Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002121.1 Hibiscus syriacus cultivar Beakdansim tig00004347_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: 35815
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2292 original size:29 final size:29
Alignment explanation
Indices: 2253--2333 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2243 TATGTGATAT
*
2253 GAGAACATGACATGAGCTACATGATCACCA
1 GAGAA-ATGACATGAGCTACATGATCACAA
2283 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
2312 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
2334 ACATATGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:2436 original size:15 final size:15
Alignment explanation
Indices: 2418--2451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2408 GAGGGTATAA
2418 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
2433 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
2448 TAGT
1 TAGT
2452 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:4440 original size:24 final size:24
Alignment explanation
Indices: 4404--4457 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
4394 TCGGAATCCT
4404 CTGCTCAACAGGAGATACACTCCA
1 CTGCTCAACAGGAGATACACTCCA
*
4428 CTGCTCAATAGGAGATACACTCCA
1 CTGCTCAACAGGAGATACACTCCA
4452 CTGCTC
1 CTGCTC
4458 GAGTGTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (24 bp):
CTGCTCAACAGGAGATACACTCCA
Found at i:9253 original size:29 final size:29
Alignment explanation
Indices: 9214--9294 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
9204 TATGTGATAT
*
9214 GAGAACATGACATGAGCTACATGATCACCA
1 GAGAA-ATGACATGAGCTACATGATCACAA
9244 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
9273 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
9295 ACATATGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:11703 original size:23 final size:22
Alignment explanation
Indices: 11670--11754 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
11660 TTTTGTACAG
*
11670 AGGGAATCGATACCCCCCTTGA
1 AGGGAACCGATACCCCCCTTGA
* *
11692 AGAGGAACCGATTCCCCCTTTGA
1 AG-GGAACCGATACCCCCCTTGA
* * *
11715 ATGGAAACCGATTCCCTCCTTG-
1 A-GGGAACCGATACCCCCCTTGA
* *
11737 AGGGAATCAATACCCCCC
1 AGGGAACCGATACCCCCC
11755 ACGGGTTCTG
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
21 12 0.24
22 3 0.06
23 34 0.68
24 1 0.02
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATACCCCCCTTGA
Found at i:13124 original size:31 final size:32
Alignment explanation
Indices: 13051--13129 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 32
13041 ACAAAAATAT
13051 TAAATCTATAATTTTA-TAAATAAAAAATTATGA
1 TAAAT-TAT-ATTTTATTAAATAAAAAATTATGA
* * *
13084 T-TATTATATTTTATTAAA-ATAAAATTATTA
1 TAAATTATATTTTATTAAATAAAAAATTATGA
13114 TAAATTATA-TTTATTA
1 TAAATTATATTTTATTA
13130 TTTATTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 24 0.60
31 13 0.32
32 2 0.05
33 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (32 bp):
TAAATTATATTTTATTAAATAAAAAATTATGA
Found at i:13725 original size:24 final size:23
Alignment explanation
Indices: 13672--13727 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
13662 ATTTGTAATA
13672 TTTATT-TTAAAAATAATATTAT
1 TTTATTGTTAAAAATAATATTAT
*
13694 TATT-TTGTTAATAAATAATATTGT
1 T-TTATTGTTAA-AAATAATATTAT
13718 TTTATTGTTA
1 TTTATTGTTA
13728 TCATTGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.28
24 18 0.62
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTATTGTTAAAAATAATATTAT
Found at i:14291 original size:23 final size:23
Alignment explanation
Indices: 14265--14314 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
14255 ACCTATTTTA
* *
14265 TTATATAAGAGCTACCTATTACG
1 TTATATAAGAGATACCTAATACG
* *
14288 TTATATAAGCGATACCTAATATG
1 TTATATAAGAGATACCTAATACG
14311 TTAT
1 TTAT
14315 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGAGATACCTAATACG
Found at i:14368 original size:23 final size:23
Alignment explanation
Indices: 14342--14396 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
14332 CCAGTAATTA
*
14342 ACCTATTTTATTATATAAGTGTT
1 ACCTATTTTATTATATAAGTGGT
**
14365 ACCTATTACATTATATAAGTGGT
1 ACCTATTTTATTATATAAGTGGT
14388 ACCTATTTT
1 ACCTATTTT
14397 GCTTGATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGTGGT
Found at i:14538 original size:87 final size:87
Alignment explanation
Indices: 14391--14754 Score: 532
Period size: 87 Copynumber: 4.2 Consensus size: 87
14381 AAGTGGTACC
* * *
14391 TATTTTGCTTGATAATATTTTCAGTAATTAACCTATTATATTATATAAGCGCTACCTATTACATT
1 TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
** *
14456 ATATAAGTTGTACCTAATATGT
66 ATATAAGCGGTACCTAATATAT
* *
14478 TATTTTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACATATTACATT
1 TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
* * *
14543 ATATAAGTGTTACCTAATATGT
66 ATATAAGCGGTACCTAATATAT
* * * *
14565 TATTGTGTTTGATAATGTTTCCAGTAATTAACTTATTTTATTATATAAGTGCTACCTATTACATT
1 TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
14630 ATATAAGCGGTACCTAATATAT
66 ATATAAGCGGTACCTAATATAT
* * *
14652 TATTGTACTTGATAATG-TTTCTAGTAATTAACCTATTTTATTATATAAGTGCTACTTATTACAT
1 TATTGTGCTTGATAATGTTTTC-AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
*
14716 TATATAAACGGTACCTAATATAT
65 TATATAAGCGGTACCTAATATAT
*
14739 TATTGTACTTGATAAT
1 TATTGTGCTTGATAAT
14755 ATTTCCGATT
Statistics
Matches: 256, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
86 3 0.01
87 253 0.99
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (87 bp):
TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
ATATAAGCGGTACCTAATATAT
Found at i:14630 original size:23 final size:23
Alignment explanation
Indices: 14604--14654 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
14594 AACTTATTTT
* *
14604 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
* *
14627 ATTATATAAGCGGTACCTAATAT
1 ATTATATAAGCGCTACCTAATAC
14650 ATTAT
1 ATTAT
14655 TGTACTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:14647 original size:174 final size:173
Alignment explanation
Indices: 14247--14760 Score: 729
Period size: 174 Copynumber: 3.0 Consensus size: 173
14237 TAACAAATTA
* *
14247 AGTAATTAACCTATTTTATTATATAAGAGCTACCTATTACGTTATATAAGCGATACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGAGCTACCTATTACATTATATAAGCGGTACCTAATATGT
* * * *
14312 TATTGTGCTTGATAATATTTCCAGTAATTAACCTATTTTATTATATAAGTGTTACCTATTACATT
66 TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGTGCTACATATTACATT
*
14377 ATATAAGTGGTACC---TA--T-TT-TGCTTGATAATATTTTC
131 ATATAAGTGGTACCTAATATTTATTGTGCTTGATAATATTTCC
* * **
14413 AGTAATTAACCTATTATATTATATAAGCGCTACCTATTACATTATATAAGTTGTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGAGCTACCTATTACATTATATAAGCGGTACCTAATATGT
* *
14478 TATTTTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGCTACATATTACATT
66 TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGTGCTACATATTACATT
* * *
14543 ATATAAGTGTTACCTAATATGTTATTGTGTTTGATAATGTTTCC
131 ATATAAGTGGTACCTAATAT-TTATTGTGCTTGATAATATTTCC
* * *
14587 AGTAATTAACTTATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGGTACCTAATATAT
1 AGTAATTAACCTATTTTATTATATAAGAGCTACCTATTACATTATATAAGCGGTACCTAATATGT
* *
14652 TATTGTACTTGATAATG-TTTCTAGTAATTAACCTATTTTATTATATAAGTGCTACTTATTACAT
66 TATTGTGCTTGATAATGTTTTC-AGTAATTAACCTATTTTATTATATAAGTGCTACATATTACAT
** *
14716 TATATAAACGGTACCTAATATATTATTGTACTTGATAATATTTCC
130 TATATAAGTGGTACCTAATAT-TTATTGTGCTTGATAATATTTCC
14761 GATTAAATGA
Statistics
Matches: 306, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
166 131 0.43
169 2 0.01
172 1 0.00
173 6 0.02
174 166 0.54
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (173 bp):
AGTAATTAACCTATTTTATTATATAAGAGCTACCTATTACATTATATAAGCGGTACCTAATATGT
TATTGTGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGTGCTACATATTACATT
ATATAAGTGGTACCTAATATTTATTGTGCTTGATAATATTTCC
Found at i:16184 original size:15 final size:15
Alignment explanation
Indices: 16146--16208 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
16136 TTTTGTCTGG
*
16146 ATTATGAATATTACATT
1 ATTAT-AATAATA-ATT
*
16163 ATAATAATAATAATT
1 ATTATAATAATAATT
*
16178 ATTATAATCATAATT
1 ATTATAATAATAATT
*
16193 ATTACAATAA-AATT
1 ATTATAATAATAATT
16207 AT
1 AT
16209 AATTATTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
14 6 0.15
15 24 0.60
16 6 0.15
17 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATAATAATT
Found at i:20618 original size:63 final size:63
Alignment explanation
Indices: 20507--20627 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
20497 TAAAAATGAT
* * * *
20507 AAATATATATTAAATTATTTGTATACAAATTTTATTAAATATATATATAAATTATAAATAATTG
1 AAATATATATTAAATTATTTGTATACAAAATATAATAAATATAAATAT-AATTATAAATAATTG
* *
20571 AAAT-TATATTAAGTTATTTGTGTA-AAAATATAATAAATTATAAATATAATTATAAAT
1 AAATATATATTAAATTATTTGTATACAAAATATAATAAA-TATAAATATAATTATAAAT
20628 TTAATTTCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 20 0.40
63 26 0.52
64 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (63 bp):
AAATATATATTAAATTATTTGTATACAAAATATAATAAATATAAATATAATTATAAATAATTG
Found at i:22324 original size:12 final size:12
Alignment explanation
Indices: 22307--22340 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
22297 TTATCGCAAA
22307 TTCGCGTTGCAT
1 TTCGCGTTGCAT
22319 TTCGCGTTGCAT
1 TTCGCGTTGCAT
22331 TTCGCGTTGC
1 TTCGCGTTGC
22341 GATAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:22420 original size:20 final size:21
Alignment explanation
Indices: 22395--22446 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
22385 TTTTCCCAAT
*
22395 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
22415 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
22436 TCGCAATGCGA
1 TCGCAATGCGA
22447 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:22460 original size:20 final size:20
Alignment explanation
Indices: 22435--22569 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
22425 AATTGGGAAA
22435 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
22455 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
22475 ATCACAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
22496 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
22516 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
22536 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
22556 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
22570 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:22497 original size:61 final size:61
Alignment explanation
Indices: 22432--22569 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
22422 GCGAATTGGG
* *
22432 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCACAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * * * * *
22493 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
*
22554 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
22570 TTTCAAAGCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:22767 original size:22 final size:22
Alignment explanation
Indices: 22739--22780 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22729 CTCTCTCACC
