Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004630.1 Hibiscus syriacus cultivar Beakdansim tig00010362_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: 64526
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5269 original size:20 final size:20
Alignment explanation
Indices: 5240--5285 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5230 CTTGAGGAAG
*
5240 TGGTTCCACAACTTCACATT
1 TGGTTTCACAACTTCACATT
5260 TGGTTTCACAACTTCACATT
1 TGGTTTCACAACTTCACATT
5280 TGGTTT
1 TGGTTT
5286 TAGGGCTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (20 bp):
TGGTTTCACAACTTCACATT
Found at i:8625 original size:23 final size:24
Alignment explanation
Indices: 8598--8649 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
8588 TGAGTGAAGG
8598 TTAAAAATATTTTTATA-TTAGTA
1 TTAAAAATATTTTTATATTTAGTA
8621 TTAAAAATATTTTTATATTTTAGTA
1 TTAAAAATATTTTTATA-TTTAGTA
8646 TTAA
1 TTAA
8650 GGTTGACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.63
25 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TTAAAAATATTTTTATATTTAGTA
Found at i:11892 original size:117 final size:118
Alignment explanation
Indices: 11685--11916 Score: 322
Period size: 117 Copynumber: 2.0 Consensus size: 118
11675 GAAGATTTAG
* * *
11685 TCGAGGTAGACTTATTTCACTATTACTCAAGGGAAGATCAAATCTTAAAAGAGAGGGATCTGTTC
1 TCGAGATAGACTTATTCCACTATTACTCAAGGGAAGATCAAACCTTAAAAGAGAGGGATCTGTTC
* * *
11750 CATTTCTTCTTTAGAAAAAATCATATCTGGGGACGTTGATTCATTCCATTGAA
66 CACTTCTTCTTGAGAAAAAATCATATATGGGGACGTTGATTCATTCCATTGAA
* * * * *
11803 TCGAGATAGACTTGTTCCACTGTTACTC-ATGGAAGATCAAACCTTGAAAGAGAGGGATTTGTTC
1 TCGAGATAGACTTATTCCACTATTACTCAAGGGAAGATCAAACCTTAAAAGAGAGGGATCTGTTC
* ** *
11867 CGCTTCTTCTTGAGTTAAAATCATATATGGGGATGTTGATTCATTCCATT
66 CACTTCTTCTTGAGAAAAAATCATATATGGGGACGTTGATTCATTCCATT
11917 ATTCTTCATG
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
117 75 0.76
118 24 0.24
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (118 bp):
TCGAGATAGACTTATTCCACTATTACTCAAGGGAAGATCAAACCTTAAAAGAGAGGGATCTGTTC
CACTTCTTCTTGAGAAAAAATCATATATGGGGACGTTGATTCATTCCATTGAA
Found at i:12037 original size:134 final size:134
Alignment explanation
Indices: 11797--12087 Score: 393
Period size: 134 Copynumber: 2.2 Consensus size: 134
11787 GATTCATTCC
* * ** *
11797 ATTGAATCGAGATAGACTTGTTCCACTGTTACTCATGGAAGATCAAACCTTGAAAGAGAGGGATT
1 ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
* ** * * * *
11862 TGTTCCGCTTCTTCTTGAGTTAAAATCATATATGGGGATGTTGATTCATTCCATTATTCTTCATG
66 TGTTACGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGG
11927 GAAG
131 GAAG
* * * *
11931 ATTGAATCGAGGTAGAATTGTTCCACTGTCACTCAAAGAATATCAAATCTTGAAAGGGAGGGATC
1 ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
* * * *
11996 TGTTATGCTTCTTCTTGAGGGAAAATCAGATCTTAGGATGTTGATTCATTCCACTCTTCTTCAGG
66 TGTTACGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGG
12061 GAAG
131 GAAG
*
12065 ATTTAATCGAGGTAGACTTGTTC
1 ATTGAATCGAGGTAGACTTGTTC
12088 TTCTTGTTTT
Statistics
Matches: 135, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (134 bp):
ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
TGTTACGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGG
GAAG
Found at i:13314 original size:10 final size:10
Alignment explanation
Indices: 13299--13329 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
13289 ATTTATTCTC
13299 TTTTTCTTTT
1 TTTTTCTTTT
13309 TTTTTCTTTT
1 TTTTTCTTTT
13319 TTTTTCTTTT
1 TTTTTCTTTT
13329 T
1 T
13330 CCTTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:13318 original size:7 final size:7
Alignment explanation
Indices: 13294--13379 Score: 59
Period size: 7 Copynumber: 11.4 Consensus size: 7
13284 CATTTATTTA
13294 TTCTCTTT
1 TTCT-TTT
13302 TTCTTTT
1 TTCTTTT
13309 TT-TTTCT
1 TTCTTT-T
13316 TT-TTTT
1 TTCTTTT
13322 TTCTTTT
1 TTCTTTT
*
13329 TCCTTTTT
1 TTC-TTTT
13337 TTCATTTTAT
1 TTC--TTT-T
13347 TTCTTTCTT
1 TTC-TT-TT
13356 TTCTTTT
1 TTCTTTT
*
13363 TTCATTT
1 TTCTTTT
*
13370 TTCATTT
1 TTCTTTT
13377 TTC
1 TTC
13380 ATTCTTCAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
6 6 0.09
7 35 0.51
8 12 0.17
9 11 0.16
10 5 0.07
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (7 bp):
TTCTTTT
Found at i:13326 original size:26 final size:26
Alignment explanation
Indices: 13297--13371 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
13287 TTATTTATTC
*
13297 TCTTTTTCTTTTTTTTTCTTTTTTTT
1 TCTTTTTCTTTTTTTTTCATTTTTTT
* *
13323 TCTTTTTC-CTTTTTTTCATTTTATT
1 TCTTTTTCTTTTTTTTTCATTTTTTT
*
13348 TCTTTCTT-TTCTTTTTTCATTTTT
1 TCTTT-TTCTTTTTTTTTCATTTTT
13372 CATTTTTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 19 0.46
26 22 0.54
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (26 bp):
TCTTTTTCTTTTTTTTTCATTTTTTT
Found at i:13338 original size:10 final size:9
Alignment explanation
Indices: 13299--13364 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
13289 ATTTATTCTC
13299 TTTTTCTTT
1 TTTTTCTTT
13308 TTTTT-TCTT
1 TTTTTCT-TT
*
13317 TTTTT-TTC
1 TTTTTCTTT
*
13325 TTTTTCCTT
1 TTTTTCTTT
13334 TTTTTCATTT
1 TTTTTC-TTT
*
13344 TATTTCTTT
1 TTTTTCTTT
*
13353 CTTTTCTTT
1 TTTTTCTTT
13362 TTT
1 TTT
13365 CATTTTTCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
8 7 0.15
9 32 0.70
10 7 0.15
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:13350 original size:35 final size:33
Alignment explanation
Indices: 13299--13377 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
13289 ATTTATTCTC
* * * *
13299 TTTTTCTTTTTTTTTCTTTTTTTTTCTTTTTCCTT
1 TTTTTCATTTTATTTC-TTTCTTTTCTTTTTCC-A
*
13334 TTTTTCATTTTATTTCTTTCTTTTCTTTTTTCA
1 TTTTTCATTTTATTTCTTTCTTTTCTTTTTCCA
13367 TTTTTCATTTT
1 TTTTTCATTTT
13378 TCATTCTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 11 0.28
34 14 0.36
35 14 0.36
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTTTCATTTTATTTCTTTCTTTTCTTTTTCCA
Found at i:13371 original size:9 final size:8
Alignment explanation
Indices: 13297--13364 Score: 68
Period size: 8 Copynumber: 8.0 Consensus size: 8
13287 TTATTTATTC
13297 TCTTTTTCT
1 TCTTTTT-T
13306 T-TTTTTT
1 TCTTTTTT
13313 TCTTTTTT
1 TCTTTTTT
13321 T-TTCTTTT
1 TCTT-TTTT
13329 TCCTTTTTT
1 T-CTTTTTT
13338 TCATTTTATT
1 TC-TTTT-TT
13348 TCTTTCTTT
1 TCTTT-TTT
13357 TCTTTTTT
1 TCTTTTTT
13365 CATTTTTCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
7 4 0.08
