Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006187.1 Hibiscus syriacus cultivar Beakdansim tig00014725_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: 44136
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2341 original size:15 final size:14
Alignment explanation
Indices: 2321--2350 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2311 CTTTGAAAGT
2321 AAATAATAATTAATA
1 AAATAATAA-TAATA
2336 AAATAATAATAATA
1 AAATAATAATAATA
2350 A
1 A
2351 GGGTCCGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:3065 original size:21 final size:23
Alignment explanation
Indices: 3037--3132 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 23
3027 AAACGAAAAC
*
3037 TAAATGAATATGTTCGTGAAC-G
1 TAAATGAATATGTTCGTGAACAA
* *
3059 T-AATGAACATGTTTGTGAACATA
1 TAAATGAATATGTTCGTGAACA-A
** *
3082 TAAATGAATATGTTCGCAAACAT
1 TAAATGAATATGTTCGTGAACAA
* *
3105 TAAACT-AACATGTTCGCGAACAA
1 TAAA-TGAATATGTTCGTGAACAA
3128 TAAAT
1 TAAAT
3133 AAACAAAGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.29
22 2 0.03
23 23 0.39
24 17 0.29
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (23 bp):
TAAATGAATATGTTCGTGAACAA
Found at i:6868 original size:22 final size:21
Alignment explanation
Indices: 6822--6867 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
6812 GTATATCTTT
*
6822 AAATAATATTTAAATACTTAA
1 AAATAATATTTAAATAATTAA
6843 AAATAAATATTTAAATAATATAA
1 AAAT-AATATTTAAATAAT-TAA
6866 AA
1 AA
6868 TTGAATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAATATTTAAATAATTAA
Found at i:14770 original size:48 final size:50
Alignment explanation
Indices: 14694--14787 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
14684 AATTAGCATA
14694 TTATATTTTTTATTTAAGTATTTAAAATATTTTC-TATTAAAATAAGTAT
1 TTATATTTTTTATTTAAGTATTTAAAATATTTTCTTATTAAAATAAGTAT
*
14743 TTATATTTATTT-TTT-ATTATTTAAAATATTTTCTTATTAAAATAA
1 TTATATTT-TTTATTTAAGTATTTAAAATATTTTCTTATTAAAATAA
14788 TATATAAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
48 17 0.40
49 22 0.52
50 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (50 bp):
TTATATTTTTTATTTAAGTATTTAAAATATTTTCTTATTAAAATAAGTAT
Found at i:14918 original size:27 final size:27
Alignment explanation
Indices: 14847--14918 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
14837 CATAAAAAAT
*
14847 AAATATTTTAGTTACTTATTTTACTTAA
1 AAATATTTTAGATACTTATTTTAC-TAA
*
14875 AAA-A-TTTAAATACTTATTTCTA-TAA
1 AAATATTTTAGATACTTATTT-TACTAA
*
14900 AAATATTTTAGATATTTAT
1 AAATATTTTAGATACTTAT
14919 CTGGAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 6 0.16
26 14 0.38
27 14 0.38
28 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (27 bp):
AAATATTTTAGATACTTATTTTACTAA
Found at i:20352 original size:18 final size:18
Alignment explanation
Indices: 20329--20363 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20319 CGATGACGGT
*
20329 ATCATATATGGCTGCGGC
1 ATCATAAATGGCTGCGGC
20347 ATCATAAATGGCTGCGG
1 ATCATAAATGGCTGCGG
20364 TGGCTGATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (18 bp):
ATCATAAATGGCTGCGGC
Found at i:22086 original size:17 final size:18
Alignment explanation
Indices: 22043--22083 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
22033 AAATTATATT
22043 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
22060 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
22078 ATTAAA
1 AGTAAA
22084 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:23550 original size:16 final size:16
Alignment explanation
Indices: 23529--23559 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23519 ACCTATTTTC
23529 AACCTAACATGTAATG
1 AACCTAACATGTAATG
*
23545 AACCTAATATGTAAT
1 AACCTAACATGTAAT
23560 TGACTCAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (16 bp):
AACCTAACATGTAATG
Found at i:23761 original size:15 final size:14
Alignment explanation
