Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007854.1 Hibiscus syriacus cultivar Beakdansim tig00110214_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: 276407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:182172 original size:21 final size:20
Alignment explanation
Indices: 182148--182218 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
182138 TTACATTATA
182148 TTTTTATTGAATTTTATTCAT
1 TTTTTATT-AATTTTATTCAT
* *
182169 TTTTAATTCATTTTTATTACA-
1 TTTTTATT-AATTTTATT-CAT
*
182190 TTTTTATTTATTTTA-T-AT
1 TTTTTATTAATTTTATTCAT
182208 TTTTTA-TAATT
1 TTTTTATTAATT
182219 AATATTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
17 5 0.12
18 6 0.15
19 1 0.02
20 5 0.12
21 22 0.54
22 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTTATTAATTTTATTCAT
Found at i:182177 original size:11 final size:10
Alignment explanation
Indices: 182147--182208 Score: 70
Period size: 11 Copynumber: 5.9 Consensus size: 10
182137 TTTACATTAT
*
182147 ATTTTTATTG
1 ATTTTTATTC
*
182157 AATTTTATTC
1 ATTTTTATTC
182167 ATTTTTAATTC
1 ATTTTT-ATTC
182178 ATTTTTATTAC
1 ATTTTTATT-C
*
182189 ATTTTTATTT
1 ATTTTTATTC
182199 ATTTTATATT
1 ATTTT-TATT
182209 TTTTATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
10 21 0.47
11 24 0.53
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:183981 original size:13 final size:13
Alignment explanation
Indices: 183963--183989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
183953 AATTACTCCC
183963 CCTTACTTTAACA
1 CCTTACTTTAACA
183976 CCTTACTTTAACA
1 CCTTACTTTAACA
183989 C
1 C
183990 TTCTCCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (13 bp):
CCTTACTTTAACA
Found at i:186108 original size:20 final size:20
Alignment explanation
Indices: 186071--186109 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
186061 AGATTGAGTG
* * *
186071 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
186091 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
186110 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:193112 original size:15 final size:15
Alignment explanation
Indices: 193092--193256 Score: 145
Period size: 15 Copynumber: 10.5 Consensus size: 15
193082 TAATAAGGTT
193092 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
193107 ATTTATTTAAAAATA
1 ATTTATTTTAAAATA
*
193122 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
193137 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
193152 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
193167 AATTATTATAAAATATCGA
1 ATTTATT-TTAAA-AT--A
193186 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
193204 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
193218 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
193236 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
193250 ATTTATT
1 ATTTATT
193257 AGTATGGATT
Statistics
Matches: 125, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
14 22 0.18
15 70 0.56
16 6 0.05
17 3 0.02
18 11 0.09
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:193243 original size:32 final size:32
Alignment explanation
Indices: 193204--193279 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
193194 TTTTAAAATA
193204 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
193236 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
193268 ATTTGTTTTAAA
1 ATTTATTTTAAA
193280 ATATGAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:193364 original size:22 final size:22
Alignment explanation
Indices: 193339--193533 Score: 147
Period size: 22 Copynumber: 8.0 Consensus size: 22
193329 AATTTATTAG
193339 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
193361 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
193385 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
193415 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
193437 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
193461 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
193491 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
193513 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
193534 TAATTTATTA
Statistics
Matches: 140, Mismatches: 13, Indels: 40
0.73 0.07 0.21
Matches are distributed among these distances:
22 68 0.49
23 4 0.03
24 4 0.03
25 4 0.03
26 20 0.14
27 4 0.03
28 20 0.14
29 4 0.03
30 4 0.03
31 4 0.03
32 4 0.03
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:193373 original size:54 final size:54
Alignment explanation
