Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002526.1 Hibiscus syriacus cultivar Beakdansim tig00005139_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: 153185
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5817 original size:60 final size:62
Alignment explanation
Indices: 5749--5870 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 62
5739 AGGTCTTTAT
* * *
5749 TATCTATTTACCTTTGAATA-TTAAAGATAA-TTATA-TATTAAATATTTCAAATTAAAATAA
1 TATCTATTTAACTTTGAATAGTAAAAGA-AATTTATACTATTAAATATTTAAAATTAAAATAA
* * *
5809 TATCTATTTAAGTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTAAAATTAAAATA
1 TATCTATTTAACTTTGAATAGTAAAAGAAATTTATA-CTATTAAATATTTAAAATTAAAATA
5871 TATTACTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
60 20 0.38
61 11 0.21
63 21 0.40
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (62 bp):
TATCTATTTAACTTTGAATAGTAAAAGAAATTTATACTATTAAATATTTAAAATTAAAATAA
Found at i:7566 original size:63 final size:63
Alignment explanation
Indices: 7486--7607 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
7476 GGTATTTATC
* * ** *
7486 ATCTCTTTAACTTTGAATATTAAATGTAA-TTATATAATTTCT-AATATTTTAAATTAAAATAAT
1 ATCTATTTAACTTTGAATAGTAAAAATAATTTATAT-ATTT-TGAATATTTCAAATTAAAATAAT
* *
7549 ATCTATTTAAGTTTGAATAGTAAAAATAGTTTATATATTTTGAATATTTCAAATTAAAA
1 ATCTATTTAACTTTGAATAGTAAAAATAATTTATATATTTTGAATATTTCAAATTAAAA
7608 GATATTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 43 0.86
64 6 0.12
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (63 bp):
ATCTATTTAACTTTGAATAGTAAAAATAATTTATATATTTTGAATATTTCAAATTAAAATAAT
Found at i:10210 original size:12 final size:12
Alignment explanation
Indices: 10190--10220 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10180 AAAATCATTT
10190 AAATATATTTTA
1 AAATATATTTTA
*
10202 AAATTTATTTTA
1 AAATATATTTTA
10214 AAATATA
1 AAATATA
10221 GATTGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:10219 original size:22 final size:20
Alignment explanation
Indices: 10203--10502 Score: 170
Period size: 22 Copynumber: 13.7 Consensus size: 20
10193 TATATTTTAA
10203 AATTTATTTTAAAATATAGATT
1 AATTTATTTTAAAATAT--ATT
*
10225 GATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATAT--ATT
* **
10247 GATTTATTTTAAAATATGAAA
1 AATTTATTTTAAAATAT-ATT
*
10268 AAATTATTTTAAAATATTGATT
1 AATTTATTTTAAAATA-T-ATT
* **
10290 GATTTATTTTAAAATATAGAAA
1 AATTTATTTTAAAATAT--ATT
10312 AATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATAT--ATT
* **
10334 GATTTATTTTAAAATATGAAAA
1 AATTTATTTTAAAATAT--ATT
* *
10356 AAATTATTTTAAAATACGGATT
1 AATTTATTTTAAAATA--TATT
* *
10378 GATTTATTTTAAAATATGGA-A
1 AATTTATTTTAAAATAT--ATT
10399 AATTTTATTTTAAAATATGGATT
1 AA-TTTATTTTAAAATAT--ATT
*
10422 GATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATAT--ATT
* **
10444 GATTTATTTTAAAATATGGAAAA
1 AATTTATTTTAAAATAT---ATT
10467 AATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATAT--ATT
*
10489 GATTTATTTTAAAA
1 AATTTATTTTAAAA
10503 AATTTATTAT
Statistics
Matches: 229, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.08
22 192 0.84
23 19 0.08
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
AATTTATTTTAAAATATATT
Found at i:10253 original size:44 final size:44
Alignment explanation
Indices: 10204--10502 Score: 402
Period size: 44 Copynumber: 6.8 Consensus size: 44
10194 ATATTTTAAA
* ***
10204 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
* *
10248 ATTTATTTTAAAATAT-GAAAAAATTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
*
10291 ATTTATTTTAAAATATAGAAAAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
* * *
10335 ATTTATTTTAAAATATGAAAAAAATTATTTTAAAATACGGATTG
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
*
10379 ATTTATTTTAAAATATGGAAAATTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
*** ***
10423 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAAAA
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGG-ATTG
***
10468 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAA
10503 AATTTATTAT
Statistics
Matches: 231, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
43 38 0.16
44 157 0.68
45 36 0.16
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.46
Consensus pattern (44 bp):
ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
Found at i:10272 original size:66 final size:66
Alignment explanation
Indices: 10201--10502 Score: 426
Period size: 66 Copynumber: 4.6 Consensus size: 66
10191 AATATATTTT
*
10201 AAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
10266 A
66 A
* * *** *
10267 AAAA-TTATTTTAAAATATTGATTGATTTATTTTAAAATATAGAAAAATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
10331 A
66 A
*** * *** * * *
10332 TTGATTTATTTTAAAATATGAAAAAAATTATTTTAAAATACGGATTGATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
10397 A
66 A
*
10398 AAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-G
10463 AA
65 AA
10465 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAA
10503 AATTTATTAT
Statistics
Matches: 202, Mismatches: 32, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
65 56 0.28
66 107 0.53
67 39 0.19
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (66 bp):
AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
A
Found at i:10583 original size:31 final size:31
Alignment explanation
Indices: 10525--10584 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
10515 TAGTTGTATG
*
10525 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
10556 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
10585 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:14279 original size:22 final size:22
Alignment explanation