Indices: 23723--23761 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
23713 TTTATATTTT
23723 TTATAATTCT-TATA
1 TTATAATT-TGTATA
23737 TTATAATTTGTATA
1 TTATAATTTGTATA
23751 TTATAAATTTG
1 TTAT-AATTTG
23762 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:23767 original size:71 final size:70
Alignment explanation
Indices: 23683--23826 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 70
23673 TTATGATAAT
*
23683 TAAATTTAGTTTTTATAATAATT-ACAATTCTTTATATTTTTTATAATTCTTATATTAT-AATTT
1 TAAATTTAGTTTTTATAATAATTCA-AATTCTTTATATTATTTATAATTCTTATATTATAAATTT
23746 GTATATTA
65 -TAT-TTA
*
23754 TAAATTT-GATTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTT
1 TAAATTTAG-TTTTTATAATAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTT
23818 TATTTA
65 TATTTA
23824 TAA
1 TAA
23827 TCACCAAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
70 7 0.10
71 55 0.81
72 6 0.09
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (70 bp):
TAAATTTAGTTTTTATAATAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTT
ATTTA
Found at i:23789 original size:19 final size:20
Alignment explanation
Indices: 23765--23810 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
23755 AAATTTGATT
23765 TTTATATTAATTCA-AATTC
1 TTTATATTAATTCATAATTC
*
23784 TTTATATT-ATTTATAATTC
1 TTTATATTAATTCATAATTC
23803 -TTATATTA
1 TTTATATTA
23811 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTAATTCATAATTC
Found at i:23824 original size:13 final size:14
Alignment explanation
Indices: 23790--23826 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
23780 ATTCTTTATA
23790 TTATTTAT-AATTC
1 TTATTTATAAATTC
23803 TTATATTATAAATT-
1 TTAT-TTATAAATTC
23817 TTATTTATAA
1 TTATTTATAA
23827 TCACCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:24415 original size:23 final size:23
Alignment explanation
Indices: 24389--24450 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
24379 ATCAATGTAC
*
24389 CAATTCAGCAAGTATCATTGCAT
1 CAATTCAGCAAGCATCATTGCAT
*
24412 CAATTCAGCAACCATCATTGCAT
1 CAATTCAGCAAGCATCATTGCAT
24435 CAATTCAGCAAGCATC
1 CAATTCAGCAAGCATC
24451 CTACATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.26
Consensus pattern (23 bp):
CAATTCAGCAAGCATCATTGCAT
Found at i:27375 original size:15 final size:15
Alignment explanation
Indices: 27361--27469 Score: 71
Period size: 15 Copynumber: 7.0 Consensus size: 15
27351 ATCTTTATAA
*
27361 AATTTATATTAATAA
1 AATTTATATTAATAT
27376 ACTATTTATAATTATATTAT
1 A--ATTTAT-ATTA-A-TAT
* *
27396 AATTAATATTAGTAT
1 AATTTATATTAATAT
*
27411 AATTAATATTAATATT
1 AATTTATATTAATA-T
*
27427 AACTTATATTAATAT
1 AATTTATATTAATAT
*
27442 AA--TATATT-TTAT
1 AATTTATATTAATAT
*
27454 AATTTGTAATTAATAT
1 AATTTAT-ATTAATAT
27470 TAATATAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.07
13 6 0.08
14 2 0.03
15 23 0.31
16 16 0.21
17 10 0.13
18 9 0.12
19 1 0.01
20 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
AATTTATATTAATAT
Found at i:27473 original size:34 final size:32
Alignment explanation
Indices: 27395--27513 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 32
27385 AATTATATTA
* *
27395 TAATTAATATTAGTATAAT-TAATATTAATAT
1 TAATTAATATTAATATAATATATTATTAATAT
* *
27426 TAACTT-ATATTAATATAATATATTTTATAATTT
1 TAA-TTAATATTAATATAATATATTAT-TAATAT
* * *
27459 GTAATTAATATTAATATAAAATA-TAGT-CTAT
1 -TAATTAATATTAATATAATATATTATTAATAT
* *
27490 AAAGTTAATATTAATATAAAATAT
1 TAA-TTAATATTAATATAATATAT
27514 GTTATAAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
30 2 0.03
31 36 0.51
32 7 0.10
33 8 0.11
34 18 0.25
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (32 bp):
TAATTAATATTAATATAATATATTATTAATAT
Found at i:27501 original size:31 final size:29
Alignment explanation
Indices: 27463--27521 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
27453 TAATTTGTAA