Indices: 193309--193904 Score: 364
Period size: 54 Copynumber: 11.3 Consensus size: 54
193299 TGTAGTTGTG
193309 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
193363 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
*
193417 TGAATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTT-AAATAA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-A
** ** * ** * * *
193461 TTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAAATA
1 TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
193515 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* * * * * ***
193568 ---ATTTATTT-GTATAGATTAATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA
1 TGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATA
** ** * ** * * *
193627 TGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATA
193681 TGGATTGATTTATTTT-AA-AA--TA-T-G-A---ATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* *
193725 TGGATTGATTTATTTTAAATAAATTATTAGTATAGATTGATTTATTTT-AAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* * * * * * ***
193778 ---ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA
1 TGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATA
193837 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
193891 TGGATTGATTTATT
1 TGGATTGATTTATT
193905 ATTGTAGTTG
Statistics
Matches: 421, Mismatches: 67, Indels: 108
0.71 0.11 0.18
Matches are distributed among these distances:
43 4 0.01
44 42 0.10
45 13 0.03
46 8 0.02
47 1 0.00
48 2 0.00
49 12 0.03
50 33 0.08
51 1 0.00
52 9 0.02
53 27 0.06
54 187 0.44
55 10 0.02
56 9 0.02
57 8 0.02
58 15 0.04
59 4 0.01
60 4 0.01
61 1 0.00
62 25 0.06
63 6 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
Found at i:193442 original size:76 final size:76
Alignment explanation
Indices: 193339--193989 Score: 737
Period size: 76 Copynumber: 8.3 Consensus size: 76
193329 AATTTATTAG
193339 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
193404 TTATTTTAAAA
66 TTATTTTAAAA
*
193415 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
193480 TTATTTTAAAA
66 TTATTTTAAAA
193491 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
193556 TTATTTTAAATAA
66 TTATTTT-AA-AA
* *
193569 TTTATTTGTATAGATTAATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTA
1 --TA--TG----GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTA
193627 TGGATTGATTTATTTTAAAA
57 TGGATTGATTTATTTTAAAA
** ** * ** * * * *
193647 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATT
1 TATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATT
193709 GATTTATTTTAAAA
63 GATTTATTTTAAAA
*
193723 TATGGATTGATTTATTTTAAATAAATTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTT--A-AAA-TA-T-G----GATTGATTTATTTTAAATAATTTATTAGT
*
193788 ATAGATTGATTTATTTTAAAA
56 ATGGATTGATTTATTTTAAAA
***
193809 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
193874 TGATTTATTTTAAAA
62 TGATTTATTTTAAAA
*** *
193889 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1 TATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
193954 TGATTTATTTTAAAA
62 TGATTTATTTTAAAA
193969 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
193990 TAATTTATTA
Statistics
Matches: 502, Mismatches: 37, Indels: 72
0.82 0.06 0.12
Matches are distributed among these distances:
69 4 0.01
70 18 0.04
71 1 0.00
72 3 0.01
73 1 0.00
74 2 0.00
75 1 0.00
76 187 0.37
77 7 0.01
78 6 0.01
79 3 0.01
80 169 0.34
81 4 0.01
82 4 0.01
84 6 0.01
85 11 0.02
86 70 0.14
87 2 0.00
88 2 0.00
89 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (76 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
TTATTTTAAAA
Found at i:193461 original size:210 final size:209
Alignment explanation
Indices: 193227--193855 Score: 862
Period size: 210 Copynumber: 3.0 Consensus size: 209
193217 AATTTATTAG
* *
193227 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTGTTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
*** *
193292 TTATTATTGTAGTTGTGTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
* * *
193357 AAAATATGGATTGATTTATTTTA-AATAATTTA-TT-AGTATGGATTGATTTA-T-TT-TA-AAA
127 AAAATA---ATTGATTT-GTATAGAATAATTTATTTAAATATGGATTGATTTATTATTGTAGAAA
193415 TATGAATTGATTTATTTTAAAA
188 TATGAATTGATTTATTTTAAAA
*
193437 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
193502 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
66 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * *** *
193566 TAATTTATTTGTATAGATTAATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
