Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005536.1 Hibiscus syriacus cultivar Beakdansim tig00012804_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: 58714
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3319 original size:22 final size:21
Alignment explanation
Indices: 3294--3334 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3284 AGCTCGTATC
3294 ATTGCACCGAAGTGCACATAGA
1 ATTGCACCGAAGTGC-CATAGA
*
3316 ATTGCACCGTAGTGCCATA
1 ATTGCACCGAAGTGCCATA
3335 TAATAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
ATTGCACCGAAGTGCCATAGA
Found at i:3373 original size:21 final size:21
Alignment explanation
Indices: 3347--3434 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
3337 ATAATGTCTA
3347 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
*
3368 TAAGGACTACATATCATTCCT
1 TAAGGACCACATATCATTCCT
3389 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
3410 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
3431 TAAG
1 TAAG
3435 AATCATATAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:5003 original size:64 final size:62
Alignment explanation
Indices: 4853--5008 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 62
4843 TAATGAAGGT
** * * ** *
4853 ATGCATCGATGCACTACTGATGCATCGATGTATAAATGCATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCA-TACCAATGCATCGATGCATAAATGCATTCGATGTTCTATTATTAAAGAG
* * *
4916 ATGCATCGATGCATGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCTATT-TTAAA-AG
1 ATGCATCGATGCATACC-AATGCATCGATGCA-TAAATGCATTCGATG-TTCTATTATTAAAGAG
4979 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACCAATGCATCGAT
5009 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
62 2 0.03
63 27 0.35
64 39 0.51
65 9 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCATACCAATGCATCGATGCATAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:11691 original size:30 final size:31
Alignment explanation
Indices: 11657--11744 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 31
11647 GAAAAAGAAT
*
11657 ATGTGATATGTGAAAGTGAATCATATGA-AA
1 ATGTGATATGTGAAAGTGAACCATATGATAA
* *
11687 ATGTGCTACGT-ACAAGTGAACCATATGATTAA
1 ATGTGATATGTGA-AAGTGAACCATATGA-TAA
*
11719 ATTTGATATGTGAAAGTGAACCATAT
1 ATGTGATATGTGAAAGTGAACCATAT
11745 ATATATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.02
30 23 0.48
32 23 0.48
33 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (31 bp):
ATGTGATATGTGAAAGTGAACCATATGATAA
Found at i:11748 original size:2 final size:2
Alignment explanation
Indices: 11741--11765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11731 AAAGTGAACC
11741 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11766 AGAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11992 original size:31 final size:32
Alignment explanation
Indices: 11945--12080 Score: 111
Period size: 31 Copynumber: 4.3 Consensus size: 32
11935 GTTCTACAAA
* *
11945 ACATATAGACAGAATTACCTATTTCTTTCGGG
1 ACATATGGACAAAATTACCTATTTCTTTCGGG
* *
11977 -CATATGGACAAAATTACCTATGTCTTTTGGG
1 ACATATGGACAAAATTACCTATTTCTTTCGGG
* ** *
12008 ACATATGGACAATA-TACCTATGTTC-TAAGGA
1 ACATATGGACAAAATTACCTAT-TTCTTTCGGG
** *
12039 ACATATGGAC-AGTTTACCTAGGTTC-TTCGGG
1 ACATATGGACAAAATTACCTA-TTTCTTTCGGG
*
12070 ACCTATGGACA
1 ACATATGGACA
12081 GTTGTCGAGG
Statistics
Matches: 83, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.01
31 68 0.82
32 14 0.17
