Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009354.1 Hibiscus syriacus cultivar Beakdansim tig00113158_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: 72739
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4231 original size:20 final size:20
Alignment explanation
Indices: 4206--4258 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4196 GACCAACGAA
4206 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
4226 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
4246 TTCGCAACGCGAA
1 TTCGCAACGCGAA
4259 TATATAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:4270 original size:20 final size:20
Alignment explanation
Indices: 4247--4334 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
4237 GTTTCCAATT
* *
4247 TCGCAACGCGAATATATAAA
1 TCGCAACGCGAATTTGTAAA
** * **
4267 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
* *
4287 TTCGCAACTCGAATCTGTAAA
1 -TCGCAACGCGAATTTGTAAA
4308 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
4328 TCGCAAC
1 TCGCAAC
4335 ACAGAAGTCA
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 39 0.75
21 13 0.25
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:4351 original size:20 final size:20
Alignment explanation
Indices: 4328--4454 Score: 191
Period size: 20 Copynumber: 6.3 Consensus size: 20
4318 AATTTGTAAA
*
4328 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
4348 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
4368 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
4388 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
4408 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
4428 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
4448 TCGCAAC
1 TCGCAAC
4455 GCGAACTCCA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:4392 original size:60 final size:60
Alignment explanation
Indices: 4328--4495 Score: 250
Period size: 60 Copynumber: 2.8 Consensus size: 60
4318 AATTTGTAAA
4328 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
*
4388 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
* * * * *
4448 TCGCAACGC-GAACTCCAATTTCGCAACGTGAATAGT-AAAATCGCAACA
1 TCGCAACACAGAAGT-CAAATTCGCAACGCG-ATAGTCAAATTCGCAACA
4496 AATCTATATG
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
59 3 0.03
60 91 0.92
61 5 0.05
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (60 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:4471 original size:40 final size:39
Alignment explanation
Indices: 4328--4474 Score: 186
Period size: 40 Copynumber: 3.7 Consensus size: 39
4318 AATTTGTAAA
* * * *
4328 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACGC-GAAGTCAAATTCGCAACACAAAAGTCAAAT
* *
4368 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAATTCGCAACACAAAAGTCAAAT
4408 TCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGA-AGTCAAATTCGCAACACAAAAGTCAAAT
* *
4448 TCGCAACGCGAACTCCAATTTCGCAAC
1 TCGCAACGCGAAGT-CAAATTCGCAAC
4475 GTGAATAGTA
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.03
40 94 0.97
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.17
Consensus pattern (39 bp):
TCGCAACGCGAAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:4874 original size:40 final size:40
Alignment explanation
Indices: 4830--4913 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
4820 ACAATTTGAA
*
4830 ATTCGTAACGCGATTTCACTATTCGCGTTACGATTTTACT
1 ATTCGCAACGCGATTTCACTATTCGCGTTACGATTTTACT
** * *
4870 ATTCGCATTGCGATTTTACTATTCGCGTTGCGATTTTACT
1 ATTCGCAACGCGATTTCACTATTCGCGTTACGATTTTACT
4910 ATTC
1 ATTC
4914 ACGTTGTGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.43
Consensus pattern (40 bp):
ATTCGCAACGCGATTTCACTATTCGCGTTACGATTTTACT
Found at i:4986 original size:21 final size:20
Alignment explanation
Indices: 4839--4988 Score: 147
Period size: 20 Copynumber: 7.4 Consensus size: 20
4829 AATTCGTAAC
* *
4839 GCGATTTCACTATTCGCGTT
1 GCGATTTTACTATTCACGTT
* * *
4859 ACGATTTTACTATTCGCATT
1 GCGATTTTACTATTCACGTT
*
4879 GCGATTTTACTATTCGCGTT
1 GCGATTTTACTATTCACGTT
4899 GCGATTTTACTATTCACGTT
1 GCGATTTTACTATTCACGTT
* *
4919 GTGATTTTACTATTCAAGTT
1 GCGATTTTACTATTCACGTT
** *
4939 GTTATTTTTACTATTTACGTT
1 GCGA-TTTTACTATTCACGTT
** * *
4960 AAGATTTTTACAATTCACGCT
1 GCGA-TTTTACTATTCACGTT
4981 GCGATTTT
1 GCGATTTT
4989 GGAAATTGAG
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
20 79 0.72
21 31 0.28
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (20 bp):
GCGATTTTACTATTCACGTT
Found at i:7306 original size:31 final size:31
Alignment explanation
Indices: 7271--7356 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
7261 GAGTATTACT
7271 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
*
7302 GAGCTCGACTTGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
* *
7333 AAGCTCGACTGGACTCGAAAACTC
1 GAGCTCGACTCGACTCGAAAACTC
7357 GCGAGCTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAACTCTGAAATG
Found at i:8699 original size:42 final size:42
Alignment explanation
Indices: 8640--8726 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
8630 GTTCTGAAAT
*
8640 ATAAACATTCGAGAATCATAAAAAGCAAAGTTGTTGGAGATG
1 ATAAACATCCGAGAATCATAAAAAGCAAAGTTGTTGGAGATG
8682 ATAAACATCCGAGAATCATAAAAAGCAAAGTTGTTGGAGATG
1 ATAAACATCCGAGAATCATAAAAAGCAAAGTTGTTGGAGATG
8724 ATA
1 ATA
8727 TGGAATCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (42 bp):
ATAAACATCCGAGAATCATAAAAAGCAAAGTTGTTGGAGATG
Found at i:13207 original size:3 final size:3
Alignment explanation
Indices: 13199--13224 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13189 TATTTGTTTT
13199 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
