Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000141.1 Hibiscus syriacus cultivar Beakdansim tig00000256_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: 89967
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1212 original size:20 final size:20
Alignment explanation
Indices: 1189--1226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1179 TCGGTTTTCC
1189 CGGTT-TTCAGCCGGTTCTTT
1 CGGTTCTTCA-CCGGTTCTTT
*
1209 CGGTTCTTTACCGGTTCT
1 CGGTTCTTCACCGGTTCT
1227 GTGCTAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.05, C:0.26, G:0.24, T:0.45
Consensus pattern (20 bp):
CGGTTCTTCACCGGTTCTTT
Found at i:3185 original size:18 final size:18
Alignment explanation
Indices: 3162--3198 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3152 GTCACAATCA
3162 TTAGAAACTCAAGATTTG
1 TTAGAAACTCAAGATTTG
3180 TTAGAAACTCAAGATTTG
1 TTAGAAACTCAAGATTTG
3198 T
1 T
3199 ACTCATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
TTAGAAACTCAAGATTTG
Found at i:3969 original size:31 final size:32
Alignment explanation
Indices: 3932--4017 Score: 122
Period size: 31 Copynumber: 2.7 Consensus size: 32
3922 TAGGTTCAAA
3932 TCAATATCAGATCGGTTGATTTTTGGGTCGG-
1 TCAATATCAGATCGGTTGATTTTTGGGTCGGC
*
3963 TTAATATCAGATCGGTTAGA-TTTTGGGTCGGC
1 TCAATATCAGATCGGTT-GATTTTTGGGTCGGC
* *
3995 TCAATACCAGATCGATTGATTTT
1 TCAATATCAGATCGGTTGATTTT
4018 CGATTTGAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 29 0.60
32 19 0.40
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (32 bp):
TCAATATCAGATCGGTTGATTTTTGGGTCGGC
Found at i:5800 original size:31 final size:31
Alignment explanation
Indices: 5757--5867 Score: 150
Period size: 31 Copynumber: 3.6 Consensus size: 31
5747 AGTTTCAAAA
* * *
5757 GTAATAAAATGGTCACTTATGTTATCGATTT
1 GTAACAAAATGGTCACTAACGTTATCGATTT
** *
5788 GTAGGAAAATGGTCACTAACGATATCGATTT
1 GTAACAAAATGGTCACTAACGTTATCGATTT
* *
5819 GTAACAAAATGCTCACTAACGTTATCAATTT
1 GTAACAAAATGGTCACTAACGTTATCGATTT
5850 GTAACAAAATGGTCACTA
1 GTAACAAAATGGTCACTA
5868 CACCATTATC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (31 bp):
GTAACAAAATGGTCACTAACGTTATCGATTT
Found at i:12421 original size:16 final size:16
Alignment explanation
Indices: 12400--12438 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12390 AGAGTTACCC
*
12400 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
* *
12416 GACCTGTTATGAACTT
1 GACCTGTTATCAACCT
12432 GACCTGT
1 GACCTGT
12439 AATTGACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:12447 original size:16 final size:16
Alignment explanation
Indices: 12415--12456 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
12405 GTTTTCAACC
*
12415 TGACCTGTTATGAACT
1 TGACCTGTAATGAACT
12431 TGACCTGTAATTG-ACT
1 TGACCTGTAA-TGAACT
*
12447 TAACCTGTAA
1 TGACCTGTAA
12457 ATGATCTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (16 bp):
TGACCTGTAATGAACT
Found at i:12672 original size:19 final size:19
Alignment explanation
Indices: 12636--12675 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12626 AAATTTGACT
*
12636 TTTATATTAATTCCAATTC
1 TTTATATTAATTACAATTC
* *
12655 TTTATATTATTTATAATTC
1 TTTATATTAATTACAATTC
12674 TT
1 TT
12676 GTATTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:17248 original size:16 final size:15
Alignment explanation
Indices: 17223--17264 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 15
17213 TAAATTATTT
17223 ATAATTAATATTAAA
1 ATAATTAATATTAAA
17238 ATAATTAAATATT--A
1 ATAATT-AATATTAAA
17252 AT-ATTAATATTAA
1 ATAATTAATATTAA
17265 CTTATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.25
13 3 0.12
14 3 0.12
15 6 0.25