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
ACATATGGACAAAATTACCTATTTCTTTCGGG
Found at i:12018 original size:32 final size:32
Alignment explanation
Indices: 11945--12030 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 32
11935 GTTCTACAAA
* * *
11945 ACATATAGACAGAATTACCTATTTCTTTCGGG
1 ACATATGGACAAAATTACCTATGTCTTTCGGG
*
11977 -CATATGGACAAAATTACCTATGTCTTTTGGG
1 ACATATGGACAAAATTACCTATGTCTTTCGGG
*
12008 ACATATGGACAATA-TACCTATGT
1 ACATATGGACAAAATTACCTATGT
12031 TCTAAGGAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 36 0.75
32 12 0.25
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (32 bp):
ACATATGGACAAAATTACCTATGTCTTTCGGG
Found at i:12754 original size:19 final size:19
Alignment explanation
Indices: 12728--12777 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
12718 TATTGTTTAT
12728 TACTGTTCATA-CAGTATAG
1 TACTGTTCATAGC-GTATAG
*
12747 TGCTGTTCATAGCGTATAG
1 TACTGTTCATAGCGTATAG
12766 TACTGTTCATAG
1 TACTGTTCATAG
12778 ATACATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (19 bp):
TACTGTTCATAGCGTATAG
Found at i:13640 original size:22 final size:23
Alignment explanation
Indices: 13615--13659 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
13605 TGTAGCAGGG
* *
13615 TACTGTTC-ACGGTATTGTTCAA
1 TACTATTCAACGGTACTGTTCAA
13637 TACTATTCATACGGTACTGTTCA
1 TACTATTCA-ACGGTACTGTTCA
13660 CTGTTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (23 bp):
TACTATTCAACGGTACTGTTCAA
Found at i:14183 original size:21 final size:20
Alignment explanation
Indices: 14157--14214 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
14147 ATCCTCTAGC
*
14157 AAAAGGATTGATCCCTTTGA
1 AAAAGGATCGATCCCTTTGA
* *
14177 CCAAAGGATCGATCCCCTTGA
1 -AAAAGGATCGATCCCTTTGA
14198 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
14215 GGATAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTTGA
Found at i:14202 original size:41 final size:41
Alignment explanation
Indices: 14137--14214 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
14127 ATTTTTTGCT
* * *
14137 CAAACGATCGATCCTCTAGCAAAAGGATTGATCCCTTTGAC
1 CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTTTGAC
* *
14178 CAAAGGATCGATCCCCTTGAAAAAGGATCGATCCCTT
1 CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTT
14215 GGATAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTTTGAC
Found at i:14204 original size:20 final size:20
Alignment explanation
Indices: 14142--14212 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
14132 TTGCTCAAAC
* * *
14142 GATCGATCCTCTAGCAAAAG
1 GATCGATCCCCTTGAAAAAG
* * *
14162 GATTGATCCCTTTGACCAAAG
1 GATCGATCCCCTTGA-AAAAG
14183 GATCGATCCCCTTGAAAAAG
1 GATCGATCCCCTTGAAAAAG
14203 GATCGATCCC
1 GATCGATCCC
14213 TTGGATAACA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 24 0.59
21 17 0.41
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GATCGATCCCCTTGAAAAAG
Found at i:16725 original size:2 final size:2
Alignment explanation
Indices: 16718--16750 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16708 ATGTAAATCG
16718 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16751 GAAAATCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20736 original size:12 final size:12
Alignment explanation
Indices: 20721--20754 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20711 TCCACATTTT
20721 TTTATATATACA
1 TTTATATATACA
*