13225 GGTGGAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18162 original size:2 final size:2
Alignment explanation
Indices: 18155--18199 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18145 CTTTATTCAA
18155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18197 AT A
1 AT A
18200 ATTATCAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20266 original size:7 final size:7
Alignment explanation
Indices: 20254--20278 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20244 ATGCGGATTT
20254 ATAAATC
1 ATAAATC
20261 ATAAATC
1 ATAAATC
20268 ATAAATC
1 ATAAATC
20275 ATAA
1 ATAA
20279 GCGTCGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAAATC
Found at i:40251 original size:27 final size:27
Alignment explanation
Indices: 40213--40267 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
40203 TAACACAGTT
40213 ATCAACCACAATTAAAACCAGGCATAA
1 ATCAACCACAATTAAAACCAGGCATAA
*
40240 ATCAACCACAATTAAAACCAGGTATAA
1 ATCAACCACAATTAAAACCAGGCATAA
40267 A
1 A
40268 ATGTAATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (27 bp):
ATCAACCACAATTAAAACCAGGCATAA
Found at i:41461 original size:17 final size:17
Alignment explanation
Indices: 41439--41491 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
41429 TTAATAAAGT
*
41439 TAGTTCTTTGATTAAAC
1 TAGTTCATTGATTAAAC
* *
41456 TAGTTCATTCATTTAAC
1 TAGTTCATTGATTAAAC
*
41473 TAGTTCATTAATTAAAC
1 TAGTTCATTGATTAAAC
41490 TA
1 TA
41492 ACTCTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (17 bp):
TAGTTCATTGATTAAAC
Found at i:45020 original size:21 final size:21
Alignment explanation
Indices: 44996--45038 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
44986 AAAGAAAACT
*
44996 TTTTGAA-TAGTTTTTGAGTTG
1 TTTTGAAGT-GTTTTTGAATTG
*
45017 TTTTTAAGTGTTTTTGAATTG
1 TTTTGAAGTGTTTTTGAATTG
45038 T
1 T
45039 GTTTAACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (21 bp):
TTTTGAAGTGTTTTTGAATTG
Found at i:45043 original size:21 final size:21
Alignment explanation
Indices: 45005--45044 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44995 TTTTTGAATA
* *
45005 GTTTTTGAGTTGTTTTTAAGT
1 GTTTTTGAATTGTGTTTAAGT
45026 GTTTTTGAATTGTGTTTAA
1 GTTTTTGAATTGTGTTTAA
45045 CCTAGTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (21 bp):
GTTTTTGAATTGTGTTTAAGT
Found at i:46495 original size:70 final size:70
Alignment explanation
Indices: 46362--46494 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 70
46352 GTAGTTGTTC
* * * * *
46362 CTAATCACAAATGTTAAAAAAATAAATTTTAAGGGTAACTCCATATAACAAGCATTGAAAAAATT
1 CTAATAACAAATATTAAAAAAATAAATTTTAAGAGTAACTCCATACAACAAACATTGAAAAAATT
46427 GGTCT
66 GGTCT
* * * *
46432 CTAATAACAAATATTTAAAAAATAAATTTTAAGAGTATGCT-CATAACAATAAATATTGAAAAA
1 CTAATAACAAATATTAAAAAAATAAATTTTAAGAGTA-ACTCCAT-ACAACAAACATTGAAAAA
46495 TGAATTTCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
70 36 0.69
71 16 0.31
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (70 bp):
CTAATAACAAATATTAAAAAAATAAATTTTAAGAGTAACTCCATACAACAAACATTGAAAAAATT
GGTCT
Found at i:46606 original size:30 final size:30
Alignment explanation
Indices: 46572--46657 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
46562 ACTCTACCCC
* *
46572 TAATAACAAATATTGAAGAAATTGGACTCA
1 TAATAACAAATATTAAAAAAATTGGACTCA
*
46602 TAATAACAAGA-ATTAAAAAAATTGGACTCT
1 TAATAACAA-ATATTAAAAAAATTGGACTCA
* * *
46632 TAATAATAAATTTTTAAAAATATTGG
1 TAATAACAAA-TATTAAAAAAATTGG
46658 TAAAAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
29 1 0.02
30 33 0.70
31 13 0.28
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (30 bp):
TAATAACAAATATTAAAAAAATTGGACTCA
Found at i:58320 original size:20 final size:20
Alignment explanation
Indices: 58295--58387 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
58285 TTTTCCCAAT
58295 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
58315 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
58335 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
58356 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
58377 TCGCAATGCGA
1 TCGCAATGCGA
58388 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:58337 original size:41 final size:41
Alignment explanation
Indices: 58292--58387 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
58282 CGATTTTCCC
*
58292 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
58333 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
58374 AAATCGCAATGCGA
1 AATTCGCAATGCGA
58388 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:58400 original size:41 final size:41
Alignment explanation
Indices: 58314--58448 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
58304 GAATAAGTAA
* * * *
58314 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
58355 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
58396 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
58437 TTCGCAACGCGA
1 ATCGCAACGCGA
58449 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:58401 original size:20 final size:20
Alignment explanation
Indices: 58376--58470 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
58366 AATTGAGAAA
*
58376 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
58396 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
58417 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
58437 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
58457 TTCGCAACGCGATA
1 ATCGCAACGCGATA
58471 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:58686 original size:22 final size:22
Alignment explanation
Indices: 58658--58701 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
58648 CACTCTCTCA
58658 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