131 TAATTGATTTGTATAGAATAATTTA-TTT-AAATATGGATTGATTTATTATTGTAGAAATATGAA
193631 TTGATTTATTTTAAAA
194 TTGATTTATTTTAAAA
193647 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
* *
193712 TTATTTTAAAATATGGATTGATTTATTTTAAATAAATTATTAGTATAGATTGATTTATTTT-AAA
66 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * *** *
193776 TAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
131 TAATTGATTTGTATAGAATAATTTA-TTT-AAATATGGATTGATTTATTATTGTAGAAATATGAA
193841 TTGATTTATTTTAAA
194 TTGATTTATTTTAAA
193856 TAATTTATTA
Statistics
Matches: 390, Mismatches: 20, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
201 3 0.01
202 15 0.04
204 2 0.01
205 5 0.01
206 64 0.16
207 3 0.01
208 4 0.01
209 3 0.01
210 291 0.75
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (209 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
TAATTGATTTGTATAGAATAATTTATTTAAATATGGATTGATTTATTATTGTAGAAATATGAATT
GATTTATTTTAAAA
Found at i:193587 original size:18 final size:18
Alignment explanation
Indices: 193534--193593 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
193524 TTATTTTAAA
* *
193534 TAATTTATTAGTATGGAT
1 TAATTTATTTGTATAGAT
*
193552 TGATTTATTT-TA-A-A-
1 TAATTTATTTGTATAGAT
193566 TAATTTATTTGTATAGAT
1 TAATTTATTTGTATAGAT
193584 TAATTTATTT
1 TAATTTATTT
193594 TAAAATATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.26
15 3 0.09
16 1 0.03
17 3 0.09
18 18 0.53
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TAATTTATTTGTATAGAT
Found at i:193606 original size:22 final size:22
Alignment explanation
Indices: 193581--193743 Score: 128
Period size: 22 Copynumber: 6.8 Consensus size: 22
193571 TATTTGTATA
*
193581 GATTAATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
***
193603 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
193629 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
193651 GATTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
193679 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
*
193705 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
193727 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
193744 TAAATTATTA
Statistics
Matches: 113, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
22 53 0.47
23 5 0.04
24 6 0.05
25 5 0.04
26 24 0.21
27 2 0.02
28 10 0.09
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:193685 original size:80 final size:82
Alignment explanation
Indices: 193599--193999 Score: 418
Period size: 80 Copynumber: 5.0 Consensus size: 82
193589 TATTTTAAAA
*
193599 TATGGATTGATTTA-TT-AT-TGTAGTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA
1 TATGGATTGATTTATTTAATATTTA-TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA
193661 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
*
193679 TATGGATTGATTTATTTTAA-A---A---TATGAATTGATTTATTTTAAAATATGGATTGATTTA
1 TATGGATTGATTTA-TTTAATATTTATTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA
*
193737 TTTTAAATAAATTATTAG
65 TTTTAAATAATTTATTAG
* *
193755 TATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTT-AAT-ATTTA-TTGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
193820 TTA--TT--AT--TGTAGTT-G
62 TTATTTTAAATAATTTA-TTAG
193835 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTT-AAT-ATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTGAT
*
193900 TTA--TT--AT--TGTAGTT-G
62 TTATTTTAAATAATTTA-TTAG
*
193915 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTT-AAT-ATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTGAT
193980 TTATTTTAAATAATTTATTA
62 TTATTTTAAATAATTTATTA
194000 TTGTAGTTGT
Statistics
Matches: 287, Mismatches: 11, Indels: 40
0.85 0.03 0.12
Matches are distributed among these distances:
76 69 0.24
77 2 0.01
79 3 0.01
80 160 0.56
81 2 0.01
82 7 0.02
83 1 0.00
84 4 0.01
85 2 0.01
86 37 0.13
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (82 bp):
TATGGATTGATTTATTTAATATTTATTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAG
Found at i:193762 original size:28 final size:30
Alignment explanation
Indices: 193730--193807 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 30
193720 AAATATGGAT
193730 TGATTTATTTTAAATAAATTATTAGTATAGA
1 TGATTTATTTTAAATAAATTATTAGTATA-A
* *
193761 TTGATTTATTTTAAATAATTTATTTGTATAGA
1 -TGATTTATTTTAAATAAATTATTAGTATA-A
193793 TTGATTTATTTTAAA
1 -TGATTTATTTTAAA
193808 ATATGGATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (30 bp):
TGATTTATTTTAAATAAATTATTAGTATAA
Found at i:193799 original size:18 final size:18
