAATTAAATATCATTCAAATTTTCTCA
* ** * *
22330 AAATTTCTATTCGATCCGATTACCGAA-TTTTTTTCAGACTTTAACATGTTATAGTTTTTAACAC
260 AAATTTATAACCGATCCAATTACC-AATTTTTTTTCAAACTTTAACATGTTATAGTTTTTAACAC
* *
22394 AAATTCCGAATCAAAAATCTGATTCTCAAAAGAATGTCATTCTTGGAGGTAAAATATTCATTTAT
324 AAATTCCGAATCAAAAATCCGATTATCAAAAGAATGTCATTCTTGGAGGTAAAATATTCATTTAT
* *
22459 GGAATAAAATTTCTTTTTGACAAAATTACCACTTAGGTCCCTAAACTTTTCCTAAACTTTTACTT
389 GGAATAAAATTTCTTTTTAACAAAATTACCACTTAGGTCCCTAAACATTTCCTAAACTTTTACTT
** * *
22524 TTACCGCTAAACTTTTAAATTTATGTTTTGGTC
454 TTACAACTAAACTTTAAAATGTATGTTTTGGTC
22557 AC
1 AC
22559 TAACCTAAAT
Statistics
Matches: 459, Mismatches: 26, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
486 453 0.99
487 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (486 bp):
ACGAAACTTGATAATTACATCCATTCCAAGCCACTTGCTAATTATCATATTCCTAAAGTCAAAGA
TGAACAAATTAATTTGTCCTTTACAACTTTACCATCAACTTTTCTAAAAATTTCATTATTGCCAT
TTTCATCCAATAATTCAAATTGAACATGGAAATAAATTCTCAAATTCAATGATCCATATTATTTT
CCATAATTTTAAAATGTGGAAATAATATTTCTAGGCTTAATTAAATATCATTCAAATTTTCTCAA
AATTTATAACCGATCCAATTACCAATTTTTTTTCAAACTTTAACATGTTATAGTTTTTAACACAA
ATTCCGAATCAAAAATCCGATTATCAAAAGAATGTCATTCTTGGAGGTAAAATATTCATTTATGG
AATAAAATTTCTTTTTAACAAAATTACCACTTAGGTCCCTAAACATTTCCTAAACTTTTACTTTT
ACAACTAAACTTTAAAATGTATGTTTTGGTC
Found at i:26861 original size:12 final size:12
Alignment explanation
Indices: 26823--26905 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
26813 ATTTCCGACT
26823 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
26835 TG-ATACATGACC
1 TGAATTC-TGTTC
26847 TGAATTCTGTTC
1 TGAATTCTGTTC
* * *
26859 TGATTTCTGATA
1 TGAATTCTGTTC
*
26871 TGGATTCTGTTC
1 TGAATTCTGTTC
26883 T-AATATCTGTTC
1 TGAAT-TCTGTTC
26895 TGAATTCTGTT
1 TGAATTCTGTT
26906 TTGATTTTTG
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
11 5 0.09
12 42 0.79
13 6 0.11
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:26865 original size:48 final size:48
Alignment explanation
Indices: 26809--26912 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
26799 AAATATTTTA
*
26809 TCTGATTTCCGACT-TGAATTCTGTTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCCGA-TATGAATTCTGTTCTAATATC-TGACCTGAATTCTGT
* * **
26857 TCTGATTTCTGATATGGATTCTGTTCTAATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGTTCTAATATCTGACCTGAATTCTGT
*
26905 TTTGATTT
1 TCTGATTT
26913 TTGATATCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 1 0.02
48 46 0.96
49 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTCTGTTCTAATATCTGACCTGAATTCTGT
Found at i:26877 original size:24 final size:24
Alignment explanation
Indices: 26809--26919 Score: 91
Period size: 24 Copynumber: 4.6 Consensus size: 24
26799 AAATATTTTA
*
26809 TCTGATTTCCGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
* **
26833 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGATATGAATTCTGT
*
26857 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
26881 TCTAATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
26905 TTTGATTTTTGATAT
1 TCTGATTTCTGATAT
26920 CTCCGTTTAC
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:33419 original size:80 final size:80
Alignment explanation
Indices: 33286--33577 Score: 476
Period size: 80 Copynumber: 3.6 Consensus size: 80
33276 AGTCCCTATA
*
33286 GATCTAAGGATGTCCTTAGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
1 GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
*
33351 TAAGGTAACCATACG
66 TAAGGTAACCCTACG
*
33366 GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTGTGCT
1 GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
*
33431 TAAGGTAACCCTACA
66 TAAGGTAACCCTACG
* * **
33446 GATCTAAGGATGTCATTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTTCCTTAACTGTGTGCT
1 GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
33511 TAAGGTAACCCTACG
66 TAAGGTAACCCTACG
* * * *
33526 GATCTAAGGATGTCCTCGGGTAGACCCAAGGTATAGCCTTAGGTTGGCTCCC
1 GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCC
33578 CTTTTTGTTG
Statistics
Matches: 196, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 196 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (80 bp):
GATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
TAAGGTAACCCTACG
Found at i:36330 original size:3 final size:3
Alignment explanation
Indices: 36322--36459 Score: 235
Period size: 3 Copynumber: 46.3 Consensus size: 3
36312 TTAATATATT
36322 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
36367 TAA T-A TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36414 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
36460 GATATGGGTA
Statistics
Matches: 130, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
2 4 0.03
3 123 0.95
4 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:36915 original size:113 final size:113
Alignment explanation
Indices: 36783--37569 Score: 1279
Period size: 113 Copynumber: 6.9 Consensus size: 113
36773 AGAATTATGC
* * *
36783 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
36848 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