58680 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
58702 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:58974 original size:20 final size:20
Alignment explanation
Indices: 58951--58988 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58941 TTAGTTTCTC
58951 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
58971 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
58989 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:60329 original size:18 final size:18
Alignment explanation
Indices: 60308--60352 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
60298 TCCACTTCGG
*
60308 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
60326 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
60344 GAGCCATCA
1 GAGCCATCA
60353 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:60878 original size:19 final size:20
Alignment explanation
Indices: 60835--60890 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
60825 TGCAACACGA
60835 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
60855 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
60874 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
60891 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:60898 original size:14 final size:14
Alignment explanation
Indices: 60879--60936 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
60869 ATGCGAAATG
60879 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
60893 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
60909 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
60925 AAAATCGCAACG
1 AAAATCGCAACG
60937 CGAAATGAAA
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:60921 original size:32 final size:33
Alignment explanation
Indices: 60863--60953 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
60853 GGAAATGGCT
*
60863 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
60896 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
60928 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
60954 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:60947 original size:19 final size:19
Alignment explanation
Indices: 60843--60958 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
60833 GAAAATGACT
***
60843 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAA
*
60863 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
60882 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
60896 ATCGCAACGCGAAATG-AA
1 ATCGCAACGCGAAATGAAA
*
60914 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
60928 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
60947 ATCGCAATGCGA
1 ATCGCAACGCGA
60959 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.36
20 9 0.12
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:60989 original size:14 final size:15
Alignment explanation
Indices: 60970--61046 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 15
60960 TTGTGTTTCG
60970 CGTTGCGATTTTGT-
1 CGTTGCGATTTTGTC
*
60984 CGTTGCGATTTCATTTC
1 CGTTGCGATTT--TGTC
*
61001 GCGTTGCGATTTTCATTTC
1 -CGTTGCGA-TTT--TGTC
61020 GCGTTGCGATTTTGT-
1 -CGTTGCGATTTTGTC
61035 CGTTGCGATTTT
1 CGTTGCGATTTT
61047 CATTTCGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 23 0.41
16 4 0.07
18 11 0.20
19 18 0.32
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (15 bp):
CGTTGCGATTTTGTC
Found at i:60999 original size:19 final size:18
Alignment explanation
Indices: 60965--61103 Score: 123
Period size: 19 Copynumber: 7.9 Consensus size: 18
60955 GCGATTTGTG
60965 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
60981 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
60997 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
61016 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
61032 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
61049 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
61068 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
61088 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
61104 TAAGTTTCGT
Statistics
Matches: 101, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 6 0.06
17 2 0.02
18 13 0.13
19 41 0.41
20 17 0.17
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:61030 original size:51 final size:52
Alignment explanation
Indices: 60965--61082 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 52
60955 GCGATTTGTG
* ***
60965 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
61016 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
61068 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
61083 AGTCATTTCG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 27 0.44
52 23 0.38
53 11 0.18
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (52 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
Found at i:61081 original size:20 final size:19
Alignment explanation
Indices: 61047--61101 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
61037 TTGCGATTTT
*
61047 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
61066 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
61086 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
61102 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:61118 original size:39 final size:38
Alignment explanation
Indices: 60984--61120 Score: 133
Period size: 39 Copynumber: 3.7 Consensus size: 38
60974 GCGATTTTGT
60984 CGTTGCGA-TTTCATTTCGCGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCG
*
61021 CGTTGCGA-TTT--TGT--CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCG
* *** **
61054 CATTGCGATAGCCATTTCCGCGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATTTCG
* *
61093 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTTCA-TTTCGCGTTGCGA
61121 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
33 26 0.33
35 2 0.03
36 2 0.03
37 11 0.14
39 35 0.44
40 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.42
Consensus pattern (38 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCG
Found at i:62987 original size:14 final size:14
Alignment explanation
Indices: 62968--63003 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
62958 ATTGTTTAAT
62968 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
62982 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
62996 TGATTTGT
1 TGATTTGT
63004 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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:63142 original size:19 final size:19
Alignment explanation
Indices: 63120--63187 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
63110 ATCGCAACGA
*
63120 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
63139 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
63158 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
63172 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
63188 TTTCATTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:63230 original size:20 final size:20
Alignment explanation
Indices: 63205--63261 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
63195 TCGCATTGCG
*
63205 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
63225 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
63245 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
63262 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:63659 original size:14 final size:14
Alignment explanation
Indices: 63627--63660 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
63617 GATTGTTTAA
63627 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
63641 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
63655 TTGATT
1 TTGATT
63661 GTTTAATTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:64232 original size:14 final size:14
Alignment explanation
Indices: 64213--64248 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
64203 ATTGTTTAAT
64213 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
64227 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
64241 TGATTTGT
1 TGATTTGT
64249 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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:64833 original size:14 final size:14
Alignment explanation
Indices: 64801--64834 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
64791 GATTGTTTAA
64801 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
64815 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
64829 TTGATT
1 TTGATT
64835 GTTTAATTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:65048 original size:588 final size:589
Alignment explanation
Indices: 63225--65212 Score: 3880
Period size: 588 Copynumber: 3.4 Consensus size: 589
63215 TGCGATAACC
63225 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
63290 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
63355 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTG-AA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
63419 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
63484 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
63549 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
63614 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTGTTTAATTGATGTGTACA
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTGTTTAATTGATGTGTACA
63679 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
456 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
63744 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
521 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
63809 TGCG
586 TGCG
63813 ATTTTCGCGTTGCGATAACCA-TTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
63877 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTG-AAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
63941 AAGTGCACACAT-AAA-ACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
64004 ATGTTTGGTTAAGTACTTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
64069 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
64134 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
64199 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGA-TTGTTTAATTGATGTGTAC
64264 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
455 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
64329 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
520 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
64394 TTGCG
585 TTGCG
64399 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
64464 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
64529 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
64594 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
64659 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
64724 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
64788 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTGTTTAATTGATGTGTACA
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTGTTTAATTGATGTGTACA
64853 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
456 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
*
64918 CAGACTATCGCAACGCGAAATGTCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
521 CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
64983 TGCG
586 TGCG
*
64987 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