27463 TTAATATTAATATAAAATATAGTCTATAAAG
1 TTAATATTAATATAAAATAT-GT-TATAAAG
27494 TTAATATTAATATAAAATATGTTATAAA
1 TTAATATTAATATAAAATATGTTATAAA
27522 TTATATAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 2 0.07
31 20 0.71
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (29 bp):
TTAATATTAATATAAAATATGTTATAAAG
Found at i:27707 original size:21 final size:20
Alignment explanation
Indices: 27631--27707 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
27621 AATTAACATT
* *
27631 AATATAAACTATATAGTATATT
1 AATATAAACTATA-GGT-TATA
*
27653 AATATAAACTATAGTTTATA
1 AATATAAACTATAGGTTATA
* *
27673 AATTATATATTATAGGTTATA
1 AA-TATAAACTATAGGTTATA
27694 AAGTATAAACTATA
1 AA-TATAAACTATA
27708 TAGTACACTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 5 0.11
21 27 0.60
22 13 0.29
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
AATATAAACTATAGGTTATA
Found at i:27724 original size:117 final size:117
Alignment explanation
Indices: 27516--27728 Score: 254
Period size: 117 Copynumber: 1.8 Consensus size: 117
27506 TAAAATATGT
* * ***
27516 TATAAATTATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTGTAGTTT
1 TATAAACTATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTATAAAGT
* *
27581 ATAAACTATAAACTATATTAACATAAATTATAGTTAAGATAATTAACATTAA
66 ATAAACTATAAACTACACTAACATAAATTATAGTTAAGATAATTAACATTAA
* *
27633 TATAAACTATATAGTATA-TTAATATAAACTATAGTTTATA-AATTATATATT-ATA-GGTTATA
1 TATAAACTATATAGTATAGTT--TATAAACTATAGTTAATATAATTA-ATATTAATATAG-TATA
* * *
27694 AAGTATAAACTATATAGTACACTAATATAAATTAT
62 AAGTATAAACTATAAACTACACTAACATAAATTAT
27729 TGATTATAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
116 3 0.04
117 55 0.69
118 22 0.28
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (117 bp):
TATAAACTATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTATAAAGT
ATAAACTATAAACTACACTAACATAAATTATAGTTAAGATAATTAACATTAA
Found at i:27799 original size:57 final size:55
Alignment explanation
Indices: 27738--27868 Score: 156
Period size: 57 Copynumber: 2.3 Consensus size: 55
27728 TTGATTATAA
* *
27738 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATATATAC-TATAAATA-ATT-TATACATAAATAT
* * *
27795 ACTATAGGTTATATATACATAGTTTATATATACTATACATAATTTATACATAAATGT
1 ACTATAGGTTACATAT--ATAGTTTATATATACTATAAATAATTTATACATAAATAT
*
27852 ACTATAAGTTACATATA
1 ACTATAGGTTACATATA
27869 GTTTACATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
55 1 0.02
57 39 0.61
58 3 0.05
59 19 0.30
60 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (55 bp):
ACTATAGGTTACATATATAGTTTATATATACTATAAATAATTTATACATAAATAT
Found at i:27801 original size:24 final size:21
Alignment explanation
Indices: 27750--27815 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
27740 TATAGGTTAC
27750 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
*
27770 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATATACAT
*
27793 ATACTATAGGTTATATATACAT
1 ATA-TATAGTTTATATATACAT
27815 A
1 A
27816 GTTTATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.18
21 2 0.05
22 18 0.46
23 8 0.21
24 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:27816 original size:15 final size:16
Alignment explanation
Indices: 27791--27831 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
27781 GTATATATAC
27791 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
27807 ATATAC-ATAGTTTAT
1 ATATACTATAGGTTAT
27822 ATATACTATA
1 ATATACTATA
27832 CATAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:27840 original size:20 final size:19
Alignment explanation
Indices: 27804--27842 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
27794 TACTATAGGT
*
27804 TATATATACATAGTTTATA
1 TATATATACATAATTTATA
27823 TATACTATACATAATTTATA
1 TATA-TATACATAATTTATA
27843 CATAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (19 bp):
TATATATACATAATTTATA
