Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002373.1 Hibiscus syriacus cultivar Beakdansim tig00004846_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: 114301
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:10113 original size:11 final size:11
Alignment explanation
Indices: 10097--10122 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10087 AATCTTGTTT
10097 AAAATAATATC
1 AAAATAATATC
10108 AAAATAATATC
1 AAAATAATATC
10119 AAAA
1 AAAA
10123 ACCATGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATATC
Found at i:12901 original size:2 final size:2
Alignment explanation
Indices: 12854--12883 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12844 GTATTTGCGG
12854 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
12884 GAATAAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13397 original size:23 final size:23
Alignment explanation
Indices: 13371--13429 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
13361 TGGCATTTCA
13371 ATGCATTTCTACGCGGCACTACG
1 ATGCATTTCTACGCGGCACTACG
* * *
13394 ATGCAATTCTACGGGGCACTTCG
1 ATGCATTTCTACGCGGCACTACG
* *
13417 GTGCATTTATACG
1 ATGCATTTCTACG
13430 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (23 bp):
ATGCATTTCTACGCGGCACTACG
Found at i:14950 original size:12 final size:12
Alignment explanation
Indices: 14935--14964 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
14925 TTCTTGTCCA
14935 TTTTCTTCTTCT
1 TTTTCTTCTTCT
14947 TTTTCTTCTTCT
1 TTTTCTTCTTCT
14959 TTTTCT
1 TTTTCT
14965 GGTCTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:19350 original size:2 final size:2
Alignment explanation
Indices: 19343--19373 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19333 AATAATAAAC
19343 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19374 TAGGTAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20548 original size:16 final size:15
Alignment explanation
Indices: 20520--20557 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
20510 AAATATGTAA
*
20520 ATTATATATATATAT
1 ATTATATATATATAC
20535 ATTATATAATATATAC
1 ATTATAT-ATATATAC
20551 ATTATAT
1 ATTATAT
20558 GGACAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATATATATATAC
Found at i:21086 original size:15 final size:15
Alignment explanation
Indices: 21063--21094 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21053 TTTTTGTGTT
*
21063 TCAAGAGAAACTGTC
1 TCAAAAGAAACTGTC
21078 TCAAAAGAAACTGTC
1 TCAAAAGAAACTGTC
21093 TC
1 TC
21095 GAGTGAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (15 bp):
TCAAAAGAAACTGTC
Found at i:21196 original size:37 final size:37
Alignment explanation
Indices: 21150--21385 Score: 228
Period size: 37 Copynumber: 6.6 Consensus size: 37
21140 TGTTTCAAGG
*
21150 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
** *
21187 GAAACTGTCTCAAGAGAGATGAAATTT-GTT-TAAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
* * **
21222 GAAAACAGAT-TC---AGAG-----ATTTTGTT-TCAAGG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTAGTTCT-AAAA
* **
21252 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTACGA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
21288 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
21325 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
21362 GAAACTGTTTCAAGAGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
21386 CTTTGTTTCA
Statistics
Matches: 169, Mismatches: 15, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
28 5 0.03
29 11 0.07
30 4 0.02
32 4 0.02
33 4 0.02
35 5 0.03
36 41 0.24
37 95 0.56
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
Found at i:21277 original size:102 final size:102
Alignment explanation
Indices: 21080--21329 Score: 349
Period size: 103 Copynumber: 2.4 Consensus size: 102
21070 AAACTGTCTC
* * * *
21080 AAAAGAAACTGTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTGTTT
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAAGATTTTGTTT
21145 CAAGGGAAAATGTCTCAAGAGAGACAAAATTTAGTTCT
66 CAAGGGAAAATGTCTCAAGAGAGACAAAATTT-GTTCT
* *
21183 AAAAGAAACTGTCTCAAGAGAGATGAAATTTGTTTAAAGGAAAACAGATTC-AGAGATTTTGTTT
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAAGATTTTGTTT
* *
21247 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTT
66 CAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTCT
** * * *
21284 ACGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAAA
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTT-GTT-TAAAGGAAAA
21330 TGTCTCAAGA
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 30 0.23
102 46 0.35
103 55 0.42
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (102 bp):
AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAAGATTTTGTTT
CAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTCT
Found at i:21280 original size:36 final size:36
