Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002291.1 Hibiscus syriacus cultivar Beakdansim tig00004660_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: 75400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2400 original size:21 final size:20
Alignment explanation
Indices: 2374--2426 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
2364 TCCACAAAAG
2374 TTCAAATTAATCCATAATT-T
1 TTCAAATTAAT-CATAATTAT
*
2394 TTCCAAATAAAGTCATAATTAT
1 TT-CAAATTAA-TCATAATTAT
*
2416 TTTAAATTAAT
1 TTCAAATTAAT
2427 TTATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
TTCAAATTAATCATAATTAT
Found at i:3229 original size:16 final size:17
Alignment explanation
Indices: 3208--3240 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3198 TTATTGAAAT
3208 AAAGCATAT-CGGGTAG
1 AAAGCATATCCGGGTAG
*
3224 AAAGCATGTCCGGGTAG
1 AAAGCATATCCGGGTAG
3241 GATTGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (17 bp):
AAAGCATATCCGGGTAG
Found at i:3895 original size:46 final size:46
Alignment explanation
Indices: 3840--3934 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
3830 ATCTCGAATA
*
3840 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGGTATTCATAT
1 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
* *
3886 TTGATGACTTTTGTCTTTAATGAAACTTGTTCTAGGATATTCATAT
1 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
3932 TTG
1 TTG
3935 GGATCAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (46 bp):
TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
Found at i:11389 original size:24 final size:24
Alignment explanation
Indices: 11357--11407 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
11347 ACAACATTAA
11357 TTCCTCCTATATTTACTT-AAGTAG
1 TTCCTCCTATATTTACTTCAA-TAG
*
11381 TTCCTCCTATATTTGCTTCAATAG
1 TTCCTCCTATATTTACTTCAATAG
11405 TTC
1 TTC
11408 ATTCGATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCCTCCTATATTTACTTCAATAG
Found at i:11619 original size:19 final size:21
Alignment explanation
Indices: 11580--11619 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11570 ATATAAAATT
*
11580 ATATTATTTAAATTATTGTTA
1 ATATTATTTAAAATATTGTTA
11601 ATATT-TTTAAAAT-TTGTTA
1 ATATTATTTAAAATATTGTTA
11620 TTAGGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATATTATTTAAAATATTGTTA
Found at i:13471 original size:19 final size:19
Alignment explanation
Indices: 13447--13485 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13437 TCGAATGCAT
13447 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
13466 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
13485 T
1 T
13486 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:13610 original size:64 final size:65
Alignment explanation
Indices: 13433--13595 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
13423 TGATTAATTG
* * * *
13433 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
13498 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
13561 A
65 A
13562 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
13596 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:21034 original size:19 final size:19
Alignment explanation
Indices: 21010--21048 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21000 TCGAATGCAT
21010 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
21029 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
21048 T
1 T
21049 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:21065 original size:65 final size:64
Alignment explanation
Indices: 20947--21155 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
20937 TATTCAAAGG
* *
20947 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
21008 ATTC
61 ATTT
21012 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
21077 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
21141 CATGCATCGATGCAC
1 CATGCACCGATGCAC
21156 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:21173 original size:64 final size:65
Alignment explanation
Indices: 20996--21158 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
20986 GAATTAATTG
* * * *
20996 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
21061 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
21124 A
65 A
21125 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
21159 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:22386 original size:64 final size:63