8 21 0.40
9 20 0.38
10 7 0.13
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TCTTTTTT
Found at i:13380 original size:7 final size:7
Alignment explanation
Indices: 13354--13387 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
13344 TATTTCTTTC
*
13354 TTTTCTT
1 TTTTCAT
13361 TTTTCAT
1 TTTTCAT
13368 TTTTCAT
1 TTTTCAT
13375 TTTTCAT
1 TTTTCAT
*
13382 TCTTCA
1 TTTTCA
13388 GGCAAAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:13385 original size:34 final size:34
Alignment explanation
Indices: 13309--13385 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
13299 TTTTTCTTTT
*
13309 TTTTTC-TT-TTTTTTTCTTTTTCCTTTTTTTCA
1 TTTTTCATTCTTTTTTTCTTTTTCCTATTTTTCA
*
13341 -TTTT-ATTTCTTTCTTTTCTTTTTTC-ATTTTTCA
1 TTTTTCA-TTCTTT-TTTTCTTTTTCCTATTTTTCA
13374 TTTTTCATTCTT
1 TTTTTCATTCTT
13386 CAGGCAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
31 4 0.11
32 2 0.05
33 10 0.27
34 20 0.54
35 1 0.03
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTTCATTCTTTTTTTCTTTTTCCTATTTTTCA
Found at i:18277 original size:26 final size:26
Alignment explanation
Indices: 18241--18298 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
18231 TGAGATACGA
18241 GCCCACCATAATACACATAAGGTCAT
1 GCCCACCATAATACACATAAGGTCAT
* *
18267 GCCCACCATAATACATATAAGGTCGT
1 GCCCACCATAATACACATAAGGTCAT
18293 GCCCAC
1 GCCCAC
18299 TATATTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (26 bp):
GCCCACCATAATACACATAAGGTCAT
Found at i:27759 original size:23 final size:24
Alignment explanation
Indices: 27721--27765 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
27711 TAAATAGTGC
27721 AATAAAAAAATGAAAACAAAATAA
1 AATAAAAAAATGAAAACAAAATAA
* *
27745 AATAAAAAGAT-AAAAGAAAAT
1 AATAAAAAAATGAAAACAAAAT
27766 TAGTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (24 bp):
AATAAAAAAATGAAAACAAAATAA
Found at i:31290 original size:6 final size:6
Alignment explanation
Indices: 31275--31346 Score: 54
Period size: 6 Copynumber: 11.0 Consensus size: 6
31265 AAGGGCACGT
* * *
31275 AATAAG AATAGA AATAAA AATAAA AATAAA AATATAA TATAATA TAATATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATA-AA AATAA-A -AATA-AA
*
31327 TATAATA AATATAA AATAAA
1 AATAA-A AATA-AA AATAAA
31347 TAAATAACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
6 29 0.55
7 18 0.34
8 5 0.09
9 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (6 bp):
AATAAA
Found at i:31320 original size:10 final size:10
Alignment explanation
Indices: 31305--31353 Score: 68
Period size: 10 Copynumber: 5.2 Consensus size: 10
31295 TAAAAATAAA
31305 AATATAATAT
1 AATATAATAT
31315 AATATAATAT
1 AATATAATAT
31325 AATATAATA-
1 AATATAATAT
*
31334 AATATAAAAT
1 AATATAATAT
31344 AA-ATAA-AT
1 AATATAATAT
31352 AA
1 AA
31354 CAACAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 4 0.11
9 12 0.32
10 21 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATAATAT
Found at i:31325 original size:15 final size:15
Alignment explanation
Indices: 31305--31353 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
31295 TAAAAATAAA
31305 AATATAATATAATAT
1 AATATAATATAATAT
31320 AATATAATATAATA-
1 AATATAATATAATAT
*
31334 AATATAAAATAA-AT
