Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000720.1 Hibiscus syriacus cultivar Beakdansim tig00001398_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: 72114
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2439 original size:21 final size:20
Alignment explanation
Indices: 2413--2452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2403 TAATTATATT
2413 AATTTTATTAATTATAATGTG
1 AATTTTATTAATTA-AATGTG
* *
2434 AATTTTTTTTATTAAATGT
1 AATTTTATTAATTAAATGT
2453 TAGTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
AATTTTATTAATTAAATGTG
Found at i:13186 original size:2 final size:2
Alignment explanation
Indices: 13174--13216 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
13164 AATTATAATA
*
13174 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13217 TTCAATTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13730 original size:22 final size:21
Alignment explanation
Indices: 13670--13730 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 21
13660 GAGAAGGAAC
13670 AAAATCAAGTTATAAAAATAAAA
1 AAAATCAAG-TA-AAAAATAAAA
*
13693 AGAAATCCAAATAAAAAATAAAA
1 A-AAAT-CAAGTAAAAAATAAAA
*
13716 AAAATCAAGTCAAAA
1 AAAATCAAGTAAAAA
13731 GAAGGAAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 8 0.24
22 4 0.12
23 12 0.36
24 6 0.18
25 3 0.09
ACGTcount: A:0.70, C:0.08, G:0.05, T:0.16
Consensus pattern (21 bp):
AAAATCAAGTAAAAAATAAAA
Found at i:16633 original size:17 final size:18
Alignment explanation
Indices: 16611--16644 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16601 GCTTTAAGAT
16611 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
16628 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
16645 TGTTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:20898 original size:22 final size:22
Alignment explanation
Indices: 20870--20916 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
20860 ACAATAAATT
20870 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
20892 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
20914 TTT
1 TTT
20917 AAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:22411 original size:182 final size:182
Alignment explanation
Indices: 22063--22721 Score: 977
Period size: 182 Copynumber: 3.6 Consensus size: 182
22053 GATCCAAATA
* * * *
22063 AAAAATGTATCGATCCATATCAATATAACAAGTAAAAATATGACAAAATCGGT-T-TAATTATGA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA--ATGA
* * * * * * *
22126 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAATATCGATTAGATTGAA-ATAAGTATTGATA
64 CAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACA
* *
22190 CTTTGAGAATTTAAAAGAGAAGCAGTAA-AGCGTCTATAAAGTGTCGATACTTTAT
127 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* *
22245 AAAAATGTATAGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAAGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
*
22310 AAACCGGTAAAGCGCTACTGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
22375 GGGAATTTAAAAGAGAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
22427 AAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGA-TAAATCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* *
22491 AAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
22556 GGGAATTTAAAAGAGAAGCAGTAATAGCGCTTATAAAGTGTCGATACTTTAT
131 GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* *
22608 AAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * * * *
22673 AAACCGATAAAGTGCTACCAGATATTTTGAATGTGTCGATACTTTAATA
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
22722 AGTACGCGTA
Statistics
Matches: 433, Mismatches: 39, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
180 4 0.01
181 210 0.48
182 216 0.50
183 1 0.00
184 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:22714 original size:363 final size:363
Alignment explanation
Indices: 22063--22721 Score: 1006
Period size: 363 Copynumber: 1.8 Consensus size: 363
22053 GATCCAAATA
* *
22063 AAAAATGTATCGATCCATATCAATATAACAAGTAAAAATATGACAAAATCGGTTTAATTATGACA
1 AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTTGAA-TATGACA
* * * * *
22128 AAACCGGTAAAGCGCTACCGGATATGTTGAAAATATCGATTAGATTGAAATAAGTATTGATACTT
65 AAACAGGTAAAGCGCTACCGAATATATTGAAAATATCGATTAGATTGAAATAAGTATCGACACTT