20733 TTTATATATATA
1 TTTATATATACA
*
20745 TATATATATA
1 TTTATATATA
20755 GTTTACAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTATATATACA
Found at i:20866 original size:36 final size:36
Alignment explanation
Indices: 20766--21052 Score: 218
Period size: 37 Copynumber: 7.5 Consensus size: 36
20756 TTTACAGATG
* *
20766 ATTTTTGAAAATACGTATATGATATATAGTTTTTAAAAC
1 ATTTTTGAAAAT---TATATAATATATAATTTTTAAAAC
* *
20805 ATTTTTTGAAACTATATATATTATATAATTTTTAAAAC
1 A-TTTTTGAAAAT-TATATAATATATAATTTTTAAAAC
* *
20843 ATTTTCGAAAATTATATAATATATAGTTTTTAAAAC
1 ATTTTTGAAAATTATATAATATATAATTTTTAAAAC
* * * *
20879 ATTTTTAAAAAATTATATATTATATAATTTTT-GAAT
1 ATTTTT-GAAAATTATATAATATATAATTTTTAAAAC
* * * *
20915 TTTTTTTAAAATATATATAATATATAGTTTTTTAAATC
1 ATTTTTGAAAAT-TATATAATATATA-ATTTTTAAAAC
* * *
20953 A-TTTTGAAAACTTATATAATATATTATTTTGGAAAAA
1 ATTTTTGAAAA-TTATATAATATATAATTTT-TAAAAC
* *
20990 ATATTTATGAAAACAATTATATATTATATAGTTTTTCAAAAAC
1 AT-TTT-TG--AA-AATTATATAATATATAATTTTT--AAAAC
*
21033 ATGTTTGAAAATATATATAA
1 ATTTTTGAAAAT-TATATAA
21053 ATTTAAAATA
Statistics
Matches: 196, Mismatches: 36, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
35 5 0.03
36 50 0.26
37 60 0.31
38 27 0.14
39 12 0.06
40 12 0.06
41 2 0.01
42 20 0.10
43 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (36 bp):
ATTTTTGAAAATTATATAATATATAATTTTTAAAAC
Found at i:20932 original size:73 final size:74
Alignment explanation
Indices: 20766--21138 Score: 273
Period size: 73 Copynumber: 5.0 Consensus size: 74
20756 TTTACAGATG
* **
20766 ATTTTTGAAAATACGTATATGATATATAGTTTTTAAAACATTTTTTGAAACTATATATATTATAT
1 ATTTTTGAAAATA--TATATAATATATAGTTTTTAAAACATTTTTAAAAACT-TATATATTATAT
20831 AATTTTTAAAAC
63 AATTTTTAAAAC
* *
20843 ATTTTCGAAAAT-TATATAATATATAGTTTTTAAAACATTTTTAAAAAATTATATATTATATAAT
1 ATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTAAAAACTTATATATTATATAAT
* *
20907 TTTT-GAAT
66 TTTTAAAAC
* * * * * *
20915 TTTTTTTAAAATATATATAATATATAGTTTTTTAAATCA-TTTTGAAAACTTATATAATATATTA
1 ATTTTTGAAAATATATATAATATATAG-TTTTTAAAACATTTTTAAAAACTTATATATTATATAA
* *
20979 TTTTGGAAAAA
65 TTTT-TAAAAC
* * * *
20990 ATATTTATGAAAACAATTATATATTATATAGTTTTTCAAAAACATGTTT-GAAA---ATATA-TA
1 AT-TTT-TGAAAA-TA-TATATAATATATAGTTTTT--AAAACATTTTTAAAAACTTATATATTA
*
21050 TA-AA--TTTAAAAT
60 TATAATTTTTAAAAC
* * * * * * **
21062 ATTTTTTTCAAAATATATTATATTATATGGTTTTGAAAACCATTTTTAAAATCATATATAAAATA
1 A--TTTTTGAAAATATA-TATAATATATAGTTTTTAAAA-CATTTTTAAAAACTTATATATTATA
*
21127 TAATTTTAAAAA
62 TAATTTTTAAAA
21139 ATATATTTAT
Statistics
Matches: 236, Mismatches: 37, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
69 4 0.02
70 8 0.03
71 18 0.08
72 21 0.09
73 63 0.27
74 49 0.21
75 7 0.03
76 9 0.04
77 21 0.09
78 12 0.05
79 13 0.06
80 8 0.03
81 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (74 bp):
ATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTAAAAACTTATATATTATATAAT
TTTTAAAAC
Found at i:22450 original size:12 final size:13
Alignment explanation
Indices: 22433--22464 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
22423 TCAAATCGAA
22433 TAATTTTAA-TTT
1 TAATTTTAATTTT
22445 TAATTTTAATTTT
1 TAATTTTAATTTT
22458 TAATTTT
1 TAATTTT
22465 TGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:22465 original size:7 final size:6
Alignment explanation
Indices: 22433--22464 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
22423 TCAAATCGAA