Indices: 14254--14295 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14244 GGCTGCCTAA
*
14254 CTTTGAAATTTAAAGCAGCCCC
1 CTTTGAAAATTAAAGCAGCCCC
*
14276 CTTTGAAAATTCAAGCAGCC
1 CTTTGAAAATTAAAGCAGCC
14296 ACCGGCTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (22 bp):
CTTTGAAAATTAAAGCAGCCCC
Found at i:24205 original size:2 final size:2
Alignment explanation
Indices: 24198--24224 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24188 ATCAAGTTAT
24198 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 T
24225 CCATGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41933 original size:2 final size:2
Alignment explanation
Indices: 41926--41958 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41916 AGAAAAATAA
41926 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41959 AATTCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43417 original size:18 final size:18
Alignment explanation
Indices: 43394--43429 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43384 AAATATTACA
*
43394 TACAATTTGGACAAAACG
1 TACAATTTGAACAAAACG
43412 TACAATTTGAACAAAACG
1 TACAATTTGAACAAAACG
43430 AACTTGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (18 bp):
TACAATTTGAACAAAACG
Found at i:44307 original size:72 final size:72
Alignment explanation
Indices: 44228--44372 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
44218 ATCAAGGGAG
*
44228 AAATTGATGGCCCAATAGTAAATTTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAA
1 AAATTGATGACCCAATAGTAAATTTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAA
44293 GGGACTT
66 GGGACTT
* *
44300 AAATTGATGACCCAATTGTAAATTTTTTAAAGTTGTAGTTCGGTTTAGGAACCTGTGGAAGTTAA
1 AAATTGATGACCCAATAGTAAATTTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAA
44365 GGGACTT
66 GGGACTT
44372 A
1 A
44373 TCCTTGAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (72 bp):
AAATTGATGACCCAATAGTAAATTTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAA
GGGACTT
Found at i:45134 original size:22 final size:22
Alignment explanation
Indices: 45096--45152 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
45086 CGGTTTTATC
*
45096 GTTAACATTTGATCGGT-TAGACT
1 GTTAAC-TTTGACCGGTCT-GACT
45119 GTTAACTTTGACCGGTCTGACT
1 GTTAACTTTGACCGGTCTGACT
*
45141 GTTGACTTTGAC
1 GTTAACTTTGAC
45153 TTTGACCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (22 bp):
GTTAACTTTGACCGGTCTGACT
Found at i:46119 original size:34 final size:34
Alignment explanation
Indices: 46076--46144 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
46066 GCTCTGAAAT
46076 TAATAAATCAACCTCGTATACCAATATGACTATA
1 TAATAAATCAACCTCGTATACCAATATGACTATA
46110 TAATAAATCAACCTCGTATACCAATATGACTATA
1 TAATAAATCAACCTCGTATACCAATATGACTATA
46144 T
1 T
46145 TATATGACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.30
Consensus pattern (34 bp):
TAATAAATCAACCTCGTATACCAATATGACTATA
Found at i:47186 original size:36 final size:36
Alignment explanation
Indices: 47146--47226 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
47136 CATCGACTGA
*
47146 TAATTCCTTATATGTGGCAGGTTCAGTCGCTGCTAG
1 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
*
47182 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTGG
1 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
47218 TAATTCCTT
1 TAATTCCTT
47227 GAATAGGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
Found at i:47238 original size:31 final size:33
Alignment explanation
Indices: 47146--47258 Score: 97
Period size: 36 Copynumber: 3.3 Consensus size: 33
47136 CATCGACTGA
* *
47146 TAATTCCTTATATGTGGCAGGTTCAGTCGCTGCTAG
1 TAATTCCTTA-AAGT-G-AGGTTCAGTCGCTGCTGG
47182 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTGG
1 TAATTCCTTAAA-GT-G-AGGTTCAGTCGCTGCTGG
* * *
47218 TAATTCCTTGAA-T-AGGTTCAG-CACCGACTGG
1 TAATTCCTTAAAGTGAGGTTCAGTCGCTG-CTGG
47249 TAATTCCTTA
1 TAATTCCTTA
47259 TGGACCTAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.04
31 21 0.30
34 1 0.01
35 1 0.01
36 43 0.62
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (33 bp):
TAATTCCTTAAAGTGAGGTTCAGTCGCTGCTGG
Found at i:54293 original size:20 final size:21
Alignment explanation
Indices: 54268--54319 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54258 TTTTCCCAAT
*
54268 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
54288 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
54309 TCGCAATGCGA
1 TCGCAATGCGA
54320 TACTGACTAT
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:54333 original size:20 final size:20
Alignment explanation
Indices: 54308--54421 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
54298 AATTGGGAAA
*
54308 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
54328 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
54348 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
54369 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
54389 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
54409 TTCGCAACGCGAT
1 ATCGCAACGCGAT
54422 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:54352 original size:61 final size:61
Alignment explanation
Indices: 54305--54421 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
54295 GCGAATTGGG
* * * * *
54305 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
54366 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
54422 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:54987 original size:20 final size:20
Alignment explanation
Indices: 54941--54997 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
54931 TTCGAGAATG
*
54941 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGAAAATA
**
54961 ACTATCGCAACGC-AAAATAA
1 AAAATCGCAACGCGAAAAT-A
