Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007951.1 Hibiscus syriacus cultivar Beakdansim tig00110374_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: 657610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:587507 original size:21 final size:21
Alignment explanation
Indices: 587481--587524 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
587471 GACTGCATGA
587481 GATATCTCGACGCCTTCAAGG
1 GATATCTCGACGCCTTCAAGG
587502 GATATCTCGACGCCTTCAAGG
1 GATATCTCGACGCCTTCAAGG
587523 GA
1 GA
587525 ATATTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (21 bp):
GATATCTCGACGCCTTCAAGG
Found at i:603935 original size:21 final size:21
Alignment explanation
Indices: 603911--603950 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
603901 AAAAAATATT
603911 TAAAAAATT-ATTATTTTTACA
1 TAAAAAATTAATT-TTTTTACA
*
603932 TAAAATATTAATTTTTTTA
1 TAAAAAATTAATTTTTTTA
603951 ATATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAAAATTAATTTTTTTACA
Found at i:604119 original size:2 final size:2
Alignment explanation
Indices: 604112--604150 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
604102 ACTGTTGTGA
604112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
604151 AATAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:606953 original size:18 final size:18
Alignment explanation
Indices: 606899--606955 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
606889 TTTTTATGTG
* *
606899 AAGTGGTTTAGGGGTTTT
1 AAGTGGTTTAGAGTTTTT
*
606917 AAGTGATTTTAGAGTTTTT
1 AAGTG-GTTTAGAGTTTTT
606936 AAGTGGTTTAGAGTTTTT
1 AAGTGGTTTAGAGTTTTT
606954 AA
1 AA
606956 AATTGTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (18 bp):
AAGTGGTTTAGAGTTTTT
Found at i:613157 original size:20 final size:20
Alignment explanation
Indices: 613110--613161 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
613100 TCTGATGAAC
613110 AGTATCGATACTGATTGAAGA
1 AGTATCGATACTGATTG-AGA
613131 AGTATCGATACTGATGTG-GA
1 AGTATCGATACTGAT-TGAGA
*
613151 GGTATCGATAC
1 AGTATCGATAC
613162 CAAGATGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.41
21 15 0.52
22 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTGATTGAGA
Found at i:613913 original size:23 final size:22
Alignment explanation
Indices: 613873--613932 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
613863 GTCGAGGGTT
** *
613873 CTATGTGGTTTTTGGGGACAAAA
1 CTATGTGGTCATTCGGGAC-AAA
613896 CTATGTGGTCATTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
613918 -TATGTGG-CACTTCGG
1 CTATGTGGTCA-TTCGG
613933 TGCAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 12 0.36
22 3 0.09
23 16 0.48
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:613923 original size:21 final size:23
Alignment explanation
Indices: 613887--613932 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
613877 GTGGTTTTTG
613887 GGGACAAAACTATGTGGTCA-TTC
1 GGGACAAAACTATGTGG-CACTTC
613910 GGGAC-AAA-TATGTGGCACTTC
1 GGGACAAAACTATGTGGCACTTC
613931 GG
1 GG
613933 TGCAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 12 0.55
22 3 0.14
23 5 0.23
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (23 bp):
GGGACAAAACTATGTGGCACTTC
Found at i:613938 original size:21 final size:22
Alignment explanation
Indices: 613887--613944 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
613877 GTGGTTTTTG
*
613887 GGGACAAAACTATGTGGTCATTC
1 GGGAC-AAATTATGTGGTCATTC
613910 GGGACAAA-TATGTGG-CACTTC
1 GGGACAAATTATGTGGTCA-TTC
613931 GGTG-CAAATTATGT
1 GG-GACAAATTATGT
613945 AAGCAATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.06
21 16 0.50
22 9 0.28
23 5 0.16
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (22 bp):
GGGACAAATTATGTGGTCATTC
Found at i:616488 original size:18 final size:20
Alignment explanation
Indices: 616465--616512 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
616455 TAATTAGTAC
*
616465 AATAAATTATT-ATAAA-AT
1 AATAAAATATTAATAAATAT
616483 AATAAAATATTAAATAAATAT
1 AATAAAATATT-AATAAATAT
616504 AATAAAATA
1 AATAAAATA
616513 AAAAATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.38
20 5 0.19
21 11 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAATATTAATAAATAT
Found at i:616518 original size:21 final size:20
Alignment explanation
Indices: 616476--616520 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
616466 ATAAATTATT
**
616476 ATAAAATAATAAAATATTAA
1 ATAAAATAATAAAATAAAAA
616496 ATAAATATAATAAAATAAAAA
1 ATAAA-ATAATAAAATAAAAA
616517 ATAA
1 ATAA
616521 GATTTTTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
ATAAAATAATAAAATAAAAA
Found at i:616554 original size:21 final size:21
Alignment explanation
Indices: 616530--616584 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
616520 AGATTTTTAC
616530 CTTCTAAAAACTATGAAAAAG
1 CTTCTAAAAACTATGAAAAAG
616551 CTTCTAAAAACTATGAAAAAG
1 CTTCTAAAAACTATGAAAAAG
* *
616572 CTACTTAAAACTA
1 CTTCTAAAAACTA
616585 GATATAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.25
