Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006373.1 Hibiscus syriacus cultivar Beakdansim tig00015331_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: 96373
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:952 original size:57 final size:60
Alignment explanation
Indices: 889--1018 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 60
879 TTGGATGACT
* * * *
889 ATTTTGTAACTTTTAATAGTCGGA-GACTCGACAAAGTAACACCCTATAGTT-CA-GATC
1 ATTTTGTAACTTTTAATAATCAGATGACTCAACAAAGTAACACCCTATAATTGCAGGATC
* * *
946 ATTTTGTAACTTTTAATAATCAGATGACTCAACAAATTAACATCCTGTAATTGCAGGATC
1 ATTTTGTAACTTTTAATAATCAGATGACTCAACAAAGTAACACCCTATAATTGCAGGATC
1006 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
1019 ACCCTTAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 22 0.35
58 22 0.35
59 2 0.03
60 13 0.21
61 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAATCAGATGACTCAACAAAGTAACACCCTATAATTGCAGGATC
Found at i:5140 original size:38 final size:38
Alignment explanation
Indices: 5085--5179 Score: 172
Period size: 38 Copynumber: 2.5 Consensus size: 38
5075 TATGAAATGT
*
5085 CAGCTGATGCTGAGCTTGACCCCCACACACAATAGGCA
1 CAGCTGATGCTGAGCTTGACCCCCACACACAATAAGCA
*
5123 CAGTTGATGCTGAGCTTGACCCCCACACACAATAAGCA
1 CAGCTGATGCTGAGCTTGACCCCCACACACAATAAGCA
5161 CAGCTGATGCTGAGCTTGA
1 CAGCTGATGCTGAGCTTGA
5180 TATTCAATGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (38 bp):
CAGCTGATGCTGAGCTTGACCCCCACACACAATAAGCA
Found at i:10281 original size:15 final size:16
Alignment explanation
Indices: 10255--10284 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10245 TCAAGTCTTT
10255 TTTTTCTATTATATTG
1 TTTTTCTATTATATTG
10271 TTTTTCT-TTATATT
1 TTTTTCTATTATATT
10285 TGGCTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTCTATTATATTG
Found at i:13311 original size:19 final size:20
Alignment explanation
Indices: 13287--13327 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
13277 GAAATGTTAA
13287 AAAAAT-TAATGTTTTAGGT
1 AAAAATATAATGTTTTAGGT
13306 AAAAATATAATGTTTTAGGT
1 AAAAATATAATGTTTTAGGT
13326 AA
1 AA
13328 TTTTTTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (20 bp):
AAAAATATAATGTTTTAGGT
Found at i:29188 original size:77 final size:77
Alignment explanation
Indices: 29078--29225 Score: 226
Period size: 77 Copynumber: 1.9 Consensus size: 77
29068 TGGAAGGGTA
* * * * *
29078 TTCCTTTGTCTCCTGGCTACTACTTACCTGCCGCGCTTCAATTC-TTTTTCCTTTTTCGTAGGCT
1 TTCCATTGCCTCCAGGCTACTACTTACCTGCCGCCCTGCAATTCTTTTTTCC-TTTTCGTAGGCT
29142 TCAATATAGAGTC
65 TCAATATAGAGTC
*
29155 TTCCATTGCCTCCAGGCTATTACTTACCTGCCGCCCTGCAATTCTTTTTTCCTTTTCGTAGGCTT
1 TTCCATTGCCTCCAGGCTACTACTTACCTGCCGCCCTGCAATTCTTTTTTCCTTTTCGTAGGCTT
29220 CAATAT
66 CAATAT
29226 TGAAGCCTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
77 57 0.89
78 7 0.11
ACGTcount: A:0.15, C:0.30, G:0.14, T:0.42
Consensus pattern (77 bp):
TTCCATTGCCTCCAGGCTACTACTTACCTGCCGCCCTGCAATTCTTTTTTCCTTTTCGTAGGCTT
CAATATAGAGTC
Found at i:38409 original size:2 final size:2
Alignment explanation
Indices: 38402--38435 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38392 GGGTCTTACG
38402 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
38436 GCTCACTAAA
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:41424 original size:3 final size:3
Alignment explanation
Indices: 41416--41486 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
41406 TGGCTGAAGC
* * * *
41416 TCT TCT TCT TCT TCA TCT TCT TCC TCC TCT TCC TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
41464 TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC
41487 ATATTCACCT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:41507 original size:6 final size:6
Alignment explanation
Indices: 41498--41555 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
41488 TATTCACCTC
* * * * * *
41498 CATCAT CATCGT CATCGT CGTCGT CATCAT CATTGT CGTCGT CATCCT
1 CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT
*
41546 CATCCT CATC
1 CATCGT CATC
41556 TCCACTGGCT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.17, C:0.36, G:0.12, T:0.34
Consensus pattern (6 bp):
CATCGT
Found at i:41524 original size:18 final size:18
