Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004435.1 Hibiscus syriacus cultivar Beakdansim tig00009727_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: 157011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:435 original size:21 final size:21
Alignment explanation
Indices: 369--435 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
359 GTGAATCGGG
*
369 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
389 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
411 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
432 CTCT
1 CTCT
436 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:4317 original size:21 final size:21
Alignment explanation
Indices: 4293--4362 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
4283 TCATTCCTCG
4293 AGAGCCCCCTCCCACCGTTCA
1 AGAGCCCCCTCCCACCGTTCA
* * ** * *
4314 AGAGGCCACTGTCATCGTTGA
1 AGAGCCCCCTCCCACCGTTCA
** *
4335 AGAGGTCCCTCCCACCATTCA
1 AGAGCCCCCTCCCACCGTTCA
4356 AGAGCCC
1 AGAGCCC
4363 GATTCACATT
Statistics
Matches: 34, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (21 bp):
AGAGCCCCCTCCCACCGTTCA
Found at i:4317 original size:41 final size:41
Alignment explanation
Indices: 4238--4362 Score: 99
Period size: 41 Copynumber: 3.0 Consensus size: 41
4228 ACCCGACTCG
* * * * * * *
4238 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGCC
1 CCTATCATTCCTCGAGAGCCCCCTCCCACCGTTCAAGAGCC
4279 CCTATCATTCCTCGAGAGCCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGCCCCCTCCCACCGTTCAAGA-GCC
* * * * ** *
4321 ACTGTCA-TCGTTGAAGAGGTCCCTCCCACCATTCAAGAGCC
1 CCTATCATTCCTCG-AGAGCCCCCTCCCACCGTTCAAGAGCC
4362 C
1 C
4363 GATTCACATT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 38 0.57
42 29 0.43
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (41 bp):
CCTATCATTCCTCGAGAGCCCCCTCCCACCGTTCAAGAGCC
Found at i:5727 original size:14 final size:14
Alignment explanation
Indices: 5708--5743 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5698 ATTGTTTAAT
5708 TGATTTGTAAAAAA
1 TGATTTGTAAAAAA
**
5722 TGATTTGTAAAAGT
1 TGATTTGTAAAAAA
5736 TGATTTGT
1 TGATTTGT
5744 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAAA
Found at i:6059 original size:24 final size:24
Alignment explanation
Indices: 5995--6059 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
5985 AAAAATCATC
* *
5995 CAAA-TCCGAGTATTGACCAAGAT
1 CAAAGTCCGAATACTGACCAAGAT
* * *
6018 TAAAGTCCGAGTATTGACCAAGAT
1 CAAAGTCCGAATACTGACCAAGAT
* *
6042 CAAATTTCGAATACTGAC
1 CAAAGTCCGAATACTGAC
6060 TAGTACTCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (24 bp):
CAAAGTCCGAATACTGACCAAGAT
Found at i:10790 original size:21 final size:20
Alignment explanation
Indices: 10747--10792 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
10737 TAACCGTCGA
*
10747 TATTTATTATTTTTTTATTT
1 TATTTATTATTTTTTTATCT
10767 TATTATATTATATTTTTT-TCT
1 TATT-TATTAT-TTTTTTATCT
10788 TATTT
1 TATTT
10793 TGTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTATTATTTTTTTATCT
Found at i:21344 original size:2 final size:2
Alignment explanation
Indices: 21337--21362 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21327 ATTTAAATTC
21337 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
21363 TTACAAAATT
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:23986 original size:30 final size:30
Alignment explanation
Indices: 23888--23989 Score: 149
Period size: 30 Copynumber: 3.5 Consensus size: 30
23878 ATTCTTTAAA
* *
23888 AAAACTAGTGATATTCCGTCGCTATTCTTT
1 AAAACTAGTGATGTTCCGTCTCTATTCTTT
23918 AAAACTAGTGA--TT--GTCTCTATTCTTT
1 AAAACTAGTGATGTTCCGTCTCTATTCTTT
23944 AAAACTAGTGATGTTCCGTCTCTATTCTTT
1 AAAACTAGTGATGTTCCGTCTCTATTCTTT
*
23974 AAAACTGGTGATGTTC
1 AAAACTAGTGATGTTC
23990 TGGCGTTGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
26 23 0.35
28 4 0.06
30 39 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (30 bp):
AAAACTAGTGATGTTCCGTCTCTATTCTTT
Found at i:34959 original size:20 final size:20
Alignment explanation
Indices: 34934--35024 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
34924 ACTGAATTTT
* *
34934 AAATTCGCAATACAAAAATC
1 AAATTCGCAACACAAAAGTC
* * *
34954 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAGTC
*
34974 AAATTCGCAACACAAAAGTA
1 AAATTCGCAACACAAAAGTC
* * *
34994 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAGTC
*
35014 AAATTCACAAC
1 AAATTCGCAAC
35025 GCGAAACACA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACACAAAAGTC
Found at i:34989 original size:40 final size:40
Alignment explanation
Indices: 34934--35024 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
34924 ACTGAATTTT
* *
34934 AAATTCGCAATACAAAAATCAAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAATAAAATTCGCAACGCGATAGTC
*
34974 AAATTCGCAACACAAAAGTAAAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAATAAAATTCGCAACGCGATAGTC
*
35014 AAATTCACAAC
1 AAATTCGCAAC
35025 GCGAAACACA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (40 bp):
AAATTCGCAACACAAAAATAAAATTCGCAACGCGATAGTC
Found at i:35025 original size:20 final size:20
Alignment explanation
Indices: 34952--35028 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
34942 AATACAAAAA
34952 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAG
* * *
34972 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACGCGATAG
*
34992 TAAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAG
*
35012 TCAAATTCACAACGCGA
1 TCAAATTCGCAACGCGA
35029 AACACAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATAG
Found at i:35165 original size:22 final size:22
Alignment explanation
Indices: 35140--35190 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
35130 CTACGGCGGC
*
35140 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
*
35162 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
35184 ATCCGTC
1 ATCCGTC
35191 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:39273 original size:59 final size:59
Alignment explanation
Indices: 39178--39290 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
39168 TTTTACATTG
39178 AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTA-TTTTTTGCTTGTTTATTGTA
1 AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTATTGTA
*
39236 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTA
1 AAAGTTGATTTGTTTAA-TTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTA
39291 ATTGATTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
58 17 0.33
59 20 0.38
60 15 0.29
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (59 bp):
AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTATTGTA
Found at i:39394 original size:20 final size:20
Alignment explanation
Indices: 39369--39418 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
39359 GTTGAAGGTA
39369 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
39389 CAAATTCGCAACGCTAAAGT
1 CAAATTCGCAACGCGAAAGT
39409 CAAATTCGCA
1 CAAATTCGCA
39419 TTGCGATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:51356 original size:12 final size:12
Alignment explanation
Indices: 51335--51368 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
51325 GGTTGTGGGT
*
51335 TTTGAGATTGTG
1 TTTGATATTGTG
51347 TTTGATATTGTG
1 TTTGATATTGTG
*
51359 TTTGGTATTG
1 TTTGATATTG
51369 GAAATGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:51985 original size:16 final size:15
Alignment explanation
Indices: 51962--52001 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
51952 AGAAATCATT
51962 AAAAAATTATATAGAA
1 AAAAAATTATATA-AA
* *
51978 ATAAAATTATGTAAA
1 AAAAAATTATATAAA
51993 AAAAAATTA
1 AAAAAATTA
52002 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAAATTATATAAA
Found at i:52201 original size:39 final size:39
Alignment explanation
Indices: 52157--52290 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
52147 ACTAAAACCT
*
52157 GTTGCGAATTT-AAATTCGTGTTGCGAATTTGAAAATCTA
1 GTTGCGAATTTGAAATTC-TGTTGCGAATTTGAAATTCTA
* *
52196 GTTGCGGATTTGAAATTCAGTTGCGAATTT-AAATTCGT-
1 GTTGCGAATTTGAAATTCTGTTGCGAATTTGAAATTC-TA
* *
52234 GTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCT-GTTGCGAATTTGAAATTCTA
52273 GTTGCGAATTTGAAATTC
1 GTTGCGAATTTGAAATTC
52291 CGCGTTACGA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
38 21 0.26
39 49 0.60
40 12 0.15
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCTGTTGCGAATTTGAAATTCTA
Found at i:52247 original size:58 final size:58
Alignment explanation
Indices: 52157--52306 Score: 264
Period size: 58 Copynumber: 2.6 Consensus size: 58
52147 ACTAAAACCT
52157 GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTCA
1 GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTCA
52215 GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTCA
1 GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTCA
* *
52273 GTTGCGAATTTGAAATTCCGCGTTACGAATTTGA
1 GTTGCGAATTT-AAATT-CGTGTTGCGAATTTGA
52307 TTTTTGTGTT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
58 69 0.78
59 5 0.06
60 14 0.16
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (58 bp):
GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATTCA
Found at i:52323 original size:20 final size:20
Alignment explanation
Indices: 52156--52440 Score: 147
Period size: 20 Copynumber: 14.4 Consensus size: 20
52146 AACTAAAACC
**
52156 TGTTGCGAATTT-AAATTCG
1 TGTTGCGAATTTGACTTTCG
***
52175 TGTTGCGAATTTGAAAATC-
1 TGTTGCGAATTTGACTTTCG
* **
52194 TAGTTGCGGATTTGAAATTC-