Alignment explanation
Indices: 21240--21542 Score: 246
Period size: 36 Copynumber: 8.4 Consensus size: 36
21230 ATTCAGAGAT
*
21240 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
21276 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
21312 TTTAG-TTCTAAAAGAAAATGTCTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* *
21349 TTTAG-TTCTAAAAGAAACTGTTTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
** *******
21386 CTTTGTTTCAAG-GAAAACAAAT-TCAA-AG-TTTTTTT
1 -TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* **
21421 TTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
21457 TTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
21493 TTTGTTT-TA-AGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
21527 CTTTGTTTCAAG-GAAA
1 -TTTGTTTCAAGAGAAA
21543 ACAAATTCGA
Statistics
Matches: 217, Mismatches: 37, Indels: 26
0.77 0.13 0.09
Matches are distributed among these distances:
33 2 0.01
34 42 0.19
35 11 0.05
36 82 0.38
37 73 0.34
38 7 0.03
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:21477 original size:181 final size:172
Alignment explanation
Indices: 21150--21526 Score: 556
Period size: 181 Copynumber: 2.1 Consensus size: 172
21140 TGTTTCAAGG
**
21150 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGATGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
* * **
21215 TTTAAAGGAAAACAGATTCAGAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
66 TTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTTG
*
21280 TTTTACGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
131 TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTT-GTT-T-AAA
*
21325 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTTTCAAGAGAGACAAAACTTT
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAA-TTT
* *
21390 GTTTCAAGGAAAACAAATTCAAAGTTTTTTTTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAA
65 GTTTAAAGGAAAACAAATTCAAAG-----ATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAA
* *
21455 AATTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAATTTGTTTTAA
125 AATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTAAA
*
21503 GAAATTGTCTCAAGAGAGACAAAA
1 GAAAATGTCTCAAGAGAGACAAAA
21527 CTTTGTTTCA
Statistics
Matches: 183, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
175 58 0.32
176 24 0.13
178 25 0.14
179 1 0.01
180 3 0.02
181 72 0.39
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (172 bp):
GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
TTTAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTTG
TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTAAA
Found at i:21532 original size:141 final size:140
Alignment explanation
Indices: 21295--21605 Score: 484
Period size: 141 Copynumber: 2.2 Consensus size: 140
21285 CGAGAAAATG
* *
21295 TCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAA
1 TCTCAAGAGAGACAAAATTT-GTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAA
*
21360 AAGAAACTGTTTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTTTTTG
65 AAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAG----TTTTTTG
21425 TTTCAAGGGAAACCA
126 TTTCAAGGGAAACCA
* *
21440 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAATTT-GTT-T-TA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAA
* *
21502 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCGAAGTTTTTTGTTTCA
66 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTGTTTCA
21567 AGGGAAACCA
131 AGGGAAACCA
*
21577 TCGCAAGAGAGACAAAATTTGTTTTAAGA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGA
21606 AACTGTAATC
Statistics
Matches: 158, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
137 50 0.32
141 51 0.32
142 1 0.01
143 3 0.02
144 33 0.21
145 20 0.13
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (140 bp):
TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAA
AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTGTTTCA
AGGGAAACCA
Found at i:22928 original size:95 final size:95
Alignment explanation
Indices: 22765--22947 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 95
22755 AATATGTAAA
* * *
22765 TACCTTTATCAGATTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
1 TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGG
*
22830 GACAACTCAAGCTTTATTGTATAGCATAAT
66 GACAACTCAAGATTTATTGTATAGCATAAT
* *
22860 TACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGTGTTTAACCAATTG-CTCTAGAG
1 TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCT-TAGAG
*
22924 GGACAACTCAAGATTTATTTTATA
65 GGACAACTCAAGATTTATTGTATA
22948 TATATAATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGG
GACAACTCAAGATTTATTGTATAGCATAAT
Found at i:24658 original size:10 final size:10
Alignment explanation
Indices: 24645--24687 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
