Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006085.1 Hibiscus syriacus cultivar Beakdansim tig00014428_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: 116394
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:254 original size:69 final size:68
Alignment explanation
Indices: 133--264 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 68
123 TCAAACTATG
* *
133 AGATTGATCAAGCATAATCATTTCGAATCACTGAACTACTTCACTCGAAGATCATAGAGCATCTA
1 AGATTGATCAAGCACAATCATTTCGAATCACTGAACTACTCCACTCGAAGATCATAGAGCATCTA
198 ATA
66 ATA
201 AGATTGATCAAGCACAATCATTTCTGAATCACTGAA-TCACTCCACTCGAAGATCATAGAGCATC
1 AGATTGATCAAGCACAATCATTTC-GAATCACTGAACT-ACTCCACTCGAAGATCATAGAGCATC
265 AAGAGAGAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
68 24 0.40
69 36 0.60
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (68 bp):
AGATTGATCAAGCACAATCATTTCGAATCACTGAACTACTCCACTCGAAGATCATAGAGCATCTA
ATA
Found at i:1203 original size:32 final size:32
Alignment explanation
Indices: 1167--1283 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 32
1157 GGAACAATGA
**
1167 GGGCA-TCTTTGAAGATTCAACATCAAATGCTG
1 GGGCATTCTTTG-AGATTCAACATCAAATATTG
* * *
1199 GGGCATTTTTTGAGATTTAACATCAAATATTT
1 GGGCATTCTTTGAGATTCAACATCAAATATTG
* *
1231 GGGCATTTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TTCTTTGAGATTCAACATCAAATATTG
*
1264 GGGCA-TCTTTGGGAATTCAA
1 GGGCATTCTTTGAG-ATTCAA
1284 TATCCTGATG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
31 6 0.08
32 32 0.44
33 34 0.47
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (32 bp):
GGGCATTCTTTGAGATTCAACATCAAATATTG
Found at i:1211 original size:33 final size:32
Alignment explanation
Indices: 1174--1269 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 32
1164 TGAGGGCATC
**
1174 TTTGAAGATTCAACATCAAATGCTGGGGCATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
* *
1207 TTTGAGATTTAACATCAAATATTTGGGCATTTT
1 TTTGAGATTCAACATCAAATATTGGGGCA-TTT
*
1240 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
1270 CTTTGGGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
32 22 0.40
33 33 0.60
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:2677 original size:99 final size:101
Alignment explanation
Indices: 2456--2687 Score: 242
Period size: 100 Copynumber: 2.3 Consensus size: 101
2446 ATTTTCCAAG
* * * **
2456 TTTTGTCTCTCTTGAGACAG-TTCCCTTGAAACAAAATATTTGAATCTATTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTGGAATAAATTTCCCTTGAAACAAA
** ** * *
2520 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAA
66 TTTCGTCTCCCTTGAGACAGGTTCCCTTGAAACAAA
* * **
2556 GTTTGTCTCTCTTGAGATAGTTTCTCTTGAAA-ATAAACATTGGAA-AAATTTCCCTTGAAATGA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAACATTGGAATAAATTTCCCTTGAAACAA
* *
2619 ATTT-GTCTCTC-TGAGATAGGTTCCCTTGAAACAAAA
65 ATTTCGTCTCCCTTGAGACAGGTTCCCTTGAAAC-AAA
2655 TTTTGTCTCTCTTGAGACAGTTT-TCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCT-CTTGAAAC
2688 TTCAATCTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
98 16 0.15
99 36 0.33
100 37 0.34
101 19 0.18
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (101 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTGGAATAAATTTCCCTTGAAACAAA
TTTCGTCTCCCTTGAGACAGGTTCCCTTGAAACAAA
Found at i:2883 original size:84 final size:84
Alignment explanation
Indices: 2782--2991 Score: 241
Period size: 83 Copynumber: 2.5 Consensus size: 84
2772 CAGCTTCGAG
* * * * *
2782 GGCAC-TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGATCTTTGAGT
1 GGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGTCAACC-AAAGACCCTCGAGT
* * *
2845 TCGACTATGC-TCAGCTCTAA
65 TCAACTACGCAT-AGCTCCAA
* * * * * *
2865 GGCACATCATTTGCAGCATAGCTTAAGTCGA-AAGGGCTATATGTCAACCAAAGACCCTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGTCAACCAAAGACCCTCGAGTT
2929 CAACTACGCATAGCTCCAA
66 CAACTACGCATAGCTCCAA
2948 GGCACATCATTTACAGCATAACTCAAGG-AAGAAGGGCTATCTGT
1 GGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGT
2992 AAATAAAATT