1 T-GTTGCGAATTTGACTTTCG
* **
52214 AGTTGCGAATTT-AAATTCG
1 TGTTGCGAATTTGACTTTCG
***
52233 TGTTGCGAATTTGAAAATC-
1 TGTTGCGAATTTGACTTTCG
* **
52252 TAGTTGCGGATTTGAAATTC-
1 T-GTTGCGAATTTGACTTTCG
* * *
52272 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAATTTG-ACTTTCG
* * * *
52293 CGTTACGAATTTGATTTTTG
1 TGTTGCGAATTTGACTTTCG
*
52313 TGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTGACTTTCG
* *
52333 CGTTGTGAATTTGAC-TTCTG
1 TGTTGCGAATTTGACTTTC-G
*
52353 TGTTGCG-ATTT-ACAGATTCG
1 TGTTGCGAATTTGAC--TTTCG
* *
52373 CGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTGACTTTCG
* * *
52393 CGTTGTGAATTTGACTTTTG
1 TGTTGCGAATTTGACTTTCG
*
52413 TGTTGCGAATTTGACTTCCG
1 TGTTGCGAATTTGACTTTCG
52433 TGTTGCGA
1 TGTTGCGA
52441 TTTACGTATT
Statistics
Matches: 215, Mismatches: 38, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.04
19 52 0.24
20 135 0.63
21 18 0.08
22 2 0.01
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGACTTTCG
Found at i:52335 original size:40 final size:41
Alignment explanation
Indices: 52273--52461 Score: 169
Period size: 40 Copynumber: 4.7 Consensus size: 41
52263 TTGAAATTCA
* * * **
52273 GTTGCGAATTTGA-AATTCCGCGTTACGAATTTGATTTTTGT
1 GTTGCGAATTTGACTATT-CGCGTTGCGAATTTGACTTCCGT
* *
52314 GTTGCGAATTTGACTA-TCGCGTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTCCGT
* *
52354 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGACTAT-CGC
1 GTTGCGAATTTGAC-TATTCGCGTTGCGAATTTGACT-TCCGT
* * *
52394 GTTGTGAATTTGACT-TTTGTGTTGCGAATTTGACTTCCGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTCCGT
*
52434 GTTGCG-ATTT-ACGTATTAGCGTTGCGAA
1 GTTGCGAATTTGAC-TATTCGCGTTGCGAA
52462 ATTAGAAACT
Statistics
Matches: 122, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
38 4 0.03
39 11 0.09
40 85 0.70
41 19 0.16
42 3 0.02
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (41 bp):
GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTCCGT
Found at i:52457 original size:60 final size:59
Alignment explanation
Indices: 52298--52440 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 59
52288 TTCCGCGTTA
* *
52298 CGAATTTGATTTTTGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTG
1 CGAATTTGA-CTTCGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTG
* *
52358 CG-ATTT-ACAGATTCGCGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTTTGTGTTG
1 CGAATTTGAC---TTCGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTG
52418 CGAATTTGACTTCCGTGTTGCGA
1 CGAATTTGACTT-CGTGTTGCGA
52441 TTTACGTATT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
58 1 0.01
59 6 0.08
60 59 0.82
61 4 0.06
62 2 0.03
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (59 bp):
CGAATTTGACTTCGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTG
Found at i:60094 original size:15 final size:15
Alignment explanation
Indices: 60074--60108 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
60064 GACTAAGATT
60074 AAAAATAAAAAAAGG
1 AAAAATAAAAAAAGG
* *
60089 AAAAATAATAAAATG
1 AAAAATAAAAAAAGG
60104 AAAAA
1 AAAAA
60109 CTTGCATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAATAAAAAAAGG
Found at i:61132 original size:22 final size:21
Alignment explanation
Indices: 61100--61146 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
61090 TAATTATTTT
61100 AAAAATTAAAT-AAAAATACAA
1 AAAAATTAAATAAAAAATA-AA
61121 AAAACATTAAATAAAAAATAAA
1 AAAA-ATTAAATAAAAAATAAA
61143 AAAA
1 AAAA
61147 TTAGGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAATTAAATAAAAAATAAA
Found at i:62052 original size:18 final size:17
Alignment explanation
Indices: 62029--62075 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
62019 TATTTATGAG
62029 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
62047 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTAA
*
62064 GAAATTGGAATC
1 GGAATTGGAATC
62076 CAATTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:62745 original size:5 final size:5
Alignment explanation
Indices: 62735--62762 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
62725 ATTAGAAATT
62735 CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGA
62763 AATAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:62965 original size:266 final size:263
Alignment explanation
Indices: 62479--62983 Score: 660
Period size: 266 Copynumber: 1.9 Consensus size: 263
62469 AATTAGAAAT
* *
62479 CCGACTCGACACGACACAAAATAATAAAAAAATATTTTTATTCAATAAAATCATTGACTTAATTG
1 CCGACCCGACACGACACAAAATAATAAAAAAATATTTTTATTCAATAAAATCAGTGACTTAATTG
* * *
62544 AAAAAAAATTTATATATAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
66 AAAAAAAATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
* * * * * **