24635 TATAGTATTT
24645 AAAAAAAATA
1 AAAAAAAATA
*
24655 AAAAGAAATA
1 AAAAAAAATA
*
24665 AAAAATAATA
1 AAAAAAAATA
*
24675 AAAAATAATA
1 AAAAAAAATA
24685 AAA
1 AAA
24688 TACATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:24669 original size:17 final size:17
Alignment explanation
Indices: 24647--24689 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
24637 TAGTATTTAA
24647 AAAAAATAA-AAAGAAAT
1 AAAAAATAATAAA-AAAT
24664 AAAAAATAATAAAAAAT
1 AAAAAATAATAAAAAAT
24681 AATAAAATA
1 AA-AAAATA
24690 CATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAATAATAAAAAAT
Found at i:28039 original size:2 final size:2
Alignment explanation
Indices: 28032--28086 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
28022 ATATGTAAAT
28032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28074 TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA
28087 CATTATATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29662 original size:22 final size:22
Alignment explanation
Indices: 29637--29683 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29627 TAAATTATTT
* *
29637 AAATTATTTATGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
29659 AAATGATTTACGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
29681 AAA
1 AAA
29684 ATTTTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (22 bp):
AAATGATTTACGTTTATGTGTA
Found at i:33075 original size:34 final size:32
Alignment explanation
Indices: 33037--33128 Score: 112
Period size: 34 Copynumber: 2.8 Consensus size: 32
33027 AATGGTAATA
* *
33037 AACAAAATTATCAAAATCAATTAACAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAA-AAAAA-TCC
*
33071 AACAAAATAAACAAAATAAATTTTAAAAAAATCC
1 AACAAAATTAACAAAATAAA--TTAAAAAAATCC
*
33105 AACCAAATTAACAAAATAAATTAA
1 AACAAAATTAACAAAATAAATTAA
33129 TTATTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.08
34 38 0.75
35 5 0.10
36 4 0.08
ACGTcount: A:0.64, C:0.14, G:0.01, T:0.21
Consensus pattern (32 bp):
AACAAAATTAACAAAATAAATTAAAAAAATCC
Found at i:35437 original size:16 final size:16
Alignment explanation
Indices: 35413--35461 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
35403 ATATCTTCAA
* *
35413 AAAAAATTAAGTAAAT
1 AAAATATTAAATAAAT
*
35429 AAAATATTAAATAATT
1 AAAATATTAAATAAAT
*
35445 TAAATAGTTAAATAAAT
1 AAAATA-TTAAATAAAT
35462 TACTAACAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:37339 original size:20 final size:20
Alignment explanation
Indices: 37314--37368 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
37304 ATGTTAAGGG
37314 ATGCATCGATACACTGTAGA
1 ATGCATCGATACACTGTAGA
37334 ATGCATCGATACACTGTAGA
1 ATGCATCGATACACTGTAGA
*
37354 ATGCATCGATGCACT
1 ATGCATCGATACACT
37369 TCAAGGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATGCATCGATACACTGTAGA
Found at i:41008 original size:24 final size:20
Alignment explanation
Indices: 40981--41038 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 20
40971 GCATAAGGAG
*
40981 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
* *
41005 TGCAACGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
41025 TGCATCGATGCACT
1 TGCATCGATGCACT
41039 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:42593 original size:23 final size:23
Alignment explanation
Indices: 42557--42626 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
42547 TCTTAGGGAT
* *
42557 AATTTTATATGGCACTTCGGTGC
1 AATTCTATACGGCACTTCGGTGC
* *
42580 AATTCTATGCGGCACTTCGATGC
1 AATTCTATACGGCACTTCGGTGC
*
42603 AATTCTATACAGCACTTCGGTGC
1 AATTCTATACGGCACTTCGGTGC
42626 A
1 A
42627 TTTATATGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (23 bp):
AATTCTATACGGCACTTCGGTGC
Found at i:50938 original size:7 final size:7
Alignment explanation
Indices: 50926--50997 Score: 78
Period size: 7 Copynumber: 10.6 Consensus size: 7
50916 ATGCCACGTC
50926 AGAAGGA
1 AGAAGGA
50933 AGAAGGA
1 AGAAGGA
50940 AGGAAGGA
1 A-GAAGGA
50948 AGAAGGA
1 AGAAGGA
*
50955 AGAATGA
1 AGAAGGA
*
50962 AGAATGA
1 AGAAGGA
50969 AGAAGG-
1 AGAAGGA
50975 AGAA-GA
1 AGAAGGA
*
50981 AGAA-AA
1 AGAAGGA
*
50987 AGTAGGA
1 AGAAGGA
50994 AGAA
1 AGAA
50998 ATGAAGAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
5 1 0.02
6 12 0.21
7 36 0.64
8 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (7 bp):
AGAAGGA
Found at i:50943 original size:11 final size:10
Alignment explanation
Indices: 50926--50997 Score: 69
Period size: 11 Copynumber: 7.1 Consensus size: 10
50916 ATGCCACGTC
50926 AGAAGGAAGA
1 AGAAGGAAGA
50936 AGGAAGGAAGGA
1 A-GAAGGAA-GA
50948 AGAAGGAAGA
1 AGAAGGAAGA
50958 ATGAA-GAATGA
1 A-GAAGGAA-GA
50969 AGAAGG-AGA
1 AGAAGGAAGA
*
50978 AGAA-GAAAA
1 AGAAGGAAGA
*
50987 AGTAGGAAGA
1 AGAAGGAAGA
50997 A
1 A
50998 ATGAAGAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
8 1 0.02
9 11 0.21
10 16 0.31
11 21 0.40
