Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004000.1 Hibiscus syriacus cultivar Beakdansim tig00008716_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: 56930
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:955 original size:38 final size:36
Alignment explanation
Indices: 903--982 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 36
893 TTCTCTAATG
903 AAATATAAGATTAAATTTATTAAATTATTTAAAATT
1 AAATATAAGATTAAATTTATTAAATTATTTAAAATT
* *
939 AAATATTAAGAATTAAATTTATTGAATTATTTTAAATT
1 AAATA-TAAG-ATTAAATTTATTAAATTATTTAAAATT
977 AGAATA
1 A-AATA
983 AAATCAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
36 5 0.13
37 4 0.10
38 26 0.67
39 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (36 bp):
AAATATAAGATTAAATTTATTAAATTATTTAAAATT
Found at i:1095 original size:20 final size:20
Alignment explanation
Indices: 1058--1097 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1048 GTCTAGACGT
* **
1058 TTTAATTTAAATGTAAATAA
1 TTTAATTGAAATCAAAATAA
1078 TTTAATTGAAATCAAAATAA
1 TTTAATTGAAATCAAAATAA
1098 AAATTTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
TTTAATTGAAATCAAAATAA
Found at i:8580 original size:29 final size:29
Alignment explanation
Indices: 8538--8626 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
8528 GTGAAGCCGT
*
8538 AGGTCGCCATGCACTTCAGGCGACCAAGG
1 AGGTCGCCATGCACTCCAGGCGACCAAGG
*
8567 AGGTCGCCATGCACTCCAGGCGACCAAAG
1 AGGTCGCCATGCACTCCAGGCGACCAAGG
*
8596 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCAGGCGACCAAGG
8625 AG
1 AG
8627 TGAGTGCAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.25, C:0.33, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCAGGCGACCAAGG
Found at i:8659 original size:32 final size:32
Alignment explanation
Indices: 8618--8682 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
8608 ACTCCGGGCG
*
8618 ACCAAGGAGTGAGTGCAAGCTATCCATGGAGC
1 ACCAAGGAGTGAGTGCAAGCTATCCAGGGAGC
**
8650 ACCAAGGAGTGAGTGTGAGCTATCCAGGGAGC
1 ACCAAGGAGTGAGTGCAAGCTATCCAGGGAGC
8682 A
1 A
8683 TTGCATGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.34, T:0.15
Consensus pattern (32 bp):
ACCAAGGAGTGAGTGCAAGCTATCCAGGGAGC
Found at i:8903 original size:23 final size:23
Alignment explanation
Indices: 8873--8918 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
8863 CATGCATGCG
8873 TTGCATCCATAGCTGGGAGATTC
1 TTGCATCCATAGCTGGGAGATTC
8896 TTGCATCCATAGCTGGGAGATTC
1 TTGCATCCATAGCTGGGAGATTC
8919 CAGCGTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
TTGCATCCATAGCTGGGAGATTC
Found at i:9292 original size:28 final size:29
Alignment explanation
Indices: 9261--9336 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
9251 TAGGGTAAAA
9261 TTAAAATT-TAGTTA-ATTAGTTTGTTAGT
1 TTAAAATTATA-TTATATTAGTTTGTTAGT
*
9289 TT-AAGTTATATTATATTAGTTTGTTAGT
1 TTAAAATTATATTATATTAGTTTGTTAGT
**
9317 TTAAGTTATATATTATATTA
1 TTAAAAT-TATATTATATTA
9337 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.17
28 20 0.49
29 2 0.05
30 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (29 bp):
TTAAAATTATATTATATTAGTTTGTTAGT
Found at i:9738 original size:17 final size:17
Alignment explanation
Indices: 9716--9774 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
9706 GATAATTTCC
9716 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
*
9733 GTTTAAAAATAT-TTAGT
1 GTTTAAAAAAATATT-GT
* *
9750 GTTTTTTAAAAAATATTTT
1 G--TTTAAAAAAATATTGT
9769 GTTTAA
1 GTTTAA
9775 TTTATATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 18 0.55
19 11 0.33
20 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:12957 original size:49 final size:49
Alignment explanation
Indices: 12900--13107 Score: 339
Period size: 49 Copynumber: 4.3 Consensus size: 49