54981 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
54998 CCAAAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATA
Found at i:55003 original size:20 final size:19
Alignment explanation
Indices: 54941--55008 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
54931 TTCGAGAATG
*
54941 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAAAA
** *
54961 ACTATCGCAACGCAAAATAA
1 AAAATCGCAACGCGAAA-AA
**
54981 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAAAA
55000 AAAATCGCA
1 AAAATCGCA
55009 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 12 0.32
20 26 0.68
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAAAA
Found at i:55026 original size:19 final size:19
Alignment explanation
Indices: 55004--55188 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
54994 GAAACCAAAA
*
55004 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
55023 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
55042 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
55061 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
55081 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
55097 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
55114 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
55128 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
55147 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
55167 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
55187 TC
1 TC
55189 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55082 original size:39 final size:38
Alignment explanation
Indices: 55004--55188 Score: 147
Period size: 33 Copynumber: 5.1 Consensus size: 38
54994 GAAACCAAAA
*
55004 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
55042 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-ATTGCGATTTTCATT
* * * **
55081 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* **
55114 TCGCGTTGCGA--TTC-TCTCG--TTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* * *
55147 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCATTGCGATTTTCATT
55187 TC
1 TC
55189 AACCAAAAGA
Statistics
Matches: 121, Mismatches: 15, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.02
33 38 0.31
34 11 0.09
35 1 0.01
36 3 0.02
37 1 0.01
38 23 0.19
39 29 0.24
40 13 0.11
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:55165 original size:20 final size:20
Alignment explanation
Indices: 55131--55188 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
55121 GCGATTCTCT
**
55131 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
55151 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
55171 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
55189 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:58851 original size:12 final size:12
Alignment explanation
Indices: 58834--58858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58824 TCTTCGGGGA
58834 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58846 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58858 C
1 C
58859 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:59067 original size:24 final size:24
Alignment explanation
Indices: 59033--59086 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
59023 CTGAATCATC
* *
59033 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAA
*
59057 ATCAAAGTCCGGGTATTGACCAAA
1 ATCAAAATCCGGGTATTGACCAAA
59081 ATCAAA
1 ATCAAA
59087 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAA
Found at i:60169 original size:20 final size:20
Alignment explanation
Indices: 60144--60193 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
60134 ATTCATTTGA
*
60144 CTATCGCAATACGAAAATGG
1 CTATCGCAACACGAAAATGG
**
60164 CTATCGCAACGTGAAAATGG
1 CTATCGCAACACGAAAATGG
*
60184 TTATCGCAAC
1 CTATCGCAAC
60194 GAGAAAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
CTATCGCAACACGAAAATGG
Found at i:60194 original size:20 final size:20
Alignment explanation
Indices: 60156--60201 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
60146 ATCGCAATAC
*
60156 GAAAATGGCTATCGCAACGT
1 GAAAATGGCTATCGCAACGA
*
60176 GAAAATGGTTATCGCAACGA
1 GAAAATGGCTATCGCAACGA
60196 GAAAAT
1 GAAAAT
60202 CGCAATGCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (20 bp):
GAAAATGGCTATCGCAACGA
Found at i:60244 original size:14 final size:14
Alignment explanation
Indices: 60225--60277 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 14
60215 GAAAATCGCA
60225 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
*
60239 TTGCGATTTCATTTCG
1 TTGCGATTT--TCTCG
60255 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
60271 TTGCGAT
1 TTGCGAT
60278 AGCCATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 16 0.48
16 8 0.24
18 9 0.27
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:60260 original size:18 final size:16
Alignment explanation
Indices: 60220--60270 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
60210 GAAATGAAAA
60220 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
*
60236 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTT--TC
60252 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
60268 TCG
1 TCG
60271 TTGCGATAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.31
16 11 0.38
18 9 0.31
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:62301 original size:20 final size:19
Alignment explanation
Indices: 62266--62332 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
62256 GAAACTTAAA
62266 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
62285 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
62305 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
62324 ATCGCAACG
1 ATCGCAACG