Consensus pattern (21 bp):
CTTCTAAAAACTATGAAAAAG
Found at i:623064 original size:25 final size:24
Alignment explanation
Indices: 623036--623093 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
623026 AATAAAAGAA
** *
623036 ATTTATTTGATCTATTATAATAAAT
1 ATTTATTTGATAAAATAT-ATAAAT
*
623061 ATTTAATTTTATAAAATATATAAAT
1 ATTT-ATTTGATAAAATATATAAAT
623086 ATTTATTT
1 ATTTATTT
623094 AATTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTATTTGATAAAATATATAAAT
Found at i:625286 original size:12 final size:12
Alignment explanation
Indices: 625269--625293 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
625259 AGTCGAGTAG
625269 AATACCAAATTT
1 AATACCAAATTT
625281 AATACCAAATTT
1 AATACCAAATTT
625293 A
1 A
625294 GTCATAGTAA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AATACCAAATTT
Found at i:634289 original size:32 final size:31
Alignment explanation
Indices: 634217--634306 Score: 128
Period size: 32 Copynumber: 2.9 Consensus size: 31
634207 CCAAGAAGGG
** *
634217 TTACCTATGT-CTTTCAAGACATATGGATAGT
1 TTACCTATGTCCTTT-GGGACATATGGATAGA
634248 TTACCTATGTCCTTTGGGACATATGGATAGGA
1 TTACCTATGTCCTTTGGGACATATGGATA-GA
634280 TTACCTATGTCCTTTGGGACATATGGA
1 TTACCTATGTCCTTTGGGACATATGGA
634307 CAAATACTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 22 0.41
32 32 0.59
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTCCTTTGGGACATATGGATAGA
Found at i:636909 original size:17 final size:17
Alignment explanation
Indices: 636887--636937 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
636877 GAGGTACCAC
636887 CTGACCGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
636904 CTGACCGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
*
636921 CTGACTGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
636938 TTTAGTATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (17 bp):
CTGACCGAAAAGTCAAG
Found at i:640379 original size:19 final size:19
Alignment explanation
Indices: 640289--640373 Score: 152
Period size: 19 Copynumber: 4.4 Consensus size: 19
640279 AACTATAAGA
*
640289 AAAGTTTCAAAACTCTTATT
1 AAAGTTTCAAAACTCTT-GT
640309 AAAGTTTCAAAACTCTTGT
1 AAAGTTTCAAAACTCTTGT
640328 AAAGTTTCAAAACTCTTGT
1 AAAGTTTCAAAACTCTTGT
640347 AAAGTTTCAAAACTCTTGT
1 AAAGTTTCAAAACTCTTGT
640366 AAAGTTTC
1 AAAGTTTC
640374 GTAACTTCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
19 47 0.73
20 17 0.27
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
AAAGTTTCAAAACTCTTGT
Found at i:640593 original size:2 final size:2
Alignment explanation
Indices: 640582--640635 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
640572 TTATAAAAAC
640582 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
640623 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
640636 TATGTTAGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:644331 original size:55 final size:55
Alignment explanation
Indices: 644265--644822 Score: 395
Period size: 55 Copynumber: 10.1 Consensus size: 55
644255 AATCTTCGTC
* * * *
644265 AATCGTGTCTGCTCCCCATTTTTCCAGAGAATACAAGACTCAAACGATTCTCGAT
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
* ** *
644320 AATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATGAGACTCGAACAATTCTCAAT
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
** * *
644375 AATCGTG-CATGCTCCCTATTTTCTTCAGAGAGA-ATGAGACTCGAACAA-TCTTCAACG
1 AATCGTGTC-TGCTCCCTATTTT-TTCAGAGA-ATACAAGACTCAAACAATTC-TCAA-T
* * ** * *
644432 AA-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * * ** * *
644486 AATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * ** * *
644541 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * * ** * * *
644596 AAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAGAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
** * *
644651 AATCGTGTCTGCTCCCTATTTTCTTCAGAGAGA-ATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTT-TTCAGAGA-ATACAAGACTCAAACAATTC-TCAAT
* * ** * *
644707 AAACGTGTCTGCTCCCTATTTCTTT-AGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTT-TTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * ** * *
644762 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
644817 AATCGT
1 AATCGT
644823 TGGGAAACCT
Statistics
Matches: 465, Mismatches: 25, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
54 5 0.01
55 361 0.78
56 95 0.20
57 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (55 bp):
AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
Found at i:644676 original size:221 final size:221
Alignment explanation
Indices: 644248--644818 Score: 868
Period size: 221 Copynumber: 2.6 Consensus size: 221
644238 AGGGAGTAAA
** * * ** * *
644248 ACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTT-TTCCAGAGAATACAAGACTCAAACG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTT-CAGAGAGTATGAGACTCGAACA
* * *
644311 AT-TCTCGATAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAA
65 ATCT-TCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAA
