Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005596.1 Hibiscus syriacus cultivar Beakdansim tig00013020_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: 110761
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1695 original size:23 final size:23
Alignment explanation
Indices: 1669--1712 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1659 GATCAACGGT
1669 AAACGGGTCGGGTCAGGTCGGGC
1 AAACGGGTCGGGTCAGGTCGGGC
* *
1692 AAACGGGTCGTGTCGGGTCGG
1 AAACGGGTCGGGTCAGGTCGG
1713 AACCTGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.48, T:0.16
Consensus pattern (23 bp):
AAACGGGTCGGGTCAGGTCGGGC
Found at i:7714 original size:15 final size:15
Alignment explanation
Indices: 7679--7708 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7669 TGAAATGACT
*
7679 GTTGCATCAGCTGTA
1 GTTGCATCAGATGTA
7694 GTTGCATCAGATGTA
1 GTTGCATCAGATGTA
7709 TCTGCAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (15 bp):
GTTGCATCAGATGTA
Found at i:9134 original size:2 final size:2
Alignment explanation
Indices: 9127--9153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9117 AAAATAATCC
9127 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
9154 TGACTTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10319 original size:597 final size:597
Alignment explanation
Indices: 9186--11548 Score: 4636
Period size: 597 Copynumber: 4.0 Consensus size: 597
9176 TTTACTTTTC
* *
9186 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGATCGACCCAGGTTTCCGTTGATAAT
1 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
*
9251 CATTCTAGTAATACTAATGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
66 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
9316 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
131 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
9381 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
196 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
9446 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
261 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
9511 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
326 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
*
9576 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATATGCAGCTTTTGTTGGGGGATGACCCCAAT
391 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
9641 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
456 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
9706 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
521 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
9771 CTGAAGAGCCAT
586 CTGAAGAGCCAT
*
9783 ATTACATGGGGAAATTAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
1 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
9848 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
66 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
9913 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
131 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
9978 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
196 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
10043 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
261 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
10108 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
326 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
10173 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
391 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
10238 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
456 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
10303 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
521 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
10368 CTGAAGAGCCAT
586 CTGAAGAGCCAT
10380 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
1 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