1 AATATAATATAATAT
31348 AA-ATAA
1 AATATAA
31354 CAACAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 5 0.16
14 13 0.41
15 14 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:31326 original size:29 final size:28
Alignment explanation
Indices: 31292--31362 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
31282 ATAGAAATAA
*
31292 AAATAAAAATAA-AAATATAATAT-AAT
1 AAATAAAAATAATAAATATAAAATAAAT
*
31318 ATAATATAATATAATAAATATAAAATAAAT
1 A-AATA-AAAATAATAAATATAAAATAAAT
* *
31348 AAATAACAACAATAA
1 AAATAAAAATAATAA
31363 TAAAAGATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 1 0.03
27 4 0.11
28 13 0.36
29 14 0.39
30 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (28 bp):
AAATAAAAATAATAAATATAAAATAAAT
Found at i:31525 original size:6 final size:6
Alignment explanation
Indices: 31491--31560 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
31481 ACAAGCCCAT
* * *
31491 AAAATA ATAATA TAATATA ATATATA AAAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA -AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA
* *
31540 GATAAATA ACAATA ATAATA A
1 -A-AAATA AAAATA AAAATA A
31561 CAAAAGATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 5 0.09
6 31 0.58
7 12 0.23
8 5 0.09
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (6 bp):
AAAATA
Found at i:31535 original size:25 final size:25
Alignment explanation
Indices: 31491--31560 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
31481 ACAAGCCCAT
* * * *
31491 AAAATAATAATATAATATAATATATA
1 AAAATAAAAATA-AAAATAAAATAGA
31517 AAAATAAAAATAAAAATAAAATAGA
1 AAAATAAAAATAAAAATAAAATAGA
* * *
31542 TAAATAACAATAATAATAA
1 AAAATAAAAATAAAAATAA
31561 CAAAAGATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 26 0.70
26 11 0.30
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (25 bp):
AAAATAAAAATAAAAATAAAATAGA
Found at i:31546 original size:13 final size:12
Alignment explanation
Indices: 31489--31557 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 12
31479 TAACAAGCCC
31489 ATAAAATAAT-A
1 ATAAAATAATAA
*
31500 ATATAAT-AT-A
1 ATAAAATAATAA
*
31510 AT-ATATAA-AA
1 ATAAAATAATAA
31520 ATAAAAATAA-AA
1 AT-AAAATAATAA
31532 ATAAAATAGATAA
1 ATAAAATA-ATAA
31545 ATAACAATAATAA
1 ATAA-AATAATAA
31558 TAACAAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 2 0.04
10 9 0.19
11 12 0.26
12 10 0.21
13 10 0.21
14 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (12 bp):
ATAAAATAATAA
Found at i:31554 original size:31 final size:32
Alignment explanation
Indices: 31491--31560 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
31481 ACAAGCCCAT
* *
31491 AAAATAATAATATAATATAATATATAAAAATA
1 AAAATAATAATATAAAATAATAAATAAAAATA
*
31523 AAAATAA-AA-ATAAAATAGATAAATAACAATA
1 AAAATAATAATATAAAATA-ATAAATAAAAATA
*
31554 ATAATAA
1 AAAATAA
31561 CAAAAGATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.21
31 19 0.58
32 7 0.21
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (32 bp):
AAAATAATAATATAAAATAATAAATAAAAATA
Found at i:31563 original size:12 final size:11
Alignment explanation
Indices: 31489--31560 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
