Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005161.1 Hibiscus syriacus cultivar Beakdansim tig00011643_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: 83211
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6358 original size:29 final size:29
Alignment explanation
Indices: 6305--6365 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
6295 ATTTCGGTCC
** * *
6305 CTAAACTTTCAAAGTTTATACTTTAGTCA
1 CTAAACTTTCAAAACTTACACTTTAATCA
*
6334 CTAAACTTTCAAAACTTACATTTTAATCA
1 CTAAACTTTCAAAACTTACACTTTAATCA
6363 CTA
1 CTA
6366 GACAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (29 bp):
CTAAACTTTCAAAACTTACACTTTAATCA
Found at i:16059 original size:11 final size:11
Alignment explanation
Indices: 16043--16102 Score: 95
Period size: 11 Copynumber: 5.5 Consensus size: 11
16033 ACCAACAACC
16043 ATAACAAACTA
1 ATAACAAACTA
16054 ATAACAAACTA
1 ATAACAAACTA
16065 ATAAC-AACTA
1 ATAACAAACTA
*
16075 ATAACAAGCTA
1 ATAACAAACTA
16086 ATAACAAACTA
1 ATAACAAACTA
*
16097 TTAACA
1 ATAACA
16103 CTCTAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
10 10 0.22
11 35 0.78
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:16075 original size:21 final size:22
Alignment explanation
Indices: 16043--16102 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
16033 ACCAACAACC
16043 ATAACAAACTAATAACAAACTA
1 ATAACAAACTAATAACAAACTA
*
16065 ATAAC-AACTAATAACAAGCTA
1 ATAACAAACTAATAACAAACTA
*
16086 ATAACAAACTATTAACA
1 ATAACAAACTAATAACA
16103 CTCTAACATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (22 bp):
ATAACAAACTAATAACAAACTA
Found at i:18353 original size:21 final size:22
Alignment explanation
Indices: 18328--18417 Score: 134
Period size: 21 Copynumber: 4.3 Consensus size: 22
18318 ACCAATAACC
18328 ATAACAAACTAATAAC-AACTA
1 ATAACAAACTAATAACAAACTA
18349 ATAACAAACTAATAAC-AACTA
1 ATAACAAACTAATAACAAACTA
18370 ATAAC-AACTAATAACAAACTA
1 ATAACAAACTAATAACAAACTA
*
18391 ATAACAAAC-CATAACAAACTA
1 ATAACAAACTAATAACAAACTA
*
18412 TTAACA
1 ATAACA
18418 CTCTAACAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
20 10 0.15
21 52 0.80
22 3 0.05
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (22 bp):
ATAACAAACTAATAACAAACTA
Found at i:18404 original size:10 final size:11
Alignment explanation
Indices: 18328--18417 Score: 134
Period size: 10 Copynumber: 8.5 Consensus size: 11
18318 ACCAATAACC
18328 ATAACAAACTA
1 ATAACAAACTA
18339 ATAAC-AACTA
1 ATAACAAACTA
18349 ATAACAAACTA
1 ATAACAAACTA
18360 ATAAC-AACTA
1 ATAACAAACTA
18370 ATAAC-AACTA
1 ATAACAAACTA
18380 ATAACAAACTA
1 ATAACAAACTA
*
18391 ATAACAAAC-C
1 ATAACAAACTA
18401 ATAACAAACTA
1 ATAACAAACTA
*
18412 TTAACA
1 ATAACA
18418 CTCTAACAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
10 39 0.53
11 34 0.47
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:18405 original size:31 final size:32
Alignment explanation
Indices: 18328--18417 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 32
18318 ACCAATAACC
18328 ATAACAAACTAATAACAACTAATAACAAACTA
1 ATAACAAACTAATAACAACTAATAACAAACTA
18360 ATAAC-AACTAATAACAACTAATAACAAACTA
1 ATAACAAACTAATAACAACTAATAACAAACTA
* *
18391 ATAACAAAC-CATAACAAACTATTAACA
1 ATAACAAACTAATAAC-AACTAATAACA
18418 CTCTAACAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 36 0.67
32 18 0.33
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (32 bp):
ATAACAAACTAATAACAACTAATAACAAACTA
Found at i:36913 original size:20 final size:21
Alignment explanation
Indices: 36877--36934 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
36867 CCAAACCATT
** *
36877 ACAAATATCAAGTAGAAGCAA
1 ACAAATATCAAACAGAACCAA
*
36898 GC-AATATCAAACAGAACCAA
1 ACAAATATCAAACAGAACCAA
*
36918 ACAAATATAAAACAGAA
1 ACAAATATCAAACAGAA
36935 TAAAGCAGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.12
Consensus pattern (21 bp):
ACAAATATCAAACAGAACCAA
Found at i:39371 original size:18 final size:18
Alignment explanation
Indices: 39321--39629 Score: 149
Period size: 18 Copynumber: 17.1 Consensus size: 18
39311 TTTCAATTAA
*
39321 TATATATGTTTATAT-TAA
1 TATATA-GTTTATATATAC
39339 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