16 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTAATATTAAA
Found at i:17271 original size:22 final size:20
Alignment explanation
Indices: 17221--17277 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
17211 AATAAATTAT
17221 TTATAATTAATATTAAAATAA
1 TTAT-ATTAATATTAAAATAA
*
17242 TTAAATATTAATATTAATATTAA
1 TT--ATATTAATATTAA-AATAA
17265 CTTATATTAATAT
1 -TTATATTAATAT
17278 AATCTAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.06
22 21 0.68
23 6 0.19
24 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATTAATATTAAAATAA
Found at i:17358 original size:31 final size:31
Alignment explanation
Indices: 17297--17480 Score: 96
Period size: 31 Copynumber: 5.8 Consensus size: 31
17287 TATAATTTAT
17297 AATTAATATTAATATAAA--ATATGGTCTATAA
1 AATTAATATTAATATAAACTATAT-GT-TATAA
17328 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATATGTTATAA
* * *
17358 AATTATATAGTATAGTTTATAAACTATA-ATTA-AT
1 AATTA-ATA-T-TA--ATATAAACTATATGTTATAA
* *
17392 AATTAATATT-A-ATACATTATA-GTTTATAA
1 AATTAATATTAATATAAACTATATG-TTATAA
* * * * *
17421 ACTATTTATTATATTAATATAAATTATATATAAGAT
1 A--A-TTA--ATATTAATATAAACTATATGTTATAA
*
17457 AATTAACATTAATATAAACTATAT
1 AATTAATATTAATATAAACTATAT
17481 ATTACATTAT
Statistics
Matches: 120, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
27 8 0.07
28 3 0.03
29 2 0.02
30 6 0.05
31 43 0.36
32 7 0.06
33 12 0.10
34 14 0.12
35 12 0.10
36 13 0.11
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (31 bp):
AATTAATATTAATATAAACTATATGTTATAA
Found at i:17448 original size:15 final size:15
Alignment explanation
Indices: 17428--17480 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
17418 TAAACTATTT
17428 ATTATATTAATATAA
1 ATTATATTAATATAA
*
17443 ATTATATATAAGAT-A
1 ATTATAT-TAATATAA
*
17458 ATTAACATTAATATAA
1 ATT-ATATTAATATAA
*
17474 ACTATAT
1 ATTATAT
17481 ATTACATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTATATTAATATAA
Found at i:17515 original size:21 final size:21
Alignment explanation
Indices: 17489--17543 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
17479 ATATTACATT
*
17489 ATTATAAACTATAGTTTATAA
1 ATTATAAACTATAGGTTATAA
* *
17510 ATTATATACTATGGGTTATAA
1 ATTATAAACTATAGGTTATAA
*
17531 AGTATAAACTATA
1 ATTATAAACTATA
17544 TAGTACACTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTATAAACTATAGGTTATAA
Found at i:17613 original size:20 final size:22
Alignment explanation
Indices: 17590--17647 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
17580 GGTTACATAT
17590 ATAGTTTATATA-ACATATA-A
1 ATAGTTTATATATACATATACA
*
17610 ATAGATTGTATATATACATATACT
1 ATAG-TT-TATATATACATATACA
*
17634 ATAGGTTATATATA
1 ATAGTTTATATATA
17648 TAGTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
ATAGTTTATATATACATATACA
Found at i:17625 original size:24 final size:25
Alignment explanation
Indices: 17596--17649 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
17586 ATATATAGTT
*
17596 TATATAACATATA-AATAGATTGTA
1 TATATAACATATACAATAGATTATA
* *
17620 TATAT-ACATATACTATAGGTTATA
1 TATATAACATATACAATAGATTATA
17644 TATATA
1 TATATA
17650 GTTTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATAACATATACAATAGATTATA
Found at i:17649 original size:13 final size:13
Alignment explanation
Indices: 17627--17660 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17617 GTATATATAC
17627 ATATACTATAGGTT
1 ATATA-TATAGGTT
*
17641 ATATATATAGTTT
1 ATATATATAGGTT
17654 ATATATA
1 ATATATA
17661 ATATACATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATATATAGGTT
Found at i:17708 original size:55 final size:57
Alignment explanation