22193 TGAGAATTTAAAAGAGAAGCAGTAAAGCGTCTATAAAGTGTCGATACTTTATAAAAATGTATAGA
130 TGAGAATTTAAAAGAGAAGCAGTAAAGCGTCTATAAAGTGTCGATACTTTATAAAAATGTATAGA
*
22258 TCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAAGACAAAACCGGTAAAGC
195 TCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAAGACAAAACCGATAAAGC
**
22323 GCTACTGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGGAATTTAAAAG
260 GCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGGAATTTAAAAG
22388 AGAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
325 AGAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
*
22427 AAAAATGTATCGATCCATAACAATATAA-AAGGTAAAAATATGA-TAAATCGGTCTCGAA-ATGA
1 AAAAATGTATCGATCCATAACAATATAACAA-GTAAAAATATGACAAAATCGGT-T-GAATATGA
* * * *
22489 CAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACA
63 CAAAACAGGTAAAGCGCTACCGAATATATTGAAAATATCGATTAGATTGAA-ATAAGTATCGACA
*
22552 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCG-CTTATAAAGTGTCGATACTTTATAAAAATGT
127 CTTTGAGAATTTAAAAGAGAAGCAGTAA-AGCGTC-TATAAAGTGTCGATACTTTATAAAAATGT
* * * *
22616 ATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATGACAAAACCGAT
190 ATAGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAAGACAAAACCGAT
* * *
22681 AAAGTGCTACCAGATATTTTGAATGTGTCGATACTTTAATA
255 AAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
22722 AGTACGCGTA
Statistics
Matches: 266, Mismatches: 23, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
361 4 0.02
362 41 0.15
363 179 0.67
364 40 0.15
365 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (363 bp):
AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTTGAATATGACAA
AACAGGTAAAGCGCTACCGAATATATTGAAAATATCGATTAGATTGAAATAAGTATCGACACTTT
GAGAATTTAAAAGAGAAGCAGTAAAGCGTCTATAAAGTGTCGATACTTTATAAAAATGTATAGAT
CCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAAGACAAAACCGATAAAGCG
CTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGGAATTTAAAAGA
GAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:24729 original size:22 final size:24
Alignment explanation
Indices: 24683--24733 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
24673 TTTTTGTTTT
* *
24683 TTATATAAAATGATAGTATTGTTA
1 TTATATAAAATGATAGAACTGTTA
24707 TTATATAAAATGATA-AACT-TTA
1 TTATATAAAATGATAGAACTGTTA
24729 TTATA
1 TTATA
24734 AATACAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 15 0.60
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
TTATATAAAATGATAGAACTGTTA
Found at i:25219 original size:33 final size:33
Alignment explanation
Indices: 25182--25248 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
25172 AAATAGATGG
25182 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
25215 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
25248 A
1 A
25249 CTTAAGATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:25455 original size:18 final size:18
Alignment explanation
Indices: 25432--25470 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25422 GAAAAAATAT
*
25432 GAAGAAAAAAATATGGAG
1 GAAGAAAAAAAGATGGAG
* *
25450 GAAGAAGAAAAGATTGAG
1 GAAGAAAAAAAGATGGAG
25468 GAA
1 GAA
25471 ATGAGGAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (18 bp):
GAAGAAAAAAAGATGGAG
Found at i:25656 original size:13 final size:13
Alignment explanation
Indices: 25638--25664 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25628 TTGAAAAAGT
25638 GGATATTCCAAGC
1 GGATATTCCAAGC
25651 GGATATTCCAAGC
1 GGATATTCCAAGC
25664 G
1 G
25665 AAATTGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (13 bp):
GGATATTCCAAGC
Found at i:27039 original size:19 final size:19
Alignment explanation
Indices: 27015--27063 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
27005 AATGTAGGGT
27015 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
27034 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
27053 TAATTTTGTAT
1 TAATTTTGTAT
27064 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:27879 original size:201 final size:201
Alignment explanation
Indices: 27512--28677 Score: 1689
Period size: 201 Copynumber: 5.8 Consensus size: 201
27502 GTAAATATAT
* * *
27512 GTGTCGCTACAGTTATAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
27577 GGTAATTTTTCAATATAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
* * *
27642 ATCGACACTTGTGGAATTTGTTTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGGTGCACG
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
27707 CATAAA
196 CATAAA
* *
27713 GTGTCGATACATTTATAAAAGGTATCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
*
27778 GGTAATTTTTCAATGTAACCGGTATAAATATACC-GATTTTATGAGAGAATAGGTCTACATAATG
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAG-TTTTAAGAGAGAATAGGTCTACATAATG
* ** *
27842 TATTGACACTTGTGGAATTTGTGTAAATACCTTTTGTCCAGAATGAATGCCCAAA--AGGAGTGC
130 TATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTA-G-GTGC
27905 ACGCATAAA
193 ACGCATAAA
* *
27914 GTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
27979 GGTAATTTTTCAATGTAACTGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
** * * * *
28044 AGT-GACACTTGTGGAATTTGTGTTTATATTTTTTGTCTAGAATGAATGCCCAAACTAAGTGCAT
131 A-TCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
28108 GCATAAA
195 GCATAAA
* * * * *
28115 GTGTCAATACATTTACAAAAAGTATCGATCCCAGAAATATCGAAAGCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
28180 TGTAATTTTTCAATGTAACCGGTATAAATATATCAGTTTTAAGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
* ** *
28245 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGCCCAGAATGAATGCCCAAACTAGGTGCACG
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
28310 CATAAA
196 CATAAA
*
28316 ATGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
28380 TGT-ATTTTTCAATGTAATCGGTATAAATATACCAGTTTTAAGAGAGAATATGTCTACATAATGC
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
* ** * * * *
28444 ATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCATAATAAATGCCCAAACTAAGTGCACG
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
28509 CATAAA
196 CATAAA
** *
28515 GTGTCGATTTATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
28580 GGTAATTTTTTAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAATAGGTTTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
* * * **
28645 GTCGGCACTTTTTAAATTT-TGTCGATACTTTTT
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTT
28678 TAAATTTTGC
Statistics
Matches: 881, Mismatches: 74, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
199 165 0.19
200 58 0.07
201 655 0.74
202 2 0.00
203 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (201 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAGAGAATAGGTCTACATAATGT
ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
CATAAA
Found at i:29321 original size:2 final size:2
Alignment explanation
Indices: 29314--29343 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29304 ATGGGGAATG
29314 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
29344 CCGGATACTA
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:31459 original size:6 final size:6
Alignment explanation
Indices: 31445--31491 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
31435 TTTCATATGT
* * * *
31445 AATTGG AATTTG AATTTG AATTTA AATTTC AATTTG AGTTTG AATTT
1 AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG AATTT
31492 CAATATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (6 bp):
AATTTG
Found at i:31466 original size:18 final size:18
Alignment explanation
Indices: 31445--31495 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
31435 TTTCATATGT
* *
31445 AATTGGAATTTGAATTTG
1 AATTTGAATTTCAATTTG
*
31463 AATTTAAATTTCAATTTG
1 AATTTGAATTTCAATTTG
*
31481 AGTTTGAATTTCAAT
1 AATTTGAATTTCAAT
31496 ATAAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (18 bp):
AATTTGAATTTCAATTTG
Found at i:32600 original size:200 final size:200
Alignment explanation
Indices: 32225--33614 Score: 1879
Period size: 200 Copynumber: 7.0 Consensus size: 200
32215 AGTAATCTCT
* *
32225 AGAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCG
1 AGAATGAATGGCCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
* *
32290 AAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
65 AAAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* * *
32355 TCAGTTTTATGTGAGAATAGGTCTATATAATGTATCGATACTTTTTAAATTTGTGTCGATACGTT
130 CCAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
32420 TTGACC