12890 AGACCTCATC
*
12900 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGGTAGTAATG
1 ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
* * *
12949 ATTAGTAATAATAAAATTATTATTAATATTTAATGGTTTGGTAGTAATA
1 ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
12998 ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
1 ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
* **
13047 ATTAGTAATAATTAAATTATTGTTAATATTTAATGATTTAATAGTAATG
1 ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
13096 ATT--TAATAATTA
1 ATTAGTAATAATTA
13108 TTAGTAATAA
Statistics
Matches: 150, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 9 0.06
49 141 0.94
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (49 bp):
ATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGGTAGTAATG
Found at i:13094 original size:21 final size:20
Alignment explanation
Indices: 13070--13121 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
13060 AAATTATTGT
*
13070 TAATATTTAATGATTTAATAG
1 TAATATTTAAT-AATTAATAG
*
13091 TAATGATTTAATAATTATTAG
1 TAAT-ATTTAATAATTAATAG
*
13112 TAATAATTAA
1 TAATATTTAA
13122 ATTATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
TAATATTTAATAATTAATAG
Found at i:13096 original size:14 final size:14
Alignment explanation
Indices: 13077--13103 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13067 TGTTAATATT
13077 TAATGATTTAATAG
1 TAATGATTTAATAG
13091 TAATGATTTAATA
1 TAATGATTTAATA
13104 ATTATTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAG
Found at i:13335 original size:19 final size:18
Alignment explanation
Indices: 13315--13366 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
13305 AAATATTTTA
13315 ATAATGATTTTAATA-TT
1 ATAATGATTTTAATATTT
*
13332 -TAATGA-TTTGATGATTT
1 ATAATGATTTTAAT-ATTT
13349 AGTAATGATTTTAATATT
1 A-TAATGATTTTAATATT
13367 ATGATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 2 0.07
19 9 0.32
20 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (18 bp):
ATAATGATTTTAATATTT
Found at i:13358 original size:11 final size:11
Alignment explanation
Indices: 13342--13616 Score: 136
Period size: 12 Copynumber: 22.2 Consensus size: 11
13332 TAATGATTTG
*
13342 ATGATTTAGTA
1 ATGATTTAATA
13353 ATGATTTTAATA
1 ATGA-TTTAATA
13365 TTATGATTTAATA
1 --ATGATTTAATA
13378 ATGATTTAGTAATA
1 ATGA-TT--TAATA
*
13392 ATCATTATAATA
1 ATGATT-TAATA
13404 ATGATTTAATA
1 ATGATTTAATA
13415 ATGACTTTAATA
1 ATGA-TTTAATA
* * * * * *
13427 TTTAATGATTTG
1 ATGATTTA-ATA
*
13439 ATGATTTAGTA
1 ATGATTTAATA
13450 ATGATTTTATAATA
1 ATGA--TT-TAATA
*
13464 ATCATTATAATA
1 ATGATT-TAATA
13476 ATGATTTAGTAATA
1 ATGA-TT--TAATA
*
13490 ATCATTATAATA
1 ATGATT-TAATA
13502 ATGATTTAATA
1 ATGATTTAATA
* *
13513 ATAATGATAATA
1 ATGAT-TTAATA
13525 ATGATTTAATAATA
1 ATGA-TT--TAATA
*
13539 ATCATTATAATA
1 ATGATT-TAATA
13551 ATGATTTAATAGTA
1 ATGATTT-A-A-TA
*
13565 ATGATTTAGTA
1 ATGATTTAATA
13576 ATGATTTTATAATA
1 ATGA--TT-TAATA
13590 ATGATTTAATTATA
1 ATGATTT-A--ATA
13604 ATGATTTAATA
1 ATGATTTAATA
13615 AT
1 AT
13617 TATTACTAAT
Statistics
Matches: 207, Mismatches: 31, Indels: 52
0.71 0.11 0.18
Matches are distributed among these distances:
11 46 0.22
12 76 0.37
13 23 0.11
14 62 0.30
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:13362 original size:35 final size:35
Alignment explanation
Indices: 13311--13458 Score: 129
Period size: 35 Copynumber: 4.5 Consensus size: 35
13301 CATAAAATAT
*
13311 TTTAATAATGATTTTAATATTTAATGATTTGATGA
1 TTTAGTAATGATTTTAATATTTAATGATTTGATGA
*
13346 TTTAGTAATGATTTTAATA-TT-ATGATTTAATAATGA
1 TTTAGTAATGATTTTAATATTTAATGA-TT--TGATGA
* * *
13382 TTTAGTAAT-A--ATCAT-TATAAT-A----ATGA
1 TTTAGTAATGATTTTAATATTTAATGATTTGATGA