Indices: 17574--17709 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 57
17564 TTGTCTATAA
*
17574 ACTATAGGTTACATATATAGTTTATATAACATATAAATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATATAACATATAAATAGATTGTATACATACATAT
* * *
17631 ACTATAGGTTATATATATAGTTTATATATA-ATATACATAG-TT-TATACATACATGT
1 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATACATACATAT
* *
17686 ATTATAAGTTACATATATAGTTTA
1 ACTATAGGTTACATATATAGTTTA
17710 CATGTATACA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
55 32 0.45
56 2 0.03
57 36 0.51
58 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (57 bp):
ACTATAGGTTACATATATAGTTTATATAACATATAAATAGATTGTATACATACATAT
Found at i:17791 original size:7 final size:7
Alignment explanation
Indices: 17781--17812 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
17771 TATGTTTAAT
17781 GTTTAGG
1 GTTTAGG
17788 GTTTAGG
1 GTTTAGG
17795 GTTTAGG
1 GTTTAGG
17802 GTTTAGG
1 GTTTAGG
17809 GTTT
1 GTTT
17813 CTATAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:17791 original size:14 final size:14
Alignment explanation
Indices: 17774--17812 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17764 TAGGGTCTAT
*
17774 GTTTAATGTTTAGG
1 GTTTAAGGTTTAGG
*
17788 GTTTAGGGTTTAGG
1 GTTTAAGGTTTAGG
*
17802 GTTTAGGGTTT
1 GTTTAAGGTTT
17813 CTATAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:17865 original size:13 final size:15
Alignment explanation
Indices: 17839--17888 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
17829 TAATGTACTT
*
17839 TATATGGTTTATATA
1 TATATAGTTTATATA
*
17854 TGTA-AG-TTATATA
1 TATATAGTTTATATA
17867 TATATAGTTTATATA
1 TATATAGTTTATATA
17882 TACTATA
1 TA-TATA
17889 CATAGTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.34
14 3 0.10
15 12 0.41
16 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:17868 original size:15 final size:13
Alignment explanation
Indices: 17839--17883 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
17829 TAATGTACTT
*
17839 TATATGGTTTATA
1 TATATAGTTTATA
*
17852 TATGTAAGTTATATA
1 TATAT-AGTT-TATA
17867 TATATAGTTTATA
1 TATATAGTTTATA
17880 TATA
1 TATA
17884 CTATACATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.44
14 7 0.26
15 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:17904 original size:20 final size:20
Alignment explanation
Indices: 17865--17904 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17855 GTAAGTTATA
* *
17865 TATATATAGTTTATATATAC
1 TATACATAGTTTATACATAC
*
17885 TATACATAGTTTGTACATAC
1 TATACATAGTTTATACATAC
17905 ATGTACTATA
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:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (20 bp):
TATACATAGTTTATACATAC
Found at i:17930 original size:35 final size:36
Alignment explanation
Indices: 17890--17963 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 36
17880 TATACTATAC
* *
17890 ATAGTTT-GTACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
17925 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
17962 AT
1 AT
17964 TAACTATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 7 0.22
37 25 0.78
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:18143 original size:20 final size:20
Alignment explanation
Indices: 18089--18429 Score: 167
Period size: 20 Copynumber: 16.1 Consensus size: 20
18079 TTTAGGGTTT
*
18089 TATAAACTATATACTTTATA
1 TATAAACTATATAATTTATA
* *
18109 TTATATACTTATATACTTTATA
1 -TATAAAC-TATATAATTTATA
18131 TATAAACTATATAATTTATACA
1 TATAAACTATATAATTTAT--A
*
18153 TAGTATATA-TAATTTATAGTTTATA
1 TA-TA-A-ACT-A--TATAATTTATA
*
18178 TTAATAAACAATATAATTTATA
1 -T-ATAAACTATATAATTTATA
* *
18200 CATAGTA-TATATAATTTATA