62609 TATTTTCGGGTCGATCCGATTTTTTTCACCCTAAACACGAACCCGACCCCGACCCGAATATTACA
131 TATTTTCGAGTCG---CGAGTATTTTCACCCTAAACACAAACCCGACCCCGACCCAAATACCACA
*
62674 CTTAAAAACCCAACCCGAACAAAATAAAGTTTCA-CCGACCCGAATATATGAATTAGAAATTCGA
193 CTTAAAAAACCAACCCGAACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATTCGA
62738 CCCGAC
258 CCCGAC
* * * *
62744 CCGACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAAT-AGTGACTTAATT
1 CCGACCCGACACGACACAAAATAATAAAAAAATATTTTTATTCAAT-AAAATCAGTGACTTAATT
** *
62808 GAAAAAAATATATATAGAGAGGGGTATTATTGTAATTATTCCTATTTATATAAGGTGAAATTATA
65 GAAAAAAA-ATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
* * *
62873 TATATTTTTGAGTCG-G-GTATTTTCACCCTAAACCCAAACTCGA-CCCGACCCAAATACCACAC
129 TATATTTTCGAGTCGCGAGTATTTTCACCCTAAACACAAACCCGACCCCGACCCAAATACCACAC
*
62935 TTAAAAAAACCGACCCGACTCGATCAAAATAAAGTTTCACCCGACCCGA
194 TT-AAAAAACCAACCCGA----A-CAAAATAAAGTTTCACCCGACCCGA
62984 TCCGAAATAA
Statistics
Matches: 207, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
260 18 0.09
261 35 0.17
262 1 0.00
265 61 0.29
266 83 0.40
267 9 0.04
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (263 bp):
CCGACCCGACACGACACAAAATAATAAAAAAATATTTTTATTCAATAAAATCAGTGACTTAATTG
AAAAAAAATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
TATTTTCGAGTCGCGAGTATTTTCACCCTAAACACAAACCCGACCCCGACCCAAATACCACACTT
AAAAAACCAACCCGAACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATTCGACCC
GAC
Found at i:64719 original size:18 final size:18
Alignment explanation
Indices: 64696--64743 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
64686 TATATGTTTT
64696 TAAAATATAAAATTCTAC
1 TAAAATATAAAATTCTAC
*
64714 TAAAAT-TATAAGTTCTAC
1 TAAAATATA-AAATTCTAC
* *
64732 CAAAACATAAAA
1 TAAAATATAAAA
64744 ATATCATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAATATAAAATTCTAC
Found at i:79024 original size:35 final size:35
Alignment explanation
Indices: 78950--79017 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
78940 TTCATGTTTA
78950 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* * *
78985 AAATTCCAAAATATTTTAATTACATTCTAAACC
1 AAATTCCAAAACACTTCAATTACATTCTAAACC
79018 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:79061 original size:35 final size:35
Alignment explanation
Indices: 79020--79094 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
79010 TCTAAACCTT
79020 AAATTAAAGTATTTTCGAATTTAGGG-TTTAAAATG
1 AAATTAAAGTATTTTCGAATTT-GGGATTTAAAATG
* * * *
79055 TAATTAAATTATTTTGGAATTTGGGATTTAGAATG
1 AAATTAAAGTATTTTCGAATTTGGGATTTAAAATG
79090 AAATT
1 AAATT
79095 GAGGATTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.43
Consensus pattern (35 bp):
AAATTAAAGTATTTTCGAATTTGGGATTTAAAATG
Found at i:86473 original size:32 final size:32
Alignment explanation
Indices: 86411--86474 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
86401 TACTCATGTA
*
86411 CATGCATACATATATTATTTTTATAGTGATAT
1 CATGCATACATATATTATTTTAATAGTGATAT
*
86443 CATGCATA-ATTTATTATGCTTTAATA-TGATAT
1 CATGCATACATATATTAT--TTTAATAGTGATAT
86475 TATGTGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 14 0.50
33 6 0.21
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (32 bp):
CATGCATACATATATTATTTTAATAGTGATAT
Found at i:86684 original size:22 final size:22
Alignment explanation
Indices: 86659--86843 Score: 197
Period size: 22 Copynumber: 8.8 Consensus size: 22
86649 GAGGGTTTAT
*
86659 AGTGGTCATTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* * *
86681 AGTGGTTCTTCGGGACGTATCT
1 AGTGGTCCTTCGGGACATATCC
*
86703 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
* *
86725 AGTGGTCCTTCAGGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
86747 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* * *
86769 AGTGGTTCTTCAGGAC--GT--
1 AGTGGTCCTTCGGGACATATCC
86787 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* * *
86809 AGTGGTTCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACATATCC
86828 A-TGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
86844 AATATTTACT
Statistics
Matches: 138, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
18 26 0.19
19 1 0.01
20 2 0.01
22 109 0.79
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:86724 original size:44 final size:42
Alignment explanation
Indices: 86656--86843 Score: 260
Period size: 44 Copynumber: 4.5 Consensus size: 42
86646 GTCGAGGGTT
* *
86656 TATAGTGGTCATTCGGGACATATCCAGTGGTTCTTCGGGACG
1 TATAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGACG
* *
86698 TATCTAGTGGTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACG
1 TA--TAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGACG
86742 TATCCAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGACG
1 TAT--AGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGACG
86786 --TAGTGGTCCTTCGGGACATATCCAGTGGTTCTT-AGGGACG
1 TATAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCA-GGACG
86826 TA-A-TGGTCCTTCGGGACA
1 TATAGTGGTCCTTCGGGACA
86844 AATATTTACT
Statistics
Matches: 133, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
39 1 0.01
40 52 0.39
41 1 0.01
42 4 0.03
44 75 0.56
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (42 bp):
TATAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGACG
Found at i:86773 original size:66 final size:62
Alignment explanation
Indices: 86658--86824 Score: 217
Period size: 66 Copynumber: 2.6 Consensus size: 62
86648 CGAGGGTTTA
* * * *
86658 TAGTGGTCATTCGGGACATATCCAGTGGTTCTTCGGGACGTATCTAGTGGTCCTTCGGGACG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCGGGACATATCCAGTGGTCCTTCAGGACG
* * * *
86720 TATCCAGTGGTCCTTCAGGACGTATCCAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCAGGAC
1 --T--AGTGGTCCTTCGGGACATATCCAGTGGTTCTTCGGGACATATCCAGTGGTCCTTCAGGAC
86785 G
62 G
*
86786 TAGTGGTCCTTCGGGACATATCCAGTGGTTCTTAGGGAC
1 TAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCGGGAC
86825 GTAATGGTCC
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
62 34 0.38
64 2 0.02
66 53 0.60
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (62 bp):
TAGTGGTCCTTCGGGACATATCCAGTGGTTCTTCGGGACATATCCAGTGGTCCTTCAGGACG
Found at i:92923 original size:22 final size:22
Alignment explanation
Indices: 92895--93038 Score: 188
Period size: 22 Copynumber: 6.7 Consensus size: 22
92885 GAGGGTTTAT
*
92895 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACGTATCC
*
92917 AGTGGTCCTTCGGGACGTATCT
1 AGTGGTCCTTCGGGACGTATCC
92939 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
92961 AGTGGTCCTTCAGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
* * * *
92983 AGTGGTCATTCAGGACATATTC
1 AGTGGTCCTTCGGGACGTATCC
*
93005 AGTGGTCCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACGTATCC
93024 A-TGGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
93039 AAATATTCAC
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.12
19 1 0.01
22 96 0.87
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:95609 original size:3 final size:3
Alignment explanation
Indices: 95603--95650 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
95593 TCATCATTTT
*
95603 TTA TTA -TA TT- TTC TTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
95647 TTA T
1 TTA T
95651 ATAGATGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:95934 original size:2 final size:2
Alignment explanation
Indices: 95910--95966 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
95900 TTTAAATACA
*
95910 AT AT AG AT AT A- AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
95949 TT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT
95967 TTAAGAGTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:103956 original size:10 final size:11
Alignment explanation
Indices: 103930--103956 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
103920 AATTATTTTG
103930 ATTTTTATTTA
1 ATTTTTATTTA
103941 ATTTTTATTTA
1 ATTTTTATTTA
103952 ATTTT
1 ATTTT
103957 CTCGTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTA
Found at i:104853 original size:43 final size:43
Alignment explanation
Indices: 104792--104875 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
104782 CCATCATATT
**
104792 ACTAATAATTATTAAATTTGGGGTAAGGTATATAAATGATCCA
1 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATCCA
104835 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATC
1 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATC
104876 TTTCAACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (43 bp):
ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATCCA
Found at i:113588 original size:12 final size:11
Alignment explanation
Indices: 113571--113610 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
113561 ATTGGACCTA
113571 AAAAATTAAAAT
1 AAAAA-TAAAAT
113583 AAAAATAAGAAT
1 AAAAATAA-AAT
113595 AAAAAT-AAAT
1 AAAAATAAAAT
113605 AAAAAT
1 AAAAAT
113611 GTATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.33
11 4 0.15
12 14 0.52
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:113707 original size:37 final size:37
Alignment explanation
Indices: 113665--113976 Score: 298
Period size: 37 Copynumber: 8.4 Consensus size: 37
113655 GTTTTCTAAA
*
113665 ATATATTATATATATTTTCCAAAAAAGTCTT-AAAATT
1 ATATATTATATATATTTT-CAAAAAAGTTTTCAAAATT
* * * *
113702 ATATATTATACATATTTTCGAAAAATGATTTCAAAACT
1 ATATATTATATATATTTTC-AAAAAAGTTTTCAAAATT
* * *
113740 ATATATTATATATATTTTTTCAAAAATATTTTTTTAAAATC
1 ATATATTATATATA--TTTTCAAAAA-A-GTTTTCAAAATT
*