22433 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
22465 TGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:23633 original size:20 final size:20
Alignment explanation
Indices: 23608--23645 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23598 TTTGGTTCAC
23608 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
23628 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
23646 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:23869 original size:33 final size:34
Alignment explanation
Indices: 23806--23870 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
23796 AAAATATTTA
*
23806 TATATTTTCTTTAAAAAATTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAATTAAAATCATAAAATT
*
23840 TATATTTT-TTTACAAAATTGAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAATT-AAAATCATAAAA
23871 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (34 bp):
TATATTTTCTTTAAAAAATTAAAATCATAAAATT
Found at i:29766 original size:2 final size:2
Alignment explanation
Indices: 29759--29826 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
29749 AAATATTTTA
29759 AT AT AT AT AT AT 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 AT AT AT AT AT AT
29801 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
29827 TGAAATCCAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30429 original size:15 final size:15
Alignment explanation
Indices: 30389--30430 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
30379 AAAAAATAAC
*
30389 ATTTTAATATATTTAT
1 ATTTTAAT-TTTTTAT
30405 A-TTTATATTTTTTAT
1 ATTTTA-ATTTTTTAT
30420 ATTTTAATTTT
1 ATTTTAATTTT
30431 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTAATTTTTTAT
Found at i:31958 original size:21 final size:22
Alignment explanation
Indices: 31911--31959 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
31901 TTGGGGTAAG
*
31911 TGGGTGGCTTAGTCGGAGGAGT
1 TGGGTGGCTTAGTCGGAGGACT
*
31933 T-GGTGGCTTGGTCGGAGG-CT
1 TGGGTGGCTTAGTCGGAGGACT
31953 TGGGTGG
1 TGGGTGG
31960 AGGATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.08, C:0.10, G:0.53, T:0.29
Consensus pattern (22 bp):
TGGGTGGCTTAGTCGGAGGACT
Found at i:32012 original size:39 final size:38
Alignment explanation
Indices: 31933--32322 Score: 232
Period size: 39 Copynumber: 10.2 Consensus size: 38
31923 TCGGAGGAGT
* * * **
31933 TGGTGGCTTGGTCGGAGGCTTGGGTGGA-G-GATAAGT
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAGATAAAC
* *
31969 TGGTGGCTTGGTTGGCGCCTTGGGTGGTGGAGAGTAAAC
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAGA-TAAAC
* * * * * **
32008 TGGTGGCTTGGGTGGTGCTTTTGGAGGAGGACCATAAGT
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGA-GATAAAC
*
32047 TGGAGGCTTGGTTGGTGCCTTGGGTGGAGG-G-TAAAC
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAGATAAAC
** * * **
32083 TGGTGGCTTAGG-TGGTGTTTTTGGCGGAGGAGCATAAGT
1 TGGTGGCTT-GGTTGGTGCCTTGGGTGGAGGAG-ATAAAC
* *
32122 TGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGGGTAAAC
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGA-GATAAAC
* * * *** * * * **
32161 CGGTGACTTGGGTGGTATTTTTGGCGGAGGAGCATGAGT
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAG-ATAAAC
* *
32200 TGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGAGTAGAC
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAGA-TAAAC
* * * * * ***
32239 CGGTGGCTTGGGTGGTGCTTTTGGAGGAGGAGCATAGGT