31479 TAACAAGCCC
31489 ATAAAATAATA
1 ATAAAATAATA
*
31500 ATATAAT-ATA
1 ATAAAATAATA
* *
31510 AT-ATATAAAA
1 ATAAAATAATA
*
31520 ATAAAAATAAAA
1 AT-AAAATAATA
31532 ATAAAATAGATAA
1 ATAAAATA-AT-A
31545 ATAACAATAATA
1 ATAA-AATAATA
31557 ATAA
1 ATAA
31561 CAAAAGATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
9 2 0.04
10 9 0.18
11 12 0.24
12 15 0.31
13 7 0.14
14 4 0.08
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:31629 original size:195 final size:193
Alignment explanation
Indices: 31297--31685 Score: 525
Period size: 195 Copynumber: 2.0 Consensus size: 193
31287 AATAAAAATA
* * *
31297 AAAATAAAAATATAATATAATATAATATAATATAATAAATATAAAATAAATAAATAACAACAATA
1 AAAATAAAAATATAATATAATATAATAAAATAAAATAAAAATAAAATAAATAAATAACAACAATA
* * *
31362 ATAAAAGATCCGGACAAAAATGAGTGTCTACTATTATTATAGGTTTGACTATACCTTTTACGATA
66 ATAAAAGATCAGGACAAAAACGAGTGTCTA-TATTATTATAGGTTTGACTATACCTTTGACGATA
* * *
31427 GTTCTTCAATGGTTGCTCAGGACT-CCGGAATGGTTCAGGTGTTGGTCACTGTTAACAAGCCCAT
130 GTTCTTCAATGGCTGC-CAGGACTACCGGAATGGTTCAGGTGTTGGTCACAGTCAACAAGCCCAT
* * *
31491 AAAATAATAATATAATATAATAT-ATAAAAATAAAAATAAAAATAAAATAGATAAATAACAATAA
1 AAAATAAAAATATAATATAATATAAT-AAAAT-AAAATAAAAATAAAATAAATAAATAACAACAA
* *
31555 TAATAACAAAAGATCAGGACGAAAACGAGTGT-T-TGTTATTATAGGTTTGACTATACCTTTGAC
64 TAAT---AAAAGATCAGGACAAAAACGAGTGTCTATATTATTATAGGTTTGACTATACCTTTGAC
* * **
31618 GATATTTCTTCAATGGCTGCCATGACTATGGGAATGGTTCAGGTGTTGGTCACAGTCAACAAGCC
126 GATAGTTCTTCAATGGCTGCCAGGACTACCGGAATGGTTCAGGTGTTGGTCACAGTCAACAAGCC
31683 CAT
191 CAT
31686 CTCTCCATTG
Statistics
Matches: 171, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
193 2 0.01
194 32 0.19
195 114 0.67
197 1 0.01
198 22 0.13
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (193 bp):
AAAATAAAAATATAATATAATATAATAAAATAAAATAAAAATAAAATAAATAAATAACAACAATA
ATAAAAGATCAGGACAAAAACGAGTGTCTATATTATTATAGGTTTGACTATACCTTTGACGATAG
TTCTTCAATGGCTGCCAGGACTACCGGAATGGTTCAGGTGTTGGTCACAGTCAACAAGCCCAT
Found at i:43511 original size:36 final size:36
Alignment explanation
Indices: 43463--43597 Score: 216
Period size: 36 Copynumber: 3.8 Consensus size: 36
43453 ATCCATTATC
*
43463 AGCTTTGATACATTCGTGTATCAATGTAATCATATT
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATT
*
43499 AGCTTTGGTACATTCGTGTATCAATGTTATCATATT
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATT
* *
43535 AGCTTTGATACATTCGTGTATCAATATTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATT
* *
43571 AGCTTTGGTACATTGGTGTATCAATGT
1 AGCTTTGATACATTCGTGTATCAATGT
43598 CCAGCACCGT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (36 bp):
AGCTTTGATACATTCGTGTATCAATGTTATCATATT
Found at i:45122 original size:49 final size:49
Alignment explanation
Indices: 45061--45285 Score: 306
Period size: 49 Copynumber: 4.6 Consensus size: 49
45051 GAGAGTCATA
* *
45061 GGTGCATGTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGTATAAC
1 GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* * * *
45110 AGTGCATTTCGGCATAAAAGGTGCCAATAATAAAAGTTAAATGTATAAC
1 GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* * * **
45159 GGTGCATTTCGTCATAAAAGGTGCCACAAAGGAAAGCCAAATGCATAAC