12 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (10 bp):
AGAAGGAAGA
Found at i:50952 original size:3 final size:3
Alignment explanation
Indices: 50926--51014 Score: 54
Period size: 3 Copynumber: 27.3 Consensus size: 3
50916 ATGCCACGTC
*
50926 AGA AGGA AGA AGGA AGGA AGGA AGA AGGA AGA ATGA AGA ATGA AGA AGG
1 AGA A-GA AGA A-GA A-GA A-GA AGA A-GA AGA A-GA AGA A-GA AGA AGA
* * * *
50975 AGA AGA AGA AAA AGTA GGA AGA A-A TGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA A
51015 ATTGTTGTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
2 1 0.01
3 43 0.62
4 25 0.36
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:50981 original size:16 final size:17
Alignment explanation
Indices: 50926--51006 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 17
50916 ATGCCACGTC
*
50926 AGAAGGAAGAAGGAAGGA
1 AGAATGAAGAAGG-AGGA
* *
50944 AGGAA-GAAGGAAGAATGA
1 A-GAATGAA-GAAGGAGGA
50962 AGAATGAAGAAGGA-GA
1 AGAATGAAGAAGGAGGA
* *
50978 AGAA-GAAAAAGTAGGA
1 AGAATGAAGAAGGAGGA
50994 AGAAATGAAGAAG
1 AG-AATGAAGAAG
51007 AAAAAGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.14
16 10 0.20
17 10 0.20
18 17 0.33
19 7 0.14
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (17 bp):
AGAATGAAGAAGGAGGA
Found at i:55991 original size:20 final size:21
Alignment explanation
Indices: 55961--55999 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
55951 ACCACTTAAT
55961 TATTAATTCTTTTACTTTTAC
1 TATTAATTCTTTTACTTTTAC
*
55982 TATTAA-TCTTTTAGTTTT
1 TATTAATTCTTTTACTTTT
56000 GTCAATCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (21 bp):
TATTAATTCTTTTACTTTTAC
Found at i:56438 original size:59 final size:58
Alignment explanation
Indices: 56358--56525 Score: 180
Period size: 59 Copynumber: 2.8 Consensus size: 58
56348 TTAAATTTAA
* * *
56358 ATTTACATTTTAACATTAAAAATATATTTTATTTTATCTTAGATTATTTTATATATTTT
1 ATTTTCATTTTAAC-TTAAAAATATATTTTATCTTATTTTAGATTATTTTATATATTTT
***
56417 ATTTTCATTTTAACTTAAAAAATATATTTTAGTCTTATTTTA-ACTTA-AAAATATATTTT
1 ATTTTCATTTTAACTT-AAAAATATATTTTA-TCTTATTTTAGA-TTATTTTATATATTTT
* * *
56476 AGTCTT-ATTTTAGCTTAAAAATATATTTTAATCTTATTTTAGCTTATTTT
1 A-TTTTCATTTTAACTTAAAAATATATTTT-ATCTTATTTTAGATTATTTT
56526 TTTAATTTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 28 0.31
59 48 0.53
60 14 0.16
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (58 bp):
ATTTTCATTTTAACTTAAAAATATATTTTATCTTATTTTAGATTATTTTATATATTTT
Found at i:56444 original size:30 final size:28
Alignment explanation
Indices: 56364--56587 Score: 165
Period size: 29 Copynumber: 7.8 Consensus size: 28
56354 TTAAATTTAC
56364 ATTTTAACATTAAAAATATATTTTATTTT
1 ATTTTAAC-TTAAAAATATATTTTATTTT
* ***
56393 ATCTTAGA-TTATTTTATATATTTTATTTT
1 ATTTTA-ACTTA-AAAATATATTTTATTTT
*
56422 CATTTTAACTTAAAAAATATATTTTAGTCTT
1 -ATTTTAACTT-AAAAATATATTTTA-TTTT
*
56453 ATTTTAACTTAAAAATATATTTTAGTCTT
1 ATTTTAACTTAAAAATATATTTTA-TTTT
* *
56482 ATTTTAGCTTAAAAATATATTTTAATCTT
1 ATTTTAACTTAAAAATATATTTT-ATTTT
* *
56511 ATTTTAGCTT----AT-TTTTTTAATTTTT
1 ATTTTAACTTAAAAATATATTTT-A-TTTT
* *
56536 ATCTTAACTTATGAAATATATTTTACTTTT
1 ATTTTAACTTA-AAAATATATTTTA-TTTT
* *
56566 ATTTTAA-TTTAATATATATTTT
1 ATTTTAACTTAAAAATATATTTT
56588 TAAAAGTAAA
Statistics
Matches: 161, Mismatches: 20, Indels: 29
0.77 0.10 0.14
Matches are distributed among these distances:
24 7 0.04
25 13 0.08
28 13 0.08
29 77 0.48
30 42 0.26
31 9 0.06
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (28 bp):
ATTTTAACTTAAAAATATATTTTATTTT
Found at i:56546 original size:25 final size:24
Alignment explanation
Indices: 56501--56547 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
56491 TAAAAATATA
* *
56501 TTTTAATCTTATTTTAGCTTATTT
1 TTTTAATCTTATCTTAACTTATTT
*
56525 TTTTAATTTTTATCTTAACTTAT
1 TTTTAA-TCTTATCTTAACTTAT
56548 GAAATATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTAATCTTATCTTAACTTATTT
Found at i:62522 original size:21 final size:22
Alignment explanation
Indices: 62475--62555 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 22
62465 ACACTAGTTA
62475 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
62498 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
62519 GTGCATCGATGCACTCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
62542 GTGCATCGATGCAC
1 GTGCATCGATGCAC
62556 TCTGCTGTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.36
23 32 0.64
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:64829 original size:21 final size:21
Alignment explanation
Indices: 64803--64845 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
64793 AAAAGGGGGA
64803 GAAGATGTGTTATA-ATAAGGG
1 GAAGATGTGTTATAGA-AAGGG
64824 GAAGATGTGTTATAGAAAGGG
1 GAAGATGTGTTATAGAAAGGG
64845 G
1 G
64846 GTAATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (21 bp):
GAAGATGTGTTATAGAAAGGG
Found at i:64880 original size:13 final size:14