62333 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:62340 original size:14 final size:14
Alignment explanation
Indices: 62321--62378 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
62311 ATGCGAAATG
62321 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
62335 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
62351 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
62367 AAAATCGCAACG
1 AAAATCGCAACG
62379 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:62363 original size:32 final size:33
Alignment explanation
Indices: 62305--62383 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
62295 GGAAATGGCT
*
62305 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62338 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62370 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
62384 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:62431 original size:14 final size:14
Alignment explanation
Indices: 62412--62469 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
62402 TTTCATTTCG
62412 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
62426 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
62442 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
62458 CGTTGCGATTTT
1 CGTTGCGATTTT
62470 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62476 original size:33 final size:33
Alignment explanation
Indices: 62395--62485 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
62385 ACAAATCGCA
*
62395 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62428 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62460 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
62486 AGCCATTTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:62521 original size:20 final size:20
Alignment explanation
Indices: 62472--62524 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
62462 GCGATTTTCA
*
62472 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
62492 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
62512 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
62525 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:64003 original size:15 final size:15
Alignment explanation
Indices: 63985--64026 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
63975 AACATCCATA
*
63985 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
64000 AATCCACAAAATCAAAC
1 AAT-C-CAAAATCAAAC
64017 AATCCAAAAT
1 AATCCAAAAT
64027 ATAATGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:64011 original size:17 final size:17
Alignment explanation
Indices: 63989--64022 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
63979 TCCATAAATC
*
63989 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
64006 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
64023 AAATATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:72576 original size:18 final size:18
Alignment explanation
Indices: 72550--72594 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
72540 GTCGATCAGA
*
72550 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
72568 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
72586 TGATGGCTC
1 TGATGGCTC
72595 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:73933 original size:20 final size:20
Alignment explanation
Indices: 73908--73945 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
73898 AATAGTTTCT
73908 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
73928 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
73946 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:74463 original size:20 final size:20
Alignment explanation
Indices: 74438--74531 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
74428 GATTATGTAT
74438 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
74458 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
74478 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
74499 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
74519 TATCGCATTGCGA
1 TATCGCGTTGCGA
74532 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:74532 original size:20 final size:20
Alignment explanation
Indices: 74418--74532 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
74408 CGCTTTGAAA
*
74418 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
74439 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
74459 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
74479 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
74500 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
74520 ATCGCATTGCGAT
1 ATCGCATTGCGAT
74533 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:74550 original size:21 final size:21
Alignment explanation
Indices: 74521--74613 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
74511 ATAGTCAGTA
74521 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
74542 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
74562 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
74583 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
74603 TCGCATTGCGA
1 TCGCATTGCGA
74614 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:74551 original size:41 final size:41
Alignment explanation
Indices: 74460--74594 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
74450 AAAGTCAGTA
* * * ** *
74460 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
74500 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
74542 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
74583 TCGCGTTGCGAT
1 TCGCGTTGCGAT
74595 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:74595 original size:41 final size:41
Alignment explanation