39357 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
***
39375 TA-ATAAACTATATA-A-
1 TATATAGTTTATATATAC
*
39390 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
39408 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
39428 TATACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
*
39448 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
39466 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
39486 TATACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
39506 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
39524 TA-AT-G--AACTATATAG
1 TATATAGTTTA-TATATAC
39539 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
39557 TA-AT-GAACTATATATAA
1 TATATAG-TTTATATATAC
*
39574 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
39592 CATATAGTCTATATATA-
1 TATATAGTTTATATATAC
39609 TCATATAGTTTATATATAC
1 T-ATATAGTTTATATATAC
39628 TA
1 TA
39630 ATAAACTATA
Statistics
Matches: 216, Mismatches: 49, Indels: 52
0.68 0.15 0.16
Matches are distributed among these distances:
14 1 0.00
15 10 0.05
16 13 0.06
17 32 0.15
18 108 0.50
19 18 0.08
20 14 0.06
21 16 0.07
22 4 0.02
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:39394 original size:33 final size:33
Alignment explanation
Indices: 39350--39653 Score: 309
Period size: 33 Copynumber: 9.5 Consensus size: 33
39340 ATATAGTTTA
* *
39350 TATATACTATATAGTTTATATATACTAATAAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
39383 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
39409 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
39441 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
39467 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
39499 TATATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
39532 TATATAGTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* * *
39565 TATATATAATGTATAGTTTATATATACCATAT-AGTC
1 --TATATAATATATAGTTTATATATACTA-ATGA-AC
*
39601 TATATATATCATATAGTTTATATATACTAATAAAC
1 TATATA-AT-ATATAGTTTATATATACTAATGAAC
*
39636 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
39654 GGGTTTAGGA
Statistics
Matches: 226, Mismatches: 22, Indels: 46
0.77 0.07 0.16
Matches are distributed among these distances:
25 42 0.19
26 2 0.01
32 2 0.01
33 115 0.51
34 8 0.04
35 36 0.16
36 21 0.09
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:39420 original size:58 final size:58
Alignment explanation
Indices: 39351--39606 Score: 341
Period size: 58 Copynumber: 4.2 Consensus size: 58
39341 TATAGTTTAT
* *
39351 ATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
* *
39409 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
*
39467 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC-------C
* *
39532 TATATAGTATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACC
1 -ATATACTATATAGTTTATATATACTAATGAAC--TATATAATATATAGTTTATATATACC
39593 ATATAGTCTATATA
1 ATATA--CTATATA
39607 TATCATATAG
Statistics
Matches: 179, Mismatches: 7, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
58 112 0.63
60 5 0.03
61 1 0.01
62 6 0.03
65 1 0.01
66 30 0.17
68 24 0.13
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (58 bp):
ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:39463 original size:91 final size:90
Alignment explanation
Indices: 39350--39606 Score: 295
Period size: 91 Copynumber: 2.8 Consensus size: 90
39340 ATATAGTTTA
* *
39350 TATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGTATATACCATATAC
1 TATATAATATATAGTTTATATATACTAATAAACTATATAAT-TATAGTTTATATATACCATATAC
39415 TATATAGGTTATATATACTAATGAAC
65 TATATAGGTTATATATACTAATGAAC
* * * * * *
39441 TATATAATATATAGTTTGTATATAC-CATATACTATATAGGTTATA-TATACTA-ATGAACTATA
1 TATATAATATATAGTTTATATATACTAATAAACTATATA-ATTATAGTTTA-TATAT--ACCATA
* *
39503 TAATATATAGTTTATATATACTAATGAAC
62 TACTATATAGGTTATATATACTAATGAAC
* *
39532 TATATAGTATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACCATAT
1 TATATAATATATAGTTTATATATACTAATAAAC--TATATAAT-TATAGTTTATATATACCATAT
39597 AGTCTATATA
63 A--CTATATA
39607 TATCATATAG
Statistics
Matches: 135, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
89 4 0.03