10445 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
66 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
*
10510 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAGGGATTACGTGGCTGCCC
131 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
10575 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
196 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
10640 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
261 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
*
10705 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGAGAGGGCTTTCG
326 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
10770 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
391 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
10835 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
456 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
10900 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
521 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
10965 CTGAAGAGCCAT
586 CTGAAGAGCCAT
10977 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
1 ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
11042 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
66 CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
*
11107 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAGGGATTACGTGGCTGCCC
131 AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
11172 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
196 TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
11237 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
261 AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
11302 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
326 TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
*
11367 AAGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
391 AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
*
11432 CACAAGGATGCTTTGGAGATTGCGAGGAGATTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
456 CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
11497 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTT
521 GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTT
11549 CGTGGTGCCC
Statistics
Matches: 1755, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
597 1755 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (597 bp):
ATTACATGGGGAAATCAGGTGGTAGGAAAAAGAAGGGTAGTTCGAACCAGGTTTCCGTTGATAAT
CATTCTAGTAATACTAGTGCACATGCTAATGGTGGTGTTGATTTAGACTCTTCTATATTTTTGAA
AAGAGCCCATGAACTCAAAGAGGAAGGCAATAAGAGGTTTCAGAATAAGGATTACGTGGCTGCCC
TTAAACACTATGATGATGCTCTTAAGCTTATCCCCAAAACACACCCCGACCGAGCTGTCTTTCAC
AGCAACCGAGCCGCTTGCTTGATGCAAATGAAACCCGCTGATTATGACACCGTGATTGCTGAGTG
TAATATGGCTCTTCAGGTTCAGCCTCGGTTCTCCCGAGCACTTCTTAGGAGGGCGAGGGCTTTCG
AGGCTATTAGGAAGTATGAAATGGCGATGCAGGATGTGCAGCTTTTGTTGGGGGATGACCCCAAT
CACAAGGATGCTTTGGAGATTGCGAGGAGGTTAAGGACTGCATTGGGTACTCTCCAGGAGGCTCA
GCAAGACCTCCAGAGCCGTCCCTCCCCGGCTGCACTCGGGGCTTCTGCTGTTACCGAGGCTGAAC
CTGAAGAGCCAT
Found at i:17484 original size:53 final size:51
Alignment explanation
Indices: 17422--17533 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 51
17412 AAATTTTAGG
*
17422 GTGGACACTTCCTGTAAAATAAACAACTAACA-TAAAGAAATTCAGATTTCAAA
1 GTGGACACTTCCAGTAAAATAAACAACTAACATTAAA-AAA-TCAGATTTC-AA
* * *
17475 GTGGACACTTTCAGTAAAATAAACAATTAATATTAAAAAATCAGATTTCAA
1 GTGGACACTTCCAGTAAAATAAACAACTAACATTAAAAAATCAGATTTCAA
17526 GATGGACA
1 G-TGGACA
17534 TGTGATCACC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
51 3 0.06
52 15 0.28
53 31 0.58
54 4 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (51 bp):
GTGGACACTTCCAGTAAAATAAACAACTAACATTAAAAAATCAGATTTCAA
Found at i:17825 original size:37 final size:37
Alignment explanation
Indices: 17752--17826 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
17742 GTTGGAAAAT
* *
17752 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
