Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007262.1 Hibiscus syriacus cultivar Beakdansim tig00019247_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: 90777
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1052 original size:21 final size:21
Alignment explanation
Indices: 1026--1079 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1016 GTGGCAGGTG
*
1026 CATGGATGCACTACAGTGGTA
1 CATGGATGCACTACAGGGGTA
* *
1047 CATGGATGCACTGCAGGGGTG
1 CATGGATGCACTACAGGGGTA
1068 CATGGATGCACT
1 CATGGATGCACT
1080 TTGACACCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
CATGGATGCACTACAGGGGTA
Found at i:3537 original size:18 final size:18
Alignment explanation
Indices: 3483--3545 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
3473 AACTTAAATA
* *
3483 AATAATTCAAAGTTATTT
1 AATAATTTAAAGTTAATT
**
3501 AATAATTTAAA-AAAATT
1 AATAATTTAAAGTTAATT
3518 AATAATTTAAAGTTAATT
1 AATAATTTAAAGTTAATT
*
3536 AACAATTTAA
1 AATAATTTAA
3546 TCAAATTGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
17 14 0.38
18 23 0.62
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AATAATTTAAAGTTAATT
Found at i:3552 original size:35 final size:35
Alignment explanation
Indices: 3478--3545 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3468 AGTATAACTT
* * *
3478 AAATAAATAATTCAAAGTTATTTAATAATTTAAAA
1 AAATTAATAATTCAAAGTTAATTAACAATTTAAAA
*
3513 AAATTAATAATTTAAAGTTAATTAACAATTTAA
1 AAATTAATAATTCAAAGTTAATTAACAATTTAA
3546 TCAAATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (35 bp):
AAATTAATAATTCAAAGTTAATTAACAATTTAAAA
Found at i:6774 original size:2 final size:2
Alignment explanation
Indices: 6767--6795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6757 AGTCAAACTT
6767 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6796 TGTTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:17257 original size:24 final size:24
Alignment explanation
Indices: 17173--17258 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 24
17163 TAAATGGATA
* * * *
17173 TATCAAAACATAATTCAAGTCAGA
1 TATCAGAACAGAATCCAAGTCAGG
* * *
17197 TATCAGAACAAAATCCAGGTCATG
1 TATCAGAACAGAATCCAAGTCAGG
* * *
17221 TATAAGAATAGAATCCATGTCAGG
1 TATCAGAACAGAATCCAAGTCAGG
*
17245 TATCATAACAGAAT
1 TATCAGAACAGAAT
17259 TCAAATCGGA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (24 bp):
TATCAGAACAGAATCCAAGTCAGG
Found at i:21563 original size:41 final size:39
Alignment explanation
Indices: 21518--21597 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 39
21508 TTAATTAAAT
*
21518 TATTATTATTTTACTTTTTTAGTGATTTATGCAAAGGATCA
1 TATTATTATTTTACTTTTTTAGTGA--TATACAAAGGATCA
21559 TATTATTATTTTACTTTTTTAGTGATATACAAAGGATCA
1 TATTATTATTTTACTTTTTTAGTGATATACAAAGGATCA
21598 GGCCCGAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 13 0.34
41 25 0.66
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (39 bp):
TATTATTATTTTACTTTTTTAGTGATATACAAAGGATCA
Found at i:24356 original size:15 final size:17
Alignment explanation
Indices: 24336--24368 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24326 TTCTGATTTT
24336 TTAAATT-CAAG-TAGA
1 TTAAATTGCAAGATAGA
24351 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
24368 T
1 T
24369 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:24400 original size:96 final size:98
Alignment explanation
Indices: 24206--24438 Score: 348
Period size: 96 Copynumber: 2.4 Consensus size: 98
24196 TTCTTTTTCT
*
24206 TTTTTCTTTTTTGTAATTGTTT-TGATTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATATAT
1 TTTTT-TTTTTTGTAATT-TTTCTGA--TTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGAT
*
24270 AAATAAAATACATTGAAATTAGATAAATAAACATATTA
62 -AATAAAATACATTGAAATTAGATAAATAAACATACTA
24308 TTTTTTTTTTTGTAATTTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGAT-A-A
1 TTTTTTTTTTTGTAATTTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAATA
24371 AAATACATTGAAATTAGATAAATAAACATACTA
66 AAATACATTGAAATTAGATAAATAAACATACTA
* *
24404 -ATTTTTTTTTGTAATTTTTTCTGTTTTTTTAAATT
1 TTTTTTTTTTTGTAA-TTTTTCTGATTTTTTAAATT
24439 TTTCTGATTT
Statistics
Matches: 125, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
95 13 0.10
96 52 0.42
97 1 0.01
99 36 0.29
100 3 0.02
101 15 0.12
102 5 0.04
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (98 bp):
TTTTTTTTTTTGTAATTTTTCTGATTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAATA
AAATACATTGAAATTAGATAAATAAACATACTA
Found at i:24431 original size:115 final size:115
Alignment explanation
Indices: 24312--24525 Score: 376
Period size: 115 Copynumber: 1.9 Consensus size: 115
24302 ATATTATTTT
* *
24312 TTTTTTTGTAATTTTTCTGATTTTTT-AAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATA
1 TTTTTTT-AAATTTTTCTGATTTTTTAAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATA
24376 CATTGAAATTAGATAAATAAACATACTAATTTTTTTTTGTAATTTTTTCTG
65 CATTGAAATTAGATAAATAAACATACTAATTTTTTTTTGTAATTTTTTCTG
*
24427 TTTTTTTAAATTTTTCTGATTTTTTAAAATTCAAGTAGATTAAATTACAAGATATATAAAAATAC
1 TTTTTTTAAATTTTTCTGATTTTTTAAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATAC
*
24492 ATTGAAATTAGATAAATAAACATATTAATTTTTT
66 ATTGAAATTAGATAAATAAACATACTAATTTTTT
24526 AAAACATAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 17 0.18
115 77 0.82
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (115 bp):
TTTTTTTAAATTTTTCTGATTTTTTAAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATAC
ATTGAAATTAGATAAATAAACATACTAATTTTTTTTTGTAATTTTTTCTG
Found at i:24432 original size:19 final size:19
Alignment explanation
Indices: 24408--24457 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
24398 ATACTAATTT
*
24408 TTTTTTGTAATTTTTTCTG-
1 TTTTTT-TAAATTTTTCTGA
24427 TTTTTTTAAATTTTTCTGA
1 TTTTTTTAAATTTTTCTGA
*
24446 TTTTTTAAAATT
1 TTTTTTTAAATT
24458 CAAGTAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (19 bp):
TTTTTTTAAATTTTTCTGA
Found at i:24440 original size:18 final size:18
Alignment explanation
Indices: 24408--24454 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
24398 ATACTAATTT
*
24408 TTTTTTGTAATTTTTTCTG
1 TTTTTT-TAAATTTTTCTG
24427 TTTTTTTAAATTTTTCTG
1 TTTTTTTAAATTTTTCTG
*
24445 ATTTTTTAAA
1 TTTTTTTAAA
24455 ATTCAAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (18 bp):
TTTTTTTAAATTTTTCTG
Found at i:25119 original size:21 final size:21
Alignment explanation
Indices: 25091--25143 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
25081 ACCGTGATTG
*
25091 CGGCCGTCGCGGGCGCTATTA
1 CGGCCGTCGCGGACGCTATTA
* *
25112 CGGTCGTCGCGGACGCTATTG
1 CGGCCGTCGCGGACGCTATTA
25133 CGGCCGTCGCG
1 CGGCCGTCGCG
25144 AGTAACTCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.34, G:0.40, T:0.19
Consensus pattern (21 bp):
CGGCCGTCGCGGACGCTATTA
Found at i:34751 original size:17 final size:16
Alignment explanation
Indices: 34729--34765 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
34719 TATCACATTC
34729 ATATATATAATTTTAAA
1 ATATATAT-ATTTTAAA
*
34746 ATATATATTTTTTAAA
1 ATATATATATTTTAAA
34762 ATAT
1 ATAT
34766 CTGAAAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATATATTTTAAA
Found at i:39183 original size:31 final size:31
Alignment explanation
Indices: 39148--39208 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
39138 ATAAGGCAAG
*
39148 TGATCACATCTTAATTAAA-TAAAAATGAATA
1 TGATCACATCTTAA-AAAATTAAAAATGAATA
39179 TGATCACATCTTAAAAAATTAAAAATGAAT
1 TGATCACATCTTAAAAAATTAAAAATGAAT