113781 ATATATTATAT-T-TTTT-AAAAACGTTTTCAAAATT
1 ATATATTATATATATTTTCAAAAAAGTTTTCAAAATT
* **
113815 ATATATTATATAT-TTTTCTAAAATTTTTTCAAAATT
1 ATATATTATATATATTTTCAAAAAAGTTTTCAAAATT
*
113851 ATATATTATATAGATTTTCAAAAATA-TTTTCAAAATT
1 ATATATTATATATATTTTCAAAAA-AGTTTTCAAAATT
* * *
113888 ATATATTATATATA-TTTGAAAAATGTTTTCAAAACT
1 ATATATTATATATATTTTCAAAAAAGTTTTCAAAATT
* * *
113924 ACATATTGTATATATTTTCGAACAATA-TTTTCAAAATT
1 ATATATTATATATATTTTC-AA-AAAAGTTTTCAAAATT
* *
113962 GTATACTATATATAT
1 ATATATTATATATAT
113977 ATATATATAT
Statistics
Matches: 225, Mismatches: 36, Indels: 27
0.78 0.12 0.09
Matches are distributed among these distances:
34 20 0.09
35 5 0.02
36 63 0.28
37 65 0.29
38 41 0.18
39 7 0.03
40 6 0.03
41 18 0.08
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAAAAGTTTTCAAAATT
Found at i:113818 original size:111 final size:111
Alignment explanation
Indices: 113665--113976 Score: 346
Period size: 111 Copynumber: 2.8 Consensus size: 111
113655 GTTTTCTAAA
* * * * *
113665 ATATATTATATATATTTTCCAAAAAAGTCTT-AAAATTATATATTATACATATTTTCGAAAAATG
1 ATATATTATATATA-TTT-GAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAAT-
* *
113729 ATTTCAAAACTATATATTATATATATTTTTTCAAAAATATTTTTTTAAAATC
63 ATTTCAAAATTATATATTATATATA-TTTTTCAAAAATA--TTTTCAAAATC
* * * * *
113781 ATATATTATAT-T-TTTTAAAAACGTTTTCAAAATTATATATTATATAT-TTTTCTAAAATTTTT
1 ATATATTATATATATTTGAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATATT
* *
113843 TCAAAATTATATATTATATAGA-TTTTCAAAAATATTTTCAAAATT
66 TCAAAATTATATATTATATATATTTTTCAAAAATATTTTCAAAATC
* * * *
113888 ATATATTATATATATTTGAAAAATGTTTTCAAAACTACATATTGTATATATTTTCGAACAATATT
1 ATATATTATATATATTTGAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATA-T
* *
113953 TTCAAAATTGTATACTATATATAT
65 TTCAAAATTATATATTATATATAT
113977 ATATATATAT
Statistics
Matches: 167, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
107 20 0.12
108 1 0.01
109 42 0.25
110 9 0.05
111 43 0.26
112 19 0.11
113 21 0.13
115 1 0.01
116 11 0.07
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (111 bp):
ATATATTATATATATTTGAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATATT
TCAAAATTATATATTATATATATTTTTCAAAAATATTTTCAAAATC
Found at i:113881 original size:73 final size:74
Alignment explanation
Indices: 113665--113974 Score: 319
Period size: 73 Copynumber: 4.2 Consensus size: 74
113655 GTTTTCTAAA
* * *
113665 ATATATTATATATATTTTCCAAAAAAGTCTT-AAAATTATATATTATACATATTTTCGAAAAATG
1 ATATATTATATAT-TTTT-CAAAAATGTTTTCAAAATTATATATTATATATATTTTCGAAAAAT-
*
113729 A-TTTCAAAACT
63 ATTTTCAAAATT
* * *
113740 ATATATTATATATATTTTTTCAAAAATATTTTTTTAAAATCATATATTATAT-T-TTTT--AAAA
1 ATATA-T-TATATA-TTTTTC-AAAA-ATGTTTTCAAAATTATATATTATATATATTTTCGAAAA
**
113801 ACGTTTTCAAAATT
61 ATATTTTCAAAATT
* * *
113815 ATATATTATATATTTTTCTAAAATTTTTTCAAAATTATATATTATATAGATTTTC-AAAAATATT
1 ATATATTATATATTTTTCAAAAATGTTTTCAAAATTATATATTATATATATTTTCGAAAAATATT
113879 TTCAAAATT
66 TTCAAAATT
* * * * * *
113888 ATATATTATATATATTTGAAAAATGTTTTCAAAACTACATATTGTATATATTTTCGAACAATATT
1 ATATATTATATATTTTTCAAAAATGTTTTCAAAATTATATATTATATATATTTTCGAAAAATATT
113953 TTCAAAATT
66 TTCAAAATT
* *
113962 GTATACTATATAT
1 ATATATTATATAT
113975 ATATATATAT
Statistics
Matches: 199, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
70 23 0.12
71 3 0.02
72 10 0.05
73 69 0.35
74 29 0.15
75 24 0.12
76 2 0.01
77 18 0.09
78 6 0.03
79 15 0.08
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (74 bp):
ATATATTATATATTTTTCAAAAATGTTTTCAAAATTATATATTATATATATTTTCGAAAAATATT
TTCAAAATT
Found at i:113972 original size:36 final size:36
Alignment explanation
Indices: 113656--113974 Score: 255
Period size: 36 Copynumber: 8.7 Consensus size: 36
113646 CCCAAACACG
*
113656 TTTTCTAAAA-TATAT-TATATATATTTTCCAAAAA-A
1 TTTTC-AAAATTATATAT-TATATATTTTCGAAAAATA
*
113691 GTCTT-AAAATTATATATTATACATATTTTCGAAAAATGA
1 -TTTTCAAAATTATATATTAT--ATATTTTCGAAAAAT-A
*
113730 -TTTCAAAACTATATATTATATATATTTTTTC-AAAAATA
1 TTTTCAAAA-T-TATA-TAT-TATATATTTTCGAAAAATA
* * * **
113768 TTTTTTTAAAATCATATATTATAT-TTTT-TAAAAACG
1 --TTTTCAAAATTATATATTATATATTTTCGAAAAATA
* *
113804 TTTTCAAAATTATATATTATATATTTTTC-TAAAATT
1 TTTTCAAAATTATATATTATATA-TTTTCGAAAAATA
113840 TTTTCAAAATTATATATTATATAGATTTTC-AAAAATA
1 TTTTCAAAATTATATATTATAT--ATTTTCGAAAAATA
*
113877 TTTTCAAAATTATATATTATATATATTT-GAAAAATG
1 TTTTCAAAATTATATATTATATAT-TTTCGAAAAATA
* * *
113913 TTTTCAAAACTACATATTGTATATATTTTCGAACAATA
1 TTTTCAAAATTATATA-T-TATATATTTTCGAAAAATA
* *
113951 TTTTCAAAATTGTATACTATATAT
1 TTTTCAAAATTATATATTATATAT
113975 ATATATATAT
Statistics
Matches: 234, Mismatches: 24, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
34 24 0.10
35 10 0.04
36 73 0.31
37 56 0.24
38 35 0.15
39 11 0.05