90 17 0.13
91 79 0.59
92 4 0.03
93 8 0.06
94 12 0.09
95 11 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (90 bp):
TATATAATATATAGTTTATATATACTAATAAACTATATAATTATAGTTTATATATACCATATACT
ATATAGGTTATATATACTAATGAAC
Found at i:39476 original size:25 final size:25
Alignment explanation
Indices: 39442--39490 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39432 CTAATGAACT
* *
39442 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
39467 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
39491 TAATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:39683 original size:69 final size:69
Alignment explanation
Indices: 39474--39654 Score: 203
Period size: 71 Copynumber: 2.7 Consensus size: 69
39464 ACCATATACT
* * * * * *
39474 ATATAGGTTATATATACTAATGAAC-TATATAATATATAGTTTATATATACTA-ATGAACTAT--
1 ATATAGTTTATATATACTAATAAACATATATAATGTATAGTTTAGATATACCATAT-ATCTATAA
39535 ATAGT-
65 ATA-TC
* *
39540 ATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACCATATAGTCTATA
1 ATATAGTTTATATATACTAATAAAC-ATATATAATGTATAGTTTAGATATACCATATA-TCTATA
*
39605 TATATC
64 AATATC
39611 ATATAGTTTATATATACTAATAAAC-TATATAATGTATAGTTTAG
1 ATATAGTTTATATATACTAATAAACATATATAATGTATAGTTTAG
39655 GGTTTAGGAT
Statistics
Matches: 102, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
66 24 0.24
68 26 0.25
69 24 0.24
70 1 0.01
71 27 0.26
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (69 bp):
ATATAGTTTATATATACTAATAAACATATATAATGTATAGTTTAGATATACCATATATCTATAAA
TATC
Found at i:39705 original size:7 final size:7
Alignment explanation
Indices: 39690--39801 Score: 65
Period size: 7 Copynumber: 16.3 Consensus size: 7
39680 ATATGTAAAT
*
39690 TATACTA
1 TATAGTA
39697 TATAGTATA
1 TATAG--TA
*
39706 TATAGTT
1 TATAGTA
39713 TATA-TA
1 TATAGTA
*
39719 TATAATA
1 TATAGTA
39726 TATAGTA
1 TATAGTA
*
39733 TATA-AA
1 TATAGTA
*
39739 TATA-AA
1 TATAGTA
39745 CTATAGTA
1 -TATAGTA
39753 TATAGTA
1 TATAGTA
*
39760 TATA-AA
1 TATAGTA
*
39766 TATA-AA
1 TATAGTA
*
39772 CTATAGTT
1 -TATAGTA
39780 TATA-TA
1 TATAGTA
39786 TATAGTA
1 TATAGTA
*
39793 TATACTA
1 TATAGTA
39800 TA
1 TA
39802 CAAATAGTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
6 24 0.28
7 54 0.63
8 1 0.01
9 7 0.08
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (7 bp):
TATAGTA
Found at i:39720 original size:20 final size:20
Alignment explanation
Indices: 39690--40457 Score: 99
Period size: 20 Copynumber: 37.5 Consensus size: 20
39680 ATATGTAAAT
39690 TATACTATATAGT-ATATATAG
1 TATA-TATATA-TAATATATAG
*
39711 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
39731 TATATAAATATAA-ACTATAG
1 TATATATATATAATA-TATAG
39751 TATATAGTATATAA-ATATA-
1 TATATA-TATATAATATATAG
* *
39770 AACTATAGTTTAT-ATATATAG
1 TA-TATA-TATATAATATATAG
*
39791 TATATACTATACAA-ATAGT-G
1 TATATA-TATATAATATA-TAG
39811 TATATAGTTCACTAATAAACTATATA-
1 TATATA--T-A-T-AT-AA-TATATAG
*
39837 TATAGTTCATATGTAA-ACTATAG
1 TATA--T-ATATATAATA-TATAG
*
39860 T-TCATATGTA-AATATCAACTA-
1 TAT-ATATATATAATAT--A-TAG
* *
39881 TAGTTTATATGTAA-ACTATAG
1 TA-TATATATATAATA-TATAG
39902 T-TA-ATATATAAACTATATAG
1 TATATATATAT-AA-TATATAG
*
39922 T-T-TATATGTAA-ACTATAG
1 TATATATATATAATA-TATAG
*
39940 TTTATATATA-AATATCAACCTTAG
1 TATATATATATAATAT--A---TAG
39964 TATATATATAT-ATATATA-
1 TATATATATATAATATATAG
39982 TATATATATATATATATATAG
1 TATATATATATA-ATATATAG
*
40003 T-TCATATGTA-AAT-TATAG
1 TAT-ATATATATAATATATAG
*
40021 T-TCATATATATAGTA-A-A-
1 TAT-ATATATATAATATATAG
40038 TA-A-ATATA-AAT-TATAG
1 TATATATATATAATATATAG
*
40054 TTTATATAATAGTATAAAATATAG
1 --TATAT-ATA-TATAATATATAG
*
40078 TATACATATA-AAT-TATAG
1 TATATATATATAATATATAG
* * *
40096 TATGTAGTTTATATAAATATAAACCC
1 TA--TA-TATATAT-AATATATA--G
* *
40122 TAAACCATATAT-ATAT-TA-
1 TATA-TATATATAATATATAG
40140 TATATATATATAA-ACTATA-
1 TATATATATATAATA-TATAG
* *
40159 TA-ATTTATATTAATAAACTA-
1 TATATATATA-TAATATA-TAG
* * *
40179 TATAATTTATACAATATATAT
1 TAT-ATATATATAATATATAG
* * * *
40200 TATTTATA-ATTATACATAA
1 TATATATATATAATATATAG
* *
40219 TATATAAATATAAATTGTATAG
1 TATATATATAT-AA-TATATAG
* *
40241 TTTATATATAATTAATATATAA
1 TATATATAT-A-TAATATATAG
* *
40263 TTTATATATA-AACTATGTAG
