Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009345.1 Hibiscus syriacus cultivar Beakdansim tig00113128_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: 61523
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2578 original size:26 final size:25
Alignment explanation
Indices: 2541--2598 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 25
2531 CAAAATAGTA
*
2541 TTTTTTCTGAAAACCAGTAATATTT
1 TTTTTTCTGAAAACCAGTAAAATTT
2566 TTTTCTTCTGAAAACCAGTAAAATTT
1 TTTT-TTCTGAAAACCAGTAAAATTT
2592 TGTTTTT
1 T-TTTTT
2599 TTCTAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.13
26 23 0.77
27 3 0.10
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (25 bp):
TTTTTTCTGAAAACCAGTAAAATTT
Found at i:3325 original size:24 final size:24
Alignment explanation
Indices: 3298--3352 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
3288 ATAGCGTCGT
*
3298 GTAGAATTTCACATAAAGTACCAC
1 GTAGAATTGCACATAAAGTACCAC
* *
3322 GTAGAATTGCACGTAAAGTGCCAC
1 GTAGAATTGCACATAAAGTACCAC
3346 GTAGAAT
1 GTAGAAT
3353 GTACACGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (24 bp):
GTAGAATTGCACATAAAGTACCAC
Found at i:4448 original size:46 final size:46
Alignment explanation
Indices: 4396--4487 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
4386 TTGAACATAG
*
4396 ATGTTGTTCAAATCTAATATCCTTCATTGTGAAGTTGAAATTTGAC
1 ATGTTGTTCAAATCTAATATCCTTCATTGTGAAGTTAAAATTTGAC
* *
4442 ATGTTGTTCGAGTCTAATATCCTTCATTGTGAAGTTAAAATTTGAC
1 ATGTTGTTCAAATCTAATATCCTTCATTGTGAAGTTAAAATTTGAC
4488 TAAAAACTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (46 bp):
ATGTTGTTCAAATCTAATATCCTTCATTGTGAAGTTAAAATTTGAC
Found at i:9347 original size:16 final size:17
Alignment explanation
Indices: 9321--9353 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9311 TTTTAATTCA
9321 TTTGTAAAAGTAAATGT
1 TTTGTAAAAGTAAATGT
*
9338 TTTG-AAAAGTCAATGT
1 TTTGTAAAAGTAAATGT
9354 GATACCTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (17 bp):
TTTGTAAAAGTAAATGT
Found at i:14319 original size:16 final size:17
Alignment explanation
Indices: 14293--14325 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14283 TTTTAATTCA
14293 TTTGTAAAAGTAAATGT
1 TTTGTAAAAGTAAATGT
*
14310 TTTG-AAAAGTCAATGT
1 TTTGTAAAAGTAAATGT
14326 GATACATCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (17 bp):
TTTGTAAAAGTAAATGT
Found at i:15693 original size:21 final size:21
Alignment explanation
Indices: 15655--15695 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15645 GTCCTTCGGG
* *
15655 ACATATATGTAATCCTTTGGA
1 ACATATATGCAATACTTTGGA
*
15676 ACATATATGCGATACTTTGG
1 ACATATATGCAATACTTTGG
15696 TACACTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
ACATATATGCAATACTTTGGA
Found at i:33484 original size:18 final size:18
Alignment explanation
Indices: 33461--33535 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
33451 ACCGGTCACA
33461 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
33479 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
33497 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
33510 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
33528 ACCCGACC
1 ACCCGACC
33536 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:33511 original size:31 final size:31
Alignment explanation
Indices: 33465--33535 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
33455 GTCACAACCC
*
33465 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
* *
33496 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
33527 GACCCGACC
1 GACCCGACC
33536 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCATTGACCCGACCCGACCCGTT
Found at i:33539 original size:12 final size:13
Alignment explanation
Indices: 33514--33557 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
33504 CCATTGACCC
33514 GACCCGACCCGTT
1 GACCCGACCCGTT
33527 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
33539 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
33554 GACC
1 GACC
33558 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:33544 original size:7 final size:7
Alignment explanation
Indices: 33532--33565 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
33522 CCGTTGACCC
33532 GACCGTT
1 GACCGTT
33539 GACCGTT
1 GACCGTT
33546 GACCCGTT
1 GA-CCGTT
*
33554 GACCATT
1 GACCGTT
33561 GACCG
1 GACCG
33566 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:33554 original size:15 final size:15
Alignment explanation
Indices: 33534--33564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33524 GTTGACCCGA
*
33534 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
33549 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
33564 C
1 C