Alignment explanation
Indices: 193748--193803 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
193738 TTTAAATAAA
*
193748 TTATTAGTATAGATTGAT
1 TTATTTGTATAGATTGAT
*
193766 TTATTT-TA-A-A-TAAT
1 TTATTTGTATAGATTGAT
193780 TTATTTGTATAGATTGAT
1 TTATTTGTATAGATTGAT
193798 TTATTT
1 TTATTT
193804 TAAAATATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
16 2 0.06
17 3 0.10
18 14 0.45
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TTATTTGTATAGATTGAT
Found at i:193881 original size:18 final size:18
Alignment explanation
Indices: 193858--193905 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
193848 ATTTTAAATA
*
193858 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
193876 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
193898 ATTTATTA
1 ATTTATTA
193906 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:194115 original size:16 final size:16
Alignment explanation
Indices: 194094--194132 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
194084 AAAAAATCAA
194094 TTTATTTATATTTCAG
1 TTTATTTATATTTCAG
*
194110 TTTATTTATATTTTAG
1 TTTATTTATATTTCAG
*
194126 TTCATTT
1 TTTATTT
194133 TAGCAGTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (16 bp):
TTTATTTATATTTCAG
Found at i:196654 original size:2 final size:2
Alignment explanation
Indices: 196647--196681 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
196637 AAATTATTAC
196647 AT AT AT AT AT 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 AT AT AT AT AT A
196682 AAAGTTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:199070 original size:37 final size:37
Alignment explanation
Indices: 199020--199094 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
199010 TGCATGTTCA
199020 AAATTTTCTTAGCCGATTGACAATGAACACTCACTCT
1 AAATTTTCTTAGCCGATTGACAATGAACACTCACTCT
199057 AAATTTTCTTAGCCGATTGACAATGAACACTCACTCT
1 AAATTTTCTTAGCCGATTGACAATGAACACTCACTCT
199094 A
1 A
199095 GAGATGCAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (37 bp):
AAATTTTCTTAGCCGATTGACAATGAACACTCACTCT
Found at i:205888 original size:24 final size:21
Alignment explanation
Indices: 205852--205919 Score: 136
Period size: 21 Copynumber: 3.2 Consensus size: 21
205842 ACAGCAGGAA
205852 GGCCTCATCATCATCAGTACC
1 GGCCTCATCATCATCAGTACC
205873 GGCCTCATCATCATCAGTACC
1 GGCCTCATCATCATCAGTACC
205894 GGCCTCATCATCATCAGTACC
1 GGCCTCATCATCATCAGTACC
205915 GGCCT
1 GGCCT
205920 ACTGCAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (21 bp):
GGCCTCATCATCATCAGTACC
Found at i:209064 original size:2 final size:2
Alignment explanation
Indices: 209057--209081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
209047 GGCCGGTCAT
209057 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
209082 TCATTGATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:217201 original size:32 final size:32
Alignment explanation
Indices: 217160--217327 Score: 164
Period size: 32 Copynumber: 5.0 Consensus size: 32
217150 CATATATATA
217160 ATATATAATTTTTAAAATCATTTTGAAAA-ATT
1 ATATATAATTTTTAAAA-CATTTTGAAAACATT
217192 ATATATAATTTTTGAAAACATTTTGAAAACA-T
1 ATATATAATTTTT-AAAACATTTTGAAAACATT
* *
217224 ATATTATAGTTTTGAAAACATTTTGAAAACATTTAT
1 ATA-TATAATTTTTAAAACATTTTGAAAACA--T-T
*
217260 ATATTATATAGTTTTTAAAACGTTTTTGAAAAC-TT
1 ATA-TATA-A-TTTTTAAAAC-ATTTTGAAAACATT
*
217295 ATATA-ATATTTTTGAAAACATGTTGAAAACATT
1 ATATATA-ATTTTT-AAAACATTTTGAAAACATT
217328 CGTATATTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 23
0.80 0.05 0.16
Matches are distributed among these distances:
32 59 0.50
33 23 0.20
34 2 0.02
35 4 0.03
36 10 0.09
38 9 0.08
39 10 0.09
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (32 bp):
ATATATAATTTTTAAAACATTTTGAAAACATT
Found at i:217217 original size:11 final size:11
Alignment explanation
Indices: 217201--217257 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
217191 TATATATAAT
217201 TTTTGAAAACA
1 TTTTGAAAACA
217212 TTTTGAAAACA
1 TTTTGAAAACA
* *
217223 TATATT--ATA-G
1 T-T-TTGAAAACA
217233 TTTTGAAAACA
1 TTTTGAAAACA
217244 TTTTGAAAACA
1 TTTTGAAAACA
217255 TTT
1 TTT
217258 ATATATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
8 2 0.05
9 1 0.03
10 3 0.08
11 28 0.76
12 1 0.03
13 2 0.05
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:217242 original size:103 final size:103
Alignment explanation
Indices: 217135--217326 Score: 280
Period size: 103 Copynumber: 1.9 Consensus size: 103
217125 TAAAAAAAAA
*