40 12 0.05
41 10 0.04
42 3 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTTCAAAATTATATATTATATATTTTCGAAAAATA
Found at i:119662 original size:23 final size:25
Alignment explanation
Indices: 119619--119665 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
119609 TACGGATAGG
*
119619 ATTTTATAAAATTAATTAAATAATA
1 ATTTTATAAAATTAATAAAATAATA
119644 ATTTTA-AAAATTAA-AAAATAAT
1 ATTTTATAAAATTAATAAAATAAT
119666 TAAAATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTTTATAAAATTAATAAAATAATA
Found at i:122376 original size:33 final size:33
Alignment explanation
Indices: 122334--122396 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
122324 GGCGACATCG
*
122334 AAGGTCTGCTGCAACAGACGTGGTGGATGCTCC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
* *
122367 AAGGTCTGCTGCATCAGATGCGGTGGATGC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGC
122397 ATCCTCTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (33 bp):
AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
Found at i:131072 original size:21 final size:21
Alignment explanation
Indices: 131034--131074 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
131024 CATGTGTCAA
131034 AAACAAGCCAAAAACATCAGGG
1 AAACAAG-CAAAAACATCAGGG
131056 AAACAAG-AAAAAGCATCAG
1 AAACAAGCAAAAA-CATCAG
131075 AATTCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.59, C:0.20, G:0.17, T:0.05
Consensus pattern (21 bp):
AAACAAGCAAAAACATCAGGG
Found at i:132329 original size:120 final size:120
Alignment explanation
Indices: 132116--132349 Score: 459
Period size: 120 Copynumber: 1.9 Consensus size: 120
132106 GAAGCTGCTC
*
132116 TCAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCTCCCTTACCCCATTACATATGGGAACAA
1 TCAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
132181 GGGACAACCATTTATTTTTATAATTTAGTCCATCAACTTTATATAATTTAGTCCA
66 GGGACAACCATTTATTTTTATAATTTAGTCCATCAACTTTATATAATTTAGTCCA
132236 TCAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
1 TCAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
132301 GGGACAACCATTTATTTTTATAATTTAGTCCATCAACTTTATATAATTT
66 GGGACAACCATTTATTTTTATAATTTAGTCCATCAACTTTATATAATTT
132350 TTTTATGTCT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 113 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (120 bp):
TCAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
GGGACAACCATTTATTTTTATAATTTAGTCCATCAACTTTATATAATTTAGTCCA
Found at i:135910 original size:16 final size:17
Alignment explanation
Indices: 135889--135920 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
135879 TAATATATAG
135889 ATATG-ATTTTTTAAAT
1 ATATGAATTTTTTAAAT
135905 ATATGAATTTTTTAAA
1 ATATGAATTTTTTAAA
135921 AATAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATGAATTTTTTAAAT
Found at i:142829 original size:17 final size:17
Alignment explanation
Indices: 142802--142840 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
142792 AATTTACAAT
142802 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
142818 TAATTATAAATAATATC
1 TAATTATAAATAATATC
142835 TAATTA
1 TAATTA
142841 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:147028 original size:37 final size:39
Alignment explanation
Indices: 146979--147074 Score: 133
Period size: 37 Copynumber: 2.5 Consensus size: 39
146969 TTGAAAATAT
* *
146979 TTTTTGAAAACATATAATATATAGTTTTTAGAAAA-C-G
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
* *
147016 TTTTAGAAAACATATTATATATAGTTTTTAAAAAATCAA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
*
147055 TTTTTGAAAATATATAATAT
1 TTTTTGAAAACATATAATAT
147075 GATTTTGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 32 0.64
38 1 0.02
39 17 0.34
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (39 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
Found at i:147081 original size:21 final size:21
Alignment explanation
Indices: 147056--147110 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
147046 AAAAATCAAT
*
147056 TTTTGAAAATATATAATATGA
1 TTTTGAAAACATATAATATGA
*
147077 TTTTGAAAACATATAATATATA
1 TTTTGAAAACATATAATAT-GA
147099 GTTTTGAAAACA
1 -TTTTGAAAACA
147111 CATTTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.60
22 1 0.03
23 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGAAAACATATAATATGA
Found at i:147097 original size:23 final size:21
Alignment explanation
Indices: 147015--147110 Score: 69
Period size: 23 Copynumber: 4.6 Consensus size: 21
147005 TTTAGAAAAC
147015 GTTTTAGAAAACATATTATATATA
1 GTTTT-GAAAACATA-TA-ATATA
* *
147039 GTTTTTAAAA-A-ATCA-AT-
1 GTTTTGAAAACATATAATATA
*
147056 -TTTTGAAAATATATAATAT-
1 GTTTTGAAAACATATAATATA
147075 GATTTTGAAAACATATAATATATA
1 G-TTTTGAAAACATAT-A-ATATA
147099 GTTTTGAAAACA