Alignment explanation
Indices: 64849--64880 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
64839 AAAGGGGGTA
64849 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
64863 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
64875 ATTTTC
1 ATTTTC
64881 TTGAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 13 0.76
14 1 0.06
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:65356 original size:65 final size:64
Alignment explanation
Indices: 65235--65358 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
65225 TACATTTCAA
* *
65235 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTATGTACAGATGCACATACC
1 ATGCATCGATGCACTCCAGAATATTTTGAACATCGAATGCATTTTATGCACAGATGCACATACC
** *
65299 ATGCATCGATGCACTCCAGGCTCA-TTTGAAACATCGAATGTATTTTATGCATC-GATGCAC
1 ATGCATCGATGCACTCCAGAAT-ATTTTG-AACATCGAATGCATTTTATGCA-CAGATGCAC
65359 CACTAGTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 23 0.44
65 28 0.54
66 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCCAGAATATTTTGAACATCGAATGCATTTTATGCACAGATGCACATACC
Found at i:67486 original size:12 final size:12
Alignment explanation
Indices: 67469--67494 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
67459 ACAAAAAAAC
67469 AAAAAAAGCCAA
1 AAAAAAAGCCAA
67481 AAAAAAAGCCAA
1 AAAAAAAGCCAA
67493 AA
1 AA
67495 TTTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGCCAA
Found at i:67494 original size:10 final size:8
Alignment explanation
Indices: 67452--67485 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
67442 TTTTTTTTTT
67452 CAAAAAAA
1 CAAAAAAA
67460 CAAAAAAA
1 CAAAAAAA
67468 CAAAAAAA
1 CAAAAAAA
67476 GCCAAAAAAA
1 --CAAAAAAA
67486 AAGCCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:76492 original size:23 final size:22
Alignment explanation
Indices: 76410--76489 Score: 81
Period size: 23 Copynumber: 3.6 Consensus size: 22
76400 ACACTAGTTA
*
76410 GTGCATCAATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * *
76433 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
76454 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
*
76477 GCGCATCGATGCA
1 GTGCATCGATGCA
76490 CTCTGCTGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 17 0.38
23 28 0.62
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:78757 original size:21 final size:21
Alignment explanation
Indices: 78731--78773 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
78721 AAAAGGGGGA
*
78731 GAAGATGTGTTATATTAAGGG
1 GAAGATGTGTTATAGTAAGGG
78752 GAAGATGTGTTATAGTAAGGG
1 GAAGATGTGTTATAGTAAGGG
78773 G
1 G
78774 GAGTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (21 bp):
GAAGATGTGTTATAGTAAGGG
Found at i:79289 original size:64 final size:65
Alignment explanation
Indices: 79165--79320 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 65
79155 AAATTAAATT
** *
79165 TCGAATGCATTTTATGTACCGATGCACAAGGTATGCATCAATGCACTCCTGAATATTTTG-AACA
1 TCGAATGCATTTTATGTACCGATGCACAAGCCATGCATCAATGCACTCCAGAATATTTTGAAACA
* **
79229 TCGAATGCATTTTATGTACCGATGCAC-AGACCATGCATCGATGCACTCCAGGCTCA-TTTGAAA
1 TCGAATGCATTTTATGTACCGATGCACAAG-CCATGCATCAATGCACTCCAGAAT-ATTTTGAAA
*
79292 TA
64 CA
* * *
79294 TCGAATGTATTTTATGCATCGATGCAC
1 TCGAATGCATTTTATGTACCGATGCAC
79321 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 49 0.62
65 28 0.35
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAAGCCATGCATCAATGCACTCCAGAATATTTTGAAACA
Found at i:80158 original size:19 final size:20
Alignment explanation
Indices: 80134--80180 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
80124 AAATAGATTT
80134 TTTAATATTAAG-ATGTGAA
1 TTTAATATTAAGTATGTGAA
*
80153 TTTAAT-TT-AGTTTGTGAA
1 TTTAATATTAAGTATGTGAA
80171 TTTAA-ATTAA
1 TTTAATATTAA
80181 ATTGTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTAATATTAAGTATGTGAA
Found at i:80185 original size:18 final size:18
Alignment explanation
Indices: 80134--80186 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
80124 AAATAGATTT
80134 TTTAATATTAAGA-TGTGAA
1 TTTAA-ATTAA-ATTGTGAA
* **
80153 TTTAATTTAGTTTGTGAA
1 TTTAAATTAAATTGTGAA
80171 TTTAAATTAAATTGTG
1 TTTAAATTAAATTGTG
80187 TAAATTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (18 bp):
TTTAAATTAAATTGTGAA
Found at i:84242 original size:11 final size:10
Alignment explanation
Indices: 84219--84266 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
84209 TCAACAATTT
84219 CTTCTTCTTC
1 CTTCTTCTTC
84229 CTTCTTCGTTC
1 CTTCTTC-TTC
84240 CTTCCTTCTTC
1 CTT-CTTCTTC
*
84251 GTTC--CTTC
1 CTTCTTCTTC
84259 CTTCTTCT
1 CTTCTTCT
84267 AACAACCCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 7 0.22
10 10 0.31
11 11 0.34
12 4 0.12
ACGTcount: A:0.00, C:0.40, G:0.04, T:0.56
Consensus pattern (10 bp):
CTTCTTCTTC
Found at i:84245 original size:15 final size:15
Alignment explanation
Indices: 84217--84265 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