Alignment explanation
Indices: 22292--22432 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
22282 CACATTGAAT
* * *
22292 GTGCATCGATGTACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * * *
22355 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATTGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
22419 GTGCATCGATGCAC
1 GTGCATCGATGCAC
22433 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 17 0.26
64 49 0.74
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:22447 original size:24 final size:20
Alignment explanation
Indices: 22420--22477 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
22410 GCATGGGTAG
22420 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
**
22444 TGCATCGATTAACTGTAGAA
1 TGCATCGATGCACTGTAGAA
22464 TGCATCGATGCACT
1 TGCATCGATGCACT
22478 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.53
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:23266 original size:18 final size:18
Alignment explanation
Indices: 23237--23288 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
23227 GGGTCTACGC
23237 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
23255 GGTCTTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
23273 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
23289 TGTGTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:26253 original size:20 final size:21
Alignment explanation
Indices: 26214--26255 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
26204 GCGGATGAGA
26214 ATAATTAATTGGGGGAGTGTG
1 ATAATTAATTGGGGGAGTGTG
26235 ATAATTAATTGGGGG-GTGTG
1 ATAATTAATTGGGGGAGTGTG
26255 A
1 A
26256 AGGGTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (21 bp):
ATAATTAATTGGGGGAGTGTG
Found at i:29797 original size:21 final size:23
Alignment explanation
Indices: 29759--29808 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
29749 TCTTAGATAT
29759 TAAAA-AATAAATAAATAA-TTA
1 TAAAATAATAAATAAATAATTTA
* *
29780 -AAAATAATTAATATATAATTTA
1 TAAAATAATAAATAAATAATTTA
29802 TAAAATA
1 TAAAATA
29809 GGATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 3 0.12
23 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAATAAATAAATAATTTA
Found at i:29885 original size:121 final size:119
Alignment explanation
Indices: 29683--29901 Score: 293
Period size: 121 Copynumber: 1.8 Consensus size: 119
29673 ATATTAATAT
* * *
29683 AAATAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAGCTCTT
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCCT
29748 TTCTTAGATATTAAAAAATAAATAAATAATTAAAAATAATTAATATATAATTTATA
66 TTCTTAGATATT-AAAAATAAATAAAT-ATTAAAAATAATTAATATATAATTTATA
* * * *
29804 AAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATTC-AGTTATTTTAAGACTA-C-
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAG-C-TTCTAGGTACTTTAAGAC-AGCT
29866 CCTTTCTTA-ATATTGAAAAATAAATAAATATTAAAA
63 CCTTTCTTAGATATT-AAAAATAAATAAATATTAAAA
29902 CAAGATTAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
119 7 0.08
120 19 0.22
121 44 0.51
122 13 0.15
123 4 0.05
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.37
Consensus pattern (119 bp):
AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCCT
TTCTTAGATATTAAAAATAAATAAATATTAAAAATAATTAATATATAATTTATA
Found at i:29932 original size:19 final size:19
Alignment explanation
Indices: 29881--29935 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
29871 CTTAATATTG
*
29881 AAAAATAAATAAAT-A-TT
1 AAAAATAATTAAATAAGTT
29898 AAAACA-AGATTAAAATAAGTT
1 AAAA-ATA-ATT-AAATAAGTT
29919 AAAAATAATTAAATAAG
1 AAAAATAATTAAATAAG
29936 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 11 0.35
20 5 0.16
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAATAATTAAATAAGTT
Found at i:31292 original size:3 final size:3
Alignment explanation
Indices: 31286--31337 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
31276 TAATATTTAT
31286 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
31333 TAA TA
1 TAA TA
31338 TTCAAATGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31780 original size:101 final size:103
Alignment explanation
Indices: 31675--32035 Score: 345
Period size: 113 Copynumber: 3.3 Consensus size: 103
31665 ATAGAGTCAT
* * *
31675 GCAAAAGGTCGAACAAGCTCTTCTTATTATG-ACCTTCTTCCTTCTTCAGATGA-ATTATGAACT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGATATTATGAACT
** *
31738 TTCTCTGGAAAAGTTGATCCATC-AAGTGATGAATTTAA
66 TGATCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAA
* * *
31776 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA--CCTTCTTCCTTCTTCAGATGA-------T-
* *
31841 ATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAA
56 ATTATGAACTTGATCTGGAAAAGTTGATCCATCGAATGATGAATTCAA
31889 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC--CTTCTTCCTTCTTCAGATGA-------T
* * *
31953 CATTATGAACTTGACCTGGCAATGTTGATCCATCGAATGATGAATTCAA
56 -ATTATGAACTTGATCTGGAAAAGTTGATCCATCGAATGATGAATTCAA
*
32002 GCGAAAA-GTTGAACAAATTCTTCTCATTATGAAC
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC
32036 TTGCCCTGGC
Statistics
Matches: 228, Mismatches: 16, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
101 27 0.12
102 1 0.00
104 19 0.08
113 175 0.77
114 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (103 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGATATTATGAACT
TGATCTGGAAAAGTTGATCCATCGAATGATGAATTCAA
Found at i:31858 original size:113 final size:113
Alignment explanation
Indices: 31728--32037 Score: 507
Period size: 113 Copynumber: 2.7 Consensus size: 113
31718 CTTCAGATGA
** * * *
31728 ATTATGAACTTTCTCTGGAAAAGTTGATCCATC-AAGTGATGAATTTAAGC-AAAAGGTTGAACA
1 ATTATGAACTTGATCTGGCAATGTTGATCCATCGAA-TGATGAATTCAAGCGAAAA-GTTGAACA
* *
31791 AATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
64 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
31841 ATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAG
1 ATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
31906 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
66 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
31954 ATTATGAACTTGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
1 ATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
32019 TTCTTCTCATTATGAACTT
66 TTCTTCTCATTATGAACTT
32038 GCCCTGGCAA
Statistics
Matches: 185, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
113 179 0.97
114 6 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (113 bp):
ATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
Found at i:32033 original size:73 final size:73
Alignment explanation
Indices: 31946--32110 Score: 294
Period size: 73 Copynumber: 2.3 Consensus size: 73
31936 TTCAGATGAG
*
31946 TTCTTCTCATTATGAACTTGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
32011 TGAACAAA
66 TGAACAAA
* *
32019 TTCTTCTCATTATGAACTTGCCCTGGCAATGCTGATCCATCGAATTATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
*
32084 TGAACAAG
66 TGAACAAA
32092 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
32111 CTTCTTCCTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 88 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (73 bp):
TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
TGAACAAA
Found at i:32057 original size:186 final size:186
Alignment explanation
Indices: 31833--32223 Score: 719
Period size: 186 Copynumber: 2.1 Consensus size: 186
31823 TTCAGATGAG
* *
31833 TTCTTCTCATTATGAACTTGATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
31898 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
31963 TTGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
131 TCGACCTGGCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
* *
32019 TTCTTCTCATTATGAACTTGCCCTGGCAATGCTGATCCATCGAATTATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
32084 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
32149 TCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
131 TCGACCTGGCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
32205 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
32224 CTTCTTCCTT
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 198 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (186 bp):
TTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
TCGACCTGGCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAA
Found at i:32139 original size:113 final size:113
Alignment explanation
Indices: 32019--32284 Score: 469
Period size: 113 Copynumber: 2.4 Consensus size: 113
32009 GTTGAACAAA
* * * *
32019 TTCTTCTCATTATGAACTTGCCCTGGCAATGCTGATCCATCGAATTATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
*
32084 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
32132 TTCTTCTCATTATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