36896 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
36961 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
37009 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
37074 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
37122 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
37187 TATGAACATTC-CCAGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
37234 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
37299 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
*
37347 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * **
37412 CATTATGAACTCTACCTCTGAAAAAATATAATCCATCAATTTGATGATTTCAGAC
63 CATTATGAACT-T-TCTCTG-GAAAAGATAATCCATCAA-ATGATGAATTCAGGT
37467 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
37532 TATGAACCTTCTCTGGAAAAGCTAATCTTTCAAATGAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGAT
37570 AGATTTGAAT
Statistics
Matches: 629, Mismatches: 37, Indels: 16
0.92 0.05 0.02
Matches are distributed among these distances:
112 106 0.17
113 381 0.61
114 13 0.02
115 5 0.01
116 22 0.03
117 21 0.03
118 5 0.01
119 15 0.02
120 61 0.10
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
Found at i:37265 original size:338 final size:344
Alignment explanation
Indices: 36782--37558 Score: 1307
Period size: 338 Copynumber: 2.3 Consensus size: 344
36772 TAGAATTATG
* * *
36782 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* **
36847 TTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TTATGAACATTCTCCAGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAAT
36912 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
36977 AAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 AAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* * *
37042 TCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-T-TCTCTG-GAAAAGATGATCCA
261 TCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTCTGAAAAAAGATAATCCA
*
37103 TCAA-ATGATGGA-TTCAGG
326 TCAATATGAT-GATTTCAGA
*
37121 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
37186 TTATGAACATTC-CCAGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TTATGAACATTCTCCAGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAAT
37250 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
37315 AAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
196 AAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
37380 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTCTGAAAAAATATAATC
261 TCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTCTGAAAAAAGATAATC
*
37445 CATCAATTTGATGATTTCAGA
324 CATCAATATGATGATTTCAGA
37466 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
37531 TTATGAACCTTCTCTGGAAAAGCTAATC
66 TTATGAACATTCTCCAGAAAAGATAATC
37559 TTTCAAATGA
Statistics
Matches: 409, Mismatches: 20, Indels: 11
0.93 0.05 0.03
Matches are distributed among these distances:
338 197 0.48
339 72 0.18
341 21 0.05
342 1 0.00
343 5 0.01
344 17 0.04
345 84 0.21
346 12 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (344 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACATTCTCCAGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTCTGAAAAAAGATAATCCA
TCAATATGATGATTTCAGA
Found at i:37322 original size:225 final size:224
Alignment explanation
Indices: 36783--37552 Score: 1279
Period size: 225 Copynumber: 3.4 Consensus size: 224
36773 AGAATTATGC
* * *
36783 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
36848 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
**
36913 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTC-CCAGA
* *
36978 AAAGATGATCCATCAAATGATGAATTCAGGT
194 AAAGATAATCCATCAATTGATGAATTCAGGT
37009 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
37074 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
37139 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACATTCCCAGAA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCCCAGAA
37204 AAGATAATCCATCAATTGATGAATTCAGGT
195 AAGATAATCCATCAATTGATGAATTCAGGT
37234 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
37299 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAGTT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
37364 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T-CC-
* * * **
37429 CTGAAAAAATATAATCCATCAATTTGATGATTTCAGAC
190 C--AGAAAAGATAATCCATCAA-TTGATGAATTCAGGT
37467 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
37532 TATGAACCTTCTCTGGAAAAG
66 TATGAACTTTCTCTGGAAAAG
37553 CTAATCTTTC
Statistics
Matches: 517, Mismatches: 18, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
225 196 0.38
226 182 0.35
227 1 0.00
228 21 0.04
229 2 0.00
230 1 0.00
232 17 0.03
233 97 0.19
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (224 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCCAGAAA
AGATAATCCATCAATTGATGAATTCAGGT
Found at i:38500 original size:83 final size:83
Alignment explanation
Indices: 38361--38856 Score: 897
Period size: 83 Copynumber: 6.0 Consensus size: 83
38351 TCTACTATGA
* *
38361 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