22739 CATCTCCGACGAAATCCGTCCT
1 CATCTCCGACGAAATCCGTCCT
*
22761 CATCTCCGGCGAAATCCGTC
1 CATCTCCGACGAAATCCGTC
22781 TATCAACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.21
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCCT
Found at i:23068 original size:20 final size:20
Alignment explanation
Indices: 23043--23111 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
23033 GCGATTCTCT
23043 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
23063 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
**
23083 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
23103 TGTTGCGAT
1 CGTTGCGAT
23112 TTTCATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:23117 original size:20 final size:20
Alignment explanation
Indices: 23044--23121 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
23034 CGATTCTCTC
** *
23044 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
** **
23064 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
23084 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
23104 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
23122 AGAAACTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:23312 original size:25 final size:24
Alignment explanation
Indices: 23258--23312 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
23248 TGTTTATTAT
* *
23258 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
23282 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
23308 TGTTT
1 TGTTT
23313 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:24462 original size:18 final size:18
Alignment explanation
Indices: 24441--24485 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
24431 TCCACTTCGG
*
24441 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
24459 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
24477 GAGCCATCA
1 GAGCCATCA
24486 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:25015 original size:19 final size:20
Alignment explanation
Indices: 24961--25027 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
24951 TAGTTTACTT
* *
24961 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
24981 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
25001 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
25020 TCGCAACG
1 TCGCAACG
25028 ACAAAATCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:25023 original size:39 final size:34
Alignment explanation
Indices: 24980--25081 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 34
24970 GAAAATGACT
24980 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATG-AA
*
25019 ATCGCAACGAC-AAA--ATCACAATGCGAAATGAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAATGAA
25051 ATCGCAACGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAATG---ATCGCAATGCGA
25082 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
31 1 0.02
32 14 0.26
33 15 0.28
37 11 0.20
38 3 0.06
39 9 0.17
40 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
Found at i:25073 original size:19 final size:19
Alignment explanation
Indices: 24961--25081 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
24951 TAGTTTACTT
* **
24961 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
24981 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
25001 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25020 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
25034 TCACAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
25052 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25071 TCGCAATGCGA
1 TCGCAACGCGA
25082 TTTGTGTTTC
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 17 0.21
19 26 0.32
20 24 0.29
21 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:25116 original size:14 final size:14
Alignment explanation
Indices: 25094--25150 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
25084 TGTGTTTCGT
25094 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
* *
25108 GTTGTGATTTCATTTC
1 GTTGCGATTT--TGTC
25124 GCATTGCGATTTTGTC
1 G--TTGCGATTTTGTC
25140 GTTGCGATTTT
1 GTTGCGATTTT
25151 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:25124 original size:32 final size:33
Alignment explanation
Indices: 25095--25166 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
25085 GTGTTTCGTG
*
25095 TTGCGATTTTGTCGTTGTGA-TTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
25127 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
25160 TTGCGAT
1 TTGCGAT
25167 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 19 0.50
33 19 0.50
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:25181 original size:20 final size:19
Alignment explanation
Indices: 25151--25206 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
25141 TTGCGATTTT
25151 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
25170 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
25190 CATTTTCGCGTTGCGAT
1 CA-TTTCGCATTGCGAT
25207 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:27053 original size:14 final size:14
Alignment explanation
Indices: 27034--27069 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27024 ATTGTTTAAT
27034 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27048 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27062 TGATTTGT
1 TGATTTGT
27070 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27228 original size:19 final size:19
Alignment explanation
Indices: 27206--27254 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