Alignment explanation
Indices: 41503--41549 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
41493 ACCTCCATCA
*
41503 TCATCGTCATCGTCGTCG
1 TCATCATCATCGTCGTCG
*
41521 TCATCATCATTGTCGTCG
1 TCATCATCATCGTCGTCG
*
41539 TCATCCTCATC
1 TCATCATCATC
41550 CTCATCTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.34, G:0.15, T:0.36
Consensus pattern (18 bp):
TCATCATCATCGTCGTCG
Found at i:44524 original size:28 final size:28
Alignment explanation
Indices: 44480--44534 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
44470 CATTTAGTAT
* * *
44480 ACAATCAGTTAATCTAACGGGATAAGAG
1 ACAACCAGTTAAACTAACAGGATAAGAG
44508 ACAACCAGTTAAACTAACAGGATAAGA
1 ACAACCAGTTAAACTAACAGGATAAGA
44535 AACGTTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (28 bp):
ACAACCAGTTAAACTAACAGGATAAGAG
Found at i:48291 original size:13 final size:13
Alignment explanation
Indices: 48273--48302 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
48263 TTATTTTATT
48273 TTTTATCATTTAA
1 TTTTATCATTTAA
48286 TTTTATCATTTAA
1 TTTTATCATTTAA
48299 TTTT
1 TTTT
48303 TAAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTATCATTTAA
Found at i:49271 original size:27 final size:25
Alignment explanation
Indices: 49226--49298 Score: 65
Period size: 28 Copynumber: 2.7 Consensus size: 25
49216 CTCAAAATTA
* *
49226 AAAATATTTTATATATTTTATATTTT
1 AAAATATTTT-TATTTTTTAAATTTT
49252 AAAATTATCTTTTATTTTTTTAAATTTAT
1 AAAA-TAT-TTTTA-TTTTTTAAATTT-T
*
49281 TAAATATATTTTATTTTT
1 AAAATAT-TTTTATTTTT
49299 ATTTAAATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.10
27 10 0.26
28 21 0.54
29 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (25 bp):
AAAATATTTTTATTTTTTAAATTTT
Found at i:49315 original size:29 final size:27
Alignment explanation
Indices: 49225--49320 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 27
49215 ACTCAAAATT
* * *
49225 AAAA-ATATTTTATATATTTTATATTTTA
1 AAAATATATTTTAT-TTTTTTA-AATCTA
* * *
49253 AAATTATCTTTTATTTTTTTAAATTTA
1 AAAATATATTTTATTTTTTTAAATCTA
*
49280 TTAAATATATTTTATTTTTATTTAAATCTA
1 -AAAATATATTTTA-TTTT-TTTAAATCTA
49310 AAAATATATTT
1 AAAATATATTT
49321 GTCAAGATAC
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.09
28 19 0.35
29 22 0.40
30 9 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
AAAATATATTTTATTTTTTTAAATCTA
Found at i:49457 original size:23 final size:23
Alignment explanation
Indices: 49430--49473 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
49420 TTTTTAAATA
*
49430 TCTTAACTTAAATTATATTTTAT
1 TCTTAACTTAAAATATATTTTAT
*
49453 TCTTAAGTTAAAATATATTTT
1 TCTTAACTTAAAATATATTTT
49474 GGATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (23 bp):
TCTTAACTTAAAATATATTTTAT
Found at i:49496 original size:10 final size:10
Alignment explanation
Indices: 49477--49524 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
49467 ATATTTTGGA
49477 TTTAAAATAT
1 TTTAAAATAT
*
49487 TTTAATATAT
1 TTTAAAATAT
*
49497 TTTTAAA-A-
1 TTTAAAATAT
*
49505 GTTAAAATAT
1 TTTAAAATAT
49515 TTTAAAATAT
1 TTTAAAATAT
49525 ATATTTGTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
8 5 0.17
9 2 0.07
10 23 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:49496 original size:28 final size:28
Alignment explanation
Indices: 49460--49531 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
49450 TATTCTTAAG
* *
49460 TTAAAATATATTTTGGATTTAAAATATT
1 TTAAAATATATTTTGAAGTTAAAATATT
* *
49488 TTAATATAT-TTTTAAAAGTTAAAATATT
1 TTAAAATATATTTT-GAAGTTAAAATATT
49516 TTAAAATATATATTTG
1 TTAAAATATAT-TTTG
49532 TAAGGGATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 4 0.11
28 27 0.77
29 1 0.03
30 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (28 bp):
TTAAAATATATTTTGAAGTTAAAATATT
Found at i:49611 original size:24 final size:25
Alignment explanation
Indices: 49580--49633 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
49570 AAATAAAAAT
* *
49580 AAATATATTTAATAATTTAAGA-AA
1 AAATATATTTAATAAGTTAAAACAA
49604 AAATATATTTAATAAGTTAAAACAA
1 AAATATATTTAATAAGTTAAAACAA
49629 AAATA
1 AAATA
49634 AAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATATATTTAATAAGTTAAAACAA
Found at i:50645 original size:60 final size:60