Found at i:28087 original size:35 final size:36
Alignment explanation
Indices: 28047--28120 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
28037 TATACTATAC
*
28047 ATAGTTT-ATACATACATGTACTATAAGGTACATAT
1 ATAGTTTAATACATACATATACTATAAGGTACATAT
** *
28082 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGGTACATAT
28119 AT
1 AT
28121 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGGTACATAT
Found at i:28336 original size:2 final size:2
Alignment explanation
Indices: 28329--28467 Score: 55
Period size: 2 Copynumber: 72.0 Consensus size: 2
28319 TGTTTCTTTA
*
28329 AT AT AT AT AT AT AT AT AT CT AT AT AT -T ACT -T AT AT -T AGT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * *
28369 AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
28408 AT AT AA ACT AT AT AT -T TT AT AT A- AT TT AT AC AT GT AT AGT TT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
28450 AT AT AC AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
28468 TCTATATTAA
Statistics
Matches: 99, Mismatches: 23, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
1 10 0.10
2 83 0.84
3 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28461 original size:21 final size:21
Alignment explanation
Indices: 28435--28474 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28425 TATATAATTT
*
28435 ATACATGTATAGTT-TATATAC
1 ATACATATATA-TTCTATATAC
28456 ATACATATATATTCTATAT
1 ATACATATATATTCTATAT
28475 TAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (21 bp):
ATACATATATATTCTATATAC
Found at i:28529 original size:15 final size:15
Alignment explanation
Indices: 28509--28540 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28499 ATATACTTTT
28509 TATAGTTTATACATA
1 TATAGTTTATACATA
*
28524 TATAGTTTATATATA
1 TATAGTTTATACATA
28539 TA
1 TA
28541 ATTCACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:28532 original size:82 final size:83
Alignment explanation
Indices: 28368--28536 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 83
28358 TTATATTAGT
*
28368 TATACATACATATATATACTATATTAATATAAATTATAATATATAAACTATATATTTTATATAAT
1 TATACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAAT
*
28433 TTATACATGTATAGTTTA
66 TTATACATATATAGTTTA
* * * *
28451 TATACATACATATATATTCTATATTAATAT-AATAATATTTTATAAACTATATACTTTT-TATAG
1 TATACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATA-TTTTATATAA
28514 TTTATACATATATAGTTTA
65 TTTATACATATATAGTTTA
28533 TATA
1 TATA
28537 TATAATTCAC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
82 46 0.58
83 33 0.42
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (83 bp):
TATACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAAT
TTATACATATATAGTTTA
Found at i:28537 original size:13 final size:14
Alignment explanation
Indices: 28509--28598 Score: 51
Period size: 15 Copynumber: 6.1 Consensus size: 14
28499 ATATACTTTT
28509 TATAGTTTATACATA
1 TATAGTTTATA-ATA
28524 TATAGTTTAT-ATA
1 TATAGTTTATAATA
* *
28537 TATAATTCACATAA-A
1 TATAGTT--TATAATA
* * *
28552 CATAATATAT-ATA
1 TATAGTTTATAATA
28565 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
28583 TATAGTTTATAATA
1 TATAGTTTATAATA
28597 TA
1 TA
28599 AATATAGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 19
0.68 0.09 0.22
Matches are distributed among these distances:
12 1 0.02
13 15 0.26
14 5 0.09
15 23 0.40
16 4 0.07
17 3 0.05
18 7 0.12
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:28576 original size:20 final size:20
Alignment explanation
Indices: 28553--28615 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 20
28543 TCACATAAAC
*
28553 ATAATATATATATATAGCTT
1 ATAATATATATATATAGTTT
28573 ATAATA-AT-TATATAGTTT
1 ATAATATATATATATAGTTT
28591 ATAATATA-A-ATATAGTTT
1 ATAATATATATATATAGTTT
28609 AT-ATATA
1 ATAATATA
28616 AACTTATCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 5 0.12
18 26 0.65