* *
644374 TAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACGAACGTGT
128 CAAACGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACGAACGTGT
*
644439 CTGCTCCCTATTTCTTCAGAGAGTATGAG
193 CTGCTCCCTATTTCTTCAGAGAGAATGAG
*
644468 ACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATGAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA
644533 TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAA
66 TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAA
* *
644598 ACGTGTC-TGCTCCCTA-TTTCTTCAGAGAGTATGAGACTCGAAGAATCTTCAAC-AATCGTGTC
131 ACGTG-CATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACGAA-CGTGTC
644660 TGCTCCCTATTTTCTTCAGAGAGAATGAG
194 TGCTCCCTA-TTTCTTCAGAGAGAATGAG
* *
644689 ACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTTAGAGAGTATGAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA
644754 TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAA
66 TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAA
644819 TCGTTGGGAA
Statistics
Matches: 324, Mismatches: 20, Indels: 13
0.91 0.06 0.04
Matches are distributed among these distances:
219 2 0.01
220 57 0.18
221 260 0.80
222 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (221 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA
TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAA
ACGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACGAACGTGTCTG
CTCCCTATTTCTTCAGAGAGAATGAG
Found at i:644748 original size:276 final size:276
Alignment explanation
Indices: 644226--644822 Score: 929
Period size: 276 Copynumber: 2.2 Consensus size: 276
644216 TGGTTTTATC
* * * **
644226 CCCTATTGCTTCAGGGAGTA--AAACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTTTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTTTT
* * * * *
644288 CCAGAGAATACAAGACTCAAACGATTCTCGATAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTA
66 CCAGAGAATACAAGACTCAAACAATTCTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTA
*
644353 TGAGACTCGAACAATTCTCAATAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
131 TGAGACTCGAACAATTCTCAACAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
*
644418 AACAATCTTCAACGAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
196 AACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
644483 AACAATCGTGTCTGCT
261 AACAATCGTGTCTGCT
* *
644499 CTCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTT-T
* ** *
644564 T-CAGAGAGTATGAGACTCGAACAA-TCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAG
65 TCCAGAGAATACAAGACTCAAACAATTC-TCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAG
*
644627 TATGAGACTCGAAGAA-TCTTCAACAATCGTGTC-TGCTCCCTATTTTCTTCAGAGAGAATGAGA
129 TATGAGACTCGAACAATTC-TCAACAATCGTG-CATGCTCCCTATTTTCTTCAGAGAGAATGAGA
*
644690 CTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTTAGAGAGTATGAGACTCGAACAAT
192 CTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAAT
644755 CTTCAACAATCGTGTCTGCT
257 CTTCAACAATCGTGTCTGCT
644775 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
644823 TGGGAAACCT
Statistics
Matches: 296, Mismatches: 21, Indels: 11
0.90 0.06 0.03
Matches are distributed among these distances:
273 17 0.06
275 12 0.04
276 264 0.89
277 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (276 bp):
CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTTTT
CCAGAGAATACAAGACTCAAACAATTCTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTA
TGAGACTCGAACAATTCTCAACAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
AACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
AACAATCGTGTCTGCT
Found at i:645844 original size:20 final size:20
Alignment explanation
Indices: 645821--645877 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
645811 TTGAACCCTC
645821 ATTTTTTCATTTTTTTCATT
1 ATTTTTTCATTTTTTTCATT
*
645841 ATTTTTTTA-TTTTTTCATT
1 ATTTTTTCATTTTTTTCATT
*
645860 -TTTTCACTCATTTTTTTC
1 ATTTT--TTCATTTTTTTC
645878 TTCTTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
20 10 0.32
21 7 0.23
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTTCATTTTTTTCATT
Found at i:645853 original size:27 final size:29
Alignment explanation
Indices: 645821--645876 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
645811 TTGAACCCTC
*
645821 ATTTTTTCATTTTTTTCA-TTATTTTTTT
1 ATTTTTTCATTTTTTTCACTCATTTTTTT
645849 ATTTTTTCA-TTTTTTCACTCATTTTTTT
1 ATTTTTTCATTTTTTTCACTCATTTTTTT
645877 CTTCTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (29 bp):
ATTTTTTCATTTTTTTCACTCATTTTTTT
Found at i:645888 original size:27 final size:27
Alignment explanation
Indices: 645830--645889 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
645820 CATTTTTTCA
* * *
645830 TTTTTTTCATTATTTTTTTATTTTTTC
1 TTTTTTTCATCATTTTTTTACTTCTTC
*
645857 ATTTTTTCACTCATTTTTTT-CTTCTTC
1 TTTTTTTCA-TCATTTTTTTACTTCTTC
645884 TTTTTT
1 TTTTTT
645890 CTTCAAGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTTCATCATTTTTTTACTTCTTC
Done.