33565 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:34879 original size:18 final size:18
Alignment explanation
Indices: 34853--34887 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34843 TCGAAAGGAC
*
34853 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
34871 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
34888 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:38681 original size:18 final size:18
Alignment explanation
Indices: 38658--38732 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
38648 ACCGGTCACA
38658 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
38676 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
38694 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
38707 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
38725 ACCCGACC
1 ACCCGACC
38733 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:38708 original size:31 final size:31
Alignment explanation
Indices: 38662--38732 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
38652 GTCACAACCC
*
38662 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
* *
38693 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
38724 GACCCGACC
1 GACCCGACC
38733 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCATTGACCCGACCCGACCCGTT
Found at i:38736 original size:12 final size:13
Alignment explanation
Indices: 38711--38754 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
38701 CCATTGACCC
38711 GACCCGACCCGTT
1 GACCCGACCCGTT
38724 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
38736 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
38751 GACC
1 GACC
38755 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:38741 original size:7 final size:7
Alignment explanation
Indices: 38729--38762 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
38719 CCGTTGACCC
38729 GACCGTT
1 GACCGTT
38736 GACCGTT
1 GACCGTT
38743 GACCCGTT
1 GA-CCGTT
*
38751 GACCATT
1 GACCGTT
38758 GACCG
1 GACCG
38763 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:38751 original size:15 final size:15
Alignment explanation
Indices: 38731--38761 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38721 GTTGACCCGA
*
38731 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
38746 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
38761 C
1 C
38762 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:40075 original size:18 final size:18
Alignment explanation
Indices: 40049--40083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40039 TCGAAAGGAC
*
40049 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
40067 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
40084 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:44777 original size:97 final size:95
Alignment explanation
Indices: 44605--44806 Score: 253
Period size: 97 Copynumber: 2.1 Consensus size: 95
44595 ACTACTGTAG
** * **
44605 GTATCGATATTAAGAGAAAGGTATCAATACCAGGGATTCTAGAATGTAAAAATGGTATCGATGTT
1 GTATCGATACAAAGAGAAAGGTATCAATACCAGGGATTCTAGAATGTAAAAATGGTATCAATACT
*
44670 GAAAGGGAGTATCGGTACCATAATAAATAGAA
66 GAAAGAGAGTATCGGTACCATAAT--ATAGAA
* * * *
44702 GTATCGATACAAAGAGAAATGTATTAATACCATGGATTAC-AGGATGTAAAAATGGTATCAATAC
1 GTATCGATACAAAGAGAAAGGTATCAATACCAGGGATT-CTAGAATGTAAAAATGGTATCAATAC
* *
44766 TGAACGAGAGTATCGGTACCATAGTATAGAA
65 TGAAAGAGAGTATCGGTACCATAATATAGAA
*
44797 GGATCGATAC
1 GTATCGATAC
44807 CATGGTAGGG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 15 0.16
97 75 0.82
98 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (95 bp):
GTATCGATACAAAGAGAAAGGTATCAATACCAGGGATTCTAGAATGTAAAAATGGTATCAATACT
GAAAGAGAGTATCGGTACCATAATATAGAA
Found at i:45271 original size:45 final size:45
Alignment explanation
Indices: 45222--45580 Score: 409
Period size: 45 Copynumber: 8.0 Consensus size: 45
45212 AAATGGATGA
45222 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
* * * * *
45267 ATATATGAAATGCATAACGGTGCACTATAGACATGAAATGATGCT
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
* * *
45312 ATATATGAAATGCATAATAGTGCATTATAGGTATGAGAGGATGCC
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
* * *
45357 ATATATGTAATGCATAACAGAGCATTATAGGCATGAAATGATGCC
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
* * * * ** *
45402 ATATATGTAATGTATAACGGTGAATTGCATGCATGAAAGGATGCC
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
*
45447 ATA-ATGAGATGCATAACGACGT--ATTATAGGCATGAAAGGATGCC
1 ATATATGAAATGCATAAC-A-GTGCATTATAGGCATGAAAGGATGCC
* * * * *
45491 ATAAATGAGATGCATAACGGTGCATTATCGACATGAAAGGATGCC
1 ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
* * * * *
45536 ATAAATGAAAATGCACAACGGAGCATTATAAGCATGAAAGGATGC