1 TATATATATATAA-TATATAG
* *
40283 TTTCTATATAGTTCAATAGTTCATA-
1 TATATATATA--T-AATA--T-ATAG
* *
40308 TATAAACTATATAGTATTATAG
1 TATATA-TATATAATA-TATAG
* * *
40330 TTTATACATGGT-ATATATAG
1 TATATATAT-ATAATATATAG
* * *
40350 TTTATACTTTCTACATA-ATA-
1 TATATA-TATATA-ATATATAG
*
40370 TATATATATATACTATATAG
1 TATATATATATAATATATAG
* *
40390 TTTATATATATAATACATA-
1 TATATATATATAATATATAG
*
40409 TACTTTATATATAAACTATATAG
1 TA-TATATATAT-AA-TATATAG
*
40432 TTTATAT-TAT-ATATATA-
1 TATATATATATAATATATAG
40449 TATATATAT
1 TATATATAT
40458 CTATATTAGT
Statistics
Matches: 551, Mismatches: 90, Indels: 215
0.64 0.11 0.25
Matches are distributed among these distances:
14 3 0.01
15 6 0.01
16 1 0.00
17 15 0.03
18 66 0.12
19 58 0.11
20 175 0.32
21 66 0.12
22 75 0.14
23 23 0.04
24 36 0.07
25 7 0.01
26 14 0.03
27 4 0.01
28 1 0.00
29 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:39720 original size:27 final size:29
Alignment explanation
Indices: 39685--39789 Score: 87
Period size: 27 Copynumber: 3.8 Consensus size: 29
39675 AGTTCATATG
* * * *
39685 TAAATTATACTATATAGTATATATAGTTTA
1 TAAACTATAATATATAGTATATA-AATTAA
*
39715 TATA-TATAATATATAGTATATAAA-T-A
1 TAAACTATAATATATAGTATATAAATTAA
*
39741 TAAACTATAGTATATAGTATATAAA-T-A
1 TAAACTATAATATATAGTATATAAATTAA
* *
39768 TAAACTATAGTTTATA-TATATA
1 TAAACTATAATATATAGTATATA
39790 GTATATACTA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.15
27 37 0.54
28 1 0.01
29 17 0.25
30 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
TAAACTATAATATATAGTATATAAATTAA
Found at i:39796 original size:27 final size:27
Alignment explanation
Indices: 39735--39789 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
39725 ATATAGTATA
39735 TAAATATAAACTATAGTATATAGTATA
1 TAAATATAAACTATAGTATATAGTATA
*
39762 TAAATATAAACTATAGTTTATA-TATA
1 TAAATATAAACTATAGTATATAGTATA
39788 TA
1 TA
39790 GTATATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (27 bp):
TAAATATAAACTATAGTATATAGTATA
Found at i:39842 original size:24 final size:24
Alignment explanation
Indices: 39780--39858 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
39770 AACTATAGTT
*
39780 TATATATATAGTAT-ATACTATACAAA
1 TATATATATAGT-TCATA-TATA-AAC
*
39806 TAGTGTATATAGTTCACTA-ATAAAC
1 TA-TATATATAGTTCA-TATATAAAC
*
39831 TATATATATAGTTCATATGTAAAC
1 TATATATATAGTTCATATATAAAC
39855 TATA
1 TATA
39859 GTTCATATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 2 0.04
24 21 0.47
25 4 0.09
26 6 0.13
27 10 0.22
28 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (24 bp):
TATATATATAGTTCATATATAAAC
Found at i:39859 original size:42 final size:42
Alignment explanation
Indices: 39702--40030 Score: 192
Period size: 42 Copynumber: 7.9 Consensus size: 42
39692 TACTATATAG
* *
39702 TATATATAGTTTATATATATAATATATAGTAT-ATAAATATAAACTA
1 TATATATAGTTTATATGTA-AA-CTATAGT-TCAT--ATATAAACTA
* * * * *
39748 TAGTATATAGTATATAAATATAAACTATAGTTTATATATATAGTA
1 TA-TATATAGT-T-TATATGTAAACTATAGTTCATATATAAACTA
***
39793 TATACTATA-CAAATAGTGT--A-TATAGTTCACTA-ATAAACTA
1 TATA-TATAGTTTATA-TGTAAACTATAGTTCA-TATATAAACTA
* *
39833 TATATATAGTTCATATGTAAACTATAGTTCATATGTAAA-TA
1 TATATATAGTTTATATGTAAACTATAGTTCATATATAAACTA
*
39874 TCA-ACTATAGTTTATATGTAAACTATAGTTAATATATAAAC--
1 T-ATA-TATAGTTTATATGTAAACTATAGTTCATATATAAACTA
*
39915 --TATATAGTTTATATGTAAACTATAGTTTATATATAAA-TA
1 TATATATAGTTTATATGTAAACTATAGTTCATATATAAACTA
* * * *
39954 TCA-ACCT-TAGTATATATATATA-TATA-TAT-ATATATATA-TA
1 T-ATA--TATAGTTTATATGTAAACTATAGT-TCATATATAAACTA
* *
39994 TATATATAGTTCATATGTAAATTATAGTTCATATATA
1 TATATATAGTTTATATGTAAACTATAGTTCATATATA
40031 TAGTAAATAA
Statistics
Matches: 226, Mismatches: 28, Indels: 63
0.71 0.09 0.20
Matches are distributed among these distances:
38 35 0.15
39 20 0.09
40 39 0.17
41 24 0.11
42 60 0.27
43 3 0.01
44 2 0.01
45 14 0.06
46 3 0.01
47 16 0.07
48 3 0.01
49 7 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (42 bp):
TATATATAGTTTATATGTAAACTATAGTTCATATATAAACTA
Found at i:39860 original size:18 final size:18
Alignment explanation
Indices: 39837--39951 Score: 113
Period size: 18 Copynumber: 5.9 Consensus size: 18
39827 AAACTATATA
*
39837 TATAGTTCATATGTAAAC