* *
13408 TTTAATAATGACTTTAATATTTAATGATTTGATGA
1 TTTAGTAATGATTTTAATATTTAATGATTTGATGA
13443 TTTAGTAATGATTTTA
1 TTTAGTAATGATTTTA
13459 TAATAATCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
26 12 0.14
27 1 0.01
29 3 0.03
30 5 0.06
31 1 0.01
33 9 0.10
34 6 0.07
35 37 0.42
36 14 0.16
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.49
Consensus pattern (35 bp):
TTTAGTAATGATTTTAATATTTAATGATTTGATGA
Found at i:13390 original size:14 final size:13
Alignment explanation
Indices: 13351--13616 Score: 175
Period size: 14 Copynumber: 20.1 Consensus size: 13
13341 GATGATTTAG
13351 TAATGATTT-TAA
1 TAATGATTTATAA
13363 TATTATGA-TT-TAA
1 TA--ATGATTTATAA
13376 TAATGATTTAGTAA
1 TAATGATTTA-TAA
*
13390 TAATCA-TTATAA
1 TAATGATTTATAA
13402 TAATGA-TT-TAA
1 TAATGATTTATAA
*
13413 TAATGACTTTAATATT
1 TAATGA-TTT-ATA-A
13429 TAATGATTTGATGATTTA
1 TAATGATTT-AT-A---A
13447 GTAATGATTTTATAA
1 -TAATGA-TTTATAA
*
13462 TAATCA-TTATAA
1 TAATGATTTATAA
13474 TAATGATTTAGTAA
1 TAATGATTTA-TAA
*
13488 TAATCA-TTATAA
1 TAATGATTTATAA
13500 TAATGATTTAATAA
1 TAATGATTT-ATAA
13514 TAATG----ATAA
1 TAATGATTTATAA
13523 TAATGATTTAATAA
1 TAATGATTT-ATAA
*
13537 TAATCA-TTATAA
1 TAATGATTTATAA
*
13549 TAATGATTTAATAG
1 TAATGATTT-ATAA
*
13563 TAATGA-TT-TAG
1 TAATGATTTATAA
13574 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
13588 TAATGATTTAATTA
1 TAATGATTT-ATAA
13602 TAATGATTTAATAA
1 TAATGATTT-ATAA
13616 T
1 T
13617 TATTACTAAT
Statistics
Matches: 209, Mismatches: 15, Indels: 58
0.74 0.05 0.21
Matches are distributed among these distances:
9 9 0.04
11 22 0.11
12 42 0.20
13 31 0.15
14 77 0.37
15 8 0.04
16 7 0.03
18 2 0.01
19 8 0.04
20 3 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:13407 original size:26 final size:25
Alignment explanation
Indices: 13342--13629 Score: 217
Period size: 26 Copynumber: 11.6 Consensus size: 25
13332 TAATGATTTG
*
13342 ATGATT-TAGTAATGATTT-TAATA
1 ATGATTATAATAATGATTTATAATA
13365 TTATGATT-TAATAATGATTTAGTAATA
1 --ATGATTATAATAATGATTTA-TAATA
*
13392 ATCATTATAATAATGA-TT-TAATA
1 ATGATTATAATAATGATTTATAATA
* * * * * *
13415 ATGACTT-TAATATTTAATGAT-TTG
1 ATGA-TTATAATAATGATTTATAATA
*
13439 ATGATT-TAGTAATGATTTTATAATA
1 ATGATTATAATAATGA-TTTATAATA
*
13464 ATCATTATAATAATGATTTAGTAATA
1 ATGATTATAATAATGATTTA-TAATA
*
13490 ATCATTATAATAATGATTTAATAATA
1 ATGATTATAATAATGATTT-ATAATA
13516 ATG---ATAATAATGATTTAATAATA
1 ATGATTATAATAATGATTT-ATAATA
* *
13539 ATCATTATAATAATGATTTAATAGTA
1 ATGATTATAATAATGATTT-ATAATA
*
13565 ATGATT-TAGTAATGATTTTATAATA
1 ATGATTATAATAATGA-TTTATAATA
*
13590 ATGATTTAATTATAATGA-TT-TAATA
1 ATGA-TT-ATAATAATGATTTATAATA
*
13615 ATTATTACTAATAAT
1 ATGATTA-TAATAAT
13630 TATGAAATAA
Statistics
Matches: 217, Mismatches: 27, Indels: 39
0.77 0.10 0.14
Matches are distributed among these distances:
23 46 0.21
24 19 0.09
25 60 0.28
26 79 0.36
27 6 0.03
28 7 0.03
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (25 bp):
ATGATTATAATAATGATTTATAATA
Found at i:13424 original size:97 final size:98
Alignment explanation
Indices: 13311--13514 Score: 358
Period size: 97 Copynumber: 2.1 Consensus size: 98
13301 CATAAAATAT
* * *
13311 TTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTA-ATATTATGATT-T
1 TTTAATAATGACTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTATA-ATAATCATTAT
13374 AATAATGATTTAGTAATAATCATTATAATAATGA
65 AATAATGATTTAGTAATAATCATTATAATAATGA
13408 TTTAATAATGACTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTATAATAATCATTATA
1 TTTAATAATGACTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTATAATAATCATTATA
13473 ATAATGATTTAGTAATAATCATTATAATAATGA
66 ATAATGATTTAGTAATAATCATTATAATAATGA
13506 TTTAATAAT
1 TTTAATAAT
13515 AATGATAATA