38426 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* * *
38444 GCAAATTCATCTTCAAAATTCAATGATTGGTCCTGCCAAACCAGATCAAATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
38509 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
38527 GCAAATTCATCTTCAAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
*
38592 TTCCAGAAGATGCTATCG
66 TTCCAGAAGATGCTATTG
38610 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
38675 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
38693 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
38757 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
38776 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
38840 CTTCCAGAAGATGCTAT
65 CTTCCAGAAGATGCTAT
38857 GGAGCACATT
Statistics
Matches: 403, Mismatches: 9, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
83 401 1.00
84 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:39867 original size:9 final size:9
Alignment explanation
Indices: 39853--39906 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
39843 TTGACCCCAT
39853 TTCTTTTTC
1 TTCTTTTTC
*
39862 TTCTTTTTT
1 TTCTTTTTC
39871 TTCTTTTTTC
1 TTC-TTTTTC
39881 TT-TTTTTC
1 TTCTTTTTC
* *
39889 TTTTTTTTA
1 TTCTTTTTC
*
39898 TTTTTTTTC
1 TTCTTTTTC
39907 AACTTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 8 0.21
9 24 0.62
10 7 0.18
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:39875 original size:18 final size:17
Alignment explanation
Indices: 39852--39904 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
39842 CTTGACCCCA
*
39852 TTTCTTTTTCTTCTTTT
1 TTTCTTTTTTTTCTTTT
*
39869 TTT-TCTTTTTTCTTTT
1 TTTCTTTTTTTTCTTTT
*
39885 TTTCTTTTTTTTATTTT
1 TTTCTTTTTTTTCTTTT
39902 TTT
1 TTT
39905 TCAACTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTCTTTTTTTTCTTTT
Found at i:39889 original size:24 final size:25
Alignment explanation
Indices: 39852--39903 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
39842 CTTGACCCCA
*
39852 TTTCTTTTTCTTCTTTTTTTTCTTT
1 TTTCTTTTTCTTCTTTTTTTTATTT
39877 TTTCTTTTT-TTCTTTTTTTTATTT
1 TTTCTTTTTCTTCTTTTTTTTATTT
39901 TTT
1 TTT
39904 TTCAACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.87
Consensus pattern (25 bp):
TTTCTTTTTCTTCTTTTTTTTATTT
Found at i:52161 original size:15 final size:15
Alignment explanation
Indices: 52120--52161 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
52110 CCTCGGTGAG
*
52120 TTTCTTTTCTTCCTT
1 TTTCTTTTCTTTCTT
*
52135 TTTCTTTCCTTTC-T
1 TTTCTTTTCTTTCTT
52149 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
52162 GCTGAGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:52718 original size:3 final size:3
Alignment explanation
Indices: 52710--52818 Score: 182
Period size: 3 Copynumber: 36.3 Consensus size: 3
52700 TTAATATATT
*
52710 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
52758 TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52806 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
52819 GATATGGGTA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56107 original size:14 final size:14
Alignment explanation
Indices: 56088--56115 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56078 TATAATTAAA
56088 TCATACTTTAAAAT
1 TCATACTTTAAAAT
56102 TCATACTTTAAAAT
1 TCATACTTTAAAAT
56116 AATAATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TCATACTTTAAAAT
Found at i:66743 original size:32 final size:33
Alignment explanation
Indices: 66702--66766 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
66692 TGTATTGCCC
* *
66702 TGTTTACTA-TTTATTTGCCTCACTAAGTATAT
1 TGTTTACTATTTTAATTACCTCACTAAGTATAT
66734 TGTTTACTATTTTAATTACCTCACTAAGTATAT
1 TGTTTACTATTTTAATTACCTCACTAAGTATAT
66767 ACTTAGCGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (33 bp):
TGTTTACTATTTTAATTACCTCACTAAGTATAT
Found at i:86425 original size:19 final size:20
Alignment explanation
Indices: 86401--86438 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
86391 GAACCGAAAG
86401 GAACCGTTGAACC-GACTGT
1 GAACCGTTGAACCGGACTGT
86420 GAACCGTTGAACCGGACTG
1 GAACCGTTGAACCGGACTG
86439 GACCCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (20 bp):
GAACCGTTGAACCGGACTGT
Found at i:86532 original size:20 final size:20
Alignment explanation
Indices: 86499--86542 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
86489 AATTAAAAAT
* *
86499 ATATTGAAATTTGAAATATA
1 ATATTAAAACTTGAAATATA
86519 ATATTAAAACTTGAAATATA
1 ATATTAAAACTTGAAATATA
86539 ATAT
1 ATAT
86543 GAAACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATTAAAACTTGAAATATA
Found at i:86549 original size:19 final size:19
Alignment explanation
Indices: 86495--86549 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
86485 CTCGAATTAA
*
86495 AAATAT-AT-TGAAATTTG
1 AAATATAATATGAAACTTG
*
86512 AAATATAATATTAAAACTTG
1 AAATATAATA-TGAAACTTG
86532 AAATATAATATGAAACTT
1 AAATATAATATGAAACTT
86550 AAACTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 7 0.22
20 17 0.53
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (19 bp):
AAATATAATATGAAACTTG
Done.