39209 GTAATCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (31 bp):
TGATCACATCTTAAAAAATTAAAAATGAATA
Found at i:42345 original size:16 final size:17
Alignment explanation
Indices: 42324--42357 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
42314 ACTATTCACA
42324 TGAATAGTG-AATTTGG
1 TGAATAGTGAAATTTGG
42340 TGAATAGTGAAATTTGG
1 TGAATAGTGAAATTTGG
42357 T
1 T
42358 CAGTGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.38
Consensus pattern (17 bp):
TGAATAGTGAAATTTGG
Found at i:45856 original size:14 final size:14
Alignment explanation
Indices: 45837--45864 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45827 CGAAAAGGCC
45837 CATTTCCCCTAATT
1 CATTTCCCCTAATT
45851 CATTTCCCCTAATT
1 CATTTCCCCTAATT
45865 GGGGGAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (14 bp):
CATTTCCCCTAATT
Found at i:51674 original size:24 final size:24
Alignment explanation
Indices: 51592--51686 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
51582 ATTTCTTATT
* *
51592 TGAATTCTGTTTTGACATCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
51616 TGAAATCTGTTCTGAT-TCCT-AAC
1 TGAATTCTGTTCTGATAT-CTGATC
*
51639 ATGGATTCTGTTCTGATATCTGATC
1 -TGAATTCTGTTCTGATATCTGATC
* * *
51664 TGAATTATGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
51687 ATCTCTGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:51854 original size:2 final size:2
Alignment explanation
Indices: 51847--51875 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51837 CGGATGAGGG
51847 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 T
51876 GTTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54453 original size:31 final size:31
Alignment explanation
Indices: 54412--54478 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
54402 TTAACGTCCG
* *
54412 GGCACTTAAAATAATAATGGAGAAAACATTA
1 GGCACCTAAAATAATAACGGAGAAAACATTA
*
54443 GGCACCTAAAATGATAACGGAGAAAACATTA
1 GGCACCTAAAATAATAACGGAGAAAACATTA
*
54474 AGCAC
1 GGCAC
54479 TTATATGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (31 bp):
GGCACCTAAAATAATAACGGAGAAAACATTA
Found at i:57376 original size:37 final size:37
Alignment explanation
Indices: 57326--57399 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
57316 GGTGGTGACA
57326 CGTGTCACCACCTGTGT-AAAGGAAAAAACTTTAGAGT
1 CGTGTCACCACCTGTGTAAAAGG-AAAAACTTTAGAGT
57363 CGTGTCACCACCTGTGTAAAAGGAAAAACTTTAGAGT
1 CGTGTCACCACCTGTGTAAAAGGAAAAACTTTAGAGT
57400 TATAAGAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
CGTGTCACCACCTGTGTAAAAGGAAAAACTTTAGAGT
Found at i:57513 original size:17 final size:18
Alignment explanation
Indices: 57491--57528 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
57481 CTCTAAATAA
57491 TTTTAATATAATTT-TAT
1 TTTTAATATAATTTATAT
57508 TTTTAATATAATTTATAT
1 TTTTAATATAATTTATAT
57526 TTT
1 TTT
57529 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATATAATTTATAT
Found at i:57514 original size:23 final size:24
Alignment explanation
Indices: 57494--57537 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
57484 TAAATAATTT
57494 TAATATA-ATTTTATT-TTTAATA
1 TAATATATATTTTATTATTTAATA
*
57516 TAATTTATATTTTATTATTTAA
1 TAATATATATTTTATTATTTAA
57538 AGAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TAATATATATTTTATTATTTAATA
Found at i:58137 original size:20 final size:22
Alignment explanation
Indices: 58107--58153 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
58097 ATTTTGTTTC
*
58107 ATTAT-TTTAAGA-A-ATAAAA
1 ATTATATTTAAGAGAGAAAAAA
58126 ATTATATTTAAGAGAGAAAAAA
1 ATTATATTTAAGAGAGAAAAAA
58148 ATTATA
1 ATTATA
58154 AACAGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 1 0.04
22 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTATATTTAAGAGAGAAAAAA
Found at i:62463 original size:29 final size:28
Alignment explanation
Indices: 62388--62505 Score: 100
Period size: 26 Copynumber: 4.1 Consensus size: 28
62378 TATTCTTCCC
* * *
62388 TTATATTAAAATAAAAAATAAATTTTTTATT
1 TTATATTAAAA-ATAAAATAAA--ATATATT
*
62419 TTATATTATAAGATAATAATAAAATATATT
1 TTATATTA-AAAATAA-AATAAAATATATT
62449 TTATATTAAAAATAAAAATAAAATATA-T
1 TTATATTAAAAAT-AAAATAAAATATATT
62477 TTA-A-TAAGATAA-AAAATAAAATATATT
1 TTATATTAA-A-AATAAAATAAAATATATT
62504 TT
1 TT
62506 TAAAATTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
26 16 0.21
27 5 0.07
28 6 0.08
29 15 0.20
30 15 0.20
31 11 0.14
32 8 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTATATTAAAAATAAAATAAAATATATT
Found at i:72203 original size:3 final size:3
Alignment explanation
Indices: 72195--72280 Score: 109
Period size: 3 Copynumber: 28.7 Consensus size: 3
72185 ATAGACAATG
72195 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
72243 TTT TAT TGT TGT TGT TCT TGT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
72281 CTGAGTAAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:75976 original size:20 final size:21
Alignment explanation
Indices: 75951--76002 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
75941 TTTTCCCAAT
*
75951 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
75971 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
75992 TCGCAATGCGA
1 TCGCAATGCGA
76003 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:76085 original size:20 final size:20
Alignment explanation
Indices: 76033--76085 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
76023 TAATACAAAA
* *
76033 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
76053 TCGCAACACGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
76073 TCGCAACGCGATT
1 TCGCAACGCGATT
76086 TACATAGCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:76646 original size:14 final size:14
Alignment explanation
Indices: 76627--76663 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
76617 GGAAATAACT
76627 ATCGCAACGAGATA
1 ATCGCAACGAGATA
76641 ATCGCAACGAGATA
1 ATCGCAACGAGATA
76655 ATCGCAACG
1 ATCGCAACG
76664 CGGTTTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (14 bp):
ATCGCAACGAGATA
Found at i:87494 original size:8 final size:8
Alignment explanation
Indices: 87483--87542 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 8
87473 GTGAAAAATG
87483 AAAAAT-A
1 AAAAATAA
87490 AAAAATAA
1 AAAAATAA
87498 AAAAATAA
1 AAAAATAA
87506 AAAAA-AA
1 AAAAATAA
87513 ATAAAA-AA
1 A-AAAATAA
** *
87521 ATGAATGA
1 AAAAATAA
*
87529 AAAAATGA
1 AAAAATAA
87537 AAAAAT
1 AAAAAT
87543 GAGGGTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
7 11 0.24
8 34 0.76
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:87501 original size:7 final size:7
Alignment explanation
Indices: 87476--87520 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
87466 AAAATGAGTG
*
87476 AAAAATG
1 AAAAATA
87483 AAAAATA
1 AAAAATA
87490 AAAAATA
1 AAAAATA
87497 AAAAA-A
1 AAAAATA
*
87503 TAAAA-A
1 AAAAATA
87509 AAAAATA
1 AAAAATA
87516 AAAAA
1 AAAAA
87521 ATGAATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.87, C:0.00, G:0.02, T:0.11
Consensus pattern (7 bp):
AAAAATA
Found at i:87531 original size:20 final size:20
Alignment explanation
Indices: 87476--87544 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
87466 AAAATGAGTG
87476 AAAAATGAAAAATAAAAAATAA
1 AAAAATG-AAAA-AAAAAATAA
87498 AAAAAT-AAAAAAAAAATAA
1 AAAAATGAAAAAAAAAATAA
** *
87517 AAAAATGAATGAAAAAATGA
1 AAAAATGAAAAAAAAAATAA
87537 AAAAATGA
1 AAAAATGA
87545 GGGTTCAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 15 0.35
20 22 0.51