217135 AAAACGTTTTAAAAACATATATATAATATATAATTTTTAAAATC-ATTTTGAAAAATTATAT-AT
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAA-CGATTTTGAAAAATTATATAAT
*
217198 AATTTTTGAAAACATTTTGAAAACATATATTATAGTTTTG
65 -ATTTTTGAAAACATGTTGAAAACATATATTATAGTTTTG
* * * * * *
217238 AAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGAAAACTTATATAATA
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAAATTATATAATA
217303 TTTTTGAAAACATGTTGAAAACAT
66 TTTTTGAAAACATGTTGAAAACAT
217327 TCGTATATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 1 0.01
103 76 0.96
104 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (103 bp):
AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAAATTATATAATA
TTTTTGAAAACATGTTGAAAACATATATTATAGTTTTG
Found at i:217268 original size:71 final size:71
Alignment explanation
Indices: 217193--217388 Score: 232
Period size: 71 Copynumber: 2.7 Consensus size: 71
217183 TGAAAAATTA
* * *
217193 TATATAATTTTTGAAAACATTTTGAAAACATATATTATAGTTTTGAAAACATTTTGAAAACATTT
1 TATATAGTTTTTGAAAACATTTTGAAAACATATATTATAGTTTTGAAAACATGTTGAAAACATTC
217258 ATATAT
66 ATATAT
* * * *
217264 TATATAGTTTTT-AAAACGTTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATT
1 TATATAGTTTTTGAAAAC-ATTTTGAAAACATATATTATAGTTTTGAAAACATGTTGAAAACATT
*
217328 CGTATAT
65 CATATAT
** *
217335 TATATAGTTTAAGAAAAAACATTTTGAAAATTTATATATTATATGTTTTGAAAA
1 TATATAGTTTTTG--AAAACATTTTGAAAA--CATATATTATA-GTTTTGAAAA
217389 TATTATGTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
70 5 0.05
71 67 0.65
73 9 0.09
74 5 0.05
75 8 0.08
76 9 0.09
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (71 bp):
TATATAGTTTTTGAAAACATTTTGAAAACATATATTATAGTTTTGAAAACATGTTGAAAACATTC
ATATAT
Found at i:217383 original size:24 final size:27
Alignment explanation
Indices: 217356--217409 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
217346 AGAAAAAACA
217356 TTTTGAAAAT-TTA-TATAT-TATATG
1 TTTTGAAAATATTAGTATATATATATG
217380 TTTTGAAAATATTATGTATATATATATG
1 TTTTGAAAATATTA-GTATATATATATG
217408 TT
1 TT
217410 ATTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 10 0.38
25 3 0.12
27 5 0.19
28 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (27 bp):
TTTTGAAAATATTAGTATATATATATG
Found at i:217414 original size:20 final size:18
Alignment explanation
Indices: 217389--217436 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
217379 GTTTTGAAAA
*
217389 TATTATGTATATATATATGT
1 TATTATGTAT-TAT-TATAT
*
217409 TATTATTTATTATTATAT
1 TATTATGTATTATTATAT
217427 TATTAT-TATT
1 TATTATGTATT
217437 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 3 0.12
20 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TATTATGTATTATTATAT
Found at i:217431 original size:11 final size:11
Alignment explanation
Indices: 217388--217435 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
217378 TGTTTTGAAA
217388 ATATTATGTATAT
1 ATATTAT-TAT-T
*
217401 ATATATGTTATT
1 ATAT-TATTATT
217413 AT-TTATTATT
1 ATATTATTATT
217423 ATATTATTATT
1 ATATTATTATT
217434 AT
1 AT
217436 TTTTCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 8 0.26
11 11 0.35
12 3 0.10
13 7 0.23
14 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (11 bp):
ATATTATTATT
Found at i:218418 original size:13 final size:13
Alignment explanation
Indices: 218400--218431 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
218390 TTTGAGAGAC
218400 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
218413 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
218426 GAGAGA
1 GAGAGA
218432 CCAAATGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.47, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGCGCA
Found at i:218855 original size:13 final size:12
Alignment explanation
Indices: 218795--218860 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 12
218785 AAATTTAACC
218795 TTTTATTATTA-
1 TTTTATTATTAT
218806 TTTTATTATT-T
1 TTTTATTATTAT
* * *
218817 CTTTCTT-TCAT
1 TTTTATTATTAT
*
218828 TATTATTATTAT
1 TTTTATTATTAT
218840 TTTTATATATT-T
1 TTTTAT-TATTAT
218852 TTTT-TTATT
1 TTTTATTATT
218861 TATTAGCATT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.12
11 21 0.49
12 13 0.30
13 4 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:224289 original size:166 final size:164
Alignment explanation
Indices: 223853--224488 Score: 909
Period size: 166 Copynumber: 3.8 Consensus size: 164
223843 TGCAGCTTGG
* * *
223853 CTCAAGGCCAGAAGGGCTATCTG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