1 TATA-AACTATATAATTTATA
* * *
18220 -ATTATAC-ATA-ATATATAAA
1 TA-TAAACTATATA-ATTTATA
** * *
18239 TATAAGTTGTATATATTTAAA
1 TATAAACTATATA-ATTTATA
*
18260 TATAATTCATATATAATTTATA
1 TATAA-AC-TATATAATTTATA
18282 TACT-AACTATATAATTTATA
1 TA-TAAACTATATAATTTATA
*
18302 TTAATAAACTATATAGTTTATA
1 -T-ATAAACTATATAATTTATA
* * *
18324 TATAGTA-TATAATAATATAAA
1 TATA-AACTAT-ATAATTTATA
*
18345 TATAAACTATATAGTTTATA
1 TATAAACTATATAATTTATA
* *
18365 TATACACTATATAGTTTATA
1 TATAAACTATATAATTTATA
*
18385 TTAATAAACTATATAGTTTATA
1 -T-ATAAACTATATAATTTATA
* *
18407 CATAATA-TATATAGTTTATA
1 TATAA-ACTATATAATTTATA
18427 TAT
1 TAT
18430 TTTTACTTAT
Statistics
Matches: 255, Mismatches: 34, Indels: 63
0.72 0.10 0.18
Matches are distributed among these distances:
18 1 0.00
19 13 0.05
20 96 0.38
21 47 0.18
22 69 0.27
23 8 0.03
24 4 0.02
25 4 0.02
26 3 0.01
27 10 0.04
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
TATAAACTATATAATTTATA
Found at i:18170 original size:49 final size:50
Alignment explanation
Indices: 18118--18301 Score: 166
Period size: 49 Copynumber: 3.7 Consensus size: 50
18108 ATTATATACT
18118 TATATACTTTATATATAAACTATATAATTTATACATAGTATATATAA-T-
1 TATATACTTTATATATAAACTATATAATTTATACATAGTATATATAATTA
* *
18166 T-TATAGTTTATATTAATAAACAATATAATTTATACATAGTATATATAATTTA
1 TATATACTTTATA-T-ATAAACTATATAATTTATACATAGTATATATAA-TTA
* * * * * *
18218 TAATTATACATAATATATAAA-TATA-AGTTGTATATAT-TTAAATATAATTCA
1 T-A-TATACTTTATATATAAACTATATAATT-TATACATAGTATATATAATT-A
*
18269 TATATAATTTATATACT-AACTATATAATTTATA
1 TATATACTTTATATA-TAAACTATATAATTTATA
18302 TTAATAAACT
Statistics
Matches: 109, Mismatches: 14, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
47 10 0.09
48 2 0.02
49 44 0.40
50 12 0.11
51 17 0.16
52 10 0.09
53 5 0.05
54 1 0.01
55 8 0.07
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (50 bp):
TATATACTTTATATATAAACTATATAATTTATACATAGTATATATAATTA
Found at i:18219 original size:11 final size:11
Alignment explanation
Indices: 18188--18349 Score: 58
Period size: 11 Copynumber: 15.5 Consensus size: 11
18178 TTAATAAACA
18188 ATATAATTTAT
1 ATATAATTTAT
* *
18199 ACAT-A-GTAT
1 ATATAATTTAT
18208 ATATAATTTAT
1 ATATAATTTAT
* **
18219 A-ATTATACAT
1 ATATAATTTAT
* *
18229 A-AT-ATATAA
1 ATATAATTTAT
* *
18238 ATATAAGTTGT
1 ATATAATTTAT
*
18249 ATAT-ATTTAA
1 ATATAATTTAT
*
18259 ATATAATTCAT
1 ATATAATTTAT
18270 ATATAATTTAT
1 ATATAATTTAT
*
18281 ATACTAA---CT
1 ATA-TAATTTAT
18290 ATATAATTTAT
1 ATATAATTTAT
**
18301 AT-TAATAAACT
1 ATATAATTTA-T
*
18312 ATATAGTTTAT
1 ATATAATTTAT
* *
18323 ATATAGTATAT
1 ATATAATTTAT
* *
18334 A-ATAATATAA
1 ATATAATTTAT
18344 ATATAA
1 ATATAA
18350 ACTATATAGT
Statistics
Matches: 110, Mismatches: 29, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
8 3 0.03
9 15 0.14
10 33 0.30
11 52 0.47
12 7 0.06
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (11 bp):
ATATAATTTAT
Found at i:18230 original size:17 final size:17
Alignment explanation
Indices: 18190--18242 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
18180 AATAAACAAT
*
18190 ATAATTTATACATAGTATAT
1 ATAATTTATA-AT--TATAC
18210 ATAATTTATAATTATAC
1 ATAATTTATAATTATAC
* *
18227 ATAATATATAAATATA
1 ATAATTTATAATTATA
18243 AGTTGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 18 0.60
19 2 0.07
20 10 0.33
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
ATAATTTATAATTATAC
Found at i:18272 original size:21 final size:22
Alignment explanation
Indices: 18226--18279 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
18216 TATAATTATA
*
18226 CATA-ATATATAAATATAAGTT
1 CATATATATTTAAATATAAGTT
*