22 6 0.14
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAAATGAAAAAAAAAATAA
Found at i:87543 original size:8 final size:8
Alignment explanation
Indices: 87476--87544 Score: 51
Period size: 8 Copynumber: 9.0 Consensus size: 8
87466 AAAATGAGTG
87476 AAAAATG-
1 AAAAATGA
87483 AAAAAT-A
1 AAAAATGA
*
87490 AAAAATAA
1 AAAAATGA
87498 AAAAAT-A
1 AAAAATGA
87505 AAAAA--A
1 AAAAATGA
*
87511 AAATAA-AA
1 AAA-AATGA
87519 AAATGAATGA
1 AAA--AATGA
87529 AAAAATGA
1 AAAAATGA
87537 AAAAATGA
1 AAAAATGA
87545 GGGTTCAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
6 4 0.07
7 20 0.37
8 24 0.44
9 2 0.04
10 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (8 bp):
AAAAATGA
Found at i:88708 original size:52 final size:55
Alignment explanation
Indices: 88511--88926 Score: 445
Period size: 52 Copynumber: 7.9 Consensus size: 55
88501 AGGTTCCCTA
* * * *
88511 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
88566 CGATCGTTGAAGATTGTTC-AGTCTTATACTCTCTGAGGAAATA-GGGGCGGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
88619 CGATTGTTGAAGA-TGTTC-AGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACG
1 CGATTGTTGAAGATTGTTCGA-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
88673 CGATCGTTGAAGATTGTTCGAGT-GT-TA-TCTCTGAAGAAATAGGGGGCGGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
88725 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
88780 TGATTGATGAAG-TTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGAAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * *
88832 TGATTGATGAAGATTG-T-GGGTCTTATAC-CTCTGAAGAAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
88884 CG--T-TTGAAGATT-TTCGAGT-TCTATACTCCCTAAAGAAAGAGGG
1 CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
88927 AGCGAACCTG
Statistics
Matches: 317, Mismatches: 32, Indels: 28
0.84 0.08 0.07
Matches are distributed among these distances:
49 10 0.03
50 9 0.03
51 13 0.04
52 117 0.37
53 62 0.20
54 47 0.15
55 58 0.18
56 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:88743 original size:107 final size:110
Alignment explanation
Indices: 88510--88926 Score: 490
Period size: 107 Copynumber: 3.9 Consensus size: 110
88500 CAGGTTCCCT
* * * *
88510 ACGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCAGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
88575 AAGATTGTTC-AGTCTTATACTCTCTGAGGAAATA-GGGGCGGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
*
88618 ACGATTGTTGAAGA-TGTTCAGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCAGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
88682 AAGATTGTTCGAGT-GT-TA-TCTCTGAAGAAATAGGGGGCGGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * * * *
88724 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGTGATTGATG
1 ACGATTGTTGAAGATTGTTCAGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
* **
88789 AAG-TTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGAAGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
** * * * *
88831 GTGATTGATGAAGATTG-T-GGGTCTTATAC-CTCTGAAGAAATAGGGAGCAGACACG-T--TTG
1 ACGATTGTTGAAGATTGTTCAGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
* * *
88890 AAGATT-TTCGAGT-TCTATACTCCCTAAAGAAAGAGGG
66 AAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
88927 AGCGAACCTG
Statistics
Matches: 270, Mismatches: 29, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
101 5 0.02
102 4 0.01
103 23 0.09
104 25 0.09
105 26 0.10
106 31 0.11
107 140 0.52
108 16 0.06
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (110 bp):
ACGATTGTTGAAGATTGTTCAGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
Found at i:88803 original size:159 final size:160
Alignment explanation