223917 ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCC-AAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
223981 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
224015 CTCAAGGCTATAAGGGTTATCTGTGA-CACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
1 CTCAAGGCTAGAAGGGTTATC--TGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
*
224079 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
64 GCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
224144 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
129 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
224180 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAG
1 CTCAAGGCTAGAAGGGTTATC--TGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
*
224245 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
64 GCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
* *
224310 ACACTCAGCTTCGAGGGCACACCATTTGCAGCATAA
129 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * ** * * * *
224346 CTTAAGTCAAGAAGGGTTATCTGCCCACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
1 CTCAAGGCTAGAAGGGTTATCTGACCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * * * **
224411 CACACCATTTGCAGCATAACTTAAGTCAAGAAGAGTTATCTGGCAACCAAAGACCTTCGAGTTCG
65 CACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCT-G---CCAAAGACCCCCGAGTTCG
* *
224476 ACTACGCTCAGCT
126 ATTACACTCAGCT
224489 CCAAGGCATA
Statistics
Matches: 434, Mismatches: 30, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
162 18 0.04
164 91 0.21
165 143 0.33
166 154 0.35
169 28 0.06
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:225201 original size:18 final size:18
Alignment explanation
Indices: 225158--225204 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
225148 TTATATGTAC
*
225158 ATACATACATATTTATAT
1 ATACATACATATTTATAA
*
225176 ATATATACATATTT-TAA
1 ATACATACATATTTATAA
225193 ACTACATACATA
1 A-TACATACATA
225205 ATATTGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (18 bp):
ATACATACATATTTATAA
Found at i:225336 original size:12 final size:12
Alignment explanation
Indices: 225319--225343 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
225309 AAATATATAT
225319 ATTTTTGAAAAC
1 ATTTTTGAAAAC
225331 ATTTTTGAAAAC
1 ATTTTTGAAAAC
225343 A
1 A
225344 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:225372 original size:11 final size:11
Alignment explanation
Indices: 225356--225380 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
225346 TATATTATAG
225356 TTTTGAAAACA
1 TTTTGAAAACA
225367 TTTTGAAAACA
1 TTTTGAAAACA
225378 TTT
1 TTT
225381 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:225376 original size:104 final size:105
Alignment explanation
Indices: 225257--225448 Score: 273
Period size: 104 Copynumber: 1.8 Consensus size: 105
225247 TTTAAAAAAA
*
225257 AAAACGTTTTAAAAACATATATATAATATATAATTTTTAAAATC-ATTTTGAAAA-ATATAT-AT
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAA-CGATTTTGAAAACATATATAAT
*
225319 ATTTTTGAAAACATTTTTGAAAACACATATATTATAGTTTTG
65 ATTTTTGAAAACA-TGTTGAAAACACATATATTATAGTTTTG
* * * * * *
225361 AAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGAAAACTTATATAATA
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAACATATATAATA
225426 TTTTTGAAAACATGTTGAAAACA
66 TTTTTGAAAACATGTTGAAAACA
225449 TTCGTATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
103 1 0.01
104 46 0.60
105 15 0.19
106 15 0.19
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (105 bp):
AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAACATATATAATA
TTTTTGAAAACATGTTGAAAACACATATATTATAGTTTTG
Found at i:225444 original size:71 final size:74
Alignment explanation
Indices: 225314--225467 Score: 217
Period size: 71 Copynumber: 2.1 Consensus size: 74
225304 TTGAAAAATA
* *
225314 TATATA-TTTTTGAAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACA
1 TATATAGTTTTTGAAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACA
*
225378 TTTATATAT
66 TTCATATAT
* * *
225387 TATATAGTTTTT-AAAACGTTTTTG-AAA-ACTTATATAATATTTTTGAAAACATGTTGAAAACA
1 TATATAGTTTTTGAAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACA
*
225449 TTCGTATAT
66 TTCATATAT
225458 TATATAGTTT
1 TATATAGTTT
225468 AAGAAAAAAC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
71 48 0.66
72 3 0.04
73 17 0.23
74 5 0.07
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (74 bp):
TATATAGTTTTTGAAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACA
TTCATATAT
Found at i:225483 original size:73 final size:70