84207 CATCAACAAT
84217 TTCTTC-TT-CTTCC
1 TTCTTCGTTCCTTCC
84230 TTCTTCGTTCCTTCC
1 TTCTTCGTTCCTTCC
84245 TTCTTCGTTCCTTCC
1 TTCTTCGTTCCTTCC
84260 TTCTTC
1 TTCTTC
84266 TAACAACCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 26 0.76
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.57
Consensus pattern (15 bp):
TTCTTCGTTCCTTCC
Found at i:85152 original size:11 final size:10
Alignment explanation
Indices: 85135--85205 Score: 85
Period size: 11 Copynumber: 7.1 Consensus size: 10
85125 ATGCCACGTC
85135 AGAAGGAAGA
1 AGAAGGAAGA
85145 ATGAAGGAAGGA
1 A-GAAGGAA-GA
85157 AGAAGGAA-A
1 AGAAGGAAGA
*
85166 GGAAGGAA-A
1 AGAAGGAAGA
85175 AGAAGGAAGA
1 AGAAGGAAGA
85185 CAGAAGGAAGA
1 -AGAAGGAAGA
85196 AGAA-GAAGA
1 AGAAGGAAGA
85205 A
1 A
85206 ATTGTTGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
9 22 0.40
10 6 0.11
11 24 0.44
12 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.38, T:0.01
Consensus pattern (10 bp):
AGAAGGAAGA
Found at i:85156 original size:15 final size:14
Alignment explanation
Indices: 85136--85205 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 14
85126 TGCCACGTCA
85136 GAAGGAAGAATGAAG
1 GAAGGAAGAA-GAAG
85151 GAAGGAAGAAGGAAAG
1 GAAGGAAGAA-G-AAG
85167 GAAGGAA-AAGAAG
1 GAAGGAAGAAGAAG
85180 GAA-GACAGAAGGAA-
1 GAAGGA-AGAA-GAAG
85194 GAA-GAAGAAGAA
1 GAAGGAAGAAGAA
85206 ATTGTTGCTG
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
12 5 0.10
13 11 0.22
14 8 0.16
15 16 0.32
16 10 0.20
ACGTcount: A:0.59, C:0.01, G:0.39, T:0.01
Consensus pattern (14 bp):
GAAGGAAGAAGAAG
Found at i:85203 original size:20 final size:20
Alignment explanation
Indices: 85135--85204 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
85125 ATGCCACGTC
85135 AGAAGGAAGA-ATGAAGGAAGGA
1 AGAAGGAAGACA-GAAGGAA--A
*
85157 AGAAGGAA-A-GGAAGGAAA
1 AGAAGGAAGACAGAAGGAAA
85175 AGAAGGAAGACAGAAGGAAGA
1 AGAAGGAAGACAGAAGGAA-A
85196 AGAA-GAAGA
1 AGAAGGAAGA
85205 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.21
19 1 0.02
20 19 0.44
21 6 0.14
22 8 0.19
ACGTcount: A:0.59, C:0.01, G:0.39, T:0.01
Consensus pattern (20 bp):
AGAAGGAAGACAGAAGGAAA
Found at i:85919 original size:22 final size:21
Alignment explanation
Indices: 85885--85941 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
85875 ATTTAAATTT
85885 ATATTTATATTTTAACATTAAAA
1 ATATTT-TATTTTAAC-TTAAAA
* * *
85908 ATATTTTATTTTTATCTTATAT
1 ATATTTTA-TTTTAACTTAAAA
85930 ATATTTTATTTT
1 ATATTTTATTTT
85942 CATTTTAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 12 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATTTTAACTTAAAA
Found at i:85985 original size:24 final size:25
Alignment explanation
Indices: 85936--85990 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
85926 ATATATATTT
85936 TATTTTCATTTTAACTTAAAATATA
1 TATTTTCATTTTAACTTAAAATATA
* * *
85961 TTTTTTTATTTTAATTTAAAA-ATA
1 TATTTTCATTTTAACTTAAAATATA
85985 TATTTT
1 TATTTT
85991 AGTCTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTTCATTTTAACTTAAAATATA
Found at i:86034 original size:29 final size:27
Alignment explanation
Indices: 85892--86031 Score: 125
Period size: 29 Copynumber: 5.3 Consensus size: 27
85882 TTTATATTTA
85892 TATTTTAACATTAAAA-ATATTTTA---
1 TATTTTAAC-TTAAAATATATTTTATCT
* * *
85916 T-TTTTATCTT-ATATATATTTTATTT
1 TATTTTAACTTAAAATATATTTTATCT
85941 TCATTTTAACTTAAAATATATTTT-T-T
1 T-ATTTTAACTTAAAATATATTTTATCT
*
85967 TATTTTAATTTAAAAATATATTTTAGTCT
1 TATTTTAACTT-AAAATATATTTTA-TCT
*
85996 TATTTTAGCTTCAAAATATATTTTAATCT
1 TATTTTAACTT-AAAATATATTTT-ATCT
86025 TATTTTA
1 TATTTTA
86032 GCTATTTTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.02
22 10 0.10
23 6 0.06
24 1 0.01
25 10 0.10
26 14 0.15
27 9 0.09
28 11 0.11
29 32 0.33
30 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (27 bp):
TATTTTAACTTAAAATATATTTTATCT
Found at i:86229 original size:30 final size:29
Alignment explanation
Indices: 86089--86226 Score: 125
Period size: 30 Copynumber: 4.6 Consensus size: 29
86079 TTTTAATTTT
* ** *
86089 ATATATTTTTAAAACTAAATATAAGAATAAT
1 ATATATTTTTTAAGTTAAA-ATAA-AATAAA
*
86120 ATATA-TTTTTAAGTTAAAATAAGATTAAA
1 ATATATTTTTTAAGTTAAAATAA-AATAAA
* * *
86149 GTATATTTTTTAATTTAAAACAAATATAAA
1 ATATATTTTTTAAGTTAAAATAAA-ATAAA
** *
86179 ATATATTTAATAAGTTAAGATAAAATAAA
1 ATATATTTTTTAAGTTAAAATAAAATAAA
86208 ATATATTTTTTAATGTTAA
1 ATATATTTTTTAA-GTTAA
86227 GATGTGAATT
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
29 30 0.34
30 52 0.60
31 5 0.06
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATATTTTTTAAGTTAAAATAAAATAAA
Found at i:87089 original size:13 final size:13
Alignment explanation
Indices: 87071--87097 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
87061 TTACAGATGC
87071 GCATATGAAGACT
1 GCATATGAAGACT
87084 GCATATGAAGACT
1 GCATATGAAGACT
87097 G