195 TTGACC
* * * * *
32426 AGAATGAATAGCTAACGAGGTACACAAATAAAGTGTCGATACATTTATTAAACGTATCGATCCCA
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
* * *
32491 AAAATATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACTGATATAAATATAC
66 AAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
** * *
32556 TGGTTTTATGTGAGAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTTGATACGTTT
131 CAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTTT
*
32621 TGACT
196 TGACC
*
32626 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCAATCCCA
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
* *
32691 AAAACATCAAATATGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
66 AAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
* * *
32756 CAGTTTTTTGTGAGAATATGTCTACATAATGTATCGACACTTTTTAAATTTGTGTTGATACGTTT
131 CAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTTT
32821 TGACC
196 TGACC
* * * * *
32826 AGAATGAATGGCCAATGAGGTGCACAAATAAAGTGTCGATACATTTATTAAACGTATTGACCCCA
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
*
32891 AAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCAGTATAAATATAC
66 AAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
** * * *
32956 GGGTTTTATGTAAGAATAGGTCTACATAATCTATCGACACTTTTTAAATTTGTGTCGATACATTT
131 CAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTTT
33021 TGACC
196 TGACC
* ** * * * *
33026 AGAAAGAATACCCAATGGGGTGAACAAATAAAGTGTCGATACATTTA--AAATTA-TATCGATCC
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAA--AGTATCGATCC
* * * * *
33088 CAAAAACATCGAA-ACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCAGTAGAAATA
64 CAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATA
* * *
33152 TACCAG-TTCA---GAAAATAGGTCTACATAATATATCGACACTTTTTAAATTTGTGTCGATACG
128 TACCAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACG
33213 TTTTGACC
193 TTTTGACC
* *
33221 ATAATGAATGGCCAAC-AGGTGCACGAATAAAGTGTCGATACATTTA-TAAAACGTATTGATCCC
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAA-GTATCGATCCC
* * *
33284 AAAAACATCGAAGAATATAATTATAATGTAATAGGTAATTTTTCAATGTAACAGGTATAAATATA
65 AAAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* *
33349 TCAGTTTTATGTGAGAATGGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
130 CCAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
33414 TTGACC
195 TTGACC
* * * * * *
33420 AGAAAGAATGTCCAACGGGGTGTACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCACA
1 AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
* * * * * * * * *
33485 TAAACATCGAA-ACCGATAAATATCATGTAATAGGAAAATCTCCAATGTAACCGGTAGAAATATA
66 AAAACATCGAATA-AGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* * * * * * * * *
33549 CC-GGTTAAT-TAGAAAATAGATCTACATAATGTATCGACACATTTTAAAGTTATATCGATACTT
130 CCAGTTTTATGT-GAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGT
33612 TTT
194 TTT
33615 TAAATTACGC
Statistics
Matches: 1050, Mismatches: 124, Indels: 32
0.87 0.10 0.03
Matches are distributed among these distances:
193 1 0.00
194 27 0.03
195 137 0.13
196 4 0.00
198 8 0.01
199 191 0.18
200 666 0.63
201 16 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (200 bp):
AGAATGAATGGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
AAAACATCGAATAAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
CAGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTTT
TGACC
Found at i:35210 original size:19 final size:19
Alignment explanation
Indices: 35166--35213 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
35156 TAACAGAGGA
*
35166 AATTTTATATACGATTTAT
1 AATTTTGTATACGATTTAT
35185 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTTAT
35204 AATTTTGTAT
1 AATTTTGTAT
35214 GTGAATGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (19 bp):
AATTTTGTATACGATTTAT
Found at i:38379 original size:198 final size:199
Alignment explanation
Indices: 37946--38419 Score: 532
Period size: 200 Copynumber: 2.4 Consensus size: 199
37936 CATTTTCTAA
* * * *
37946 AAGTATCGACCCCAAAAACATCGAAACCAATCATTATAATGTAATAGGTAAATTAACAATGTAAC
1 AAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAC
* * * *
38011 CAGTATAAATATACTGGTTAATTACAAAATAGGTAAATATACGGTATCGACACTTGTGAAATTTG