1 TATAGTTTATATGTAAAC
*
39855 TATAGTTCATATGTAAATATCAAC
1 TATAGTTTATATG----TA--AAC
39879 TATAGTTTATATGTAAAC
1 TATAGTTTATATGTAAAC
* *
39897 TATAGTTAATATATAAAC
1 TATAGTTTATATGTAAAC
39915 TATATAGTTTATATGTAAAC
1 --TATAGTTTATATGTAAAC
*
39935 TATAGTTTATATATAAA
1 TATAGTTTATATGTAAA
39952 TATCAACCTT
Statistics
Matches: 83, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
18 48 0.58
20 18 0.22
22 2 0.02
24 15 0.18
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (18 bp):
TATAGTTTATATGTAAAC
Found at i:39929 original size:80 final size:81
Alignment explanation
Indices: 39834--40030 Score: 260
Period size: 80 Copynumber: 2.4 Consensus size: 81
39824 AATAAACTAT
* *
39834 ATATATAGTTCATATGTAAACTATAGTTCATATGTAAATATCAA-CTATAGT-T-TATATGTAAA
1 ATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCAACCT-TAGTATATATATATAAA
39896 CTATAGT-TA-ATATATAA
65 -TATA-TATATATATATAA
* * *
39913 ACTATATAGTTTATATGTAAACTATAGTTTATATATAAATATCAACCTTAGTATATATATATATA
1 A-TATATAGTTCATATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATATAAA
*
39978 TATATATATATATATAT
65 TATATATATATATATAA
*
39995 ATATATAGTTCATATGTAAATTATAGTTCATATATA
1 ATATATAGTTCATATGTAAACTATAGTTCATATATA
40031 TAGTAAATAA
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
79 1 0.01
80 45 0.44
81 41 0.40
82 16 0.16
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (81 bp):
ATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATATAAAT
ATATATATATATATAA
Found at i:39971 original size:2 final size:2
Alignment explanation
Indices: 39964--40463 Score: 86
Period size: 2 Copynumber: 248.5 Consensus size: 2
39954 TCAACCTTAG
39964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A
* * * * *
40007 TA TG TA AA T- TA TA GT- TCA TA TA TA TA GTA AA TA AA TA TA AA
1 TA TA TA TA TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA
* * *
40048 T- TA TA GTT TA TA TA -A TA GTA TA -A AA TA TA GTA TA CA TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* * * * * ** * *
40088 AA T- TA TA GTA TG TA GTT TA TA TA AA TA TA AA CCC TA AA CCA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
40131 TA TA TA T- TA TA TA TA TA TA TA AA CTA TA TA -A TT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
40171 -A TA AA CTA TA TA -A TT TA TA CA -A TA TA TA T- TA TT TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
40209 T- TA TA CA TA -A TA TA TA AA TA TA AA T- TG TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
40249 TA -A T- TA -A TA TA TA -A TT TA TA TA TA AA CTA TG TA GTT TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
*
40289 TA TA GT- TCA -A TA GT- TCA TA TA TA AA CTA TA TA GTA T- TA TA
1 TA TA -TA T-A TA TA -TA T-A TA TA TA TA -TA TA TA -TA TA TA TA
* * * * * * *
40329 GTT TA TA CA TGG TA TA TA TA GTT TA TA CTT TC TA CA TA -A TA TA
1 -TA TA TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * *
40372 TA TA TA TA TA CTA TA TA GTT TA TA TA TA TA -A TA CA TA TA CTT
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* *
40414 TA TA TA TA AA CTA TA TA GTT TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
40457 TC TA TA T
1 TA TA TA T
40464 TAGTTGTTTT
Statistics
Matches: 350, Mismatches: 87, Indels: 122
0.63 0.16 0.22
Matches are distributed among these distances:
1 29 0.08
2 285 0.81
3 36 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:40031 original size:31 final size:32
Alignment explanation
Indices: 39993--40076 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
39983 ATATATATAT
** *
39993 ATATATATAGTTCAT-ATGTAAATTATAGTTC
1 ATATATATAGTAAATAATATAAATTATAGTTC
*
40024 ATATATATAGTAAATAAATATAAATTATAGTTT
1 ATATATATAGTAAAT-AATATAAATTATAGTTC
40057 ATATA-ATAGTATAA-AATATA
1 ATATATATAGTA-AATAATATA
40077 GTATACATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 19 0.41
32 6 0.13
33 21 0.46
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (32 bp):
ATATATATAGTAAATAATATAAATTATAGTTC
Found at i:40048 original size:33 final size:31
Alignment explanation
Indices: 40011--40076 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 31
40001 AGTTCATATG
40011 TAAATTATAGTTCATATATATAGTAAATAAATA