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 57 0.56
98 45 0.44
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (98 bp):
TTTAATAATGACTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTATAATAATCATTATA
ATAATGATTTAGTAATAATCATTATAATAATGA
Found at i:13455 original size:72 final size:70
Alignment explanation
Indices: 13367--13629 Score: 247
Period size: 72 Copynumber: 3.7 Consensus size: 70
13357 TTTTAATATT
* * *
13367 ATGATTTAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGA-CTTTAATATTTA
1 ATGATTTAATAATGATTTA-TAATAATCATTATAATAATGATTTAATAATAATCATT-ATA-ATA
*
13431 ATGATTTG
63 ATGATTTA
* *
13439 ATGATTTAGTAATGATTTTATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAAT
1 ATGATTTAATAATGA-TTTATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAAT
13504 GATTTA
65 GATTTA
* * * *
13510 ATAATAATGATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAGTAATGATT-TAG
1 ATGAT--T--TAATAATGATTT-ATAATAATCATTATAATAATGATTTAATAATAATCATTATAA
13574 TAATGATTT-
61 TAATGATTTA
* * * *
13583 -T-A--TAATAATGATTTAATTATAATGATT-TAATAATTA-TTACTAATAAT
1 ATGATTTAATAATGATTT-ATAATAATCATTATAATAATGATTTAATAATAAT
13630 TATGAAATAA
Statistics
Matches: 167, Mismatches: 17, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
63 9 0.05
64 8 0.05
65 23 0.14
71 14 0.08
72 48 0.29
73 8 0.05
74 14 0.08
75 43 0.26
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (70 bp):
ATGATTTAATAATGATTTATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATG
ATTTA
Found at i:13784 original size:17 final size:16
Alignment explanation
Indices: 13744--13785 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
13734 AATGATTTAC
13744 TAATTATTATTAATAT
1 TAATTATTATTAATAT
13760 TAATTTATTATTAATATT
1 TAA-TTATTATTAATA-T
13778 TAATTATT
1 TAATTATT
13786 TGATACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 17 0.71
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTATTATTAATAT
Found at i:16141 original size:11 final size:11
Alignment explanation
Indices: 16127--16165 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
16117 ATAAACTATT
16127 CTTTAATATAA
1 CTTTAATATAA
*
16138 CTTTAACTAT-T
1 CTTTAA-TATAA
16149 CTTTAATATAA
1 CTTTAATATAA
16160 CTTTAA
1 CTTTAA
16166 CTAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:16145 original size:22 final size:22
Alignment explanation
Indices: 16120--16168 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
16110 ACAACTAATA
16120 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
16142 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
16164 AACTA
1 AACTA
16169 ATAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:16146 original size:30 final size:30
Alignment explanation
Indices: 16112--16230 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 30
16102 TACCTTAAAC
16112 AACTAATAAACTATTCTTTAATATAAC--T
1 AACTAATAAACTATTCTTTAATATAACTTT
16140 ---T--T-AACTATTCTTTAATATAACTTT
1 AACTAATAAACTATTCTTTAATATAACTTT
*
16164 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAACTTT
*
16194 AACTAAT-AACGATT-TTTAATTATAA-TTT
1 AACTAATAAACTATTCTTTAA-TATAACTTT
*
16222 -ACTACTAAA
1 AACTAATAAA
16231 ACTAATTAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
22 19 0.25
23 1 0.01
24 1 0.01
25 1 0.01
27 6 0.08
28 9 0.12
29 12 0.16
30 28 0.36
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.43
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:16185 original size:15 final size:16
Alignment explanation
Indices: 16141--16191 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
16131 AATATAACTT
16141 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
16157 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