1 GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* *
45208 GGTGCATTTTGGCATAAAAGGTGCCACTAATGAAATTTAAATGCATAAC
1 GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* *
45257 GGTGCATTTTCGACATAAAAGGTGGCACT
1 GGTGCA-TTTCGGCATAAAAGGTGCCACT
45286 CATGGTATTC
Statistics
Matches: 152, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 133 0.88
50 19 0.12
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (49 bp):
GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
Found at i:52231 original size:49 final size:50
Alignment explanation
Indices: 52169--52383 Score: 278
Period size: 49 Copynumber: 4.4 Consensus size: 50
52159 GGTGCATGTC
52169 GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTGCATTTTG
1 GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTGCATTTTG
* * * *
52219 GA-ATAAAAGGTGCCACAAAGGAAA-TTCAAATGCATAATGGTGAATTTCG
1 GACATAAAAGGTGCCACTAATGAAAGTT-AAATGCATAATGGTGCATTTTG
* * *
52268 G-TATAAAAGGTGCCACTAACGAAAGTTAAATGCATAACT-GTGCA-TTTC
1 GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAA-TGGTGCATTTTG
* * * *
52316 AACATAAAAGGTGCCACTAATGAAAGTTCAATGCATAATGGTGTATTTTT
1 GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTGCATTTTG
52366 GACATAAAAGGTGCCACT
1 GACATAAAAGGTGCCACT
52384 CATGGTATTC
Statistics
Matches: 142, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
48 5 0.04
49 112 0.79
50 25 0.18
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (50 bp):
GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTGCATTTTG
Found at i:53139 original size:27 final size:25
Alignment explanation
Indices: 53082--53153 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
53072 ACATATGAAC
*
53082 TATATATAAAACTATATAAACTATAGTT
1 TATATAT-AAACTATAT--ACTACAGTT
53110 TATATATAAACTATATACTACAGTTGT
1 TATATATAAACTATATACTACAG-T-T
* *
53137 TATTTATATACTATATA
1 TATATATAAACTATATA
53154 TAATTTATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
25 6 0.15
26 1 0.03
27 25 0.64
28 7 0.18
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (25 bp):
TATATATAAACTATATACTACAGTT
Found at i:53188 original size:15 final size:16
Alignment explanation
Indices: 53146--53188 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
53136 TTATTTATAT
*
53146 ACTATATATAATTTAT
1 ACTATATATAATTTAG
53162 ACT-TATATAATTTAG
1 ACTATATATAATTTAG
53177 ACTATATA-AATT
1 ACTATATATAATT
53189 CAAAGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
ACTATATATAATTTAG
Found at i:53449 original size:69 final size:69
Alignment explanation
Indices: 53307--53514 Score: 314
Period size: 69 Copynumber: 3.1 Consensus size: 69
53297 ATATGAACTA
* * ** *
53307 TATATATAAATTATATGGTATATACAAACTATTTATTACATAGTT-ATTAGTATATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
53371 ATAG
66 ATAG
* * *
53375 TATATATAAACAATATGGTATATATAAACTATACATCATATAATTCATTAGTATATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
53440 ATAG
66 ATAG
53444 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAG--TATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
*
53507 ATAT
66 ATAG
53511 TATA
1 TATA
53515 GTTCATTAGT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
67 19 0.15
68 37 0.29