1 TAAATTATAGTTCATATA-ATAGTAAA-AAATA
* *
40044 TAAATTATAGTTTATATAATAGTATAAAATA
1 TAAATTATAGTTCATATAATAGTAAAAAATA
40075 TA
1 TA
40077 GTATACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
32 7 0.23
33 17 0.55
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (31 bp):
TAAATTATAGTTCATATAATAGTAAAAAATA
Found at i:40143 original size:9 final size:9
Alignment explanation
Indices: 40129--40271 Score: 50
Period size: 9 Copynumber: 16.0 Consensus size: 9
40119 CCCTAAACCA
40129 TATATATAT
1 TATATATAT
40138 TATATATA-
1 TATATATAT
* *
40146 TATATAAAC
1 TATATATAT
40155 TATATA-AT
1 TATATATAT
*
40163 T-TATATTAA
1 TATATA-TAT
*
40172 TAAACTATAT
1 TATA-TATAT
* * *
40182 AATTTATAC
1 TATATATAT
*
40191 AATATATAT
1 TATATATAT
*
40200 TATTTATAAT
1 TATATAT-AT
*
40210 TATACATA-
1 TATATATAT
40218 -ATATATA-
1 TATATATAT
* *
40225 AATATAAAT
1 TATATATAT
*
40234 TGTATAGT-T
1 TATATA-TAT
40243 TATATATAAT
1 TATATAT-AT
40253 TAATATATAAT
1 T-ATATAT-AT
40264 T-TATATAT
1 TATATATAT
40272 AAACTATGTA
Statistics
Matches: 101, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
7 10 0.10
8 18 0.18
9 48 0.48
10 13 0.13
11 12 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (9 bp):
TATATATAT
Found at i:40168 original size:31 final size:32
Alignment explanation
Indices: 40130--40207 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
40120 CCTAAACCAT
*
40130 ATATATATTATATATA-TATATAAACTATATA
1 ATATATATTATATATACTATATAAACTATACA
* * **
40161 ATTTATATTA-ATAAACTATATAATTTATACA
1 ATATATATTATATATACTATATAAACTATACA
*
40192 ATATATATTATTTATA
1 ATATATATTATATATA
40208 ATTATACATA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.11
31 30 0.81
32 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATATATTATATATACTATATAAACTATACA
Found at i:40273 original size:11 final size:11
Alignment explanation
Indices: 40155--40273 Score: 66
Period size: 11 Copynumber: 10.6 Consensus size: 11
40145 ATATATAAAC
40155 TATATAATTTA
1 TATATAATTTA
**
40166 TAT-TAATAAA
1 TATATAATTTA
40176 CTATATAATTTA
1 -TATATAATTTA
*
40188 TACAATATATATTA
1 TA-TATA-AT-TTA
*
40202 TTTATAA-TTA
1 TATATAATTTA
*
40212 TACATAATATATA
1 TATATAAT-T-TA
* *
40225 AATATAA-AT-
1 TATATAATTTA
* *
40234 TGTATAGTTTA
1 TATATAATTTA
*
40245 TATATAATTAA
1 TATATAATTTA
40256 TATATAATTTA
1 TATATAATTTA
40267 TATATAA
1 TATATAA
40274 ACTATGTAGT
Statistics
Matches: 78, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
9 4 0.05
10 15 0.19
11 33 0.42
12 10 0.13
13 12 0.15
14 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (11 bp):
TATATAATTTA
Found at i:40364 original size:27 final size:27
Alignment explanation
Indices: 40315--40457 Score: 94
Period size: 27 Copynumber: 5.2 Consensus size: 27
40305 ATATATAAAC
* **
40315 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGT-TTATACTTTATACATAATA
*
40343 TATATAGTTTATACTTTCTACATAATA
1 TATATAGTTTATACTTTATACATAATA
* * ** *
40370 TATATA-TATATACTATATAGTTTATA
1 TATATAGTTTATACTTTATACATAATA
* * *
40396 TATATAATACATATACTTTATATATAA-A
1 TATATAGT--TTATACTTTATACATAATA
*
40424 CTATATAGTTTATA-TTATATATATATATA
1 -TATATAGTTTATACTT-TATACATA-ATA
40453 TATAT
1 TATAT
40458 CTATATTAGT
Statistics
Matches: 92, Mismatches: 16, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
26 22 0.24
27 34 0.37
28 15 0.16
29 21 0.23
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (27 bp):
TATATAGTTTATACTTTATACATAATA
Found at i:40407 original size:42 final size:40
Alignment explanation
Indices: 40343--40463 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 40
40333 ATACATGGTA
*
40343 TATATAGTTTATACTT-TCTACATAATATATATATATATAC
1 TATATAGTTTATA-TTATATACATAATATATATATATATAC
* *
40383 TATATAGTTTATATATATAATACAT-ATACTTTATATATAAAC
1 TATATAGTTTATAT-TAT-ATACATAATA-TATATATATATAC
* *
40425 TATATAGTTTATATTATATATATATATATATATCTATAT
1 TATATAGTTTATATTATATACATA-ATATATATATATAT
40464 TAGTTGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
39 1 0.01
40 19 0.28
41 15 0.22
42 33 0.49
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (40 bp):
TATATAGTTTATATTATATACATAATATATATATATATAC
Found at i:41267 original size:217 final size:216