17789 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
17826 A
1 A
17827 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:29895 original size:20 final size:20
Alignment explanation
Indices: 29859--29896 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29849 ATCATATTCT
**
29859 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
29879 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
29897 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:30503 original size:20 final size:21
Alignment explanation
Indices: 30453--30504 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
30443 TAGATTCATT
* *
30453 GAAAACAAA-AAAATAAAGAT
1 GAAAATAAAGAAAATAAAGAA
* *
30473 GTAAATTAAGAAAATAAA-AA
1 GAAAATAAAGAAAATAAAGAA
30493 GAAAATAAAGAA
1 GAAAATAAAGAA
30505 TAAATATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (21 bp):
GAAAATAAAGAAAATAAAGAA
Found at i:37462 original size:27 final size:26
Alignment explanation
Indices: 37432--37500 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
37422 TTTAAATGAA
37432 AATAAAATATTTTTAAATGAAGTTAAT
1 AATAAAATATTTTTAAAT-AAGTTAAT
*
37459 AATAAAATATATTT-AATAAGTTAAT
1 AATAAAATATTTTTAAATAAGTTAAT
* *
37484 ATAAAAAATAGTTTTAA
1 A-ATAAAATATTTTTAA
37501 GTTAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.25
26 13 0.36
27 14 0.39
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
AATAAAATATTTTTAAATAAGTTAAT
Found at i:37490 original size:25 final size:26
Alignment explanation
Indices: 37433--37520 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 26
37423 TTAAATGAAA
*
37433 ATAAAATATTTTTAAATGAAGTTAATA-
1 ATAAAATATATTT-AAT-AAGTTAATAT
37460 ATAAAATATATTTAATAAGTTAATAT
1 ATAAAATATATTTAATAAGTTAATAT
37486 A-AAAA-ATAGTTT--TAAGTTAATAT
1 ATAAAATATA-TTTAATAAGTTAATAT
37509 ATATAAA-ATATT
1 ATA-AAATATATT
37521 ATGAATTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
23 12 0.21
24 6 0.11
25 22 0.39
26 4 0.07
27 12 0.21
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
ATAAAATATATTTAATAAGTTAATAT
Found at i:38607 original size:18 final size:17
Alignment explanation
Indices: 38584--38647 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
38574 GAGACAATTT
38584 TTATTTATTTATTTTGAA
1 TTATTTATTTATTTTG-A
*
38602 TTATTTATTTATTTCGTA
1 TTATTTATTTATTTTG-A
*
38620 TAATTTATTTAGTTTT-A
1 TTATTTATTTA-TTTTGA
38637 TTCATTTATTT
1 TT-ATTTATTT
38648 TGAATAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 2 0.05
18 34 0.87
19 3 0.08
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (17 bp):
TTATTTATTTATTTTGA
Found at i:38671 original size:4 final size:4
Alignment explanation
Indices: 38662--38695 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
38652 TAGATTAATG
38662 ATTT ATTT ATTT ATTTT CATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT A-TTT -ATTT ATTT ATTT ATTT
38696 GAAAGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.75
5 6 0.21
6 1 0.04
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:40675 original size:6 final size:6
Alignment explanation
Indices: 40656--40726 Score: 52
Period size: 6 Copynumber: 11.8 Consensus size: 6
40646 ATGATATTGA
* * * * * *
40656 TGATGG TAATGG TGATGG TGGTGG TGGTGA TGGTGG TGGTGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
* * * *
40704 TGGTGG TGGTGA TGATGC TGATG
1 TGATGG TGATGG TGATGG TGATG
40727 TTAATGTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.13, C:0.01, G:0.52, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:40677 original size:3 final size:3
Alignment explanation
Indices: 40665--40714 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
40655 ATGATGGTAA
* * *
40665 TGG TGA TGG TGG TGG TGG TGA TGG TGG TGG TGG TGA TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
40713 TG
1 TG
40715 ATGATGCTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.06, C:0.00, G:0.60, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:40677 original size:15 final size:15