Alignment explanation
Indices: 225326--225495 Score: 187
Period size: 71 Copynumber: 2.3 Consensus size: 70
225316 TATATTTTTG
* * * *
225326 AAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATA
1 AAAACA-TTTTG-AAA-ACTTATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
**
225391 TAGTTTTT
63 TAGTTTAA
* * *
225399 AAAACGTTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATA
1 AAAAC-ATTTTGAAAACTTATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATATA
225464 GTTTAAGAA
65 GTTT---AA
*
225473 AAAACATTTTGAAAATTTATATA
1 AAAACATTTTGAAAACTTATATA
225496 TTATATGTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
71 48 0.59
72 3 0.04
73 26 0.32
74 5 0.06
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.41
Consensus pattern (70 bp):
AAAACATTTTGAAAACTTATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATATAG
TTTAA
Found at i:225541 original size:3 final size:3
Alignment explanation
Indices: 225533--225561 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
225523 TATATATATG
225533 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
225562 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:226546 original size:13 final size:13
Alignment explanation
Indices: 226528--226559 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
226518 TTTGAGAGAC
226528 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
226541 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
226554 GAGAGA
1 GAGAGA
226560 CCAAATGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.47, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGCGCA
Found at i:226938 original size:11 final size:11
Alignment explanation
Indices: 226924--226996 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
226914 AAATTTAACC
226924 TTTTATTATTA
1 TTTTATTATTA
226935 TTTTATTATT-
1 TTTTATTATTA
* *
226945 TCTTTCTT-TCA
1 T-TTTATTATTA
226956 TTATTATTATTA
1 TT-TTATTATTA
226968 TTTT-TTATATA
1 TTTTATTAT-TA
* *
226979 TTTTTTTTTTA
1 TTTTATTATTA
226990 -TTTATTA
1 TTTTATTA
226997 GCATTTTGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
10 12 0.24
11 30 0.61
12 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:227557 original size:2 final size:2
Alignment explanation
Indices: 227550--227589 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
227540 GTCATATCAA
227550 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
227590 CCTACAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228770 original size:136 final size:136
Alignment explanation
Indices: 228488--228755 Score: 421
Period size: 135 Copynumber: 2.0 Consensus size: 136
228478 ATATTATATG
* * * *
228488 TTCTAAGATTTTTTCCTATTTAATAATAAAAATTCAAATATTTTTATAGTTTCCTCTCTTATATT
1 TTCTAAGATTTTTCCCTATTTAACAATAAAAATTCAAATAATTTTATAGTTTCCTCTCATATATT
* * * *
228553 TAAACCTAAAACCTTTGAAATAACAACTATTCTTTAAATATAGGTGTTTTGGTTGGTAATGTAAC
66 TAAACATAAAACCTCTCAAATAACAACTATTCTTTAAATAGAGGTGTTTTGGTTGGTAATGTAAC
228618 AAAGAA
131 AAAGAA
*
228624 TTCTAAGATTTTTCCCTATTTAACAATAAAAATTCAAATAATTTTATGGTTTCCTCTCATA-ATT
1 TTCTAAGATTTTTCCCTATTTAACAATAAAAATTCAAATAATTTTATAGTTTCCTCTCATATATT
* * *
228688 TGAACATAAAACCTCTCAAATAACAACTATTCTTTAAATCGAGGTGTTTTGGTTGGTACTGTAAC
66 TAAACATAAAACCTCTCAAATAACAACTATTCTTTAAATAGAGGTGTTTTGGTTGGTAATGTAAC
228753 AAA
131 AAA
228756 TTTTTTTAAG
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
135 64 0.53
136 56 0.47
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (136 bp):
TTCTAAGATTTTTCCCTATTTAACAATAAAAATTCAAATAATTTTATAGTTTCCTCTCATATATT
TAAACATAAAACCTCTCAAATAACAACTATTCTTTAAATAGAGGTGTTTTGGTTGGTAATGTAAC
AAAGAA
Found at i:229383 original size:31 final size:33
Alignment explanation
Indices: 229346--229406 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
229336 TTATAAGCGT
*
229346 TTTTAAAATTAA-TAA-TATTATTT-TATTTCAA
1 TTTTAAAAATAAGTAATTA-TATTTATATTTCAA
229377 TTTTAAAAATAAGTAATTATATTTATATTT
1 TTTTAAAAATAAGTAATTATATTTATATTT
229407 ATAACTAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.42
32 8 0.31
33 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (33 bp):
TTTTAAAAATAAGTAATTATATTTATATTTCAA
Found at i:230067 original size:17 final size:17
Alignment explanation
Indices: 230045--230088 Score: 81
Period size: 16 Copynumber: 2.6 Consensus size: 17
230035 TTTGGAGAAG
230045 ATAAAAATATATTATTA
1 ATAAAAATATATTATTA
230062 AT-AAAATATATTATTA
1 ATAAAAATATATTATTA
230078 ATAAAAATATA
1 ATAAAAATATA
230089 AATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAATATATTATTA
Found at i:230734 original size:6 final size:5
Alignment explanation
Indices: 230698--230727 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
230688 AACTTTAATA
230698 AAAATT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAA
230728 ATTAAAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:243832 original size:2 final size:2
Alignment explanation
Indices: 243825--243859 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
243815 CTAGGGTAAG
243825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
243860 GGGTTAGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:245935 original size:60 final size:60
Alignment explanation
Indices: 245864--245978 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
245854 AAAATGATTA
** * *
245864 TCATTCAAAATTAGTCCTTAAAC-TTTTGAACATTTCAATTTAATCTCCAAACTATGACCT
1 TCATTCAAAATTAGTCCCCAAACTTTTTGAACAATCCAATTTAATC-CCAAACTATGACCT
* * *
245924 TCATTCTAAATTAGTCCCCAAACTTTTTGAACAATCCAATTTCATCCTAAACTAT
1 TCATTCAAAATTAGTCCCCAAACTTTTTGAACAATCCAATTTAATCCCAAACTAT
245979 ACGTATATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 28 0.60
61 19 0.40
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
TCATTCAAAATTAGTCCCCAAACTTTTTGAACAATCCAATTTAATCCCAAACTATGACCT
Found at i:251467 original size:21 final size:21
Alignment explanation
Indices: 251430--251470 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
251420 ATAGGTATTA
251430 ATAAAATTATAAATAAAAGTG
1 ATAAAATTATAAATAAAAGTG
*
251451 ATAAATTTA-AAATTAAAAGT
1 ATAAAATTATAAA-TAAAAGT
251471 TAAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
ATAAAATTATAAATAAAAGTG
Found at i:265774 original size:41 final size:41
Alignment explanation
Indices: 265723--265819 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
265713 TAAAGTTTAG
*
265723 TTTTTGTTTCATTTTAGTACACGTCGTTAAAAACTTTAGTC
1 TTTTTGTTTCATTTTAGTACACGCCGTTAAAAACTTTAGTC
*
265764 TTTTTGTTTCATTTTAGTACACGCCGTTAAAAACTTTAGTT
1 TTTTTGTTTCATTTTAGTACACGCCGTTAAAAACTTTAGTC
*
265805 TTTTTATTTCATTTT
1 TTTTTGTTTCATTTT
265820 TGTATACATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (41 bp):
TTTTTGTTTCATTTTAGTACACGCCGTTAAAAACTTTAGTC
Found at i:267947 original size:31 final size:29
Alignment explanation
Indices: 267912--267985 Score: 69
Period size: 33 Copynumber: 2.4 Consensus size: 29
267902 ATGGCTTCCC
267912 TAAAATTATAATTTT-ATATATTAATATATGA
1 TAAAATTATAATTTTGATATATT--TA-ATGA
* * *
267943 TAAAAAAATATATTTTTGTTATATTTAATGA
1 T--AAAATTATAATTTTGATATATTTAATGA
267974 TAAAATTATAAT
1 TAAAATTATAAT
267986 CTAATCCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
29 9 0.26
31 6 0.17
32 2 0.06
33 12 0.34
34 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (29 bp):
TAAAATTATAATTTTGATATATTTAATGA
Found at i:270621 original size:15 final size:18
Alignment explanation
Indices: 270601--270640 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
270591 AATTAAAATA
270601 ATATAAAAT-TTTA-AT-
1 ATATAAAATATTTATATG
270616 ATATAAAATATTTATATG
1 ATATAAAATATTTATATG
270634 ATATAAA
1 ATATAAA
270641 TTAATCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 2 0.09
18 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATAAAATATTTATATG
Found at i:270725 original size:28 final size:24
Alignment explanation
Indices: 270694--270765 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
270684 AATTTATATT
*
270694 AAAATTAATCTCTATAATATAATATTAA
1 AAAATTAATAT-T-TAAT-TAAT-TTAA
*
270722 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
*
270746 AAAATTAATATTAAATTAAT
1 AAAATTAATATTTAATTAAT
270766 ATATAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 22 0.55
25 3 0.08
26 4 0.10
27 1 0.03
28 10 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:270763 original size:11 final size:12
Alignment explanation
Indices: 270655--270767 Score: 74
Period size: 11 Copynumber: 9.3 Consensus size: 12
270645 TCTATAATAT
*
270655 ATATTAAAAATA
1 ATATTAAAATTA
*
270667 ATATT-AAATTT
1 ATATTAAAATTA
*
270678 AT-TTAAAATTT
1 ATATTAAAATTA
270689 ATATTAAAATTA
1 ATATTAAAATTA
* *
270701 ATCTCTATAATATA
1 ATAT-TAAAAT-TA
270715 ATATTAAAAAATTA
1 ATATT--AAAATTA
* *
270729 ATATT-TAATTT
1 ATATTAAAATTA
270740 AT-TTAAAAAATTA
1 ATATT--AAAATTA
270753 ATATT-AAATTA
1 ATATTAAAATTA
270764 ATAT
1 ATAT
270768 ATAATATAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.05
11 30 0.38
12 16 0.20
13 12 0.15
14 14 0.17
15 4 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTAAAATTA
Done.