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
82 1 0.01
83 79 0.76
84 24 0.23
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
GGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGTCAACCAAAGACCCTCGAGTT
CAACTACGCATAGCTCCAA
Found at i:4650 original size:16 final size:15
Alignment explanation
Indices: 4624--4653 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4614 TCTTTGTTTG
4624 TTTTATTTATTTATT
1 TTTTATTTATTTATT
4639 TTTTACTTTATTTAT
1 TTTTA-TTTATTTAT
4654 GATCTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:4661 original size:20 final size:20
Alignment explanation
Indices: 4625--4663 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4615 CTTTGTTTGT
*
4625 TTTATTTATTTATTTTTTAC
1 TTTATTTATTGATTTTTTAC
4645 TTTATTTA-TGATCTTTTTA
1 TTTATTTATTGAT-TTTTTA
4664 GGATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTATTTATTGATTTTTTAC
Found at i:8426 original size:12 final size:12
Alignment explanation
Indices: 8409--8433 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8399 ACGAGAAATA
8409 AGAAATTACAAG
1 AGAAATTACAAG
8421 AGAAATTACAAG
1 AGAAATTACAAG
8433 A
1 A
8434 AATTATAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AGAAATTACAAG
Found at i:15414 original size:19 final size:20
Alignment explanation
Indices: 15377--15415 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
15367 GACTTTACAG
15377 ATTTAATTAAAATATTTAAA
1 ATTTAATTAAAATATTTAAA
15397 ATTTAA-TAATAA-ATTTAAA
1 ATTTAATTAA-AATATTTAAA
15416 TTTCACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAATTAAAATATTTAAA
Found at i:16145 original size:2 final size:2
Alignment explanation
Indices: 16130--16166 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16120 TAAAAATAAA
16130 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16167 ATTTTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18383 original size:9 final size:9
Alignment explanation
Indices: 18369--18396 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
18359 GAAGAATCTG
18369 ATGATAAGA
1 ATGATAAGA
18378 ATGATAAGA
1 ATGATAAGA
18387 ATGATAAGA
1 ATGATAAGA
18396 A
1 A
18397 GCAACATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (9 bp):
ATGATAAGA
Found at i:25330 original size:21 final size:21
Alignment explanation
Indices: 25304--25357 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
25294 GCGCTGCATT
25304 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
25325 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
25346 TCGCGTTGCGAT
1 TCGCGTTGCGAT
25358 TTTCCTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:25394 original size:41 final size:41
Alignment explanation
Indices: 25349--25510 Score: 279
Period size: 41 Copynumber: 4.0 Consensus size: 41
25339 TTGAAAATCG
* *
25349 CGTTGCGATTTTCCTTTTCGCATTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
* * *
25390 CGTTGCGATTTTCCATATCGCGTTGCGATAGTCTACATTAT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
25431 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
25472 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
25511 AAATTAAAAA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:25397 original size:21 final size:20
Alignment explanation
Indices: 25371--25480 Score: 73
Period size: 21 Copynumber: 5.3 Consensus size: 20
25361 CCTTTTCGCA
25371 TTGCGATAGTCTACAGTGTCG
1 TTGCGATAGTCTACA-TGTCG
** * *
25392 TTGCGATTTTCCATATCG-CG
1 TTGCGATAGTCTACAT-GTCG
*
25412 TTGCGATAGTCTACATTATCG
1 TTGCGATAGTCTACA-TGTCG
* * *
25433 TTGCGAT--TTTCCATTTCGCG
1 TTGCGATAGTCTACATGT--CG
25453 TTGCGATAGTCTACAGTGTCG
1 TTGCGATAGTCTACA-TGTCG
25474 TTGCGAT
1 TTGCGAT
25481 TTTCCATTTC
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 23 0.35
21 31 0.47
22 4 0.06
23 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCTACATGTCG
Found at i:25410 original size:82 final size:82
Alignment explanation
Indices: 25324--25506 Score: 287
Period size: 82 Copynumber: 2.2 Consensus size: 82