Alignment explanation
Indices: 40487--41306 Score: 1239
Period size: 215 Copynumber: 3.8 Consensus size: 216
40477 TTTTTTCTCA
*
40487 ACTTATTACTTATTTCTATTTATT-AATTGGCCCATAACTTTTTAAA-GGAGTATAATTTAGTAC
1 ACTTATTACTTAATTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGG-GTATAATTTAGTAC
* * * * *
40550 ATTTTTATATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGTG
64 TTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTG
40609 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
129 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
40674 ATTTGCACCTGAAATTGACCCAT
194 ATTTGCATCTGAAATTGACCCAT
* * * *
40697 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATTGGTATAATTTAATAC-T
1 ACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
40761 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCTCTCATAAATGTGTGTT
66 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTGTT
* * *
40826 GTTTAATATATTTAATTTTTTATTTGTAATTTTATATTTATTCAATTTAGTCCTCCAAATTTTAT
131 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
40891 TTGCATCTAAAATTTACCCAT
196 TTGCATCTGAAATTGACCCAT
* *
40912 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAAT-GGTATAATTTAATACTT
1 ACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
40976 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTGTT
* * * *
41041 GTTTAATTTATTTAAATTTTTATTTTTAATTTCATATATGTTCAATTTAGTCCTACAAATTTTAT
131 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
41106 TTGCATATGAAATTGATCCAT
196 TTGCATCTGAAATTGACCCAT
* *
41127 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAAC-TTTTAAATGGGTATAATTTAGTATT
1 ACTTATTACTTAATTCTA-TTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA-C
* *
41191 TTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCAACTTGATCCCTCATCAATATGTG
64 TTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTG
*
41256 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
129 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
41307 ATTCTTAAAT
Statistics
Matches: 562, Mismatches: 36, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
209 50 0.09
210 55 0.10
211 2 0.00
214 16 0.03
215 295 0.52
216 32 0.06
217 112 0.20
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (216 bp):
ACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGACTTGATCCCTCATCAATGTGTGTT
GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
TTGCATCTGAAATTGACCCAT
Found at i:41617 original size:16 final size:16
Alignment explanation
Indices: 41579--41617 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41569 AACTGCTTCG
*
41579 GACCTGAACTGACAAC
1 GACCTGAACTGAAAAC
* *
41595 GATCTGAACTGAAAAT
1 GACCTGAACTGAAAAC
41611 GACCTGA
1 GACCTGA
41618 CCAGAACCCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (16 bp):
GACCTGAACTGAAAAC
Found at i:45861 original size:14 final size:14
Alignment explanation
Indices: 45832--45875 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
45822 CGTTCGTGAA
45832 CGTTCAATTATATGTT
1 CGTTC-ATT-TATGTT
45848 CGTTCATTTATGTT
1 CGTTCATTTATGTT
45862 CGTTCATTTATGTT
1 CGTTCATTTATGTT
45876 TGAACAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 20 0.71
15 3 0.11
16 5 0.18
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:46185 original size:14 final size:14
Alignment explanation
Indices: 46166--46206 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
46156 TATTTATTAT
46166 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
46180 GTTCGTTT--G-T-
1 GTTCGTTTACGTTC
46190 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
46204 GTT
1 GTT
46207 TATGTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 8 0.35
11 1 0.04
12 2 0.09
13 1 0.04
14 11 0.48
ACGTcount: A:0.05, C:0.17, G:0.24, T:0.54
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:46204 original size:20 final size:20
Alignment explanation
Indices: 46179--46218 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46169 CGTTTACGTT
*
46179 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
*
46199 CGTTCGTTTATGTTCTTTTA
1 CGTTCGTTTATGTTCGTTTA
46219 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.57