66 CGGTATAAATATACTGGTTAATGACAAAATAGATAAATATACGGTATCGACACTTGTGAAATATG
* * * * *
38076 TGTTGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTTCACGCATAAAGTACCGATACATTT
131 TGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAAGTGCACACATAAAGTACCAATACATTT
38141 ATTAG
196 A-TAG
* * * * *
38146 AAGTATCGATCTCAAAAACATCGAAACTGATAATTATGATATAATATGTAAATTTACAATGTAAC
1 AAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAC
* * ** * *
38211 CGGTATAAATATACATGTTTTATGA-AAGAATAGATCAACAT-TA-TTTATCGACACTTTTTAAA
66 CGGTATAAATATAC-TGGTTAATGACAA-AATAGAT-AA-ATATACGGTATCGACACTTGTGAAA
** * **
38273 TATGTGTCGATACATT-TT-TCCATCATGAATTCCC-AACGAAGTGCACACATAAAGTGTCAATA
127 TATGTGTCGATAC-TTATTGTCCAGAATGAATGCCCAAACGAAGTGCACACATAAAGTACCAATA
38335 CATTTA-A-
191 CATTTATAG
* * *
38342 AATTGTATCGATCCCTAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTT
1 AA--GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA
38407 ACCGGTATAAATA
64 ACCGGTATAAATA
38420 AACCGGTTTA
Statistics
Matches: 230, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
196 2 0.01
197 1 0.00
198 66 0.29
199 28 0.12
200 84 0.37
201 41 0.18
202 6 0.03
203 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (199 bp):
AAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAC
CGGTATAAATATACTGGTTAATGACAAAATAGATAAATATACGGTATCGACACTTGTGAAATATG
TGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAAGTGCACACATAAAGTACCAATACATTT
ATAG
Found at i:38479 original size:23 final size:23
Alignment explanation
Indices: 38446--38493 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
38436 AAATAGGTCA
* *
38446 ATATAATCGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
*
38469 ATATAAACGCTACCTAATATGTT
1 ATATAAACGCTACCTAATATATT
38492 AT
1 AT
38494 TATACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:39184 original size:22 final size:22
Alignment explanation
Indices: 39159--39202 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39149 ATTTACTATA
* *
39159 ATTGGGTGTTTAATGTAAATAT
1 ATTGCGTGGTTAATGTAAATAT
* *
39181 ATTGCTTGGTTGATGTAAATAT
1 ATTGCGTGGTTAATGTAAATAT
39203 TAAACCATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (22 bp):
ATTGCGTGGTTAATGTAAATAT
Found at i:40880 original size:15 final size:15
Alignment explanation
Indices: 40860--40909 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
40850 TAAAACAAAA
40860 TAAATTATAAAATAT
1 TAAATTATAAAATAT
*
40875 TAAATT-TATAATAT
1 TAAATTATAAAATAT
* *
40889 T-TATATAAAAAATAT
1 TAAAT-TATAAAATAT
40904 TAAATT
1 TAAATT
40910 TATCATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTATAAAATAT
Found at i:40900 original size:29 final size:29
Alignment explanation
Indices: 40868--40928 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
40858 AATAAATTAT
40868 AAAATATTAAATTTATAATATTTATATAA
1 AAAATATTAAATTTATAATATTTATATAA
*
40897 AAAATATTAAATTTATCATATTTATATAA
1 AAAATATTAAATTTATAATATTTATATAA
40926 AAA
1 AAA
40929 TGTATCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AAAATATTAAATTTATAATATTTATATAA
Found at i:41095 original size:21 final size:22
Alignment explanation
Indices: 41070--41112 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41060 ATTATAATAT
41070 AAATT-ACAATTTTAAATTAAA
1 AAATTAACAATTTTAAATTAAA
*
41091 AAATTAATAATTTTAAATTAAA
1 AAATTAACAATTTTAAATTAAA
41113 TTAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTAACAATTTTAAATTAAA
Found at i:41125 original size:16 final size:19
Alignment explanation
Indices: 41077--41138 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 19
41067 TATAAATTAC
41077 AATTTTAAATTAAAAAATTAAT
1 AATTTTAAATT---AAATTAAT
41099 AATTTTAAATTAAATTAAT
1 AATTTTAAATTAAATTAAT
* *
41118 -A-TTT-AATTAATTTATT
1 AATTTTAAATTAAATTAAT
41134 AATTT
1 AATTT
41139 AAGATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 10 0.28
17 4 0.11
18 3 0.08
19 8 0.22
22 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTAAATTAAATTAAT
Found at i:44553 original size:34 final size:34
Alignment explanation
Indices: 44514--44620 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
44504 TAAGTTGAAA
* * *
44514 TTTAATGTTAAATTTTGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
44548 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