25314 ATAGTTGAAA
* *
25324 ATCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCTTTTCGCATTGCGATAGTCTACAGT
1 ATCGCGTTGCGATAGTCT-AAAATAGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAGT
25388 GTCGTTGCGATTTTCCAT
65 GTCGTTGCGATTTTCCAT
* * * *
25406 ATCGCGTTGCGATAGTCTACATTATCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTG
1 ATCGCGTTGCGATAGTCTAAAATAGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAGTG
25471 TCGTTGCGATTTTCCAT
66 TCGTTGCGATTTTCCAT
*
25488 TTCGCGTTGCGATAGTCTA
1 ATCGCGTTGCGATAGTCTA
25507 CAGTAAATTA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 92 0.99
83 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (82 bp):
ATCGCGTTGCGATAGTCTAAAATAGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAGTG
TCGTTGCGATTTTCCAT
Found at i:25415 original size:20 final size:20
Alignment explanation
Indices: 25345--25500 Score: 86
Period size: 20 Copynumber: 7.7 Consensus size: 20
25335 ATAGTTGAAA
*
25345 ATCGCGTTGCGATTTTCCTT
1 ATCGCGTTGCGATTTTCCAT
* * ** * *
25365 TTCGCATTGCGATAGTCTAC
1 ATCGCGTTGCGATTTTCCAT
25385 AGT-GTCGTTGCGATTTTCCAT
1 A-TCG-CGTTGCGATTTTCCAT
* *
25406 ATCGCGTTGCGATAGTCTACATT
1 ATCGCGTTGCGAT--TTTCCA-T
25429 AT--CGTTGCGATTTTCCAT
1 ATCGCGTTGCGATTTTCCAT
* ** * *
25447 TTCGCGTTGCGATAGTCTAC
1 ATCGCGTTGCGATTTTCCAT
25467 AGT-GTCGTTGCGATTTTCCAT
1 A-TCG-CGTTGCGATTTTCCAT
*
25488 TTCGCGTTGCGAT
1 ATCGCGTTGCGAT
25501 AGTCTACAGT
Statistics
Matches: 97, Mismatches: 28, Indels: 22
0.66 0.19 0.15
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 47 0.48
21 37 0.38
22 4 0.04
23 3 0.03
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCCAT
Found at i:25598 original size:6 final size:6
Alignment explanation
Indices: 25587--25617 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
25577 AAAGACACGT
25587 ATTACC ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC ATTACC A
25618 CGACCACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:25623 original size:6 final size:6
Alignment explanation
Indices: 25614--25656 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
25604 CATTACCATT
25614 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
25657 GACGAGACGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:25623 original size:18 final size:18
Alignment explanation
Indices: 25587--25623 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25577 AAAGACACGT
**
25587 ATTACCATTACCATTACC
1 ATTACCATTACCACGACC
25605 ATTACCATTACCACGACC
1 ATTACCATTACCACGACC
25623 A
1 A
25624 CGACCACGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (18 bp):
ATTACCATTACCACGACC
Found at i:26156 original size:5 final size:5
Alignment explanation
Indices: 26148--26175 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
26138 CCGTCTCGTC
26148 TCGGT TCGGT TCGGT TCGGT TCGGT TCG
1 TCGGT TCGGT TCGGT TCGGT TCGGT TCG
26176 TGGTCGTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.39, T:0.39
Consensus pattern (5 bp):
TCGGT
Found at i:26184 original size:6 final size:6
Alignment explanation
Indices: 26173--26227 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
26163 TCGGTTCGGT
26173 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
26221 TCGTGG T
1 TCGTGG T
26228 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:26365 original size:41 final size:41
Alignment explanation
Indices: 26308--26477 Score: 232
Period size: 41 Copynumber: 4.0 Consensus size: 41
26298 TTTTTAATTT
*
26308 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
26349 ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
26390 ACTGTAGACTATCGGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 AC--T-G--TA-C--ACTATCGCAACGCGAAATGGAAAATCGCAACGAC
* * *
26439 ACTGTAAACTATCGCAATGCGAAAAGGAAAATCGCAACG
1 ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACG
26478 CGATTTTCAA
Statistics
Matches: 117, Mismatches: 4, Indels: 16
0.85 0.03 0.12
Matches are distributed among these distances:
41 72 0.62
43 1 0.01
44 3 0.03