1 ATATATG-AAATGCATAACAGTGCATTATAGGCATGAAAGGATGC
45581 TATAAATGCA
Statistics
Matches: 265, Mismatches: 43, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
43 2 0.01
44 33 0.12
45 197 0.74
46 33 0.12
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (45 bp):
ATATATGAAATGCATAACAGTGCATTATAGGCATGAAAGGATGCC
Found at i:45516 original size:179 final size:181
Alignment explanation
Indices: 45252--45580 Score: 446
Period size: 179 Copynumber: 1.8 Consensus size: 181
45242 TGCATTATAG
** * * *
45252 GCATGAAAGGATGCCATATATGAAATGCATAACGGTGCACTATAGACATGAAATGATGCTATATA
1 GCATGAAAGGATGCCATATATGAAATGCATAACGACGCACTATAGACATGAAAGGATGCCATAAA
* ** * * * *
45317 TGAAATGCATAATAGTGCATTATAGGTATGAGAGGATGCCATATATG-TAATGCATAACAGAGCA
66 TGAAATGCATAACAGTGCATTATAGACATGAAAGGATGCCATAAATGAAAATGCACAACAGAGCA
* *
45381 TTATAGGCATGAAATGATGCCATATATGTAATGTATAACGGTGAATTGCAT
131 TTATAAGCATGAAAGGATGCCATATATGTAATGTATAACGGTGAATTGCAT
* * * *
45432 GCATGAAAGGATGCCATA-ATGAGATGCATAACGACGTATTATAGGCATGAAAGGATGCCATAAA
1 GCATGAAAGGATGCCATATATGAAATGCATAACGACGCACTATAGACATGAAAGGATGCCATAAA
* * * *
45496 TGAGATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCACAACGGAGCA
66 TGAAATGCATAACAGTGCATTATAGACATGAAAGGATGCCATAAATGAAAATGCACAACAGAGCA
45561 TTATAAGCATGAAAGGATGC
131 TTATAAGCATGAAAGGATGC
45581 TATAAATGCA
Statistics
Matches: 126, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
179 76 0.60
180 50 0.40
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.24
Consensus pattern (181 bp):
GCATGAAAGGATGCCATATATGAAATGCATAACGACGCACTATAGACATGAAAGGATGCCATAAA
TGAAATGCATAACAGTGCATTATAGACATGAAAGGATGCCATAAATGAAAATGCACAACAGAGCA
TTATAAGCATGAAAGGATGCCATATATGTAATGTATAACGGTGAATTGCAT
Found at i:47413 original size:26 final size:25
Alignment explanation
Indices: 47384--47454 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 25
47374 TTCCTGAATG
47384 CATAAATAGTGTCGCGTAGAATTGCA
1 CATAAAT-GTGTCGCGTAGAATTGCA
*
47410 CAT-AAT-TGTCACGTAGAATTGCA
1 CATAAATGTGTCGCGTAGAATTGCA
47433 CATAAAGTGTGTCGCGTAGAAT
1 CATAAA-TGTGTCGCGTAGAAT
47455 GTACACGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 19 0.47
24 2 0.05
25 4 0.10
26 15 0.38
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (25 bp):
CATAAATGTGTCGCGTAGAATTGCA
Found at i:51503 original size:13 final size:14
Alignment explanation
Indices: 51476--51502 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51466 AAGAGGTAAT
51476 GATCTACAAAAAAA
1 GATCTACAAAAAAA
51490 GATCTACAAAAAA
1 GATCTACAAAAAA
51503 GTGTTCGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (14 bp):
GATCTACAAAAAAA
Found at i:54000 original size:18 final size:18
Alignment explanation
Indices: 53977--54012 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53967 CCTAGGGCAA
53977 GTTCATCTGATGGGGTAG
1 GTTCATCTGATGGGGTAG
53995 GTTCATCTGATGGGGTAG
1 GTTCATCTGATGGGGTAG
54013 CTATGCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.39, T:0.33
Consensus pattern (18 bp):
GTTCATCTGATGGGGTAG
Found at i:56321 original size:2 final size:2
Alignment explanation
Indices: 56252--56310 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
56242 TATTATGAAT
*
56252 TA TA TA TA TA TA TA TA TA GA 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
56294 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
56311 TGTAATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:58119 original size:20 final size:20
Alignment explanation
Indices: 58094--58162 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
58084 TATTATTTCA
58094 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
*
58114 AATTAATTGAAAT-TAATATTC
1 AATTAATT-AAATCT-ATATTT
*
58135 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAATC-TATATTT
58157 AATTAA
1 AATTAA
58163 CTCTATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 12 0.31
21 14 0.36
22 9 0.23
23 4 0.10
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:58130 original size:88 final size:88
Alignment explanation
Indices: 57962--58131 Score: 281
Period size: 88 Copynumber: 1.9 Consensus size: 88
57952 ACGCACCCTT
57962 TTATAGCCAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAATCTATATTTAA
1 TTATAGCCAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAATCTATATTTAA
*
58027 TTAATTGGAATTTAATAATCCTC
66 TTAATTGGAAATTAATAATCCTC
* *
58050 TTATATCCAAGTTACCCT-ATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATAATAGGG-TTTTATTATTTCAAATTAATT-AATCTATATTT
58114 AATTAATT-GAAATTAATA
64 AATTAATTGGAAATTAATA
58132 TTCAGGATTA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
87 11 0.14
88 47 0.61
89 19 0.25
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAATCTATATTTAA
TTAATTGGAAATTAATAATCCTC
Done.