1 G
87098 TTCAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:87117 original size:4 final size:4
Alignment explanation
Indices: 87108--87134 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
87098 TTCAACTATG
87108 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
87135 ACATGCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:90745 original size:5 final size:5
Alignment explanation
Indices: 90735--90814 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
90725 AACGGTCAAC
* *
90735 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
90784 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
90815 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:90756 original size:22 final size:22
Alignment explanation
Indices: 90728--90814 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
90718 AACGGTCAAC
90728 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
90750 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
90772 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
90794 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
90815 AGACCGGTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:90760 original size:17 final size:16
Alignment explanation
Indices: 90740--90815 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 16
90730 TCAACGGTCG
90740 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC-AC
*
90757 GGTCGGGTCGGGTC-G
1 GGTCGGGTCGGGTCAC
** *
90772 GGTC--AAC-GGTC-G
1 GGTCGGGTCGGGTCAC
90784 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC-AC
90801 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
90816 GACCGGTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
14 1 0.02
15 8 0.17
16 1 0.02
17 28 0.58
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.18
Consensus pattern (16 bp):
GGTCGGGTCGGGTCAC
Found at i:90829 original size:9 final size:9
Alignment explanation
Indices: 90811--90909 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
90801 GGTCGGGTCG
*
90811 GGTCAGACC
1 GGTCAAACC
90820 GGTCAAACC
1 GGTCAAACC
* *
90829 GATTCAGACC
1 G-GTCAAACC
90839 GGTCAAACC
1 GGTCAAACC
*
90848 GGTTCGAACC
1 GG-TCAAACC
*
90858 GGTTGAAACC
1 GG-TCAAACC
*
90868 GATCAAACC
1 GGTCAAACC
90877 GGTCAGAACC
1 GGTCA-AACC
*
90887 GGTTGAAAACC
1 GG-T-CAAACC
*
90898 GGTTAAACC
1 GGTCAAACC
90907 GGT
1 GGT
90910 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:90835 original size:19 final size:19
Alignment explanation
Indices: 90813--90887 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
90803 TCGGGTCGGG
90813 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
90832 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGAT
*
90851 TC-GAACCGGTTGAAACCGA-
1 TCAG-ACCGG-TCAAACCGAT
*
90870 TCAAACCGGTCAGAACCG
1 TCAGACCGGTCA-AACCG
90888 GTTGAAAACC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 3 0.06
19 37 0.79
20 7 0.15
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:90868 original size:29 final size:31
Alignment explanation
Indices: 90836--90910 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
90826 ACCGATTCAG
90836 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
90865 ACCGATCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
90895 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
90911 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 14 0.35
31 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:98106 original size:5 final size:5
Alignment explanation
Indices: 98096--98153 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
98086 AACGGTCAAC
* *
98096 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
98145 GGTCG GGTC
1 GGTCG GGTC
98154 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:98116 original size:7 final size:7
Alignment explanation
Indices: 98069--98099 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
98059 GTCAAAGAAA
*
98069 GTCAACA
1 GTCAACG
98076 GTCAACG
1 GTCAACG
98083 GTCAACG
1 GTCAACG
98090 GTCAACG
1 GTCAACG
98097 GTC
1 GTC
98100 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:98124 original size:22 final size:22
Alignment explanation
Indices: 98082--98154 Score: 119
Period size: 22 Copynumber: 3.2 Consensus size: 22
98072 AACAGTCAAC
*
98082 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
98106 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
98128 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
98150 GGTCA
1 GGTCA
98155 GACCGGTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 37 0.77
24 11 0.23
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:98148 original size:17 final size:17
Alignment explanation
Indices: 98089--98126 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
98079 AACGGTCAAC
98089 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