18247 -GTATATATTTAAATATAA-TT
1 CATATATATTTAAATATAAGTT
18267 CATATATAATTTA
1 CATATAT-ATTTA
18280 TATACTAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 18 0.67
22 5 0.19
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (22 bp):
CATATATATTTAAATATAAGTT
Found at i:29805 original size:14 final size:13
Alignment explanation
Indices: 29775--29821 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
29765 AGGACAAAAG
29775 AAAATATATTATA
1 AAAATATATTATA
29788 AAAATATAATTATTA
1 AAAATAT-ATTA-TA
29803 AAAA-A-ATT-TA
1 AAAATATATTATA
29813 AAAATATAT
1 AAAATATAT
29822 ATCCATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.20
11 1 0.03
12 5 0.17
13 7 0.23
14 5 0.17
15 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATATTATA
Found at i:32358 original size:27 final size:26
Alignment explanation
Indices: 32301--32364 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
32291 ACATACCATG
**
32301 CATCGATGCACTCAGTGTATTTGATG
1 CATCGATGCACTCAGTGTATTTGAAA
32327 CATCGATGCACTCAG-GCTATTTTGAAA
1 CATCGATGCACTCAGTG-TA-TTTGAAA
32354 CATCGAATGCA
1 CATCG-ATGCA
32365 TTTTATGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 17 0.52
27 10 0.30
28 5 0.15
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
CATCGATGCACTCAGTGTATTTGAAA
Found at i:40981 original size:45 final size:45
Alignment explanation
Indices: 40925--41027 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
40915 GCACCAATCC
*
40925 ATGCATTGATGCACCAATGAATAAATTAAACATCAAATGCATTTT
1 ATGCATCGATGCACCAATGAATAAATTAAACATCAAATGCATTTT
*
40970 ATGCATCGATGCACCAATGAATAAATTGAACATCAAATGCATTTT
1 ATGCATCGATGCACCAATGAATAAATTAAACATCAAATGCATTTT
41015 ATGCATCGATGCA
1 ATGCATCGATGCA
41028 TATACCATGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACCAATGAATAAATTAAACATCAAATGCATTTT
Found at i:41058 original size:45 final size:46
Alignment explanation
Indices: 41009--41096 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
40999 ACATCAAATG
* * *
41009 CATTTTATGCATCGATGCATATA-CCATGCATCGATGCACTCAGTA
1 CATTTGATGCATCGATGCACAAAGCCATGCATCGATGCACTCAGTA
*
41054 CATTTGATGCATCGATGCACAAAGTCATGCATCGATGCACTCA
1 CATTTGATGCATCGATGCACAAAGCCATGCATCGATGCACTCA
41097 TGCTATTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAAGCCATGCATCGATGCACTCAGTA
Found at i:42946 original size:31 final size:31
Alignment explanation
Indices: 42910--42984 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
42900 CGTGTCATGT
*
42910 ATCAAAATTTAATAAAATGATAACATAAGTA
1 ATCAAAATTTAATAAAACGATAACATAAGTA
* *
42941 ATCAAAGTTTAATAAAACGATAACATAAGTG
1 ATCAAAATTTAATAAAACGATAACATAAGTA
42972 ATCAAAATTTAAT
1 ATCAAAATTTAAT
42985 TTTTTAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (31 bp):
ATCAAAATTTAATAAAACGATAACATAAGTA
Found at i:54619 original size:21 final size:23
Alignment explanation
Indices: 54578--54636 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
54568 TTTCTTTGTT
*
54578 CTTGTAGCACTTTTTTCTCTACA
1 CTTGTAACACTTTTTTCTCTACA
* *
54601 CTTGTAACACTTTTTTCTATACT
1 CTTGTAACACTTTTTTCTCTACA
* *
54624 TTTGTGACACTTT
1 CTTGTAACACTTT
54637 CTTTATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.51
Consensus pattern (23 bp):
CTTGTAACACTTTTTTCTCTACA
Found at i:54648 original size:22 final size:23
Alignment explanation
Indices: 54602--54648 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
54592 TTCTCTACAC
* *
54602 TTGTAACACTTTTTTCTATACTT
1 TTGTAACACTTTCTTCTATAATT
*
54625 TTGTGACACTTTCTT-TATAATT
1 TTGTAACACTTTCTTCTATAATT
54647 TT
1 TT
54649 CGGTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.57
Consensus pattern (23 bp):
TTGTAACACTTTCTTCTATAATT