44582 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
44616 TTTAA
1 TTTAA
44621 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:45171 original size:21 final size:20
Alignment explanation
Indices: 45144--45213 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
45134 GGTATAAAAC
*
45144 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
45164 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
45185 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
45206 CCCTGCGG
1 -CCTGCGG
45214 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:45263 original size:21 final size:21
Alignment explanation
Indices: 45233--45285 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
45223 ATAAACTGAT
*
45233 GGGTTTGGCATATGAAGTGGA
1 GGGTTGGGCATATGAAGTGGA
*
45254 GTGTTGGGCATATGAAGTGGA
1 GGGTTGGGCATATGAAGTGGA
45275 GGGTTGGGCAT
1 GGGTTGGGCAT
45286 GTAACCCTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.06, G:0.45, T:0.28
Consensus pattern (21 bp):
GGGTTGGGCATATGAAGTGGA
Found at i:47043 original size:30 final size:32
Alignment explanation
Indices: 46979--47061 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 32
46969 TTAATAATTC
* *
46979 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATATTTACATAAATATTA-TTTAA
47013 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATATTTACATAAATATTATTTAA
47043 TATAAAATATAACTATTTA
1 TA-AAAA-ATAA-TATTTA
47062 AAAAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 6 0.14
31 4 0.09
32 6 0.14
33 24 0.55
34 4 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAAAAATAATATTTACATAAATATTATTTAA
Found at i:47544 original size:2 final size:2
Alignment explanation
Indices: 47537--47567 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47527 CTCATAAAGA
47537 AT 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 A
47568 ATCTACTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47927 original size:87 final size:87
Alignment explanation
Indices: 47781--47978 Score: 297
Period size: 87 Copynumber: 2.3 Consensus size: 87
47771 AACCGGAAAC
* * * ***
47781 ATTATCAAACACAATAACATATTAGGTACCGTTTATATAATGTAATAGGTAGTGCTTATATAATA
1 ATTATCAAACACAATAACATATTAAGTACCATTTATATAATGTAATAGATAACACTTATATAATA
47846 AAATAGATTAATTACTGAAAAT
66 AAATAGATTAATTACTGAAAAT
*
47868 ATTATCAAGCACAATAACATATTAAGTACCATTTATATAATGTAATAGATAACACTTATATAATA
1 ATTATCAAACACAATAACATATTAAGTACCATTTATATAATGTAATAGATAACACTTATATAATA
*
47933 AAATAGGTTAATTACTGAAAAT
66 AAATAGATTAATTACTGAAAAT
* * *
47955 ATTATAAAACATAACAACATATTA
1 ATTATCAAACACAATAACATATTA
47979 GATAACGCTG
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (87 bp):
ATTATCAAACACAATAACATATTAAGTACCATTTATATAATGTAATAGATAACACTTATATAATA
AAATAGATTAATTACTGAAAAT
Found at i:49497 original size:25 final size:25
Alignment explanation
Indices: 49450--49497 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
49440 AATATTATCC
* * * *
49450 AATAGTGTATTTTTAATATATTTTT
1 AATAATGTAATTTTAAAAAATTTTT
49475 AATAATGTAATTTTAAAAAATTT
1 AATAATGTAATTTTAAAAAATTT
49498 AAAATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATTTTT
Found at i:50320 original size:111 final size:111
Alignment explanation
Indices: 50055--50583 Score: 690
Period size: 109 Copynumber: 4.8 Consensus size: 111
50045 AAAATGTATC
* * * *
50055 GATATTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
** ** *
50120 ATTTACCTGATATGTTGAAAGTATATATCCTTTTCATAAAAAGGATC
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTT-ATAAAAAAAATA
* * *
50167 GATACTTTACAATATAACAGGTGAAAATATGACAAAACCAGTTTTATTATGATAAAAACGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
* *
50232 ATTTACATGATATGTTGAAAGTATCGATCATTTTATAAAAAAAATA
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAAAATA
* *
50278 GATATTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
*
50343 ATTTACCTAATATGTTGAAAGTATCGATCCTTTTAT--AAAAAATA
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAAAATA
* * * * *
50387 GATAATTTACAATATAACAGATAAAAATATGACAAAACCAGTTTTATTATGACAAAAAGGGTGAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
* * * * **
50452 ATTTACGTAATATGTTGAAAGTATCAATCTTTTTATAAAAAGGATA
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAAAATA
* * * * ** *
50498 TATACTTTACAATATAATATGT--AAATATGACAAAATCAGTTTCATTATGACAAACTC-ATAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
*
50560 ATTTACCTGATATGTTAAAAGTAT
66 ATTTACCTGATATGTTGAAAGTAT
50584 AAATATATTT
Statistics
Matches: 367, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
108 24 0.07
109 130 0.35
111 125 0.34
112 88 0.24
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (111 bp):
GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAAAATA
Found at i:50513 original size:220 final size:222
Alignment explanation
Indices: 50055--50584 Score: 755
Period size: 220 Copynumber: 2.4 Consensus size: 222
50045 AAAATGTATC
* * * *
50055 GATATTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
* * *
50120 ATTTACCTGATATGTTGAAAGTATATATCCTTTTCATAAAAAGGATCGATACTTTACAATATAAC
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTCATAAAAA-GATAGATAATTTACAATATAAC
* * * *
50185 AGGTGAAAATATGACAAAACCAGTTTTATTATGATAAAAACGGTAAAATTTACATGATATGTTGA
130 AGATAAAAATATGACAAAACCAGTTTTATTATGACAAAAACGGTAAAATTTACATAATATGTTGA
*
50250 AAGTATCGATCATTTTATAAAAAAAATA
195 AAGTATCAATCATTTTATAAAAAAAATA
* *
50278 GATATTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
* *
50343 ATTTACCTAATATGTTGAAAGTATCGATCCTTTT-ATAAAAA-ATAGATAATTTACAATATAACA
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTCATAAAAAGATAGATAATTTACAATATAACA
* * *
50406 GATAAAAATATGACAAAACCAGTTTTATTATGACAAAAAGGGTGAAATTTACGTAATATGTTGAA
131 GATAAAAATATGACAAAACCAGTTTTATTATGACAAAAACGGTAAAATTTACATAATATGTTGAA
* **
50471 AGTATCAATCTTTTTATAAAAAGGATA
196 AGTATCAATCATTTTATAAAAAAAATA
* * * ** *
50498 TATACTTTACAATATAATATGT--AAATATGACAAAATCAGTTTCATTATGACAAACTC-ATAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
*
50560 ATTTACCTGATATGTTAAAAGTATA
66 ATTTACCTGATATGTTGAAAGTATA
50585 AATATATTTT
Statistics
Matches: 277, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
217 26 0.09
218 33 0.12
220 119 0.43
222 7 0.03
223 92 0.33
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (222 bp):
GATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAA
ATTTACCTGATATGTTGAAAGTATAGATCCTTTTCATAAAAAGATAGATAATTTACAATATAACA
GATAAAAATATGACAAAACCAGTTTTATTATGACAAAAACGGTAAAATTTACATAATATGTTGAA
AGTATCAATCATTTTATAAAAAAAATA
Found at i:51239 original size:110 final size:111
Alignment explanation
Indices: 51043--51389 Score: 554
Period size: 110 Copynumber: 3.1 Consensus size: 111
51033 TAGCGCCTAT
* * * *
51043 AAAGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCGGTTTTATTATGACAAAA
1 AAAGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
*
51108 AGGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
66 ACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
*
51154 AAAGTATCGATACTTTACAATATAACATGTAAAAATATGA-TAAACCAGTTTCATTATGACAAAA
1 AAAGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
51218 ACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
66 ACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
* *
51264 AAAGGATCGATACTTTACAATATAACATGTATAAATATGACAAAACCAGTTTCATTATGACAAAA
1 AAAGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * ** * *
51329 CCGGTAAAATTTACCTAATATGTTGAAAGTATATAT-ATTTTTTAA
66 ACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
51374 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
51390 TTTGAAAGTT
Statistics
Matches: 219, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
110 126 0.58
111 93 0.42
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (111 bp):
AAAGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
ACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAA
Found at i:51397 original size:20 final size:19
Alignment explanation
Indices: 51351--51398 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
51341 ACCTAATATG
*
51351 TTGAAAGTATATATATTTT
1 TTGAAAGTATAGATATTTT
* *
51370 TTAAAAAGTATCGATACTTTT
1 TT-GAAAGTATAGATA-TTTT
51391 TTGAAAGT
1 TTGAAAGT
51399 TATGTAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (19 bp):
TTGAAAGTATAGATATTTT
Found at i:51948 original size:109 final size:110
Alignment explanation
Indices: 51820--52156 Score: 436
Period size: 109 Copynumber: 3.1 Consensus size: 110
51810 TAGCGCCTAT
* *