Indices: 74521--74613 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
74511 ATAGTCAGTA
74521 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
74562 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
74603 TCGCATTGCGA
1 TCGCATTGCGA
74614 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:77220 original size:2 final size:2
Alignment explanation
Indices: 77213--77258 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
77203 AATTGGATCC
77213 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
77255 CT CT
1 CT CT
77259 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:78825 original size:18 final size:19
Alignment explanation
Indices: 78783--78819 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
78773 AACTAAGGGT
78783 CAAGTTTTTCTTCTTTCCC
1 CAAGTTTTTCTTCTTTCCC
78802 CAAGTTTTTCTTCTTTCC
1 CAAGTTTTTCTTCTTTCC
78820 TAAGTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.30, G:0.05, T:0.54
Consensus pattern (19 bp):
CAAGTTTTTCTTCTTTCCC
Found at i:80284 original size:133 final size:134
Alignment explanation
Indices: 80046--80580 Score: 763
Period size: 133 Copynumber: 4.0 Consensus size: 134
80036 AAATTTCAAA
* * * *
80046 CCATCCAGTAAG-GAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACA--CA
1 CCATCCGGTAAGAG-AACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAA-ATGCA
* * * *
80108 AACATTCACAGGATATATAACATAATTTCAGAAACACAGAGAAATGAAGATTCACTTCCAAAGAA
64 AACATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAA
* *
80173 ATAAAT
129 AGAAAG
*
80179 CCATCCGGTAAGAGAACATACAGGAAAGCATGATAAGTAG-TTTCAGTGTGACTATAAATGCAAA
1 CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
* * *
80243 CATTTACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCATTTCCAAAGAAAG
66 CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
80308 AAAG
131 AAAG
* * * *
80312 CCATCCTGTAAGAAAAACATATGGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATTAATGCAA
1 CCATCCGGTAAG-AGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAA
* * *
80377 ACATTCACATGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTTCAAAGAA
65 ACATTCACA-GGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAA
80442 AGAAAG
129 AGAAAG
* * * *
80448 CCATACGGTGATAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGAGACTATAAATGCAAA
1 CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
* *
80513 CATTCACAGGAAATATAACATAATTTCAGAAACAGATAGAAATGAAGATTCAGTTCCAAAGAAAG
66 CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
80578 AAA
131 AAA
80581 TTTCAATAAT
Statistics
Matches: 360, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
131 1 0.00
132 16 0.04
133 110 0.31
134 81 0.22
135 87 0.24
136 65 0.18
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (134 bp):
CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
AAAG
Found at i:80557 original size:270 final size:266
Alignment explanation
Indices: 80046--80580 Score: 800
Period size: 269 Copynumber: 2.0 Consensus size: 266
80036 AAATTTCAAA
*
80046 CCATCCAGTAAGGAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
1 CCATCCAGTAAGAAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
* * * * * *
80111 ATTCACAGGATATATAACATAATTTCAGAAACACAGAGAAATGAAGATTCACTTCCAAAGAAATA
66 ATTCACAGGAAATACAACATAATTTCAAAAACAAAGAGAAATGAAGATTCAATTCCAAAGAAAGA
* * *
80176 AATCCATCCGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGTGACTATAAATGCA
131 AAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGAGACTATAAATGCA
* *
80241 AACATTTACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCATTTCCAAAGAA
196 AACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAAAGAA
80306 AGAAAG
261 AGAAAG
* * * * * **
80312 CCATCCTGTAAGAAAAACATATGGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATTAATGCAA
1 CCATCCAGTAAG-AAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTA-TAACACAA
* *
80377 ACATTCACATGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTTCAAAGAA
64 ACATTCACA-GGAAATACAACATAATTTCAAAAACAAAGAGAAATGAAGATTCAATTCCAAAGAA
* * *
80442 AGAAAGCCATACGGTGATAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGAGACTATAAA
128 AGAAAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAG-TTTCAGTGAGACTATAAA
* *
80507 TGCAAACATTCACAGGAAATATAACATAATTTCAGAAACAGATAGAAATGAAGATTCAGTTCCAA
192 TGCAAACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAA
80572 AGAAAGAAA
257 AGAAAGAAA
80581 TTTCAATAAT
Statistics
Matches: 239, Mismatches: 26, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
266 11 0.05
267 38 0.16
268 15 0.06
269 88 0.37
270 87 0.36
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (266 bp):
CCATCCAGTAAGAAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
ATTCACAGGAAATACAACATAATTTCAAAAACAAAGAGAAATGAAGATTCAATTCCAAAGAAAGA
AAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGAGACTATAAATGCA
AACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAAAGAA
AGAAAG
Found at i:83729 original size:19 final size:19
Alignment explanation
Indices: 83705--83742 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
83695 TTCCAAAATG
**
83705 TCTAGGGGTTATCGATTCC
1 TCTAGGGGGAATCGATTCC
83724 TCTAGGGGGAATCGATTCC
1 TCTAGGGGGAATCGATTCC
83743 CCCTAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (19 bp):
TCTAGGGGGAATCGATTCC
Found at i:84213 original size:46 final size:46
Alignment explanation
Indices: 84143--84255 Score: 169
Period size: 46 Copynumber: 2.5 Consensus size: 46
84133 GAGATAAGAT
** *
84143 ATGTGAT-T-ATATGAAATGGTATATGAATATGCAATATGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
84187 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
84233 ATGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