Found at i:54924 original size:21 final size:21
Alignment explanation
Indices: 54899--54942 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
54889 ATATCTTTGA
*
54899 ATCTTTGGGTTTAATATTTTT
1 ATCTTTGGATTTAATATTTTT
54920 ATCTTTGGATTTAATATTTTT
1 ATCTTTGGATTTAATATTTTT
54941 AT
1 AT
54943 TTTATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (21 bp):
ATCTTTGGATTTAATATTTTT
Found at i:56642 original size:49 final size:50
Alignment explanation
Indices: 56545--56643 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
56535 TACAAATATT
*
56545 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
56595 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
56644 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:57183 original size:42 final size:42
Alignment explanation
Indices: 57125--57244 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
57115 ATGAATTACA
* *
57125 TTCCGGAAAACCAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
* *
57167 TTCCGGAAAACAAATTACATGAAACAAACACCGGAAAACATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
* *
57209 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAA
57245 TTCGGGGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
Found at i:58759 original size:29 final size:29
Alignment explanation
Indices: 58717--58785 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
58707 GTTGACTGGC
58717 GCTATTCTGGTAAATAATTCAGTTTTGGT
1 GCTATTCTGGTAAATAATTCAGTTTTGGT
*
58746 GCTATTCTGGTAAATAATTCGGTTTTGGT
1 GCTATTCTGGTAAATAATTCAGTTTTGGT
58775 GCTATTCTGGT
1 GCTATTCTGGT
58786 TATTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (29 bp):
GCTATTCTGGTAAATAATTCAGTTTTGGT
Found at i:65359 original size:23 final size:22
Alignment explanation
Indices: 65332--65383 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
65322 TTTTAAGGGT
*
65332 TTGACCGGTCACGACCCGACCCG
1 TTGACCGGACACGACCCGA-CCG
* * *
65355 TTGACCCGACCCGACCCGATCG
1 TTGACCGGACACGACCCGACCG
65377 TTGACCG
1 TTGACCG
65384 TTGACCGGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.15
Consensus pattern (22 bp):
TTGACCGGACACGACCCGACCG
Found at i:65434 original size:29 final size:29
Alignment explanation
Indices: 65392--65463 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
65382 CGTTGACCGG
65392 TGCTATTCTGGTAAATAATTCGATTTTGA
1 TGCTATTCTGGTAAATAATTCGATTTTGA
* *
65421 TGCTATTCTGGTAAATAATTCGGTTTTGG
1 TGCTATTCTGGTAAATAATTCGATTTTGA
65450 TGCTATTCTGGTAA
1 TGCTATTCTGGTAA
65464 TTATTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (29 bp):
TGCTATTCTGGTAAATAATTCGATTTTGA
Found at i:67401 original size:18 final size:20
Alignment explanation
Indices: 67360--67402 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
67350 TTTCTGTCTC
67360 ATTATTATTTTGTTAATATT
1 ATTATTATTTTGTTAATATT
*
67380 -TTATT-TTTTGTTTAT-TT
1 ATTATTATTTTGTTAATATT
67397 ATTATT
1 ATTATT
67403 CACTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
ATTATTATTTTGTTAATATT
Found at i:71140 original size:29 final size:28
Alignment explanation
Indices: 71107--71185 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 28
71097 CGGTGATCGG
71107 TATATTTATCGATCTAACATC-GATTAGAC
1 TATATTT-TCGATCTAACATCTG-TTAGAC
71136 TATATTTTCTGATCTAACATCTGTTAGAC
1 TATATTTTC-GATCTAACATCTGTTAGAC
* *
71165 TATATTTCCCGATCAAACATC
1 TATATTT-TCGATCTAACATC
71186 CGTTGCAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 2 0.04
29 41 0.91
30 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (28 bp):
TATATTTTCGATCTAACATCTGTTAGAC
Found at i:71969 original size:23 final size:23
Alignment explanation