32197 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
32245 TTTTTCTCATTATGAACTCGACCTGGTAATGCTGATCCAT
1 TTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCAT
32285 TGATGGATTT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 145 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:32270 original size:299 final size:299
Alignment explanation
Indices: 31728--32284 Score: 911
Period size: 299 Copynumber: 1.9 Consensus size: 299
31718 CTTCAGATGA
* * * *
31728 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAA
1 ATTATGAACTTGCCCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAA
* * * *
31793 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGATCTG
66 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
* *
31858 GCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
131 GCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAAC
* *
31923 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTGGCAATGTTGATCCATCG
196 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCG
31988 AATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTC
261 AATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTC
* * *
32027 ATTATGAACTTGCCCTGGCAATGCTGATCCATCGAA-TTATGAATTCAAGCGAAAA-GTTGAACA
1 ATTATGAACTTGCCCTGGAAAAGCTGATCCATC-AAGTGATGAATTCAAGC-AAAAGGTTGAACA
*
32090 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
64 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
*
32155 TGGTAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGA
129 TGGCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGA
* *
32220 ACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCGACCTGGTAATGCTGATCCAT
194 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCAT
32285 TGATGGATTT
Statistics
Matches: 237, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
299 231 0.97
300 6 0.03
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (299 bp):
ATTATGAACTTGCCCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAA
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
GCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCG
AATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTC
Found at i:32721 original size:22 final size:22
Alignment explanation
Indices: 32696--32750 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
32686 GATAAAGCTT
*
32696 TCATCTTTGAAAA-GAGAATCTG
1 TCATCTTTGAAAAGGA-AATCTA
* *
32718 TCATGTTTAAAAAGGAAATCTA
1 TCATCTTTGAAAAGGAAATCTA
32740 TCATCTTTGAA
1 TCATCTTTGAA
32751 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGGAAATCTA
Found at i:33209 original size:54 final size:53
Alignment explanation
Indices: 33118--33251 Score: 175
Period size: 54 Copynumber: 2.6 Consensus size: 53
33108 AGAATAGCAG
* * * *
33118 GTTCGTAAAACATTTGACAGCGCATTCATCATTTCATGTGGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
* *
33171 TGTTCGTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
*
33225 --T-GTAAAACACTTGACAACACATTCATC
1 GTTCGTAAAACATTTGACAACACATTCATC
33252 CTTTTCTGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
50 24 0.33
51 1 0.01
54 47 0.65
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
Found at i:33267 original size:40 final size:40
Alignment explanation
Indices: 33223--33302 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
33213 TTTCAGCTCA
33223 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
33263 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
33303 CTTCTGCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:33333 original size:54 final size:54
Alignment explanation
Indices: 33266--33369 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
33256 TCTGTGGGAT
* *
33266 GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTC
* * *
33320 GTAAAGCATTTGACAATAAATTCATCATTTTCTGTGGCTTCTGCTCAGAT
1 GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGAT
33370 TTCTCAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTC
Found at i:35716 original size:114 final size:113
Alignment explanation
Indices: 35512--35735 Score: 331
Period size: 114 Copynumber: 2.0 Consensus size: 113
35502 AGACGATCAT
* * * * ***
35512 GCAGTTCATCTTTCAATTTCAATGATTGGTTCTGGGGTTCCTATTGAACCAGATCAGATAACTCA
1 GCAGTTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCA
*
35577 AATAACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTATGA
66 AAGAACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTATGA
* *
35625 GCAGATTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTC
1 GCAG-TTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTC
* *
35690 AAAGAACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTA
65 AAAGAACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTA
35736 CGAGAACATG
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
113 4 0.04
114 94 0.96
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (113 bp):
GCAGTTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTATGA
Found at i:37789 original size:31 final size:33
Alignment explanation
Indices: 37751--37828 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 33
37741 TCAATTTATC
*
37751 TCTTTTTTCTTTTTCCTTTTTCCTTTTT-T-TT
1 TCTTTTTTCTTTTTCATTTTTCCTTTTTATCTT
* *
37782 TCTTTTTT-TTCTCTCATTTTTTCTTTTTCATCTT
1 TCTTTTTTCTT-TTTCATTTTTCCTTTTT-ATCTT
37816 T-TTTTTTCTTTTT
1 TCTTTTTTCTTTTT
37829 TTCTTTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 2 0.05
31 22 0.58
33 9 0.24
34 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (33 bp):
TCTTTTTTCTTTTTCATTTTTCCTTTTTATCTT
Found at i:37801 original size:24 final size:23
Alignment explanation
Indices: 37753--37803 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
37743 AATTTATCTC
*
37753 TTTTTTCTTTTTCCTTTTTCCTTT
1 TTTTTTCTTTTT-CTTTTTCATTT
37777 TTTTTTCTTTTT-TTTCTCTCATTT
1 TTTTTTCTTTTTCTTT-T-TCATTT
37801 TTT
1 TTT
37804 CTTTTTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 1 0.04
24 20 0.83
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTTCTTTTTCATTT
Found at i:37808 original size:27 final size:27
Alignment explanation
Indices: 37774--37834 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
37764 TCCTTTTTCC
37774 TTTT-TTTTTC-T-TTTTTTTCTCTCATT
1 TTTTCTTTTTCATCTTTTTTT-T-TCATT
*
37800 TTTTCTTTTTCATCTTTTTTTTTCTTT
1 TTTTCTTTTTCATCTTTTTTTTTCATT
37827 TTTTCTTT
1 TTTTCTTT
37835 CTTTGTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 18 0.58
28 2 0.06
29 7 0.23
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTCTTTTTCATCTTTTTTTTTCATT
Found at i:37829 original size:21 final size:20
Alignment explanation
Indices: 37749--37832 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
37739 ATTCAATTTA
37749 TCTCTTTTTTCTTT-TTCCTTTT
1 TCTCTTTTTT-TTTCTT--TTTT
37771 TC-CTTTTTTTTTCTTTTTTT
1 TCTCTTTTTTTTTC-TTTTTT
**
37791 TCTCTCATTTTTTC--TTTT
1 TCTCTTTTTTTTTCTTTTTT
37809 TCATCTTTTTTTTTCTTTTTT
1 TC-TCTTTTTTTTTCTTTTTT
37830 TCT
1 TCT
37833 TTCTTTGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 6 0.12
19 10 0.19
20 10 0.19
21 22 0.42
22 4 0.08
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTCTTTTTTTTTCTTTTTT
Found at i:37836 original size:31 final size:29
Alignment explanation
Indices: 37755--37838 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
37745 TTTATCTCTT
* *
37755 TTTTCTTTTTCCTTTTTCCTTT-TTTTTTC
1 TTTT-TTTTTCTTTTTTTCTTTCTTTTTTC
**
37784 TTTTTTTTCTCTCATTTTTTC-TT-TTTCATC
1 TTTTTTTT-TCT--TTTTTTCTTTCTTTTTTC
37814 TTTTTTTTTCTTTTTTTCTTTCTTT
1 TTTTTTTTTCTTTTTTTCTTTCTTT
37839 GTTGGATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
27 7 0.15
28 6 0.13
29 12 0.26
30 15 0.33
31 6 0.13
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTTTTTTCTTTTTTTCTTTCTTTTTTC
Found at i:37848 original size:27 final size:26
Alignment explanation
Indices: 37818--37871 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
37808 TTCATCTTTT
*
37818 TTTTTCTTTTTTTCTTTCTTTGTTGGA
1 TTTTTC-TTTTTTCTTTCTTTGCTGGA
37845 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
37871 T
1 T
37872 GAGTATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:37922 original size:9 final size:8
Alignment explanation
Indices: 37904--37944 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
37894 TGAATACATC
37904 TTTTTCCT
1 TTTTTCCT
37912 TTTTATCC-
1 TTTT-TCCT
37920 TTTTTCCT
1 TTTTTCCT
37928 TTTTATCC-
1 TTTT-TCCT
37936 TTTTTCCT
1 TTTTTCCT
37944 T
1 T
37945 CTTCAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.21
8 17 0.59
9 6 0.21
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTCCT
Found at i:37924 original size:16 final size:16
Alignment explanation
Indices: 37903--37944 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
37893 TTGAATACAT
37903 CTTTTTCCTTTTTATC
1 CTTTTTCCTTTTTATC
37919 CTTTTTCCTTTTTATC
1 CTTTTTCCTTTTTATC