16172 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
16187 TAACT
1 TAACT
16192 TAAACTAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:16521 original size:18 final size:18
Alignment explanation
Indices: 16468--16522 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
16458 TTTGTTTACC
*
16468 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
16486 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
16498 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
16515 CTAATTTA
1 CTAATTTA
16523 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:16684 original size:27 final size:28
Alignment explanation
Indices: 16649--16712 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
16639 TATATATAAC
* *
16649 TTAACTATTTA-ACTAACTACAAACTAA
1 TTAAATATTTAGACTAACAACAAACTAA
*
16676 TTAAATA-TTAGACTAACAACACACTAA
1 TTAAATATTTAGACTAACAACAAACTAA
*
16703 TTAATTATTT
1 TTAAATATTT
16713 TTTAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 26 0.84
28 2 0.06
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (28 bp):
TTAAATATTTAGACTAACAACAAACTAA
Found at i:16846 original size:39 final size:39
Alignment explanation
Indices: 16791--16874 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
16781 AATAATAAAA
16791 CTTAAACTAACAAACTAATTAACAAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACAAAAATTTTGTTTTAC
* *
16830 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACAAAAATTTTGTTTTAC
16869 CTTAAA
1 CTTAAA
16875 TCATAAACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.38
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACAAAAATTTTGTTTTAC
Found at i:21891 original size:25 final size:25
Alignment explanation
Indices: 21863--21910 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21853 CAGTGTGACA
*
21863 TAATAAACCGGTTATTGATATATGG
1 TAATAAACCGGTAATTGATATATGG
*
21888 TAATAAATCGGTAATTGATATAT
1 TAATAAACCGGTAATTGATATAT
21911 TTATACATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (25 bp):
TAATAAACCGGTAATTGATATATGG
Found at i:35920 original size:2 final size:2
Alignment explanation
Indices: 35913--35949 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35903 TCGAAACCCA
35913 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35950 TTCACTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:36909 original size:20 final size:20
Alignment explanation
Indices: 36886--36939 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
36876 ACCCAGTTTC
36886 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
36906 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
36926 CAAATTCGCAACAC
1 CAAATTCGCAACAC
36940 TTAATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:36996 original size:59 final size:59
Alignment explanation
Indices: 36925--37036 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
36915 AACACAGAAG
*
36925 TCAAATTCGCAACACTTAATTTCAAATTCACAACT-GAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCACAACTCGAATTTCAAATTCGCAACTGAATT
* * * * **
36984 TCAAATTCGCAACTCGATTTTCGAATTCACAACTCGATTTTTGAATTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCACAACTCGAATTTCAAATTCGCAAC
37037 AGGTTTTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 16 0.36
59 29 0.64
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (59 bp):
TCAAATTCGCAACACGAATTTCAAATTCACAACTCGAATTTCAAATTCGCAACTGAATT
Found at i:37010 original size:20 final size:19
Alignment explanation
Indices: 36925--37036 Score: 116
Period size: 19 Copynumber: 5.7 Consensus size: 19
36915 AACACAGAAG
*
36925 TCAAATTCGCAACACTTAATT
1 TCAAATTCGC-A-ACTGAATT
*
36946 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
36965 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