69 71 0.56
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (69 bp):
TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
ATAG
Found at i:53485 original size:18 final size:18
Alignment explanation
Indices: 53307--53476 Score: 158
Period size: 18 Copynumber: 9.8 Consensus size: 18
53297 ATATGAACTA
* *
53307 TATATATAAATTATATGG
1 TATATATAAACTATATAG
* *
53325 TATATACAAACTATTTA-
1 TATATATAAACTATATAG
* **
53342 T-TACAT-AGTTAT-TAG
1 TATATATAAACTATATAG
53357 TATATATAAACTATATAG
1 TATATATAAACTATATAG
* *
53375 TATATATAAACAATATGG
1 TATATATAAACTATATAG
*
53393 TATATATAAACTATACA-
1 TATATATAAACTATATAG
* *
53410 T-CATAT-AATTCAT-TAG
1 TATATATAAACT-ATATAG
53426 TATATATAAACTATATAG
1 TATATATAAACTATATAG
*
53444 TATATATAAACTATATGG
1 TATATATAAACTATATAG
53462 TATATATAAACTATA
1 TATATATAAACTATA
53477 CATTATATAG
Statistics
Matches: 121, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.02
15 9 0.07
16 14 0.12
17 12 0.10
18 84 0.69
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:53530 original size:31 final size:33
Alignment explanation
Indices: 53324--53532 Score: 162
Period size: 36 Copynumber: 6.3 Consensus size: 33
53314 AAATTATATG
* ** *
53324 GTATATACAAACTATTTATTACATAGTT-ATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
* ** *
53356 GTATATATAAACTATATAGTATATATA-AACAATATG
1 GTATATATAAACTATACA-T-TATATAGTTC-AT-TA
* *
53392 GTATATATAAACTATACATCATATAATTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
* ** *
53425 GTATATATAAACTATATAGTATATATA-AACTATATG
1 GTATATATAAACTATACA-T-TATATAGTTC-AT-TA
53461 GTATATATAAACTATACATTATATAGTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
*
53494 G--TATATAAACTATATA-T-TATAGTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
53523 GTATATATAA
1 GTATATATAA
53533 CATGTATATT
Statistics
Matches: 143, Mismatches: 21, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
29 13 0.09
30 1 0.01
31 21 0.15
32 16 0.11
33 21 0.15
34 22 0.15
35 13 0.09
36 36 0.25
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (33 bp):
GTATATATAAACTATACATTATATAGTTCATTA
Found at i:53541 original size:31 final size:29
Alignment explanation
Indices: 53464--53569 Score: 112
Period size: 29 Copynumber: 3.6 Consensus size: 29
53454 CTATATGGTA
*
53464 TATATAAACTATACATTATATAGTTCATTAG
1 TATATAAACTATATA-T-TATAGTTCATTAG
53495 TATATAAACTATATATTATAGTTCATTAG
1 TATATAAACTATATATTATAGTTCATTAG
* *
53524 TATATATAACATGTATATTA-A-TTTATTA-
1 TATATA-AAC-TATATATTATAGTTCATTAG
53552 T-TATAAACATATATATTA
1 TATATAAAC-TATATATTA
53570 ATTGAAAGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
26 12 0.17
27 4 0.06
28 1 0.01
29 25 0.36
30 5 0.07
31 22 0.32
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAAACTATATATTATAGTTCATTAG
Found at i:53675 original size:61 final size:61
Alignment explanation
Indices: 53600--53741 Score: 196
Period size: 61 Copynumber: 2.3 Consensus size: 61
53590 TATAAGGATC
* * *
53600 AAATTGAACAAATTTTAAATATGAAGTTTAAATTAATAAATTGTAAC-ATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACAATT-AACTTGGACT
** * *
53661 AAATTGAAGTAATTTTAAATATGAAGCTTAAATTAATATATTGCATCAATTAACTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACAATTAACTTGGACT
*
53722 AAATTGAACAAATTTAAAAT
1 AAATTGAACAAATTTTAAAT
53742 TTGGAGATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
61 67 0.96
62 3 0.04
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACAATTAACTTGGACT
Found at i:54073 original size:103 final size:103
Alignment explanation
Indices: 53890--54078 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 103
53880 TCTCTAGAAA
* * *
53890 TTCATCTGTGTTCATCCCAAAAACACTCATTTGATCTTCACAAATACCAAAACCCAAACTATTTC
1 TTCATATGTGTTCATCCCAAAAACACTCATTTGATCTTCAAAAACACCAAAACCCAAACTATTTC
53955 ATGTTTTTTCAATCAAACACCCATAATTTCAACCCTTG
66 ATGTTTTTTCAATCAAACACCCATAATTTCAACCCTTG
* *
53993 TTCATATGTGTTCATCCTAAAAACCCTCATTTGATCTTCAAAAACACCAAAACCCAAACTATTT-
1 TTCATATGTGTTCATCCCAAAAACACTCATTTGATCTTCAAAAACACCAAAACCCAAACTATTTC
*
54057 AGTGTTTTTTCGATCAAACACC
66 A-TGTTTTTTCAATCAAACACC
54079 TAAAAATTCA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 1 0.01
103 78 0.99
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (103 bp):
TTCATATGTGTTCATCCCAAAAACACTCATTTGATCTTCAAAAACACCAAAACCCAAACTATTTC
ATGTTTTTTCAATCAAACACCCATAATTTCAACCCTTG
Found at i:58866 original size:20 final size:20
Alignment explanation
Indices: 58838--58883 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
58828 AAATACAAGT
*
58838 AATTTAAAGTTTAATGATTA
1 AATTGAAAGTTTAATGATTA
58858 AATTGAAAGTTTAATGATTA
1 AATTGAAAGTTTAATGATTA
58878 AATTGA
1 AATTGA
58884 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (20 bp):
AATTGAAAGTTTAATGATTA
Found at i:59862 original size:23 final size:24
Alignment explanation
Indices: 59836--59901 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
59826 AATATTAAAA
59836 AATTAATATTTTAAATTA-TGTTT
1 AATTAATATTTTAAATTATTGTTT
* * *
59859 AATTAAAATTTTAAAATATTTTTT
1 AATTAATATTTTAAATTATTGTTT
* *
59883 ATTTATTATTTTAATATTA
1 AATTAATATTTTAA-ATTA
59902 AATTAGACGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 16 0.47
24 15 0.44
25 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTAATATTTTAAATTATTGTTT
Found at i:60300 original size:16 final size:16
Alignment explanation
Indices: 60270--60314 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
60260 AATATTGAAA
60270 CTTGAACTC-AAAAGG
1 CTTGAACTCAAAAAGG
60285 CTTGAACTCAAAAAGG
1 CTTGAACTCAAAAAGG
60301 CTTGAACTCAAAAA
1 CTTGAACTCAAAAA
60315 AAAATTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (16 bp):
CTTGAACTCAAAAAGG
Found at i:61293 original size:15 final size:15
Alignment explanation
Indices: 61269--61307 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
61259 CAAGAACCAG
* *
61269 AAATTGTTTTTGTAA
1 AAATTATTTTTATAA
61284 AAATTA-TTTTATAA
1 AAATTATTTTTATAA
61298 AAATTATTTT
1 AAATTATTTT
61308 CAGGGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
AAATTATTTTTATAA
Found at i:61298 original size:14 final size:14
Alignment explanation
Indices: 61276--61307 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
61266 CAGAAATTGT
*
61276 TTTTGTAAAAATTA
1 TTTTATAAAAATTA
61290 TTTTATAAAAATTA
1 TTTTATAAAAATTA
61304 TTTT
1 TTTT
61308 CAGGGTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTTATAAAAATTA
Done.