Alignment explanation
Indices: 50581--50712 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
50571 ATTGGAGACC
* * ** * * *
50581 AATTTAGAATGAA-GGTCATAGTTTATGGATGAAATTAAAATGTTTAAAAGTTTAAGGACT
1 AATTTAGAAT-AATAGTCATAGTTTAGGGATGAAACAAAAATATTTAAAAGCTTAACGACT
* * *
50641 AATTTATAATAATAGTCATAGTTTAGGGATGAAACAAAAATATTTAAAAGCTTAACTATT
1 AATTTAGAATAATAGTCATAGTTTAGGGATGAAACAAAAATATTTAAAAGCTTAACGACT
50701 AATTTAGAATAA
1 AATTTAGAATAA
50713 GAGTTATAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (60 bp):
AATTTAGAATAATAGTCATAGTTTAGGGATGAAACAAAAATATTTAAAAGCTTAACGACT
Found at i:54403 original size:20 final size:20
Alignment explanation
Indices: 54348--54404 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
54338 TTTTATTTTC
* * *
54348 TGATAATCATACATTCCCAC
1 TGATAATCTTACATTTCCAA
*
54368 TGATAATCTTACATTTCTAA
1 TGATAATCTTACATTTCCAA
54388 TGATAATCTTACATTTC
1 TGATAATCTTACATTTC
54405 GTGAACCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (20 bp):
TGATAATCTTACATTTCCAA
Found at i:55923 original size:23 final size:23
Alignment explanation
Indices: 55897--55970 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
55887 AACGTGTACG
* *
55897 TTTAATGTTCGTGAACATATTTA
1 TTTAATGTTCGTAAATATATTTA
** *
55920 TTTAAAAATTCGTCAATATATTTA
1 TTT-AATGTTCGTAAATATATTTA
* * *
55944 TCTATTGTTCGTAAATATATTTT
1 TTTAATGTTCGTAAATATATTTA
55967 TTTA
1 TTTA
55971 GCATTTATTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (23 bp):
TTTAATGTTCGTAAATATATTTA
Found at i:56379 original size:11 final size:11
Alignment explanation
Indices: 56363--56399 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
56353 ACAATCATAA
56363 ACAAACGTTAT
1 ACAAACGTTAT
56374 ACAAACGTTAT
1 ACAAACGTTAT
56385 ACAAACGTTAT
1 ACAAACGTTAT
56396 ACAA
1 ACAA
56400 CATTCCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (11 bp):
ACAAACGTTAT
Found at i:61773 original size:20 final size:20
Alignment explanation
Indices: 61744--61786 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
61734 TTTTTGTTCG
*
61744 AATTTATTTAATAT-ATTTTA
1 AATTTATTT-ATATGATCTTA
*
61764 AATTTTTTTATATGATCTTA
1 AATTTATTTATATGATCTTA
61784 AAT
1 AAT
61787 GATTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTATTTATATGATCTTA
Found at i:62586 original size:33 final size:33
Alignment explanation
Indices: 62549--62623 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
62539 GGTAAGAAAT
* * * *
62549 TTATTTTTATGTTAGTAT-TTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
62582 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
62615 TT-TTTTTAT
1 TTATTTTTAT
62624 TAAAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.19
33 21 0.57
34 9 0.24
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:62616 original size:30 final size:30
Alignment explanation
Indices: 62580--62653 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
62570 TTTAAATAGT
* *
62580 TATTATTTTTATATTAATATATTATGTAAA
1 TATTATTTTTATATTAAAATAATATGTAAA
* * *
62610 TATTATTTTTTTATTAAAATAATATTTATA
1 TATTATTTTTATATTAAAATAATATGTAAA
62640 TAATTATTATTTAT
1 T-ATTATT-TTTAT
62654 TTAGAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 26 0.72
31 6 0.17
32 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TATTATTTTTATATTAAAATAATATGTAAA
Found at i:62819 original size:17 final size:17
Alignment explanation
Indices: 62797--62850 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
62787 AATGTTAATA
62797 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
62814 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
62831 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
62848 TTT
1 TTT
62851 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:64432 original size:21 final size:21
Alignment explanation
Indices: 64419--64504 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
64409 GCCCACCAGT
* *
64419 TTACATTCCGAGCCCGCAGGG
1 TTACATTCCTAGCCCCCAGGG
* *
64440 TTACATTCCAAGCCCGCAGGG
1 TTACATTCCTAGCCCCCAGGG
64461 TTACATTCCTAGCCCGCCA-GG
1 TTACATTCCTAGCCC-CCAGGG
* *
64482 TTACATGCCTAGCCCGCAGGG
1 TTACATTCCTAGCCCCCAGGG
64503 TT
1 TT
64505 TTATACCATA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.20, C:0.34, G:0.24, T:0.22