36984 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
* * *
37004 TCGAATTCACAACTCGATTT
1 TCAAATTCGCAACT-GAATT
**
37024 TTGAATTCGCAAC
1 TCAAATTCGCAAC
37037 AGGTTTTAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 39 0.48
20 34 0.41
21 9 0.11
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:38624 original size:18 final size:17
Alignment explanation
Indices: 38570--38618 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
38560 TTGGACCCTT
* *
38570 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
38588 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
38606 AGTGCATTCGATG
1 AGTGCA-TCGATG
38619 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:38638 original size:64 final size:61
Alignment explanation
Indices: 38569--38749 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 61
38559 GTTGGACCCT
*
38569 TAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCC
1 TAGTGCATCGGTGCA-T-AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCC
* * * * *
38632 ATAGTGCATCGATGCATTGCTGGTGTATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCC
1 -TAGTGCATCGGTGCATAG--AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCC
* *
38697 TCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 T-AGTGCATCGGTGCATAG-A-GTGCATCGATGCATCAAATGCATTCGATGTT
38750 CAATTTAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.45
65 50 0.50
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (61 bp):
TAGTGCATCGGTGCATAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCC
Found at i:38727 original size:65 final size:65
Alignment explanation
Indices: 38590--38749 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
38580 TGCACTAAGA
*
38590 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCATAGTGCATCGATGCATTGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTGCATCGATGCATTGCTG
* * * *
38654 GTGTATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCC-TCAGTGCATCGGTGCA-TGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAT-AGTGCATCGATGCATTGC
*
38716 TAT
64 T-G
*
38719 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
38750 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 31 0.37
65 50 0.60
66 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCATAGTGCATCGATGCATTGCTG
Found at i:39272 original size:2 final size:2
Alignment explanation
Indices: 39260--39296 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
39250 AATTGATTAA
* *
39260 AT AT CT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39297 ACTTAAGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39877 original size:21 final size:21
Alignment explanation
Indices: 39853--39896 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
39843 GAGCTGGAGG
* *
39853 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
39874 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
39895 AG
1 AG
39897 CTCCTGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:40018 original size:32 final size:32
Alignment explanation
Indices: 39982--40045 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
39972 AGGATATGAG
39982 ATTGATTTGATTTTGAAGTGGGATAGGATTGT
1 ATTGATTTGATTTTGAAGTGGGATAGGATTGT
40014 ATTGATTTGATTTTGAAGTGGGATAGGATTGT
1 ATTGATTTGATTTTGAAGTGGGATAGGATTGT
40046 CAAGAGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (32 bp):
ATTGATTTGATTTTGAAGTGGGATAGGATTGT
Found at i:40647 original size:19 final size:20
Alignment explanation
Indices: 40615--40652 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40605 TCCTCTCATC
40615 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
40634 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