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAG-ATAAAC
* * *
32278 TGGTGGCTTGGTTGGAGCCTTGGGTGGTGGTGGATAAAC
1 TGGTGGCTTGGTTGGTGCCTTGGGTGGAGG-AGATAAAC
*
32317 AGGTGG
1 TGGTGG
32323 AGCCGTCGGG
Statistics
Matches: 262, Mismatches: 78, Indels: 25
0.72 0.21 0.07
Matches are distributed among these distances:
36 49 0.19
37 4 0.02
38 6 0.02
39 199 0.76
40 4 0.02
ACGTcount: A:0.14, C:0.09, G:0.47, T:0.30
Consensus pattern (38 bp):
TGGTGGCTTGGTTGGTGCCTTGGGTGGAGGAGATAAAC
Found at i:32055 original size:78 final size:78
Alignment explanation
Indices: 31958--32307 Score: 472
Period size: 78 Copynumber: 4.5 Consensus size: 78
31948 AGGCTTGGGT
* * *
31958 GGAGGATAAGTTGGTGGCTTGGTTGGCGCCTTGGGTGGTGGAGAGTAAACTGGTGGCTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGGAGAGTAAACCGGTGGCTTGGGTGG
32023 TGCTTTTGGAGGA
66 TGCTTTTGGAGGA
* * * * *
32036 GGACCATAAGTTGGAGGCTTGGTTGGTGCCTT--G-GGTGGAGGGTAAACTGGTGGCTTAGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGGAGAGTAAACCGGTGGCTTGGGTGG
* *
32098 TGTTTTTGGCGGA
66 TGCTTTTGGAGGA
* * * *
32111 GGAGCATAAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGGGTAAACCGGTGACTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGGAGAGTAAACCGGTGGCTTGGGTGG
** *
32176 TATTTTTGGCGGA
66 TGCTTTTGGAGGA
* * * *
32189 GGAGCATGAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGAGTAGACCGGTGGCTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGGAGAGTAAACCGGTGGCTTGGGTGG
32254 TGCTTTTGGAGGA
66 TGCTTTTGGAGGA
* *
32267 GGAGCATAGGTTGGTGGCTTGGTTGGAGCCTTGGGTGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGG
32308 TGGATAAACA
Statistics
Matches: 241, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
75 67 0.28
76 1 0.00
77 1 0.00
78 172 0.71
ACGTcount: A:0.14, C:0.09, G:0.47, T:0.30
Consensus pattern (78 bp):
GGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGTGGAGAGTAAACCGGTGGCTTGGGTGG
TGCTTTTGGAGGA
Found at i:32175 original size:153 final size:156
Alignment explanation
Indices: 31958--32304 Score: 484
Period size: 153 Copynumber: 2.2 Consensus size: 156
31948 AGGCTTGGGT
* * * * *
31958 GGAGGATAAGTTGGTGGCTTGGTTGGCGCCTTGGGTGGTGGAGAGTAAACTGGTGGCTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGAGTAAACCGGTGACTTGGGTGG
* *
32023 TGCTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGA-G-G-GTAAACTG
66 TACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGAGAGTAAACCG
* *
32085 GTGGCTTAGGTGGTGTTTTTGGCGGA
131 GTGGCTTAGGTGGTGCTTTTGGAGGA
* * *
32111 GGAGCATAAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGGGTAAACCGGTGACTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGAGTAAACCGGTGACTTGGGTGG
* * * * * * *
32176 TATTTTTGGCGGAGGAGCATGAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAGAGTAGACCG
66 TACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGAGAGTAAACCG
*
32241 GTGGCTTGGGTGGTGCTTTTGGAGGA
131 GTGGCTTAGGTGGTGCTTTTGGAGGA
*
32267 GGAGCATAGGTTGGTGGCTTGGTTGGAGCCTTGGGTGG
1 GGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTGGGTGG
32305 TGGTGGATAA
Statistics
Matches: 169, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
153 103 0.61
154 1 0.01
155 1 0.01
156 64 0.38
ACGTcount: A:0.14, C:0.10, G:0.47, T:0.30
Consensus pattern (156 bp):
GGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGAGTAAACCGGTGACTTGGGTGG
TACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGAGAGTAAACCG
GTGGCTTAGGTGGTGCTTTTGGAGGA
Found at i:32818 original size:17 final size:18
Alignment explanation
Indices: 32793--32829 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
32783 TAATTATATA
32793 TATATTATTTTTATT-ATT
1 TATATTA-TTTTATTAATT
32811 TATA-TATTTTATTAATT
1 TATATTATTTTATTAATT
32828 TA
1 TA
32830 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATATTATTTTATTAATT
Found at i:33256 original size:41 final size:41
Alignment explanation
Indices: 33189--33284 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
33179 GTGCGGACCC
* * *
33189 GGGGGCGCGCCTTAGGCCACCAAGGAGTATAGCGTAGGGCA
1 GGGGTCGCGCCTTAGGCCACCAAGGAGTATAGCGCAAGGCA
* *
33230 GGTGTCGCGCCTTAGGCCACCTAGGAGTATAGCGCAAGGCA
1 GGGGTCGCGCCTTAGGCCACCAAGGAGTATAGCGCAAGGCA
33271 GGGGTCGCGCCTTA
1 GGGGTCGCGCCTTA
33285 CCTTTAACAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.26, G:0.39, T:0.16
Consensus pattern (41 bp):
GGGGTCGCGCCTTAGGCCACCAAGGAGTATAGCGCAAGGCA
Found at i:36865 original size:34 final size:33
Alignment explanation
Indices: 36827--36893 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
36817 GTAATAAACA
36827 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
36861 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
36894 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:39200 original size:17 final size:17
Alignment explanation
Indices: 39178--39211 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39168 AAAAAATTAA
39178 TTAAATAAAATAAATAC
1 TTAAATAAAATAAATAC
*
39195 TTAAATAAATTAAATAC
1 TTAAATAAAATAAATAC
39212 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAATAAAATAAATAC
Found at i:43595 original size:18 final size:18
Alignment explanation
Indices: 43574--43608 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43564 CAAACGTATC
43574 TTTTTATAATATTTATAT
1 TTTTTATAATATTTATAT
*
43592 TTTTTATAATGTTTATA
1 TTTTTATAATATTTATA
43609 AAATAAAAAA
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTATAATATTTATAT
Found at i:46658 original size:17 final size:17
Alignment explanation
Indices: 46636--46690 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
46626 GATGAGTTTT
46636 AAAAAATATTTTTTTAA
1 AAAAAATATTTTTTTAA
46653 AAAAAAT-TATTTTTTAA
1 AAAAAATAT-TTTTTTAA
**
46670 TTTAAAATA-TTTTTTAA
1 -AAAAAATATTTTTTTAA
46687 AAAA
1 AAAA
46691 TAGTTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 3 0.10
17 23 0.74
18 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAAAATATTTTTTTAA
Found at i:49165 original size:188 final size:191
Alignment explanation
Indices: 48955--49340 Score: 681
Period size: 188 Copynumber: 2.0 Consensus size: 191
48945 CGACCCGACA
48955 CGACCCGAATATATGAATTATAAACTCGACCCGACCCGAAATAATAAAAAAATTGTTTTTATTCA
1 CGACCCGAATATATGAATTATAAACTCGACCCGACCCGAAATAATAAAAAAATTGTTTTTATTCA
* *
49020 ATAAAAACAGTGACTTAATT-AAAAAAATTATATATATAGGGGTATTATTGTAATTATTTCTAAA
66 ATAAAAACAGTGACTTAATTAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAA
*
49084 TATATAAGGTAAAATTATATA-TTTTTT-CGGGTCGGGAC-GAGTATTTTTCACCCTAAACC
131 TATATAAGGTAAAATTATATATTTTTTTCCAGGTCGGGACGGA-TATTTTTCACCCTAAACC
49143 CGACCCGAATATATGAATTATAAACTCGACCCGACCCGAAATAATAAAAAAATTGTTTTTATTCA
1 CGACCCGAATATATGAATTATAAACTCGACCCGACCCGAAATAATAAAAAAATTGTTTTTATTCA
49208 ATAAAAACAGTGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAA
66 ATAAAAACAGTGACTTAATT-AAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAA
*
49273 ATATATAAGGTAAAATTATATATTTTTTTCCAGGTCGGGTCGGATATTTTTCACCCTAAACC
130 ATATATAAGGTAAAATTATATATTTTTTTCCAGGTCGGGACGGATATTTTTCACCCTAAACC
*
49335 TGACCC
1 CGACCC
49341 CGACCCGAAT
Statistics
Matches: 188, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
188 85 0.45
190 63 0.34
191 6 0.03
192 32 0.17
193 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (191 bp):
CGACCCGAATATATGAATTATAAACTCGACCCGACCCGAAATAATAAAAAAATTGTTTTTATTCA
ATAAAAACAGTGACTTAATTAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAA
TATATAAGGTAAAATTATATATTTTTTTCCAGGTCGGGACGGATATTTTTCACCCTAAACC
Found at i:49398 original size:26 final size:27
Alignment explanation
Indices: 49346--49398 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
49336 GACCCCGACC
*
49346 CGAATATCACACTTAAAAAAACCTGACT
1 CGAATATCAAACTTAAAAAAA-CTGACT
49374 CGAATATCAAACTTAAAAAAA-TGAC
1 CGAATATCAAACTTAAAAAAACTGAC
49399 CCGACCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
28 20 0.83
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.21
Consensus pattern (27 bp):
CGAATATCAAACTTAAAAAAACTGACT
Found at i:49893 original size:23 final size:21
Alignment explanation
Indices: 49843--49893 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
49833 TATGTCTGTT
* *
49843 TTATGAAAAATAATTTATTTG
1 TTATAAAAAATAATTTATTTA
49864 TTAATAAAAAATAAATTTTATTTA
1 TT-ATAAAAAAT-AA-TTTATTTA
49888 TTATAA
1 TTATAA
49894 TTATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 6 0.24
24 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TTATAAAAAATAATTTATTTA
Found at i:50046 original size:28 final size:30
Alignment explanation
Indices: 49994--50052 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
49984 CACAATGTTC
49994 AATAATATTAAAAATACATATTTATATTTT
1 AATAATATTAAAAATACATATTTATATTTT
*
50024 AATAATA-TATAAATA-ATATTTATATTTT
1 AATAATATTAAAAATACATATTTATATTTT
50052 A
1 A
50053 GAAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 14 0.50
29 7 0.25
30 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAATATTAAAAATACATATTTATATTTT
Found at i:57136 original size:23 final size:24
Alignment explanation
Indices: 57094--57146 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
57084 CGTTGGTATT
**
57094 TTTA-TTATTTTTTATATAATATC
1 TTTATTTATTTTTTATATAATAAA
57117 TTTATTTATTTATTT-T-TAATAAA
1 TTTATTTATTT-TTTATATAATAAA
57140 TTTATTT
1 TTTATTT
57147 GATTGTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 16 0.62
24 7 0.27
25 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTATTTTTTATATAATAAA
Found at i:58196 original size:21 final size:22
Alignment explanation
Indices: 58172--58220 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
58162 AACTCACACA
58172 TATTTA-TTTAAATTTAAAT-TT
1 TATTTATTTTAAA-TTAAATATT
58193 TATTTATTTTAAATTAAATAATT
1 TATTTATTTTAAATTAAAT-ATT
58216 TATTT
1 TATTT
58221 TTTCATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.48
22 6 0.24
23 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATTTTAAATTAAATATT
Found at i:58203 original size:16 final size:17
Alignment explanation
Indices: 58174--58207 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58164 CTCACACATA
58174 TTTATTTAAATTTAAAT
1 TTTATTTAAATTTAAAT
*
58191 TTTATTT-ATTTTAAAT
1 TTTATTTAAATTTAAAT
58207 T
1 T
58208 AAATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTTAAATTTAAAT
Done.