51820 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATAT-A-AA
1 AAAGTATCGATCCTTTTATAAAAATG-ATCGATACTTTACAATATAACAGGTAAAAATATGACAA
*
51882 AACCAGTTTCATTATGGAAAAAGGGTAAAATTTACCTGATATGTTG
65 AACCAGTTTCATTATGGAAAAACGGTAAAATTTACCTGATATGTTG
* ** * *
51928 AAAGTATCGATCCTTTTATAAAAAGGATTAATACTTTACAATAT-ACATGTAAAAATATGATAAA
1 AAAGTATCGATCCTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
51992 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATG-GAAAAACGGTAAAATTTACCTGATATGTTG
* * * * *
52038 AAAGTGTCTATCATTTTAT-AAAATGATCGATACTTTACAATATAACAGATATAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
52102 ATCAGTTTCATTAT-GACAAAACCAGT-AAATTTACCTAATATGTTG
66 ACCAGTTTCATTATGGA-AAAA-CGGTAAAATTTACCTGATATGTTG
52147 AAAGTATCGA
1 AAAGTATCGA
52157 CTAATATACG
Statistics
Matches: 198, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
107 13 0.07
108 29 0.15
109 80 0.40
110 76 0.38
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (110 bp):
AAAGTATCGATCCTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGGAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:52031 original size:110 final size:109
Alignment explanation
Indices: 51820--52156 Score: 434
Period size: 110 Copynumber: 3.1 Consensus size: 109
51810 TAGCGCCTAT
* * *
51820 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATAT-AAAA
1 AAAGTATCGATCCTTTTATAAAAA-GGATCGATACTTTACAATATAACA-GTAAAAATATGAAAA
* *
51883 ACCAGTTTCATTATG-GAAAAAGGGTAAAATTTACCTGATATGTTG
64 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
**
51928 AAAGTATCGATCCTTTTATAAAAAGGATTAATACTTTACAATAT-ACATGTAAAAATATGATAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACA-GTAAAAATATGA-AAA
51992 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
64 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* * * * *
52038 AAAGTGTCTATCATTTTAT-AAAATGATCGATACTTTACAATATAACAGATATAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAG-TAAAAATATGA-AAA
* * * *
52102 ATCAGTTTCATTATGACAAAACCAGT-AAATTTACCTAATATGTTG
64 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
52147 AAAGTATCGA
1 AAAGTATCGA
52157 CTAATATACG
Statistics
Matches: 201, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
107 13 0.06
108 29 0.14
109 76 0.38
110 83 0.41
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (109 bp):
AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAGTAAAAATATGAAAAAC
CAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:53291 original size:30 final size:30
Alignment explanation
Indices: 53250--53308 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
53240 AGTATAAATT
53250 TGAAAAAAAATAA-AGTTTAGATACTAAAA
1 TGAAAAAAAATAATAGTTTAGATACTAAAA
*
53279 TGAAACAAAAATAATAGTTTAGGTACTAAA
1 TGAAA-AAAAATAATAGTTTAGATACTAAA
53309 CATATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 8 0.30
31 14 0.52
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (30 bp):
TGAAAAAAAATAATAGTTTAGATACTAAAA
Found at i:53577 original size:20 final size:20
Alignment explanation
Indices: 53519--53578 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
53509 TATTATTTTA
*
53519 ATTATAAAAATTTAA-AAATA
1 ATTATAAAAA-TTAATAAATT
* *
53539 ATTAT-TAAATCTATTAAATT
1 ATTATAAAAAT-TAATAAATT
53559 ATTATAAAAATTAATAAATT
1 ATTATAAAAATTAATAAATT
53579 TAATTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 22 0.69
21 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATAAAAATTAATAAATT
Found at i:53587 original size:30 final size:29
Alignment explanation
Indices: 53538--53597 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
53528 ATTTAAAAAT
* *
53538 AATTATTAAATCTATTAAATTATTATAAA
1 AATTAATAAATCTATTAAATTATCATAAA
*
53567 AATTAATAAATTTAATTAAATTATCATAAA
1 AATTAATAAATCT-ATTAAATTATCATAAA
53597 A
1 A
53598 TAATTACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTAATAAATCTATTAAATTATCATAAA
Found at i:53620 original size:23 final size:22
Alignment explanation
Indices: 53583--53626 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
53573 TAAATTTAAT
*
53583 TAAATTATCATAAAATAATTAC
1 TAAATTATCAAAAAATAATTAC
*
53605 TAAATTCATCAAAAAATTATTA
1 TAAATT-ATCAAAAAATAATTA
53627 TTATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATTATCAAAAAATAATTAC
Done.