1 GTTTTGAAAACA
147111 CATTTTTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
16 8 0.14
17 1 0.02
18 5 0.08
19 3 0.05
20 1 0.02
21 14 0.24
22 2 0.03
23 19 0.32
24 6 0.10
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (21 bp):
GTTTTGAAAACATATAATATA
Found at i:147099 original size:97 final size:97
Alignment explanation
Indices: 146980--147189 Score: 257
Period size: 97 Copynumber: 2.1 Consensus size: 97
146970 TGAAAATATT
* * * *
146980 TTTTGAAAACATATAATATATAGTTTTTAGAAA-ACGTTTTAG-AAAAC-ATATTATATATAGTT
1 TTTTGAAAACATATAATATATAGTTTTGA-AAACACATTTTAGAAAAACGATAATATACATAG-T
* *
147042 TTTAAAAAATCAATTTTTGAAAA-TATATAATATGA
64 TTT-AAAAAT-AATTTTTAAAAACTATATAATATAA
*
147077 TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTTGAAAAACGTATAATATACATAGTT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTAGAAAAACG-ATAATATACATAGTT
*
147142 TTAAAAATGATTTTTAAAAACGTATATAATATAA
65 TTAAAAATAATTTTTAAAAAC-TATATAATATAA
*
147176 TTTTAAAAACATAT
1 TTTTGAAAACATAT
147190 TTTGAAAATA
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
96 3 0.03
97 45 0.46
98 11 0.11
99 28 0.29
100 11 0.11
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (97 bp):
TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTAGAAAAACGATAATATACATAGTTT
TAAAAATAATTTTTAAAAACTATATAATATAA
Found at i:147130 original size:38 final size:36
Alignment explanation
Indices: 147077--147197 Score: 131
Period size: 38 Copynumber: 3.2 Consensus size: 36
147067 TATAATATGA
*
147077 TTTTG-AAAACATATAATATATAGTTTTGAAAACACAT
1 TTTTGAAAAACGTATAATATATAGTTTT-AAAA-ACAT
*
147114 TTTTGAAAAACGTATAATATACATAGTTTTAAAAATGAT
1 TTTTGAAAAACGTATAATAT--ATAGTTTTAAAAA-CAT
*
147153 TTTT-AAAAACGTAT-ATAATATAATTTTAAAAACAT
1 TTTTGAAAAACGTATAAT-ATATAGTTTTAAAAACAT
147188 ATTTTGAAAA
1 -TTTTGAAAA
147198 TATATATAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
35 2 0.03
36 16 0.22
37 11 0.15
38 26 0.36
39 10 0.14
40 8 0.11
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (36 bp):
TTTTGAAAAACGTATAATATATAGTTTTAAAAACAT
Found at i:147204 original size:36 final size:35
Alignment explanation
Indices: 147076--147244 Score: 98
Period size: 37 Copynumber: 4.6 Consensus size: 35
147066 ATATAATATG
*
147076 ATTTTGAAAACATATA-ATATATAGTTTTGAAAACACAT
1 ATTTTGAAAA-ATATATA-ATATAATTTT-AAAA-ACAT
** *
147114 -TTTTGAAAAACGTATAATATACATAGTTTTAAAA-AT
1 ATTTTGAAAAATATATAATATA-AT--TTTAAAAACAT
*
147150 GATTTTTAAAAACGTATATAATATAATTTTAAAAACAT
1 -ATTTTGAAAAA--TATATAATATAATTTTAAAAACAT
* *
147188 ATTTTG-AAAATATAT-ATAGT-TTTTTAAAAGCGAT
1 ATTTTGAAAAATATATAATA-TAATTTTAAAAAC-AT
* *
147222 TTTTTAGAAACATATATAATATA
1 ATTTT-GAAAAATATATAATATA
147245 TAATTTTTGA
Statistics
Matches: 103, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
33 12 0.12
34 12 0.12
35 1 0.01
36 23 0.22
37 27 0.26
38 14 0.14
39 5 0.05
40 9 0.09
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (35 bp):
ATTTTGAAAAATATATAATATAATTTTAAAAACAT
Found at i:147256 original size:25 final size:25
Alignment explanation
Indices: 147222--147277 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
147212 TAAAAGCGAT
147222 TTTTTAGAAACATAT-ATAATATATAA
1 TTTTTAGAAA-ATATAATAATATAT-A
*
147248 TTTTT-GAAAATATAATATTATATA
1 TTTTTAGAAAATATAATAATATATA
147272 TTTTTA
1 TTTTTA
147278 ATATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 10 0.37
25 12 0.44
26 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTTAGAAAATATAATAATATATA
Found at i:147281 original size:16 final size:15
Alignment explanation
Indices: 147260--147302 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
147250 TTTGAAAATA
147260 TAATATTATATATTTT
1 TAATATTAT-TATTTT
147276 TAATATTATTA--TT
1 TAATATTATTATTTT
*
147289 TAATATTTTTATTT
1 TAATATTATTATTT
147303 ATTTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 12 0.50
15 3 0.12
16 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATATTATTATTTT
Found at i:147294 original size:24 final size:22
Alignment explanation
Indices: 147265--147311 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
147255 AAATATAATA
147265 TTATATATTTTTAATATTA-TTAT
1 TTATATATTTTT-AT-TTATTTAT
147288 TTA-ATATTTTTATTTATTTAT
1 TTATATATTTTTATTTATTTAT
147309 TTA
1 TTA
147312 ATTTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 8 0.35
23 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATATTTTTATTTATTTAT
Found at i:148705 original size:15 final size:16
Alignment explanation
Indices: 148676--148706 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
148666 CTTCATTTTA
148676 TTTTATTTTACTTTGT
1 TTTTATTTTACTTTGT
148692 TTTTATTTTA-TTTGT
1 TTTTATTTTACTTTGT
148707 CTCTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTATTTTACTTTGT
Done.