Indices: 71938--71992 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
71928 TAATTTTATT
* *
71938 TTTGAGACACATTTATCTTTGTC
1 TTTGTGACACATTTATATTTGTC
** *
71961 TTTGTGACATGTTTATATTTGTT
1 TTTGTGACACATTTATATTTGTC
*
71984 TTTATGACA
1 TTTGTGACA
71993 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.53
Consensus pattern (23 bp):
TTTGTGACACATTTATATTTGTC
Found at i:71993 original size:23 final size:22
Alignment explanation
Indices: 71949--72007 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
71939 TTGAGACACA
* * *
71949 TTTATCTTTGTCTTTGTGACAT
1 TTTATATTTGTTTTTATGACAT
71971 GTTTATATTTGTTTTTATGACAT
1 -TTTATATTTGTTTTTATGACAT
*
71994 TTT-TTTTTGTTTTT
1 TTTATATTTGTTTTT
72008 GGTAGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 10 0.31
22 3 0.09
23 19 0.59
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.68
Consensus pattern (22 bp):
TTTATATTTGTTTTTATGACAT
Found at i:72847 original size:635 final size:634
Alignment explanation
Indices: 71785--73056 Score: 2287
Period size: 635 Copynumber: 2.0 Consensus size: 634
71775 AGGAAAATAT
* *
71785 TATTTTTTTTATAATTTGTGTCATTTTTTATAGATCAAATCAATTTTTTATTTTTTGATTTTGTT
1 TATTTTTTTTATAATTTGTGTCATTTTCTATAGATCAAATCAATTTTTTATTTTTTGATTTTGGT
* *
71850 TAATCTGCGGCGGCATCGATTTTAATGTTAGTTATCGACGGTTAGTTTTTCTTTTTATTTTTAGT
66 TAATCCGCGACGGCATCGATTTTAATGTTAGTTATCGACGGTTAGTTTTTCTTTTTATTTTTAGT
* *
71915 TTTTCAATAAAAATAATTTTATTTTTGAGACACATTTATCTTTGTCTTTGTGACATGTTTATATT
131 TTTTCAATAAAAATAATTTTATTTTTGAGACACAATTATCTTTGCCTTTGTGACATGTTTATATT
*
71980 TGTTTTTATGACATTTTTTTTTGTTTTTGGTAGTTTTTGATCACTTGCCTGTTATTTTTATTTTT
196 TGTTTTTATGACATTTTTTTTTGTTTTTGGTAGTTTTCGATCACTTGCCTGTTATTTTTATTTTT
72045 TTGCAAGGTGAATTTGAAATGATCACGACTGATCAAAATGACGCGTTATATATTCTTATGACCTG
261 TTGCAAGGTGAATTTGAAATGATCACGACTGATCAAAATGACGCGTTATATATTCTTATGACCTG
*
72110 CCATTGAAAAATTGATTAATCTTAAAATGTGCCTTAGCAATATAGTCTAAACCATAATCCATTAC
326 CCATTGAAAAATTAATTAATCTTAAAATGTGCCTTAGCAATATAGTCTAAACCATAATCCATTAC
*
72175 ACAATGTTAGAAAGTACAAAAGCAAAATCGCCTCATTATTTGCAATTCCAATAGTAATTGTGTAC
391 ACAATGTTAGAAAGTACAAAAGCAAAATCGCCTCATTATTTGCAATTCCAATAGCAATTGTGTAC
*
72240 CATTTATGAGATTTATCTTATTATTGTTAAAGAATATTATCTAAAATACAATTGGATGATAACAA
456 CATTTATGAGATTTATCCTATTATTGTTAAAGAATATTATCTAAAATACAATTGGATGATAACAA
72305 ACGAAAAGAAAAAGTAAAGAACTTTCTGATTGTATGATATAGCGCATTATATATAATTGTGTGGT
521 ACGAAAAGAAAAAGTAAAGAACTTTCTGATTGTATGATATAGCGCATTATATATAATTGTGTGGT
* *
72370 ATAGCACGGTGCAGGGGGCGCGCTATATCCCACGTGTCACTCACACACG
586 ATAGCACGGTGCAGGGAGCGCGCTATATCCCACGTGTCACACACACACG
* *
72419 TATTTTTTTTATAATTTGTGTTATTTTCTATAGATCAAATCAATTTTTTCTTTTTTGATTTTGGT
1 TATTTTTTTTATAATTTGTGTCATTTTCTATAGATCAAATCAATTTTTTATTTTTTGATTTTGGT
*
72484 TAATCCGCGACGGCATCGATTTTAATGTTAGTTATCGGCGGTTAG-TTTTCTTTTTATTTTTAGT
66 TAATCCGCGACGGCATCGATTTTAATGTTAGTTATCGACGGTTAGTTTTTCTTTTTATTTTTAGT
* *
72548 TTTTTAATAAAAATACTTTTATTTTTGAGACACAATTATCTTTGCCTTTGTGACATGTTTATATT
131 TTTTCAATAAAAATAATTTTATTTTTGAGACACAATTATCTTTGCCTTTGTGACATGTTTATATT
* * *
72613 TGTTTTTATGATA-TTTTTTTTGTTTTTGGTAGTTTTCGATCGCTTGCCTGTTATTTTCGTTTTT
196 TGTTTTTATGACATTTTTTTTTGTTTTTGGTAGTTTTCGATCACTTGCCTGTTA-TTT--TTATT
*
72677 TTTTTGCAAGGTGAATTTGAAATGATCACGACTGATCAAGATGACGCGTTATATATTCTTATGAC
258 TTTTTGCAAGGTGAATTTGAAATGATCACGACTGATCAAAATGACGCGTTATATATTCTTATGAC
* *
72742 CTGCCATTGAAAAATTAATTAATCTTAAAATGTGTCTTAGCAATCTAGTCTAAACCATAATCCAT
323 CTGCCATTGAAAAATTAATTAATCTTAAAATGTGCCTTAGCAATATAGTCTAAACCATAATCCAT
72807 TACACAATGTTAGAAAGTACAAAAGCAAAATCGCCTCATTATTTGCAATTCCAATAGCAATTGTG
388 TACACAATGTTAGAAAGTACAAAAGCAAAATCGCCTCATTATTTGCAATTCCAATAGCAATTGTG
72872 TACCATTTATGAGATTTATCCTATTATTGTTAAAGAATATTATCTAAAATACAATTGGATGATAA