Consensus pattern (21 bp):
TTACATTCCTAGCCCCCAGGG
Found at i:64451 original size:42 final size:42
Alignment explanation
Indices: 64402--64504 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
64392 TCCACTTCAT
*
64402 ATGCCAAGCCCACCA-GTTTACATTCCGAGCCCG-CAGGGTTAC
1 ATGCCAAGCCC-CCAGGGTTACATTCCGAGCCCGCCA-GGTTAC
* * *
64444 ATTCCAAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTAC
1 ATGCCAAGCCCCCAGGGTTACATTCCGAGCCCGCCAGGTTAC
* *
64486 ATGCCTAGCCCGCAGGGTT
1 ATGCCAAGCCCCCAGGGTT
64505 TTATACCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.04
42 49 0.92
43 2 0.04
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
ATGCCAAGCCCCCAGGGTTACATTCCGAGCCCGCCAGGTTAC
Found at i:65086 original size:33 final size:34
Alignment explanation
Indices: 65027--65123 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
65017 AAATGTTTTT
*
65027 AAAATACAAATTATAGTATTCGAAATTTAAAATA
1 AAAATAAAAATTATAGTATTCGAAATTTAAAATA
* * * *
65061 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATAGTATTCGAAATTTAAAATA
*
65094 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATAGTATTCGAAATTTAA
65124 CATTAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (34 bp):
AAAATAAAAATTATAGTATTCGAAATTTAAAATA
Found at i:65130 original size:34 final size:33
Alignment explanation
Indices: 65025--65130 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
65015 ATAAATGTTT
*
65025 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATAGTATTCGAAATTT-AAA
* * *
65059 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATAGTATTCGAAATTTAAA
*
65091 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATAGTATTCGAAATTTAA-A
65126 TTAAA
1 TTAAA
65131 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.41
34 32 0.52
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATAGTATTCGAAATTTAAA
Found at i:65758 original size:16 final size:16
Alignment explanation
Indices: 65728--65768 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
65718 ACGAAATAAT
*
65728 GGAAGGCGCGCCCCCG
1 GGAACGCGCGCCCCCG
* *
65744 GGGACGCGCGTCCCCG
1 GGAACGCGCGCCCCCG
65760 GGAACGCGC
1 GGAACGCGC
65769 CTTCATGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.12, C:0.41, G:0.44, T:0.02
Consensus pattern (16 bp):
GGAACGCGCGCCCCCG
Found at i:65871 original size:144 final size:139
Alignment explanation
Indices: 65600--66024 Score: 568
Period size: 144 Copynumber: 3.1 Consensus size: 139
65590 ATGACATAAT
* *
65600 GGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTA
1 GGAACGCGCGTCCCCGGGAACGCGCCTTCATGT---T-G-GAAATAATAGGTACTGATATATCTA
65665 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGG
61 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGG
65730 AAGGCGCGCCCCCG
126 AAGGCGCGCCCCCG
* *
65744 GGGACGCGCGTCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTA
1 GGAACGCGCGTCCCCGGGAACGCGCCTTCATGT----TG-GAAATAATAGGTACTGATATATCTA
* *
65809 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGACATAATGG
61 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGG
65874 AAGGCGCG-CCCCG
126 AAGGCGCGCCCCCG
* * ** *
65887 GGAACGCGCCTTCATGTGAA-------T-A-G-T-GAAATAATAGGTACTGATATATCTAGTGTC
1 GGAACGCGCGTCCCCGGGAACGCGCCTTCATGTTGGAAATAATAGGTACTGATATATCTAGTGTC
65941 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGGAAGG
66 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG-AAATAATGGAAGG
66006 CGCGCCCCCG
130 CGCGCCCCCG
66016 GGAACGCGC
1 GGAACGCGC
66025 CTTCATGTCC
Statistics
Matches: 259, Mismatches: 19, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
127 79 0.31
128 16 0.06
129 15 0.06
134 1 0.00
135 1 0.00
136 1 0.00
143 19 0.07
144 126 0.49
145 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (139 bp):
GGAACGCGCGTCCCCGGGAACGCGCCTTCATGTTGGAAATAATAGGTACTGATATATCTAGTGTC
CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCG
Found at i:66200 original size:128 final size:128
Alignment explanation
Indices: 65755--66295 Score: 854
Period size: 128 Copynumber: 4.2 Consensus size: 128
65745 GGACGCGCGT
*** *
65755 CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGTAATGATATATCTAGTGTCCCCGA