84256 GGTTACACAT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 51 0.81
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:84472 original size:38 final size:38
Alignment explanation
Indices: 84404--84499 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
84394 TATAAGACAT
* *
84404 ATGATAGGTCCTACGGGACACAGATTACATCCTTCAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
* * * *
84442 ATGACAGGTCCTTCGGGATACATATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
84480 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
84500 TTTATACGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
Found at i:84493 original size:17 final size:17
Alignment explanation
Indices: 84433--84497 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
84423 ACAGATTACA
* *
84433 TCCTTCAGGATGACAGG
1 TCCTTCGGGATGATAGG
* *
84450 TCCTTCGGGATACATATGACA
1 TCCTTCGGGAT-GATA-G--G
84471 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
84488 TCCTTCGGGA
1 TCCTTCGGGA
84498 CATTTATACG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 20 0.53
18 2 0.05
19 2 0.05
20 3 0.08
21 11 0.29
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:96372 original size:2 final size:2
Alignment explanation
Indices: 96365--96395 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
96355 CACTGCACTT
96365 TC 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 TC T
96396 AAATATAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:97492 original size:16 final size:16
Alignment explanation
Indices: 97473--97506 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
97463 CAATATACGA
97473 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
97489 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
97505 AT
1 AT
97507 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:97580 original size:16 final size:18
Alignment explanation
Indices: 97548--97581 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
97538 TATTAATGTA
97548 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
97566 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
97582 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:98284 original size:130 final size:130
Alignment explanation
Indices: 98051--98298 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
98041 AATTTTCTTC
* *
98051 TAATTAGGCGGTGACATGTGTCACAAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGCGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
98116 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
98181 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGCGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
98246 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
98299 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGCGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:98736 original size:35 final size:35
Alignment explanation
Indices: 98686--98761 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
98676 AATCTGACAT
* *
98686 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
98721 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
98756 AATTGA
1 AATTGA
98762 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:99339 original size:13 final size:12
Alignment explanation
Indices: 99303--99343 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 12
99293 AATTTTTTTA
99303 TATTTAAAAAAT
1 TATTTAAAAAAT
99315 TATACTTAAAAAAT
1 TAT--TTAAAAAAT
99329 TATTTATAAAAAT
1 TATTTA-AAAAAT
99342 TA
1 TA
99344 ATTCAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TATTTAAAAAAT
Found at i:110540 original size:23 final size:23
Alignment explanation
Indices: 110474--110543 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
110464 CACCACAGTT
* *
110474 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
110497 CGTAGAATTTGCACC-ATAGTGCCG
1 CGTAGAA-ATGCACCGA-AGTGCCA
110521 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
110544 TATAAAGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:110977 original size:20 final size:21
Alignment explanation
Indices: 110930--110980 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
110920 TTTTGTGTCT
*
110930 TATCATATAACTTCTCTTTTA
1 TATCATATAACTTCTCTTTCA
110951 TATTCATATAA-TT-TCTTATCA
1 TA-TCATATAACTTCTCTT-TCA
110972 TATCATATA
1 TATCATATA
110981 GTTTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCATATAACTTCTCTTTCA
Found at i:111468 original size:45 final size:45
Alignment explanation
Indices: 111400--111500 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 45
111390 CTACCTATGT
* * * *
111400 ATCGATACACAAATCACCTTCGATGTTTTC-ATTTTAAGGGGGTGC
1 ATCGATGCACTAATCACATTCGATGTTTCCAATTTTAA-GGGGTGC
* *
111445 ATCGATGCACTAATTACATTCGATGTTTCCAATTTTAATGGGTGC
1 ATCGATGCACTAATCACATTCGATGTTTCCAATTTTAAGGGGTGC
111490 ATCGATGCACT
1 ATCGATGCACT
111501 TCCTGTGCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
45 42 0.86
46 7 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (45 bp):
ATCGATGCACTAATCACATTCGATGTTTCCAATTTTAAGGGGTGC
Found at i:115409 original size:20 final size:21
Alignment explanation
Indices: 115362--115412 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
115352 TTTTGTGTCT
*
115362 TATCATATAACTTCTCTTTTA
1 TATCATATAACTTCTCTTTCA
115383 TATTCATATAA-TT-TCTTATCA
1 TA-TCATATAACTTCTCTT-TCA
115404 TATCATATA
1 TATCATATA
115413 GTTTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCATATAACTTCTCTTTCA
Found at i:121331 original size:30 final size:29
Alignment explanation
Indices: 121247--121539 Score: 228
Period size: 30 Copynumber: 10.1 Consensus size: 29
121237 TATTCTTATA
*
121247 ATATTTTAAAATTAAGAT-A-AA-AAAA-
1 ATATTTTTAAATTAAGATAAGAATAAAAT