Alignment explanation
Indices: 40665--40717 Score: 106
Period size: 15 Copynumber: 3.5 Consensus size: 15
40655 ATGATGGTAA
40665 TGGTGATGGTGGTGG
1 TGGTGATGGTGGTGG
40680 TGGTGATGGTGGTGG
1 TGGTGATGGTGGTGG
40695 TGGTGATGGTGGTGG
1 TGGTGATGGTGGTGG
40710 TGGTGATG
1 TGGTGATG
40718 ATGCTGATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.08, C:0.00, G:0.58, T:0.34
Consensus pattern (15 bp):
TGGTGATGGTGGTGG
Found at i:42036 original size:6 final size:6
Alignment explanation
Indices: 42025--42049 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42015 AGTAGAACTG
42025 CATCTT CATCTT CATCTT CATCTT C
1 CATCTT CATCTT CATCTT CATCTT C
42050 TTTATCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CATCTT
Found at i:45950 original size:2 final size:2
Alignment explanation
Indices: 45945--45983 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45935 TATATTAATG
45945 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
45984 GTTTTAGTAT
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:46608 original size:6 final size:6
Alignment explanation
Indices: 46597--46625 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46587 TTAGAAAACA
46597 TACATG TACATG TACATG TACATG TACAT
1 TACATG TACATG TACATG TACATG TACAT
46626 ACATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
TACATG
Found at i:47478 original size:124 final size:119
Alignment explanation
Indices: 47195--47480 Score: 326
Period size: 119 Copynumber: 2.4 Consensus size: 119
47185 AAACAAAATT
* * **
47195 GAAAGTTTAGGTATTAAAATGGATCAAAACTAATAGTTT-GAGTACTAAACGCGTTAAGTTGTTA
1 GAAAGTTTAGGTATTAAAACGGACCAAAACTAATAGTTTAG-GTACTAAAAACGTTAAGTTGTTA
* * **
47259 ACAGTGGGTAATAAATGAAACAAAAACTAAACATTAGGTATGATTTGAAAGCATT
65 ACAGTAGGTAATAAATGAAACAAAAACCAAACATTAGGTATGATTTGAAAGCAAG
* * * *
47314 GAAAGTTTAGGTATTAAAACGGACCAAAAATAATAATTTAGGTAC-AAAAACGTTAATTTTTTAA
1 GAAAGTTTAGGTATTAAAACGGACCAAAACTAATAGTTTAGGTACTAAAAACGTTAAGTTGTTAA
* * *
47378 TATTAGGTATTAAAATGAAACAAAAACCAAACATTAGGTATGATTTTGAAAAAAAG-AGAG
66 CAGTAGGTAAT-AAATGAAACAAAAACCAAACATTAGGTATGA-TTTG----AAAGCA-AG
* *
47438 GAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGT
1 GAAAGTTTAGGTATTAAAACGGACCAAAACTAATAGTTTAGGT
47481 GTTAAACACA
Statistics
Matches: 140, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
118 22 0.16
119 69 0.49
120 5 0.04
123 1 0.01
124 43 0.31
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.28
Consensus pattern (119 bp):
GAAAGTTTAGGTATTAAAACGGACCAAAACTAATAGTTTAGGTACTAAAAACGTTAAGTTGTTAA
CAGTAGGTAATAAATGAAACAAAAACCAAACATTAGGTATGATTTGAAAGCAAG
Found at i:53371 original size:145 final size:144
Alignment explanation
Indices: 53109--53402 Score: 579
Period size: 145 Copynumber: 2.0 Consensus size: 144
53099 TTGCCTGAGA
53109 AAATGCCTATTTTTTTCACAGAATATACGATGAGGAACAAAAAGGGAAAGGAAAGGGAAAAAAAG
1 AAATGCCTATTTTTTTCACAGAATATACGATGAGGAACAAAAAGGGAAAGGAAAGGGAAAAAAAG
53174 AAAGAAATAAAATTCCACCAAAGTAGACTATTGGTTACATGGAGGCATGAAGCCCATGAAAATTT
66 AAAGAAATAAAATTCCACCAAAGTAGACTATTGGTTACATGGAGGCATGAAGCCCATGAAAATTT
53239 ATTTGTAAATGGAT
131 ATTTGTAAATGGAT
53253 AAATGCCTATTTTTTTCACAGAATATACGATGAGGAACAAAAAGGGAAAGGAAAGGGAAAAAAAA
1 AAATGCCTATTTTTTTCACAGAATATACGATGAGGAACAAAAAGGGAAAGGAAAGGG-AAAAAAA
53318 GAAAGAAATAAAATTCCACCAAAGTAGACTATTGGTTACATGGAGGCATGAAGCCCATGAAAATT
65 GAAAGAAATAAAATTCCACCAAAGTAGACTATTGGTTACATGGAGGCATGAAGCCCATGAAAATT
53383 TATTTGTAAATGGAT
130 TATTTGTAAATGGAT
53398 AAATG
1 AAATG
53403 ACAACTACTT
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
144 57 0.38
145 92 0.62
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.23
Consensus pattern (144 bp):
AAATGCCTATTTTTTTCACAGAATATACGATGAGGAACAAAAAGGGAAAGGAAAGGGAAAAAAAG
AAAGAAATAAAATTCCACCAAAGTAGACTATTGGTTACATGGAGGCATGAAGCCCATGAAAATTT
ATTTGTAAATGGAT
Found at i:56315 original size:16 final size:16
Alignment explanation