46 3 0.03
47 2 0.02
49 36 0.31
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (41 bp):
ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
Found at i:26428 original size:49 final size:49
Alignment explanation
Indices: 26356--26452 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
26346 GACACTGTAC
*
26356 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGG
26405 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCG
26453 CAATGCGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (49 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGG
Found at i:26492 original size:90 final size:90
Alignment explanation
Indices: 26314--26477 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 90
26304 ATTTACTGTA
* *
26314 GACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAATGGAAA
1 GACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGCAACGCGAAAAGGAAA
26379 ATCGCAACGACACTGTAGACTATCG
66 ATCGCAACGACACTGTAGACTATCG
*
26404 GACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGCAATGCGAAAAGGAAA
1 GACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGCAACGCGAAAAGGAAA
26469 ATCGCAACG
66 ATCGCAACG
26478 CGATTTTCAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (90 bp):
GACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAAACTATCGCAACGCGAAAAGGAAA
ATCGCAACGACACTGTAGACTATCG
Found at i:26497 original size:21 final size:21
Alignment explanation
Indices: 26473--26522 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
26463 AGGAAAATCG
*
26473 CAACGCGATTTTCAACTATCA
1 CAACGCGATTTTAAACTATCA
*
26494 CAACGCGATTTTAAACTATCG
1 CAACGCGATTTTAAACTATCA
26515 CAACGCGA
1 CAACGCGA
26523 AATGCAGCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (21 bp):
CAACGCGATTTTAAACTATCA
Found at i:28463 original size:2 final size:2
Alignment explanation
Indices: 28456--28483 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28446 AATAACTACA
28456 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
28484 TCATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64315 original size:18 final size:18
Alignment explanation
Indices: 64289--64328 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
64279 CTCAGATATT
*
64289 GCTTCTGTGTTAAACAAA
1 GCTTATGTGTTAAACAAA
64307 GCTTATGTGTTAAACAAA
1 GCTTATGTGTTAAACAAA
64325 GCTT
1 GCTT
64329 CACTCTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (18 bp):
GCTTATGTGTTAAACAAA
Found at i:66045 original size:21 final size:22
Alignment explanation
Indices: 66014--66080 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
66004 CTCGTATAAA
66014 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
66036 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
66057 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
66079 TG
1 TG
66081 TCCATAAGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.48
22 23 0.52
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:67787 original size:21 final size:21
Alignment explanation
Indices: 67763--67803 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
67753 TCTTGTTCGT
* *
67763 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
67784 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
67804 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:70948 original size:22 final size:22
Alignment explanation
Indices: 70931--70998 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
70921 CTCGTATAAA
70931 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70953 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70975 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70997 TG
1 TG
70999 TCCATAAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:72708 original size:21 final size:21
Alignment explanation
Indices: 72684--72728 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
72674 TCTTGTTCGT
* *
72684 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
72705 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