1 CCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTAATGATATATCTAGTGTCCCCGA
* * *
65819 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGACATAATGGAAGGCG-CG
65 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
*
65882 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
1 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTCCCCGAG
*
65947 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGGAAGGCGCGC
66 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG-AAATAATGGAAGGCGCCC
*** *
66011 CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGTAATGATATATCTAGTGTCCCCGA
1 CCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTAATGATATATCTAGTGTCCCCGA
66075 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
65 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
* *
66139 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTATCCCCGAG
1 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTCCCCGAG
* *
66204 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGAAAGGCGCGC
66 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
* * *
66267 CCCCGAGAACGCGTCTTTATGTGAATAGT
1 CCCCGGGAACGCGCCTTCATGTGAATAGT
66296 ACTCCGATTA
Statistics
Matches: 383, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
126 1 0.00
127 103 0.27
128 175 0.46
129 103 0.27
130 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (128 bp):
CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTCCCCGAG
GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
Found at i:66255 original size:256 final size:256
Alignment explanation
Indices: 65749--66288 Score: 983
Period size: 256 Copynumber: 2.1 Consensus size: 256
65739 CCCCGGGGAC
*
65749 GCGCGTCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTAGTGTC
1 GCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTAGTGTC
* *
65814 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGACATAATGGAAGGC
66 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
* *
65879 GCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
131 GCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTATCCCC
*
65944 GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGGAAG
196 GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGAAAG
66005 GCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTAGTGTC
1 GCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTAGTGTC
66070 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
66 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
66135 GCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTATCCC
131 G-CCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTATCCC
66200 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG-AAATAATGAAAG
195 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGAAAG
* * *
66261 GCGCGCCCCCGAGAACGCGTCTTTATGT
1 GCGCGCCCCCGGGAACGCGCCTTCATGT
66289 GAATAGTACT
Statistics
Matches: 274, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
256 164 0.60
257 110 0.40
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (256 bp):
GCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAATGATATATCTAGTGTC
CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
GCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTATCCCC
GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAATAATGAAAG
Found at i:66379 original size:8 final size:8
Alignment explanation
Indices: 66366--66414 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
66356 TCACAATCTT
66366 TCAAATTC
1 TCAAATTC
66374 TCAAATTC
1 TCAAATTC
66382 TCAAATTC
1 TCAAATTC
* *
66390 CCAAACTC
1 TCAAATTC
66398 T-AAATTC
1 TCAAATTC
66405 TCAAATTC
1 TCAAATTC
66413 TC
1 TC
66415 TGAAAATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 6 0.17
8 30 0.83
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.35
Consensus pattern (8 bp):
TCAAATTC
Found at i:71484 original size:29 final size:29
Alignment explanation
Indices: 71449--71504 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
71439 GTGTTGACCA
71449 TAGGTCGCCATGCACTACGGGCGACCTTG
1 TAGGTCGCCATGCACTACGGGCGACCTTG
* *
71478 TAGGTCGCTATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTACGGGCGACCT
71505 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTACGGGCGACCTTG
Found at i:71601 original size:29 final size:29
Alignment explanation
Indices: 71568--71652 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
71558 ACACAACACA
*
71568 TAGGTCGCCATGCCCTACGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
71597 TAGGTCGCCATGTCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
71626 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
71653 ACCCTCGCAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:71704 original size:23 final size:23
Alignment explanation
Indices: 71670--71729 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
71660 CACGGCTTCC
71670 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
71693 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
71716 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
71730 GTCGGATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:73282 original size:76 final size:76
Alignment explanation
Indices: 73148--73290 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 76
73138 GGTGGACACT
* * * * *
73148 GAGATCCGAATTTTCTTCAATTAATTGCTTATTTTATTGATAGTGTCCAGCCTGAAATTTTATTT
1 GAGATCCGAATTTTCTTCAATTAATTACCTATTTAAATGATAGTGTCCAGCCTAAAATTTTATTT
73213 GTTTATATCCA
66 GTTTATATCCA
* * * * *
73224 GAGATCCTAGTTTTCTTTAGTTAATTACCTATTTAAATGATAGTG-CACATCCTAAAATTTTATT
1 GAGATCCGAATTTTCTTCAATTAATTACCTATTTAAATGATAGTGTC-CAGCCTAAAATTTTATT
73288 TGT
65 TGT
73291 ACTAACTCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 1 0.02
76 55 0.98
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (76 bp):
GAGATCCGAATTTTCTTCAATTAATTACCTATTTAAATGATAGTGTCCAGCCTAAAATTTTATTT
GTTTATATCCA
Found at i:79582 original size:20 final size:20
Alignment explanation
Indices: 79557--79611 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
79547 GACCATTCGA
*
79557 CCGAGGCCATCTGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
79577 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
79597 CCGAGGCCATCCGAG
1 CCGAGGCCATCCGAG
79612 CGAGCTATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:79587 original size:10 final size:10
Alignment explanation
Indices: 79557--79611 Score: 69
Period size: 10 Copynumber: 5.5 Consensus size: 10
79547 GACCATTCGA
79557 CCGAGGCCAT
1 CCGAGGCCAT
*
79567 CTGAGAG-CAT
1 CCGAG-GCCAT
79577 CCGAGGCCAT
1 CCGAGGCCAT
79587 CCGAGAG-CAT
1 CCGAG-GCCAT
79597 CCGAGGCCAT
1 CCGAGGCCAT
79607 CCGAG
1 CCGAG
79612 CGAGCTATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 2 0.05
10 35 0.90
11 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.11
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:79725 original size:23 final size:23
Alignment explanation
Indices: 79696--79761 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
79686 CCCTCAGATT
*
79696 CCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGCATAGCTCGCTCGGATG
*
79719 CCCTCGCATAGCTCGGTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
*
79742 GCCTCG-AT-GCT--CTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
79761 C
1 C
79762 TTTCGGATGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 7 0.18
21 3 0.08
22 2 0.05
23 26 0.68
ACGTcount: A:0.11, C:0.36, G:0.29, T:0.24
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGGATG
Found at i:80176 original size:33 final size:33
Alignment explanation
Indices: 80139--80204 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
80129 TAATGTAGTA
* * *
80139 ATATCTTATATATAAAGTGATGACGTGATATAT
1 ATATCATATATATAAAGTAATGACGTGACATAT
* *
80172 ATATCATATATCTAAAGTAATGATGTGACATAT
1 ATATCATATATATAAAGTAATGACGTGACATAT
80205 GTTATATGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (33 bp):
ATATCATATATATAAAGTAATGACGTGACATAT
Found at i:91620 original size:23 final size:23
Alignment explanation
Indices: 91590--91633 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
91580 TAAATAATAA
91590 GGGAGAGAGTGAACAACCCTGGT
1 GGGAGAGAGTGAACAACCCTGGT
91613 GGGAGAGAGTGAACAACCCTG
1 GGGAGAGAGTGAACAACCCTG
91634 TCTTAGCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.39, T:0.11
Consensus pattern (23 bp):
GGGAGAGAGTGAACAACCCTGGT
Done.