*
121272 ATATTTTTAATATTTAAGATAAAAATAAAAT
1 ATATTTTTAA-A-TTAAGATAAGAATAAAAT
*
121303 ATATTTATTAAATTAAAATAAGAATAAAAT
1 ATATTT-TTAAATTAAGATAAGAATAAAAT
*
121333 ATACATTTTTAAATTAAAATAA-AAT---AT
1 AT--ATTTTTAAATTAAGATAAGAATAAAAT
* *
121360 ATATTTTTGAGTTAAGATAAGAAT-AAAT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
* * *
121388 AATATTTAATAATTTAAGATAAGAATATAAT
1 -ATATTT-TTAAATTAAGATAAGAATAAAAT
* * * *
121419 ATATTTAATAATTTAAGTTAAGAATATAAT
1 ATATTT-TTAAATTAAGATAAGAATAAAAT
* * * *
121449 ATATGTATCAAGTTAAGATAAAAATAAAAAT
1 ATAT-TTTTAAATTAAGATAAGAAT-AAAAT
* *
121480 ATATTTTTAAGTTAAGGTAAGAATAAAAT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
* *
121509 ATA-TTTTATAAGTAAGATAAGATTAAAAT
1 ATATTTTTA-AATTAAGATAAGAATAAAAT
121538 AT
1 AT
121540 TTAATATTAA
Statistics
Matches: 224, Mismatches: 26, Indels: 32
0.79 0.09 0.11
Matches are distributed among these distances:
25 24 0.11
26 4 0.02
27 11 0.05
28 8 0.04
29 34 0.15
30 102 0.46
31 33 0.15
32 8 0.04
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAATTAAGATAAGAATAAAAT
Found at i:121414 original size:86 final size:87
Alignment explanation
Indices: 121249--121511 Score: 216
Period size: 86 Copynumber: 3.0 Consensus size: 87
121239 TTCTTATAAT
* * * *
121249 ATTTTAAAATTAAGATAAAAAAAATATTTTTAATATTTAAGATAAAAATAAAATATATTTATTAA
1 ATTTTAAAATTAAAATAAAAAAAATATTTTT-AGAGTTAAGATAAAAATAAAATATATTTAATAA
121314 ATTAAAATAAGAATAAAATATAC
65 ATTAAAATAAGAATAAAATATAC
* * * *
121337 ATTTTTAAATTAAAATAAAATATATATTTTT-GAGTTAAGATAAGAAT-AAATAATATTTAATAA
1 ATTTTAAAATTAAAATAAAAAAAATATTTTTAGAGTTAAGATAAAAATAAAAT-ATATTTAATAA
* * *
121400 TTTAAGATAAGAATATAATAT--
65 ATTAAAATAAGAATAAAATATAC
** * *
121421 A-TTTAATAATTTAAGTTAAGAATATAATATATGTATCA-AGTTAAGATAAAAATAAAAATATAT
1 ATTTTAA-AA-TTAAAATAA-AA-A-AA-ATAT-TTTTAGAGTTAAGATAAAAAT-AAAATATAT
* * **
121484 TT-TTAAGTTAAGGTAAGAATAAAATATA
58 TTAATAAATTAAAATAAGAATAAAATATA
121512 TTTTATAAGT
Statistics
Matches: 140, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
83 4 0.03
84 3 0.02
85 11 0.08
86 43 0.31
88 28 0.20
89 4 0.03
90 37 0.26
91 6 0.04
92 4 0.03
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (87 bp):
ATTTTAAAATTAAAATAAAAAAAATATTTTTAGAGTTAAGATAAAAATAAAATATATTTAATAAA
TTAAAATAAGAATAAAATATAC
Found at i:121717 original size:15 final size:14
Alignment explanation
Indices: 121688--121721 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
121678 TGATTGGTGA
*
121688 AAATTAAATATATT
1 AAATTAAATAAATT
121702 AAATTAAAATAAATT
1 AAATT-AAATAAATT
121717 AAATT
1 AAATT
121722 CTCTAATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTAAATAAATT
Found at i:125797 original size:44 final size:44
Alignment explanation
Indices: 125734--125823 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
125724 TGGGGTTCCT
125734 TACAATGGTTTTTAGAATTAAACTTTTTATAGGCTCATCTGAAC
1 TACAATGGTTTTTAGAATTAAACTTTTTATAGGCTCATCTGAAC
125778 TACAATGGTTTTTAGAATTAAACTTTTTATAGGCTCATCTGAAC
1 TACAATGGTTTTTAGAATTAAACTTTTTATAGGCTCATCTGAAC
125822 TA
1 TA
125824 TCTTCTCAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (44 bp):
TACAATGGTTTTTAGAATTAAACTTTTTATAGGCTCATCTGAAC
Found at i:126801 original size:31 final size:31
Alignment explanation
Indices: 126763--126839 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
126753 AGTTACGTCG
* *
126763 GGGACCATATTGCAAACGTACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATATTGA
*
126794 GGGACCATATTGCAAACGGACTAAATATTGG
1 GGGACCATATTGCAAACGGACTAAATATTGA
**
126825 GGGATTATATTGCAA
1 GGGACCATATTGCAA
126840 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATATTGA
Found at i:141681 original size:13 final size:12
Alignment explanation
Indices: 141654--141691 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
141644 ATGTAAAACT
141654 ATATT-TTTAAA
1 ATATTGTTTAAA
141665 ATATTGTTTACAA
1 ATATTGTTTA-AA
*
141678 ATATAGTTTAAA
1 ATATTGTTTAAA
141690 AT
1 AT
141692 TCTATCGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (12 bp):
ATATTGTTTAAA
Found at i:141903 original size:16 final size:15
Alignment explanation
Indices: 141870--141912 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
141860 TTTAAGATAA
* *
141870 TTTATTAATAAATTT
1 TTTATTAAAAAATAT
141885 TTTATATAAAAAATAT
1 TTTAT-TAAAAAATAT
141901 TTTATTAAAAAA
1 TTTATTAAAAAA
141913 GTATAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATTAAAAAATAT
Found at i:142010 original size:2 final size:2
Alignment explanation
Indices: 142005--142030 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
141995 GAACATTACA
142005 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
142031 TAGTAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142247 original size:21 final size:21
Alignment explanation
Indices: 142221--142276 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
142211 CGCAACTCAG
*
142221 TTTTTAAATTCGCATTGTGAT
1 TTTTTAAATTCGCATAGTGAT
*
142242 TTTTTAAATTCGCGTAGTGAT
1 TTTTTAAATTCGCATAGTGAT
*
142263 TTTTTAATTTCGCA
1 TTTTTAAATTCGCA
142277 ATTCAGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTTAAATTCGCATAGTGAT
Found at i:142568 original size:14 final size:16
Alignment explanation
Indices: 142551--142587 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
142541 TTTTCATCTC
142551 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
142565 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
142581 TAATTTT
1 TAATTTT
142588 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:145658 original size:20 final size:20
Alignment explanation
Indices: 145633--145675 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
145623 ATCGCAACGT
145633 GAATTTGACTTTCACGTTGC