40653 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:41155 original size:21 final size:21
Alignment explanation
Indices: 41113--41155 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41103 TTTCTGGGCT
*
41113 AGGGGAATCAGTACCCATTCA
1 AGGGGAATCAGTACCCACTCA
*
41134 AGGGGAATC-GATACCCCCTCA
1 AGGGGAATCAG-TACCCACTCA
41155 A
1 A
41156 CGAATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCAGTACCCACTCA
Found at i:41817 original size:21 final size:23
Alignment explanation
Indices: 41792--41841 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
41782 CTAGCATATG
*
41792 TATATGATTCTTAAGGA-ATTA-
1 TATATGATCCTTAAGGACATTAT
* *
41813 TATATGGTCCTTATGGACATTAT
1 TATATGATCCTTAAGGACATTAT
41836 TATATG
1 TATATG
41842 GCACTACGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.58
22 4 0.17
23 6 0.25
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (23 bp):
TATATGATCCTTAAGGACATTAT
Found at i:41885 original size:23 final size:23
Alignment explanation
Indices: 41841--41885 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41831 ATTATTATAT
*
41841 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
41864 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
41886 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:47409 original size:19 final size:20
Alignment explanation
Indices: 47377--47414 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
47367 TCCTCTCATC
47377 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
47396 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
47415 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:47917 original size:21 final size:21
Alignment explanation
Indices: 47875--47917 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
47865 TTTCTGGGCT
* *
47875 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
47896 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
47917 A
1 A
47918 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:48651 original size:23 final size:23
Alignment explanation
Indices: 48607--48651 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48597 ATTATTATAT
*
48607 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
48630 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
48652 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:49869 original size:17 final size:18
Alignment explanation
Indices: 49847--49887 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
49837 TATTTTTAAA
49847 TTTTGAAATAATT-TTT-T
1 TTTTGAAA-AATTGTTTGT
49864 TTTTGAAAAATTGTTTGT
1 TTTTGAAAAATTGTTTGT
49882 TTTTGA
1 TTTTGA
49888 CGAAATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (18 bp):
TTTTGAAAAATTGTTTGT
Found at i:50662 original size:14 final size:14
Alignment explanation
Indices: 50643--50680 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
50633 GATCAATTAA
50643 ACAAATCAACTTTT
1 ACAAATCAACTTTT
50657 ACAAATCAACTTTT
1 ACAAATCAACTTTT
50671 ACAAATCAAC
1 ACAAATCAAC
50681 AAGCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:52094 original size:21 final size:21
Alignment explanation
Indices: 52070--52166 Score: 92
Period size: 21 Copynumber: 4.6 Consensus size: 21
52060 GAGTGGGACA
* *
52070 TCTTGAACGATGACAGGGGCC
1 TCTTGAACGATGAGAGGAGCC
* *
52091 TCTTGAACGGTGGGAGGAGCC
1 TCTTGAACGATGAGAGGAGCC
*
52112 TCTTTG-ATGATGAGAGGAGCC
1 TC-TTGAACGATGAGAGGAGCC
*
52133 TCTTGAATGAT-AG-GAGACGCC
1 TCTTGAACGATGAGAG-GA-GCC
52154 TCTTGAACGATGA
1 TCTTGAACGATGA
52167 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.02
20 7 0.11
21 51 0.81
22 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGAGCC
Found at i:52166 original size:42 final size:42
Alignment explanation