98106 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
98123 GGTC
1 GGTC
98127 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:98168 original size:9 final size:9
Alignment explanation
Indices: 98150--98219 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
98140 GGTCGGGTCG
*
98150 GGTCAGACC
1 GGTCAAACC
98159 GGTCAAACC
1 GGTCAAACC
*
98168 GGTTCGAACC
1 GG-TCAAACC
*
98178 GGTTGAAACC
1 GG-TCAAACC
98188 GGTCAAACC
1 GGTCAAACC
*
98197 GGTTGAAAACC
1 GG-T-CAAACC
*
98208 GGTTAAACC
1 GGTCAAACC
98217 GGT
1 GGT
98220 TTCCAGCAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 26 0.51
10 18 0.35
11 7 0.14
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:98188 original size:20 final size:21
Alignment explanation
Indices: 98163--98220 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
98153 CAGACCGGTC
*
98163 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCAAACCGGTTGA
98183 AAACCGG-TCAAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
98203 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
98221 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 11 0.31
20 23 0.66
21 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:98190 original size:29 final size:28
Alignment explanation
Indices: 98156--98219 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
98146 GTCGGGTCAG
98156 ACCGGTCAAACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTT-GAAACCGGTT-AA
98185 ACCGGTCAAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGGTTG-AAACCGGTTAA
98214 ACCGGT
1 ACCGGT
98220 TTCCAGCAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.73
30 8 0.24
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTGAAACCGGTTAA
Found at i:98220 original size:9 final size:10
Alignment explanation
Indices: 98163--98220 Score: 68
Period size: 9 Copynumber: 5.9 Consensus size: 10
98153 CAGACCGGTC
98163 AAACCGGTTCG
1 AAACCGGTT-G
98174 -AACCGGTTG
1 AAACCGGTTG
*
98183 AAACCGG-TC
1 AAACCGGTTG
98192 AAACCGGTTG
1 AAACCGGTTG
98202 AAAACCGGTT-
1 -AAACCGGTTG
98212 AAACCGGTT
1 AAACCGGTT
98221 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 18 0.43
10 15 0.36
11 9 0.21
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:99982 original size:20 final size:20
Alignment explanation
Indices: 99936--100048 Score: 131
Period size: 20 Copynumber: 5.6 Consensus size: 20
99926 TATTTCAATT
*
99936 TCAGTATCGAGACCTTC-CTA
1 TCAGTATCGATACCTTCAC-A
**
99956 TTGGTATCGATACCTTCACA
1 TCAGTATCGATACCTTCACA
*
99976 TCAGTATTGATACCTTCACA
1 TCAGTATCGATACCTTCACA
*
99996 TTAGTATCGATACCTTCACA
1 TCAGTATCGATACCTTCACA
100016 TCAGTATCGATACTACTTCA-A
1 TCAGTATCGATAC--CTTCACA
*
100037 TCAGTATAGATA
1 TCAGTATCGATA
100049 TTGTTCATCG
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
20 62 0.77
21 13 0.16
22 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
TCAGTATCGATACCTTCACA
Found at i:101245 original size:34 final size:34
Alignment explanation
Indices: 101202--101266 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
101192 AACTCCTTAG
* *
101202 TTTTTCACGGGATAAACTAGAACCTTTCCCTAGC
1 TTTTACACGGGATAAACTAGAACATTTCCCTAGC
* *
101236 TTTTACACGGGCTAAGCTAGAACATTTCCCT
1 TTTTACACGGGATAAACTAGAACATTTCCCT
101267 TTTACAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (34 bp):
TTTTACACGGGATAAACTAGAACATTTCCCTAGC
Found at i:105290 original size:22 final size:20
Alignment explanation
Indices: 105249--105291 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
105239 TTACTCTTAT
*
105249 TATATACATGCCTATTACCA
1 TATATACATGCCTATCACCA
*
105269 TATATAGATGCCTTCATCACCA
1 TATATACATGCC-T-ATCACCA
105291 T
1 T
105292 TTCACCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATACATGCCTATCACCA
Found at i:108751 original size:34 final size:34
Alignment explanation
Indices: 108712--108807 Score: 167
Period size: 34 Copynumber: 2.9 Consensus size: 34
108702 ATACACACAT
108712 ACGTATGATCTTAAATTTATGTATAAAACATTAA
1 ACGTATGATCTTAAATTTATGTATAAAACATTAA
*
108746 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
1 ACGTATGATCTTAAATTTATGTATAAAACATTAA
*
108780 ACGTATGATCTTAAA-TTATGTATTAAAC
1 ACGTATGATCTTAAATTTATGTATAAAAC
108808 TTGAAATTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 12 0.20
34 48 0.80
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (34 bp):
ACGTATGATCTTAAATTTATGTATAAAACATTAA
Found at i:113235 original size:31 final size:31
Alignment explanation
Indices: 113195--113269 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
113185 TACCTATGAT
*
113195 ATTACATCTTAAATAAATAAAAACAAAAGTA
1 ATTATATCTTAAATAAATAAAAACAAAAGTA
* *
113226 ATTATATCTTAATTAAATAAAAATAAAAGTA
1 ATTATATCTTAAATAAATAAAAACAAAAGTA
* *
113257 ACTATATTTTAAA
1 ATTATATCTTAAA
113270 ATTAATAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (31 bp):
ATTATATCTTAAATAAATAAAAACAAAAGTA
Done.