27196 ATCGCAACGA
27206 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
27225 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
27244 GAAAATCGCAA
1 GAAAATCGCAA
27255 CGAGAAAATC
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:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:27261 original size:19 final size:19
Alignment explanation
Indices: 27206--27261 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
27196 ATCGCAACGA
27206 GAAAATCGCAATGCA-AAAT
1 GAAAATCGCAATG-AGAAAT
*
27225 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
*
27244 GAAAATCGCAACGAGAAA
1 GAAAATCGCAATGAGAAA
27262 ATCGCAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:27317 original size:20 final size:20
Alignment explanation
Indices: 27292--27387 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
27282 TCGCATTGCG
*
27292 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
27312 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
27333 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
27352 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
27372 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
27388 TTCCCCGTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:27325 original size:34 final size:36
Alignment explanation
Indices: 27280--27367 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
27270 GCGATTTTCA
* *
27280 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
27314 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
27354 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
27368 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:27385 original size:40 final size:41
Alignment explanation
Indices: 27292--27387 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
27282 TCGCATTGCG
* ***
27292 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
27333 A-TTTCGAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
27372 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
27388 TTCCCCGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
39 4 0.09
40 42 0.89
41 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (41 bp):
ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
Found at i:27626 original size:20 final size:20
Alignment explanation
Indices: 27601--27650 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
27591 TTGAAGATGA
27601 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
27621 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
27641 TTGCGATTTT
1 TTGCGATTTT
27651 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:28507 original size:24 final size:24
Alignment explanation
Indices: 28480--28533 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28470 GTATTCGAAA
*
28480 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
28504 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
28528 TTTGAT
1 TTTGAT
28534 TATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:28725 original size:12 final size:12
Alignment explanation
Indices: 28708--28732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28698 ATATAATCCT
28708 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28720 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28732 G
1 G
28733 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31042 original size:19 final size:19
Alignment explanation
Indices: 31020--31150 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
31010 GGAAATTACT
31020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
31039 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
31053 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
31072 ATCGCAATGC----T-AAT
1 ATCGCAATGCGAAATGAAA
* * *
31086 TTTGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
31105 ATCGCAA--C--AA-GGGA
1 ATCGCAATGCGAAATGAAA
31119 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
31138 ATCGCAACGCGAA
1 ATCGCAATGCGAA
31151 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 29 0.35
15 4 0.05
16 3 0.04
17 3 0.04
18 4 0.05
19 41 0.49
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:31062 original size:33 final size:33
Alignment explanation
Indices: 31020--31146 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
31010 GGAAATTACT
31020 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
31053 ATCGCAATGCGAAATGAAAATCGCAATGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * * *
31085 TTTTGCAATGCAAAATGAAAATCGCAACAAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
31119 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
31147 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:31129 original size:66 final size:66
Alignment explanation
Indices: 31023--31153 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
31013 AATTACTATC
* * * *
31023 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCTAATTT
1 GCAATGCAAAATGAAAATCGCAACAAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
31088 T
66 T
*
31089 GCAATGCAAAATGAAAATCGCAACAAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAATGCAAAATGAAAATCGCAACAAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
31154 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (66 bp):
GCAATGCAAAATGAAAATCGCAACAAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
T
Found at i:31197 original size:33 final size:33
Alignment explanation
Indices: 31146--31235 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
31136 AAATCGCAAC
* * *