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:46219 original size:10 final size:10
Alignment explanation
Indices: 46180--46219 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
46170 GTTTACGTTC
*
46180 GTTCGTTTGT
1 GTTCGTTTAT
*
46190 GTTCGTTTAC
1 GTTCGTTTAT
46200 GTTCGTTTAT
1 GTTCGTTTAT
*
46210 GTTCTTTTAT
1 GTTCGTTTAT
46220 CATTTAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.07, C:0.12, G:0.20, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:66078 original size:2 final size:2
Alignment explanation
Indices: 66071--66100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66061 CTCAGTTTAC
66071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66101 GACTTAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77242 original size:24 final size:24
Alignment explanation
Indices: 77214--77274 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
77204 GCGGTAGAAA
*
77214 GTTCGATTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTGC
* *
77238 GTTCGGTTATATTCGTTTATGTGC
1 GTTCGATTATGTTCGTTTATGTGC
77262 GTTC-ATTTATGTT
1 GTTCGA-TTATGTT
77275 TAACCCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.54
Consensus pattern (24 bp):
GTTCGATTATGTTCGTTTATGTGC
Found at i:78833 original size:16 final size:16
Alignment explanation
Indices: 78812--78878 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
78802 GTCTCCAACG
78812 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
78828 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* * *
78844 TTTATTTTCGTATTCG
1 TTTATGTTCGTGTTCA
78860 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
78874 TTTAT
1 TTTAT
78879 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:78854 original size:32 final size:32
Alignment explanation
Indices: 78810--78870 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
78800 GGGTCTCCAA
*
78810 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTATTCATTTATGTTCGTGTT
* *
78842 CGTTTATTTTCGTATTCGTTTATGTTCGT
1 CGTTTATGTTCGTATTCATTTATGTTCGT
78871 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCGTATTCATTTATGTTCGTGTT
Found at i:82738 original size:17 final size:17
Alignment explanation
Indices: 82716--82748 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
82706 AAAATGATAC
82716 AACTAAACAATAAAAAG
1 AACTAAACAATAAAAAG
*
82733 AACTAAATAATAAAAA
1 AACTAAACAATAAAAA
82749 CATTTGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (17 bp):
AACTAAACAATAAAAAG
Found at i:82784 original size:26 final size:25
Alignment explanation
Indices: 82736--82802 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
82726 TAAAAAGAAC
* *
82736 TAAATAATAAAAACATTTGAACAAT
1 TAAATAATAAAAACATTAGAACAAA
82761 TAAATAATAAAAA-ATTAAGAAACAAA
1 TAAATAATAAAAACATT-AG-AACAAA
82787 TAAATAA-AAAATACAT
1 TAAATAATAAAA-ACAT
82803 AATTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 3 0.08
25 18 0.50
26 13 0.36
27 2 0.06
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (25 bp):
TAAATAATAAAAACATTAGAACAAA
Found at i:82809 original size:15 final size:15
Alignment explanation
Indices: 82758--82814 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
82748 ACATTTGAAC
* *
82758 AATTAAATAATAAAA
1 AATTAAAAAATAAAT
* *
82773 AATTAAGAAACAAAT
1 AATTAAAAAATAAAT
* *
82788 AAATAAAAAATACAT
1 AATTAAAAAATAAAT
82803 AATTAAATAAAT
1 AATTAAA-AAAT
82815 TTTTTACAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
15 28 0.88
16 4 0.12
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
AATTAAAAAATAAAT
Found at i:82810 original size:23 final size:23
Alignment explanation
Indices: 82730--82814 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
82720 AAACAATAAA
*
82730 AAGAACTAAAT-AATAAAAACATTT
1 AAGAATTAAATAAATAAAAA-A-TT
*
82754 GAACAATTAAAT-AATAAAAAATT
1 -AAGAATTAAATAAATAAAAAATT
**
82777 AAGAAACAAATAAATAAAAAA-T
1 AAGAATTAAATAAATAAAAAATT
*
82799 ACATAATTAAATAAAT
1 A-AGAATTAAATAAAT
82815 TTTTTACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 10 0.20
23 22 0.44
24 1 0.02
25 17 0.34
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (23 bp):
AAGAATTAAATAAATAAAAAATT
Done.