453 TACCATTTATGAGATTTATCCTATTATTGTTAAAGAATATTATCTAAAATACAATTGGATGATAA
*
72937 CAAACGAAAAGAAAAAGTAAAGAACTTTCTGATTGTATGATATAGCGCGTTATATATAATTGTGT
518 CAAACGAAAAGAAAAAGTAAAGAACTTTCTGATTGTATGATATAGCGCATTATATATAATTGTGT
73002 GGTATAGCACGGTGCAGGGAGCGCGCTATATCCCACGTGTCACACACACACG
583 GGTATAGCACGGTGCAGGGAGCGCGCTATATCCCACGTGTCACACACACACG
73054 TAT
1 TAT
73057 AGCGCGATGC
Statistics
Matches: 611, Mismatches: 24, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
632 38 0.06
633 95 0.16
634 103 0.17
635 375 0.61
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (634 bp):
TATTTTTTTTATAATTTGTGTCATTTTCTATAGATCAAATCAATTTTTTATTTTTTGATTTTGGT
TAATCCGCGACGGCATCGATTTTAATGTTAGTTATCGACGGTTAGTTTTTCTTTTTATTTTTAGT
TTTTCAATAAAAATAATTTTATTTTTGAGACACAATTATCTTTGCCTTTGTGACATGTTTATATT
TGTTTTTATGACATTTTTTTTTGTTTTTGGTAGTTTTCGATCACTTGCCTGTTATTTTTATTTTT
TTGCAAGGTGAATTTGAAATGATCACGACTGATCAAAATGACGCGTTATATATTCTTATGACCTG
CCATTGAAAAATTAATTAATCTTAAAATGTGCCTTAGCAATATAGTCTAAACCATAATCCATTAC
ACAATGTTAGAAAGTACAAAAGCAAAATCGCCTCATTATTTGCAATTCCAATAGCAATTGTGTAC
CATTTATGAGATTTATCCTATTATTGTTAAAGAATATTATCTAAAATACAATTGGATGATAACAA
ACGAAAAGAAAAAGTAAAGAACTTTCTGATTGTATGATATAGCGCATTATATATAATTGTGTGGT
ATAGCACGGTGCAGGGAGCGCGCTATATCCCACGTGTCACACACACACG
Found at i:73573 original size:16 final size:16
Alignment explanation
Indices: 73552--73582 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
73542 ATATAGAACC
73552 TCTGAATCATTCAACA
1 TCTGAATCATTCAACA
73568 TCTGAATCATTCAAC
1 TCTGAATCATTCAAC
73583 GCTTAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TCTGAATCATTCAACA
Found at i:73592 original size:15 final size:16
Alignment explanation
Indices: 73553--73594 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
73543 TATAGAACCT
*
73553 CTGAATCATTCAACAT
1 CTGAATCATTCAACAG
73569 CTGAATCATTCAAC-G
1 CTGAATCATTCAACAG
*
73584 CTTAATCATTC
1 CTGAATCATTC
73595 TGAAGTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (16 bp):
CTGAATCATTCAACAG
Found at i:82572 original size:17 final size:17
Alignment explanation
Indices: 82546--82612 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
82536 TGTATTAGAA
* *
82546 AAATTTATAATTAATAT
1 AAATTAATAATAAATAT
* *
82563 AAATTCATAATAAATTT
1 AAATTAATAATAAATAT
*
82580 AAAATAATAATAAATATT
1 AAATTAATAATAAATA-T
*
82598 AACATTAATTATAAA
1 AA-ATTAATAATAAA
82613 AAATATTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 27 0.68
18 3 0.08
19 10 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAATAATAAATAT
Found at i:82737 original size:18 final size:19
Alignment explanation
Indices: 82698--82738 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
82688 AACTGTAGAC
82698 AAAAAAAATATAATTAGCAT
1 AAAAAAAATATAATTA-CAT
82718 AAAAAATAAT-TAATTA-AT
1 AAAAAA-AATATAATTACAT
82736 AAA
1 AAA
82739 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.25
20 12 0.60
21 3 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAAAATATAATTACAT
Found at i:82795 original size:36 final size:33
Alignment explanation
Indices: 82723--82814 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 33
82713 AGCATAAAAA
*
82723 ATAATTA-ATTAATAAATTTAAATAAATAGTAATTAT
1 ATAATTATATTAATAAA---AAA-AAATAATAATTAT
* *
82759 ATAAATATTATTTTAATAAAAAAAAATAATATTTAT
1 AT--A-ATTATATTAATAAAAAAAAATAATAATTAT
82795 ATAATTATATTAATAAAAAA
1 ATAATTATATTAATAAAAAA
82815 TATAAAAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
33 16 0.33
34 1 0.02
36 15 0.31
37 3 0.06
38 1 0.02
39 4 0.08
40 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (33 bp):
ATAATTATATTAATAAAAAAAAATAATAATTAT
Done.