72726 TTG
1 TTG
72729 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:77065 original size:32 final size:31
Alignment explanation
Indices: 77004--77067 Score: 74
Period size: 34 Copynumber: 2.0 Consensus size: 31
76994 ATTCAGAAAT
77004 TTAAAAATAGGGTATAAAATTTTAATTTTTTC
1 TTAAAAATAGGGTATAAAATTTT-ATTTTTTC
** *
77036 TTAAAAATAATGGGTATGCAATTTTTTTTTTT
1 TTAAAAAT-A-GGGTATAAAATTTTATTTTTT
77068 ACATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 8 0.30
33 7 0.26
34 12 0.44
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (31 bp):
TTAAAAATAGGGTATAAAATTTTATTTTTTC
Found at i:77504 original size:35 final size:35
Alignment explanation
Indices: 77438--77504 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
77428 TAACATATAA
* * **
77438 TAAATTAATATCAATTCAATTGTATGTTATAAATC
1 TAAATTAACATCAATTCAATTATATACTATAAATC
77473 TAAATTAACATCAA-TCTAATTATATACTATAA
1 TAAATTAACATCAATTC-AATTATATACTATAA
77505 GATAAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (35 bp):
TAAATTAACATCAATTCAATTATATACTATAAATC
Found at i:88588 original size:21 final size:20
Alignment explanation
Indices: 88550--88606 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
88540 GGAAGGGGAC
*
88550 TATTTTTTAAAAATAATATATT
1 TATTTTTTAATAA-AATAT-TT
88572 TATTTTTTAATAAAATATTT
1 TATTTTTTAATAAAATATTT
*
88592 AATTTTTTAAATAAA
1 TATTTTTT-AATAAA
88607 TTCTCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 9 0.28
21 11 0.34
22 12 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTTAATAAAATATTT
Found at i:88589 original size:19 final size:21
Alignment explanation
Indices: 88551--88606 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
88541 GAAGGGGACT
*
88551 ATTTTTTAAA-AATAATATATTT
1 ATTTTTTAAATAA-AATAT-TTA
88573 ATTTTTT-AATAAAATATTTA
1 ATTTTTTAAATAAAATATTTA
88593 ATTTTTTAAATAAA
1 ATTTTTTAAATAAA
88607 TTCTCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 13 0.42
22 9 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTTAAATAAAATATTTA
Found at i:88607 original size:20 final size:19
Alignment explanation
Indices: 88550--88607 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 19
88540 GGAAGGGGAC
88550 TATTTTTTAAAAATAATATATT
1 TATTTTTT--AAATAA-ATATT
88572 TATTTTTT-AATAAAATATT
1 TATTTTTTAAAT-AAATATT
88591 TAATTTTTTAAATAAAT
1 T-ATTTTTTAAATAAAT
88608 TCTCAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 9 0.27
20 13 0.39
21 3 0.09
22 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTTAAATAAATATT
Found at i:91151 original size:2 final size:2
Alignment explanation
Indices: 91144--91173 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91134 TCAGGTGAGC
91144 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
91174 TAACAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99772 original size:28 final size:28
Alignment explanation
Indices: 99709--99783 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
99699 GGGGAAAGAG
* * * *
99709 ATCTCATGCAGAACCAAGACGGGGACTA
1 ATCTCATGCAGAATCAAGAAGGGAACAA
* *
99737 AGCCCATGCAGAATCAAGAAGGGAACAA
1 ATCTCATGCAGAATCAAGAAGGGAACAA
*
99765 ATCTCATGTAGAATCAAGA
1 ATCTCATGCAGAATCAAGA
99784 TGAATATTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (28 bp):
ATCTCATGCAGAATCAAGAAGGGAACAA
Found at i:99896 original size:2 final size:2
Alignment explanation
Indices: 99891--99915 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99881 GTCACGTGTG
99891 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
99916 CACAAACATA
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:103723 original size:21 final size:21
Alignment explanation
Indices: 103694--103733 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
103684 GTCAAAATGA
103694 ATCCATTTTATTAATTTTTTC
1 ATCCATTTTATTAATTTTTTC
* * *
103715 ATCCTTTTTCTTTATTTTT
1 ATCCATTTTATTAATTTTT
103734 GGGGTAAAGT
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:0.15, G:0.00, T:0.68
Consensus pattern (21 bp):
ATCCATTTTATTAATTTTTTC
Done.