19 3 0.08
20 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
ATAATATATATATATAGTTT
Found at i:30255 original size:24 final size:25
Alignment explanation
Indices: 30208--30257 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
30198 ATTAAATAAC
* *
30208 ATATTATAATTATATAATATAAAAA
1 ATATTATAATTATATAAAAAAAAAA
*
30233 ATATT-TAATTATTTAAAAAAAAAA
1 ATATTATAATTATATAAAAAAAAAA
30257 A
1 A
30258 CTAAATAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATTATAATTATATAAAAAAAAAA
Found at i:31023 original size:226 final size:226
Alignment explanation
Indices: 30613--31073 Score: 567
Period size: 226 Copynumber: 2.0 Consensus size: 226
30603 ACATAACTCA
* * *
30613 TTAATTACTAGAAACACTATTAATCATAATAACATAATAAATAGCACTTAAGTAACGTAATAAGT
1 TTAATTACTAGAAACACTATCAACCATAATAACATAATAAATAGCACTTAAATAACGTAATAAGT
* * * * *
30678 AACACATTTTCAAAGCTGATGGAGCATTACAAATTTGACGATAATAAAATATATTAATTACTTGA
66 AACACATTTTCAAAGCTGATGGAGCATTAAAAATTCGACCATAACAAAATATATTAATTACTTAA
* * * * *
30743 TTTGCTATCAATATTATCAACATATTAGGTAACACCTGAAATGTTACTAAAG-TTTAAGCTGATA
131 TTTACTATCAATATTATCAACATATAAAGTAACACCTGAAATATTACTAAAGTTTTAA-CTAATA
* *
30807 GAGTATTAGAAA-TCTAACGATAACAAAATAAG
195 GAGTATTAGAAATTCGAA-AATAACAAAATAAG
* * *
30839 TTAATTACT-GAAAACATTATCAACCTTAATAACATAATAAATAGCGCTTAAATAACGTAATAAG
1 TTAATTACTAG-AAACACTATCAACCATAATAACATAATAAATAGCACTTAAATAACGTAATAAG
* * * *
30903 TAACGCCTTTTCAAAGCTGATAGGA-CTTTTAAAAATTCGACCATAACAAAATATGTTAATTACT
65 TAACACATTTTCAAAGCTGAT-GGAGC-ATTAAAAATTCGACCATAACAAAATATATTAATTACT
* *
30967 TAATTTATTATCAATATTATCAACATA-AAAGTAATACCT-ACAATATTA-TCAAAGTTTTAACT
128 TAATTTACTATCAATATTATCAACATATAAAGTAACACCTGA-AATATTACT-AAAGTTTTAACT
* * *
31029 AATGGAGTCTTATAAATTCGAAAATAACAAAATAAG
191 AATAGAGTATTAGAAATTCGAAAATAACAAAATAAG
31065 TTAATTACT
1 TTAATTACT
31074 TATTTTGTTA
Statistics
Matches: 201, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
225 3 0.01
226 131 0.65
227 67 0.33
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (226 bp):
TTAATTACTAGAAACACTATCAACCATAATAACATAATAAATAGCACTTAAATAACGTAATAAGT
AACACATTTTCAAAGCTGATGGAGCATTAAAAATTCGACCATAACAAAATATATTAATTACTTAA
TTTACTATCAATATTATCAACATATAAAGTAACACCTGAAATATTACTAAAGTTTTAACTAATAG
AGTATTAGAAATTCGAAAATAACAAAATAAG
Found at i:31634 original size:2 final size:2
Alignment explanation
Indices: 31627--31658 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31617 ACTATAAATT
*
31627 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31659 AACTCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:32367 original size:59 final size:60
Alignment explanation
Indices: 32235--32375 Score: 180
Period size: 59 Copynumber: 2.4 Consensus size: 60
32225 CTGAGGTGGC
* * *
32235 GAAAGGCGCATCCCCGGGGACGCGCTTTACCTGGTTTTACGCTGAGTTGGATGCCACGTGT
1 GAAAGGCGCATCCCCGGGGACACGCTTTACCT-GTTTTACGCTGAGTTAGATGCCACGTAT
* *
32296 GAAAGGCGCATCCCCGGGGACACGCTTTACCT-TTATT-TGCTGA-TTCAGTTGCCACGTAT
1 GAAAGGCGCATCCCCGGGGACACGCTTTACCTGTT-TTACGCTGAGTT-AGATGCCACGTAT
*
32355 GAAAGACGCATCCCCGGGGAC
1 GAAAGGCGCATCCCCGGGGAC
32376 GCGCCTTTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
58 2 0.03
59 37 0.51
60 2 0.03
61 31 0.43
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.23
Consensus pattern (60 bp):
GAAAGGCGCATCCCCGGGGACACGCTTTACCTGTTTTACGCTGAGTTAGATGCCACGTAT
Found at i:32631 original size:31 final size:33
Alignment explanation
Indices: 32583--32661 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
32573 TTTAAATAGT
*
32583 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTTTTATTAAATAATAATTATATAAA
* *
32615 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATAATTATATAAA
*
32649 TATTATTTATTTA
1 TATTATTTTTTTA
32662 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATAATTATATAAA
Found at i:32653 original size:34 final size:31
Alignment explanation