31146 GCGAATTTAATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
31179 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
31212 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
31236 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:31199 original size:19 final size:19
Alignment explanation
Indices: 31175--31235 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
31165 GTGATTCTCT
31175 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
31194 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
31208 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
31227 CATTGCGAT
1 CGTTGCGAT
31236 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:31213 original size:14 final size:14
Alignment explanation
Indices: 31161--31217 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
31151 TTTAATTTCG
*
31161 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
31175 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
31194 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
31208 CGTTGCGATT
1 CGTTGCGATT
31218 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31361 original size:14 final size:15
Alignment explanation
Indices: 31342--31378 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
31332 CATCAATTAA
31342 ACAAATCAAC-TTTT
1 ACAAATCAACTTTTT
31356 ACAAATC-ACTTTTT
1 ACAAATCAACTTTTT
31370 ACAAATCAA
1 ACAAATCAA
31379 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAACTTTTT
Found at i:32793 original size:42 final size:41
Alignment explanation
Indices: 32734--32939 Score: 157
Period size: 42 Copynumber: 4.9 Consensus size: 41
32724 GTGAATCGAG
* *
32734 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
32776 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
32818 CTCTTTAACGATAGGAGTAGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
32860 CTTTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * *
32902 CTCTTCAACGATAGGAGTGGACTCTT-AAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAA-GGATGACAG
32940 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 30, Indels: 18
0.72 0.17 0.10
Matches are distributed among these distances:
41 9 0.07
42 105 0.84
43 11 0.09
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:32800 original size:21 final size:21
Alignment explanation
Indices: 32734--32800 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32724 GTGAATCGAG
*
32734 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
32754 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
32776 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
32797 CTCT
1 CTCT
32801 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:32875 original size:84 final size:84
Alignment explanation
Indices: 32764--32939 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
32754 CCTCTTCAAC
*
32764 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTTAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
*
32829 TAGGAGTAGACTCTTGAGG
66 TAGGAGTAGACTCTTAAGG
*
32848 GATGACAGTGGCCTTTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
*
32913 TAGGAGTGGACTCTTAAGG
66 TAGGAGTAGACTCTTAAGG
32932 GATGACAG
1 GATGACAG
32940 GCGAGTCGGG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTAGACTCTTAAGG
Found at i:33318 original size:78 final size:82
Alignment explanation
Indices: 33171--33323 Score: 242
Period size: 78 Copynumber: 1.9 Consensus size: 82
33161 AAGATAAAAC
*
33171 AAAGACAAATACTAATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
33236 TAAATTTACTTCAACCA
66 TAAATTTACTTCAACCA
* * *
33253 AAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-TTTAGCAGTATTGGCAGCAACTGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
33314 TAAATTTACT
66 TAAATTTACT
33324 AAGCAATCTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
78 33 0.49
79 1 0.01
80 3 0.04
81 4 0.06
82 26 0.39
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
TAAATTTACTTCAACCA
Found at i:35067 original size:33 final size:33
Alignment explanation
Indices: 35012--35110 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
35002 ACGAGATAAT
*
35012 GAGAATCGTAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* * *
35046 GAGAATCGCAATGCGAAATGACTATCACGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
35079 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
35111 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 44 0.79
34 12 0.21
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:35106 original size:19 final size:19
Alignment explanation
Indices: 35082--35132 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
35072 ACGACGAGAG
35082 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
35101 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
35120 AATCGCAATGCGA
1 AATCGCAACGCGA
35133 TTTGGTTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:35790 original size:20 final size:20
Alignment explanation
Indices: 35708--35815 Score: 110
Period size: 20 Copynumber: 5.4 Consensus size: 20
35698 CGCTATGTAA
* * *
35708 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
35728 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
35748 ATCTCGTTGCGATTTGT-ATT
1 ATCGCATTGCGA-TAGTCAGT
*
35768 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
35788 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
35808 ATCGCATT
1 ATCGCATT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 3 0.04
20 71 0.93
21 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Done.