65052 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
65117 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
65182 ATATTTGGTTAAGTACCTAGAATTCAATAAT
196 ATGTTTGGTTAAGTACCTAGAATTCAATAAT
65213 AATTGTTAAA
Statistics
Matches: 1388, Mismatches: 6, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
584 45 0.03
585 244 0.18
586 196 0.14
587 196 0.14
588 419 0.30
589 50 0.04
590 238 0.17
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (589 bp):
ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTGTTTAATTGATGTGTACA
TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
CAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCAT
TGCG
Found at i:66125 original size:24 final size:24
Alignment explanation
Indices: 66069--66127 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
66059 AGTAAGTATT
* *
66069 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
66093 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
66117 CGAATTTTGAT
1 CGAAATTTGAT
66128 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:66319 original size:12 final size:12
Alignment explanation
Indices: 66302--66326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66292 ATATAATCCT
66302 GAAGAAGAAAAA
1 GAAGAAGAAAAA
66314 GAAGAAGAAAAA
1 GAAGAAGAAAAA
66326 G
1 G
66327 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:68653 original size:32 final size:33
Alignment explanation
Indices: 68612--68704 Score: 170
Period size: 32 Copynumber: 2.8 Consensus size: 33
68602 GGAAATTACT
68612 ATCGCAATGCGAAATGAAAATCGCAACGAGAG-
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
68644 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
68677 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
68705 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 31 0.53
33 28 0.47
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:68734 original size:18 final size:18
Alignment explanation
Indices: 68708--68745 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
68698 CGCAACGCGA
*
68708 ATTTAATTTCGCGTTGCG
1 ATTTAATTTCGCATTGCG
*
68726 ATTTCATTTCGCATTGCG
1 ATTTAATTTCGCATTGCG
68744 AT
1 AT
68746 AGTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (18 bp):
ATTTAATTTCGCATTGCG
Found at i:68871 original size:14 final size:14
Alignment explanation
Indices: 68852--68888 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
68842 CATCAATTAA
68852 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
68866 ACAAATCACCTTTT
1 ACAAATCAACTTTT
68880 ACAAATCAA
1 ACAAATCAA
68889 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:70305 original size:21 final size:21
Alignment explanation
Indices: 70239--70305 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
70229 GTGAATCGGG
*
70239 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
70259 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
70281 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
70302 CTCT
1 CTCT
70306 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:70324 original size:42 final size:41
Alignment explanation
Indices: 70239--70361 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
70229 GTGAATCGGG
* * * * *
70239 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
70281 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
70323 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
70362 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:71108 original size:20 final size:18
Alignment explanation
Indices: 71068--71108 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
71058 CGGGTCGATC
*
71068 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGAGTG
71086 AGGTGATGGCTCTCGAAGTG
1 AGGTGATGGCTCT-G-AGTG
71106 AGG
1 AGG
71109 AAGTGGAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 1 0.05
20 6 0.30
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.24
Consensus pattern (18 bp):
AGGTGATGGCTCTGAGTG
Found at i:72450 original size:33 final size:33
Alignment explanation
Indices: 72377--72503 Score: 139
Period size: 33 Copynumber: 3.7 Consensus size: 33
72367 TAATGAAATT
*
72377 GCAACGCGGAAATGACTATCGCAATGAGAGAAATC
1 GCAACGC-GAAATGACTATCGCAACGAGAG-AATC
*
72412 GCAACGCGAAATGACTATCGCGACGAGAGAATC
1 GCAACGCGAAATGACTATCGCAACGAGAGAATC
** *
72445 GCAACGCGAAATGAAAATCGCAACGCGAATGAAAATC
1 GCAACGCGAAATGACTATCGCAA--CG-A-GAGAATC
*
72482 GCAACGCGAAATGA-AATCGCAA
1 GCAACGCGAAATGACTATCGCAA
72504 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
33 24 0.29
34 20 0.24
35 9 0.11
36 9 0.11
37 20 0.24
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (33 bp):
GCAACGCGAAATGACTATCGCAACGAGAGAATC
Found at i:72477 original size:18 final size:19
Alignment explanation
Indices: 72346--72508 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
72336 GTCATTTGGT
*
72346 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
72365 GATAATG-AAATTGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
72384 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
72402 GAGA-G-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
72419 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
72436 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
72452 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
72471 G-AATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
72489 GAAATG-AAATCGCAATGC
1 GAAATGAAAATCGCAACGC
72507 GA
1 GA
72509 TTTTGGTTTC
Statistics
Matches: 112, Mismatches: 19, Indels: 27
0.71 0.12 0.17
Matches are distributed among these distances:
14 8 0.07
15 8 0.07
16 3 0.03
17 8 0.07
18 33 0.29
19 40 0.36
20 12 0.11
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Done.