Indices: 32573--32661 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
32563 TTCAGTTTTT
* * *
32573 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
32605 ATTATATAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
32639 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
32662 AATTTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:32655 original size:15 final size:14
Alignment explanation
Indices: 32637--32699 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 14
32627 ATTAAAATAA
32637 TATTTATATAATTAT
1 TATTTAT-TAATTAT
*
32652 TATTTATTTAAAT-T
1 TATTTA-TTAATTAT
*
32666 TATTAATTAATTAT
1 TATTTATTAATTAT
32680 T-TTTATGCTAATTAT
1 TATTTAT--TAATTAT
32695 TATTT
1 TATTT
32700 TTTGTATACA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 9 0.23
14 8 0.21
15 18 0.46
16 4 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTTATTAATTAT
Found at i:34499 original size:21 final size:21
Alignment explanation
Indices: 34448--34499 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
34438 TATGTCATCT
34448 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
34469 CCGCCA-GGTTACATGT-CTAGC
1 CCG-CAGGGTTACAT-TCCTAGC
34490 CCGCAGGGTT
1 CCGCAGGGTT
34500 TTATACCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.07
21 23 0.82
22 3 0.11
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:35064 original size:34 final size:34
Alignment explanation
Indices: 35021--35127 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
35011 ATAAATGTTT
*
35021 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATAATAGTATTCGAAATTTAAAA
* * *
35055 TTAAAATACAAATAATATTATTCGAAATATAAAT
1 TTAAAATACAAATAATAGTATTCGAAATTTAAAA
* * *
35089 TTAAAATATAAATGATAGTATTCGAAATTTAACA
1 TTAAAATACAAATAATAGTATTCGAAATTTAAAA
35123 TTAAA
1 TTAAA
35128 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATAATAGTATTCGAAATTTAAAA
Found at i:35768 original size:127 final size:127
Alignment explanation
Indices: 35542--36324 Score: 1307
Period size: 127 Copynumber: 6.2 Consensus size: 127
35532 CAGGAACGCG
* * *
35542 CCCCCGAGAACGCGCCTTCACGATCCCCTAAGGAATAATAGGTATTGACATTAATAGTTCCCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
* * *
35607 GGACATAAGTGACATAATAGGATAATGATAACATATTCTCTGACAAAATAATGAAAAGCGCC
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
* * *
35669 CCCCCGGGAACGCACATTCACTGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
* *
35734 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTTTGACAAAATAATGGAAGGCGCG
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
* * * * *
35796 CCCCCGGGAACGTGCCTTCACGGTCCCCTAAGGAATAATATGTATTGATATAAATAGTTACCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
* *
35861 GGACATAAGTGATATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
35923 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
*
35988 GGACATAAGTGATATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
*
36050 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCTGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
* * *
36115 GGACATAAGTGAGATAATAGGATAATGATAATATATTCTCTGACAAAATAATGGAAGGCG-C
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
* *
36176 CCCCCGGGAACGCGCATTCACGGTCCCCTAAGGAATAATAGGTATTGTCATGAATAGTTCCCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
* * *
36241 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGAAAAAATAATGGAAGACGCG
66 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
36303 CCCCCGGGAACGCGCCTTCACG
1 CCCCCGGGAACGCGCCTTCACG
36325 TGAATAGTAC
Statistics
Matches: 614, Mismatches: 41, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
126 118 0.19
127 496 0.81
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (127 bp):
CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGG
GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC
Done.