37935 CTTTTTCCTT
1 CTTTTTCCTT
37945 CTTCAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTTTTCCTTTTTATC
Found at i:41537 original size:14 final size:14
Alignment explanation
Indices: 41503--41556 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
41493 CATAAAAATA
* *
41503 CAAATGCAAAGATG
1 CAAATGTAAATATG
41517 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
41532 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
41546 TAAATGTAAAT
1 CAAATGTAAAT
41557 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:43185 original size:20 final size:20
Alignment explanation
Indices: 43140--43205 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
43130 TTAATACTTG
* *
43140 AAAAATAAAATAAAACATTA-
1 AAAAATAATAT-AAATATTAT
43160 ATAAAATAATATAAATATTAT
1 A-AAAATAATATAAATATTAT
43181 AAAAATAATA-AATATATATAT
1 AAAAATAATATAA-ATAT-TAT
43202 AAAA
1 AAAA
43206 TTTGGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.05
20 21 0.52
21 17 0.43
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATAATATAAATATTAT
Found at i:43830 original size:21 final size:23
Alignment explanation
Indices: 43792--43841 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
43782 TCTTAGATAT
43792 TAAAA-AATAAATAAATAA-TTA
1 TAAAATAATAAATAAATAATTTA
* *
43813 -AAAATAATTAATATATAATTTA
1 TAAAATAATAAATAAATAATTTA
43835 TAAAATA
1 TAAAATA
43842 GGATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 3 0.12
23 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAATAAATAAATAATTTA
Found at i:43918 original size:121 final size:120
Alignment explanation
Indices: 43716--43943 Score: 282
Period size: 121 Copynumber: 1.9 Consensus size: 120
43706 ATATTAATAT
* ** ** * *
43716 AAATAAGATATTTATTTATTTAGAAATATCAGAAAAAGGTTTTTAGGTGCTTTAAGACAGCTCTT
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAAGGCATCCAGGTACTTTAAGACAGCTCCT
43781 TTCTTAGATATTAAAAAATAAATAAATAATTAAAA-ATAATTAATATATAATTTATA
66 TTCTTAGATATT-AAAAATAAATAAAT-ATTAAAACATAATTAATATATAATTTATA
* * * * *
43837 AAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTATTTTAAGACTG-TCC
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAAGG-CATCCAGGTACTTTAAGACAGCTCC
*
43901 TTTCTTA-ATATTGAAAAATAAATAAATATTAAAACATGATTAA
65 TTTCTTAGATATT-AAAAATAAATAAATATTAAAACATAATTAA
43944 AATAAGTTAC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
119 7 0.08
120 26 0.29
121 45 0.49
122 13 0.14
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (120 bp):
AAATAAGATATTTATTTATTTAAAAATATCAGAAAAAGGCATCCAGGTACTTTAAGACAGCTCCT
TTCTTAGATATTAAAAATAAATAAATATTAAAACATAATTAATATATAATTTATA
Found at i:45362 original size:3 final size:3
Alignment explanation
Indices: 45356--45411 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
45346 TAATATTTAT
45356 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45404 TAA TAA TA
1 TAA TAA TA
45412 TTCAAATGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51897 original size:7 final size:7
Alignment explanation
Indices: 51885--51911 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
51875 TGAGTCAGTA
51885 TGGACAC
1 TGGACAC
51892 TGGACAC
1 TGGACAC
51899 TGGACAC
1 TGGACAC
51906 TGGACA
1 TGGACA
51912 GTCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (7 bp):
TGGACAC
Found at i:54033 original size:21 final size:22
Alignment explanation
Indices: 53990--54036 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
53980 TATATTTAAA
53990 TTTGACACCTCAAAATAATTTT
1 TTTGACACCTCAAAATAATTTT
*
54012 TTTGACACCTCAAAATATTTTT
1 TTTGACACCTCAAAATAATTTT
54034 TTT
1 TTT
54037 AAAAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTGACACCTCAAAATAATTTT
Found at i:56736 original size:24 final size:25
Alignment explanation
Indices: 56686--56745 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
56676 CAGTCGAAAC
*
56686 TGCCACGTAGAATTTTGCACCGAAG
1 TGCCACGTAGAATTATGCACCGAAG
* *
56711 TGCCACGTAGAA-TATGTACCGTAG
1 TGCCACGTAGAATTATGCACCGAAG
*
56735 TGCCACATAGA
1 TGCCACGTAGA
56746 TTTGTCTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
TGCCACGTAGAATTATGCACCGAAG
Found at i:56768 original size:23 final size:23
Alignment explanation
Indices: 56750--56793 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56740 CATAGATTTG
*
56750 TCTCGAAGAACCACGTAGAATCA
1 TCTCGAAGAACCACATAGAATCA
* *
56773 TCTCGAAGGACCACAAAGAAT
1 TCTCGAAGAACCACATAGAAT