1 GAATTTGACTTTCACGTTGC
*
145653 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACGTTGC
145673 GAA
1 GAA
145676 AGTGTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
GAATTTGACTTTCACGTTGC
Found at i:145815 original size:14 final size:14
Alignment explanation
Indices: 145798--145830 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
145788 CATCAATTAA
145798 ACAAATCAAATTTT
1 ACAAATCAAATTTT
*
145812 ACAAATCAACTTTT
1 ACAAATCAAATTTT
145826 ACAAA
1 ACAAA
145831 ATACATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAAATTTT
Found at i:147204 original size:21 final size:21
Alignment explanation
Indices: 147178--147292 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
147168 GTGAATCGGG
* *
147178 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
147199 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
147220 CTCTTGAACAGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
** *
147241 CTCTTGAA-GGATGATAGGGCC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
147262 CTCTTGAATGATAGGG-GAGGC
1 CTCTTGAACGGT-GGGAGGGGC
147283 CTCTTGAACG
1 CTCTTGAACG
147293 ATGACAGATG
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
20 1 0.01
21 69 0.96
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:147244 original size:42 final size:42
Alignment explanation
Indices: 147178--147296 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 42
147168 GTGAATCGGG
* * *
147178 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
* *
147220 CTCTTGAACAGTGGGAGGGGCCTCTTGAAGGATGATAGGGCC
1 CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
*
147262 CTCTTGAA-TGATAGGG-GAGGCCTCTTGAACGATGA
1 CTCTTGAACAG-T-GGGAGAGGCCTCTTGAACGATGA
147297 CAGATGAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 63 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
Found at i:147455 original size:12 final size:12
Alignment explanation
Indices: 147436--147477 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
147426 CGGCCGCTAA
*
147436 AAATAAATTAAT
1 AAATAAATCAAT
*
147448 ACATAAATCAAT
1 AAATAAATCAAT
147460 AAATAAA-CAAAT
1 AAATAAATC-AAT
147472 AAATAA
1 AAATAA
147478 CGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:147599 original size:21 final size:21
Alignment explanation
Indices: 147574--147627 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
147564 TGCAATAATT
* *
147574 CCACGTAGAGCAACTACCTCA
1 CCACGTAAAGCAAATACCTCA
* * *
147595 TCACGCAAAGTAAATACCTCA
1 CCACGTAAAGCAAATACCTCA
147616 CCACGTAAAGCA
1 CCACGTAAAGCA
147628 GCATTGTCAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.33, G:0.13, T:0.15
Consensus pattern (21 bp):
CCACGTAAAGCAAATACCTCA
Found at i:149790 original size:22 final size:22
Alignment explanation
Indices: 149758--149812 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
149748 GATTTTACCA
149758 GAGA-TGGGACGAATTTCGTCG
1 GAGATTGGGACGAATTTCGTCG
149779 GAGATTGGGACGAATTTCGTCG
1 GAGATTGGGACGAATTTCGTCG
*
149801 GAGATGGGGACG
1 GAGATTGGGACG
149813 GATGTCCCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.24, C:0.13, G:0.42, T:0.22
Consensus pattern (22 bp):
GAGATTGGGACGAATTTCGTCG
Found at i:150006 original size:20 final size:20
Alignment explanation
Indices: 149983--150032 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
149973 TGACTTCTGT
*
149983 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
*
150003 GTTGCGATTTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
150023 GTTGCGAATT
1 GTTGCGAATT
150033 TAGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:150331 original size:19 final size:20
Alignment explanation
Indices: 150297--150334 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
150287 AAAAGAAATT
*
150297 ATTATATATGAAATATAAAA
1 ATTATATATAAAATATAAAA
150317 ATTATA-ATAAAATATAAA
1 ATTATATATAAAATATAAA
150335 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
ATTATATATAAAATATAAAA
Found at i:150350 original size:24 final size:26
Alignment explanation
Indices: 150302--150356 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
150292 AAATTATTAT
*
150302 ATATGAAATATAAAAATTATAATAAA
1 ATATGAAATATAAAAAATATAATAAA
*
150328 ATAT-AAATAAAAAAATATTATAATAAA
1 ATATGAAATATAAAAA-A-TATAATAAA
150355 AT
1 AT
150357 TATATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
27 11 0.44
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
ATATGAAATATAAAAAATATAATAAA
Found at i:150354 original size:16 final size:16
Alignment explanation
Indices: 150320--150370 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
150310 TATAAAAATT
*
150320 ATAATAAAATA-TA-A
1 ATAAAAAAATATTATA
150334 ATAAAAAAATATTATA
1 ATAAAAAAATATTATA
**
150350 ATAAAATTATATTTATA
1 ATAAAAAAATA-TTATA
150367 ATAA
1 ATAA
150371 CTCACTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
16 10 0.32
17 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAAAAATATTATA
Found at i:152918 original size:14 final size:14
Alignment explanation
Indices: 152897--152934 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
152887 ACATTTCTAA
152897 TAAC-ATATTTCCT
1 TAACTATATTTCCT
152910 TAACTATATATTTCCT
1 TAAC--TATATTTCCT
152926 TAACTATAT
1 TAACTATAT
152935 ATTAAGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
16 13 0.59
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (14 bp):
TAACTATATTTCCT
Found at i:152922 original size:16 final size:16
Alignment explanation
Indices: 152901--152937 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
152891 TTCTAATAAC
152901 ATATTTCCTTAACTAT
1 ATATTTCCTTAACTAT
152917 ATATTTCCTTAACTAT
1 ATATTTCCTTAACTAT
152933 ATATT
1 ATATT
152938 AAGACTGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTCCTTAACTAT
Done.