Indices: 88511--88926 Score: 485
Period size: 159 Copynumber: 2.6 Consensus size: 160
88501 AGGTTCCCTA
* * *
88511 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACGCGATCGTTGA
1 CGATCGTTGAAGATTGTTCGAGTCT--TA-TCTCTGAAGAAATAGGGGGCGGACACGATTGTTGA
* * * *
88576 AGATTGTTC-AGTCTTATACTCTCTGAGGAAATAGGGGCGGACACGATTGTTGAAGATGTTCAGG
63 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCGCAAACGATTGATGAAGATGTTCAGG
*
88640 TCTTATACTCTCTGAAGAAATAGAGGGCAGACG
128 TCTTATACTCTCTGAAGAAATAGAGGGAAGACG
*
88673 CGATCGTTGAAGATTGTTCGAGTGTTATCTCTGAAGAAATAGGGGGCGGACACGATTGTTGAAGA
1 CGATCGTTGAAGATTGTTCGAGTCTTATCTCTGAAGAAATAGGGGGCGGACACGATTGTTGAAGA
* * *
88738 TTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGG-GCAAACGTGATTGATGAAGTTG-T-GGGT
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCGCAAAC--GATTGATGAAGATGTTCAGGT
*
88800 CTTATACTCTCTGAAGAAATAGGGGGAAGACG
129 CTTATACTCTCTGAAGAAATAGAGGGAAGACG
* * * * * *
88832 TGATTGATGAAGATTG-T-GGGTCTTATACCTCTGAAGAAATAGGGAGCAGACACG--T-TTGAA
1 CGATCGTTGAAGATTGTTCGAGTCTTAT--CTCTGAAGAAATAGGGGGCGGACACGATTGTTGAA
* * *
88892 GATT-TTCGAGT-TCTATACTCCCTAAAGAAAGAGGG
64 GATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
88927 AGCGAACCTG
Statistics
Matches: 224, Mismatches: 24, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
154 1 0.00
155 25 0.11
156 9 0.04
157 8 0.04
158 1 0.00
159 116 0.52
160 29 0.13
161 12 0.05
162 23 0.10
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (160 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATCTCTGAAGAAATAGGGGGCGGACACGATTGTTGAAGA
TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCGCAAACGATTGATGAAGATGTTCAGGTCT
TATACTCTCTGAAGAAATAGAGGGAAGACG
Found at i:88927 original size:51 final size:50
Alignment explanation
Indices: 88866--89399 Score: 438
Period size: 51 Copynumber: 10.3 Consensus size: 50
88856 ATACCTCTGA
* * *
88866 AGAAATAGGGAGCAGACACGTTTGAAGATTTTCGAGTTCTATACTCCCTAA
1 AGAAAGAGGGAGC-GACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAG
* * * *
88917 AGAAAGAGGGAGCGAACCTGTTAGAAGATGTTCGAGTTCCATACTCCCTAG
1 AGAAAGAGGGAGCG-ACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAG
* ** *
88968 ATAAAGAGGGAATGAACCCGTTTGAAGAATATTT-GAGTTCTATTCTCCCT-G
1 AGAAAGAGGGAGCG-ACCCGTTTGAAG-AT-TTTCGAGTTCTATACTCCCTAG
* * *
89019 AAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACT-CCTAG
1 -AGAAAGAGGGAGC-GACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAG
* * ** *
89070 ATAAAGAGGGAACGAACCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTAG
1 AGAAAGAGGGAGCG-ACCCGT---TTGAAGATTTTCGAGTTCTATACTCCCTAG
89124 AGAAAGAGGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTT-TCATACTCCCTAG
1 AGAAAGAGGGAGCG-ACCCGTTT---GAAGATT-TTCGAGTTCT-ATACTCCCTAG
* * * * *
89179 ATAAAGAGGGAACGAACCTGTTTGCAGAAGATTATTCGAGTTCTATACTTCCTGAA
1 AGAAAGAGGGAGCG-ACCCGTTT---GAAGATT-TTCGAGTTCTATACTCCCT-AG
* * *
89235 AGAAAGA-GGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTTCCTGAA
1 AGAAAGAGGGAGCG-ACCCGTTTGAAGATTTTCGAGTTCTATACTCCCT-AG
* *
89286 AGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCTATACTCCCTAG
1 AGAAAGAGGGAGC-GACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAG
* * **
89337 ATAAAGAGGGA---ACTCGTAAGAAGAAGATGTTT-GAGTTCTATACTCCCTAG
1 AGAAAGAGGGAGCGACCCGT---TTGAAGAT-TTTCGAGTTCTATACTCCCTAG
89387 AGAAAGAGGGAGC
1 AGAAAGAGGGAGC
89400 AAACTCGTTT
Statistics
Matches: 405, Mismatches: 51, Indels: 53
0.80 0.10 0.10
Matches are distributed among these distances:
47 5 0.01
50 57 0.14
51 120 0.30
52 82 0.20
53 23 0.06
54 31 0.08
55 79 0.20
56 8 0.02
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (50 bp):
AGAAAGAGGGAGCGACCCGTTTGAAGATTTTCGAGTTCTATACTCCCTAG
Done.