56794 TATCCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (23 bp):
TCTCGAAGAACCACATAGAATCA
Found at i:57347 original size:22 final size:22
Alignment explanation
Indices: 57322--57371 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
57312 CACCTAGTAT
57322 CGATACTTCCCTTCTATGGTAC
1 CGATACTTCCCTTCTATGGTAC
57344 CGATACTTCCCTTCTATGGTAC
1 CGATACTTCCCTTCTATGGTAC
57366 CGATAC
1 CGATAC
57372 CTACCTCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (22 bp):
CGATACTTCCCTTCTATGGTAC
Found at i:59104 original size:19 final size:20
Alignment explanation
Indices: 59076--59117 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
59066 AACCAGATTG
59076 CCCAGAGGGA-ACAGATACC
1 CCCAGAGGGATACAGATACC
*
59095 CCCAGGGGGATACAGATACC
1 CCCAGAGGGATACAGATACC
59115 CCC
1 CCC
59118 TGAATGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.31, C:0.36, G:0.26, T:0.07
Consensus pattern (20 bp):
CCCAGAGGGATACAGATACC
Found at i:59178 original size:20 final size:21
Alignment explanation
Indices: 59153--59191 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
59143 AGAATGTCTG
59153 GGGGGTACAGATTC-CCCCCA
1 GGGGGTACAGATTCTCCCCCA
*
59173 GGGGGTACCGATTCTCCCC
1 GGGGGTACAGATTCTCCCC
59192 TGTTTAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.36, G:0.31, T:0.18
Consensus pattern (21 bp):
GGGGGTACAGATTCTCCCCCA
Found at i:60911 original size:44 final size:43
Alignment explanation
Indices: 60809--60911 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
60799 AAGTTGACAA
* * * *
60809 GTTGGCAAGTTG-CTAACTTGTGCACATGTGATAATTATCTTTG
1 GTTGGCAAGTTGAC-AACGTGAGCACATGGGATAATTATCATTG
* *
60852 GTTAGCAAGTGGACAACGTGAGCACATGGGATAATTCATCATTG
1 GTTGGCAAGTTGACAACGTGAGCACATGGGATAATT-ATCATTG
60896 GTTGGCAAGTTGACAA
1 GTTGGCAAGTTGACAA
60912 GTTATGCAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 29 0.58
44 21 0.42
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
GTTGGCAAGTTGACAACGTGAGCACATGGGATAATTATCATTG
Found at i:66094 original size:11 final size:11
Alignment explanation
Indices: 66078--66113 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
66068 ACAAGCAACC
66078 AGAATCAAGAG
1 AGAATCAAGAG
66089 AGAATCAAGAG
1 AGAATCAAGAG
66100 AGAATCAA-AG
1 AGAATCAAGAG
66110 AGAA
1 AGAA
66114 AGCATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.58, C:0.08, G:0.25, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:73101 original size:136 final size:136
Alignment explanation
Indices: 72858--73475 Score: 915
Period size: 136 Copynumber: 4.6 Consensus size: 136
72848 GTCTGAAGTT
* * *
72858 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-TGTTGGATGAATTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * **
72922 CTCCATTAGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATACCGTGAATCGAGTGA
72987 TAGGTC
131 TAGGTC
* * *
72993 GAACAAGATCTTCTCATTATGAACTTCTTATCCCTCTGTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * **
73058 CTCAATTGGAAATTTCAATCCCTTAAGCGAGGTATCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATACCGTGAATCGAGTGA
73123 TAGGTC
131 TAGGTC
*
73129 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAATT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* **
73194 CTCCATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATACCGTGAATCGAGTGA
*
73259 TAGATC
131 TAGGTC
* * * *
73265 GAATAAGTTATTCTCATTATGAACTTCTTCTCCTTCTG--GG-TGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * **
73327 CTTCACTGG-AATGTTGATCCCTCAAGCGAGGCATCACTGATT-GAAATACCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATACCGTGAATCGAGTGA
73390 TAGGTC
131 TAGGTC
*
73396 GAACAAGCTCTTCTCATTATGAACTGCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
73461 CTCCATTGGAAATGT
66 CTCCATTGGAAATGT
73476 TGGTTCACCT
Statistics
Matches: 434, Mismatches: 44, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
131 59 0.14
132 28 0.06
133 30 0.07
134 31 0.07
135 38 0.09
136 248 0.57
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATACCGTGAATCGAGTGA
TAGGTC
Found at i:74342 original size:8 final size:9
Alignment explanation
Indices: 74323--74363 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
74313 TCTCTCTTCA
74323 TTTCATTTT
1 TTTCATTTT
74332 TTTCATTTT
1 TTTCATTTT
*
74341 TTTCCTTTT
1 TTTCATTTT
74350 TTTC-TTTT
1 TTTCATTTT
74358 TCTTCA
1 T-TTCA
74364 AGCATAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCATTTT
Done.