Indices: 52070--52166 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
52060 GAGTGGGACA
* * *
52070 TCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGAGCC
1 TCTTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGAGCC
* * *
52112 TCTTTG-ATGATGAGAGGAGCCTCTTGAATGATAGGA-GACGCC
1 TC-TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGA-GCC
52154 TCTTGAACGATGA
1 TCTTGAACGATGA
52167 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 5 0.11
42 37 0.82
43 3 0.07
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
TCTTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGAGCC
Found at i:54668 original size:22 final size:23
Alignment explanation
Indices: 54643--54699 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
54633 AGATGGAGAT
* *
54643 AGACAGATTTCGCTGA-AGATGG
1 AGACAGATTTCGCTCAGAGACGG
54665 AGAC-GAATTTCG-TCAGAGACGG
1 AGACAG-ATTTCGCTCAGAGACGG
*
54687 AGACAGATGTCGC
1 AGACAGATTTCGC
54700 CGTAGAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 3 0.11
22 24 0.86
23 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.19
Consensus pattern (23 bp):
AGACAGATTTCGCTCAGAGACGG
Found at i:54842 original size:19 final size:20
Alignment explanation
Indices: 54812--54854 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
54802 GTTTCGAATT
*
54812 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATGCGCGTTG
*
54832 CGAAAAT-AAATGCGCTTTG
1 CGAAAATAAAATGCGCGTTG
54851 CGAA
1 CGAA
54855 TTTGCTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAATGCGCGTTG
Found at i:54904 original size:20 final size:20
Alignment explanation
Indices: 54848--54969 Score: 171
Period size: 20 Copynumber: 6.3 Consensus size: 20
54838 TAAATGCGCT
54848 TTGCGAATTTG-CTTTTGTG
1 TTGCGAATTTGACTTTTGTG
54867 TTGC-AA-TTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* *
54885 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
*
54905 TTGCGAATTTGACTTTTGTA
1 TTGCGAATTTGACTTTTGTG
*
54925 TTGCGAA-TTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
*
54944 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
54964 TTGCGA
1 TTGCGA
54970 TTCAATTCGC
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.03
18 14 0.15
19 23 0.25
20 52 0.57
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:54944 original size:59 final size:57
Alignment explanation
Indices: 54848--54969 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 57
54838 TAAATGCGCT
* * *
54848 TTGCGAATTTGCTTTTGTGTTGCAATTGACTTTTGTGTTGCGAATTTAACTTCTGTG
1 TTGCGAATTTGCTTTTGTATTGCAATTGACTTATGTGTTGCGAATTTAACTTATGTG
*
54905 TTGCGAATTTGACTTTTGTATTGCGAATTGACTTATGTGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTG-CTTTTGTATTGC-AATTGACTTATGTGTTGCGAATTTAACTTATGTG
54964 TTGCGA
1 TTGCGA
54970 TTCAATTCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 11 0.19
58 11 0.19
59 37 0.63
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (57 bp):
TTGCGAATTTGCTTTTGTATTGCAATTGACTTATGTGTTGCGAATTTAACTTATGTG
Found at i:54955 original size:39 final size:40
Alignment explanation
Indices: 54848--54969 Score: 171
Period size: 39 Copynumber: 3.1 Consensus size: 40
54838 TAAATGCGCT
*
54848 TTGCGAATTTG-CTTTTGTGTTGC-AA-TTGACTTTTGTG
1 TTGCGAATTTGACTTATGTGTTGCGAATTTGACTTTTGTG
* * *
54885 TTGCGAATTTAACTTCTGTGTTGCGAATTTGACTTTTGTA
1 TTGCGAATTTGACTTATGTGTTGCGAATTTGACTTTTGTG
*
54925 TTGCGAA-TTGACTTATGTGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTGTTGCGAATTTGACTTTTGTG
54964 TTGCGA
1 TTGCGA
54970 TTCAATTCGC
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
37 10 0.13
38 11 0.15
39 36 0.48
40 18 0.24
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (40 bp):
TTGCGAATTTGACTTATGTGTTGCGAATTTGACTTTTGTG
Done.