Indices: 56294--56325 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56284 TAGTGAACTC
56294 GAAGTGGCATCTTCTT
1 GAAGTGGCATCTTCTT
56310 GAAGTGGCATCTTCTT
1 GAAGTGGCATCTTCTT
56326 CTTACCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
GAAGTGGCATCTTCTT
Found at i:58799 original size:35 final size:32
Alignment explanation
Indices: 58760--58824 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 32
58750 CAGATTGAAC
*
58760 AAGCTTAAATATCTCTTCAAAGTTTCATATTACTA
1 AAGCTTAAATATC-CAT-AAA-TTTCATATTACTA
*
58795 AAGCTTAAATCTCCATAAATTTCATATTAC
1 AAGCTTAAATATCCATAAATTTCATATTAC
58825 AACTTGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 3 0.11
34 2 0.07
35 12 0.43
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (32 bp):
AAGCTTAAATATCCATAAATTTCATATTACTA
Found at i:58807 original size:33 final size:34
Alignment explanation
Indices: 58760--58824 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 34
58750 CAGATTGAAC
*
58760 AAGCTTAAATATCTCTTCA-AAGTTTCATATTACTA
1 AAGCTTAAATATCTC--CATAAATTTCATATTACTA
58795 AAGCTT-AA-ATCTCCATAAATTTCATATTAC
1 AAGCTTAAATATCTCCATAAATTTCATATTAC
58825 AACTTGAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 2 0.07
32 13 0.46
33 5 0.18
34 2 0.07
35 6 0.21
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (34 bp):
AAGCTTAAATATCTCCATAAATTTCATATTACTA
Found at i:71111 original size:33 final size:33
Alignment explanation
Indices: 71068--71142 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
71058 AACACGCTGG
* *
71068 GCATCTGAGGCCATCCGACCGAGCTATGTGAGA
1 GCATCCGAGGCCATCCGACAGAGCTATGTGAGA
* *
71101 GCATCCGAGGCCATCCGAGAGAGCTATGTGAGG
1 GCATCCGAGGCCATCCGACAGAGCTATGTGAGA
*
71134 GCAGCCGAG
1 GCATCCGAG
71143 CGAGCTATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGACAGAGCTATGTGAGA
Found at i:71668 original size:60 final size:60
Alignment explanation
Indices: 71583--71700 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
71573 AATGATCCCT
* *
71583 TGACTATAAGGTGTTGCTTTATTGAGTCACTCGACTATTAGAAGTTATAAAATGATCATC
1 TGACTATAAGGTGTTGCTTTATTGAGTCACTCGACTATTAAAAATTATAAAATGATCATC
* * *
71643 TGACTAT-AGGATGTTGCTTTGTTGAGTCTCTCGACTATTAAAAATTATCAAATGATCA
1 TGACTATAAGG-TGTTGCTTTATTGAGTCACTCGACTATTAAAAATTATAAAATGATCA
71701 CATAACTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 3 0.06
60 49 0.94
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (60 bp):
TGACTATAAGGTGTTGCTTTATTGAGTCACTCGACTATTAAAAATTATAAAATGATCATC
Found at i:76721 original size:18 final size:18
Alignment explanation
Indices: 76700--76739 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
76690 AGAGGAAACA
*
76700 AAAAAATATTTTCAATAG
1 AAAAAAGATTTTCAATAG
*
76718 AAAATAGATTTTCAATAG
1 AAAAAAGATTTTCAATAG
76736 AAAA
1 AAAA
76740 TACAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (18 bp):
AAAAAAGATTTTCAATAG
Found at i:76740 original size:18 final size:18
Alignment explanation
Indices: 76707--76741 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
76697 ACAAAAAAAT
76707 ATTTTCAATAGAAAATAG
1 ATTTTCAATAGAAAATAG
76725 ATTTTCAATAGAAAATA
1 ATTTTCAATAGAAAATA
76742 CAAAACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (18 bp):
ATTTTCAATAGAAAATAG
Found at i:77571 original size:3 final size:3
Alignment explanation
Indices: 77563--77595 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
77553 TTTATGACTA
*
77563 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
77596 TAAGAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:78502 original size:13 final size:13
Alignment explanation
Indices: 78484--78521 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
78474 TGGGTTCGTG
78484 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
* *
78497 GCTCGTTTCTATT
1 GCTCGTCTCTGTT
78510 GCTCGTCTCTGT
1 GCTCGTCTCTGT
78522 GTATCTCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.03, C:0.29, G:0.21, T:0.47
Consensus pattern (13 bp):
GCTCGTCTCTGTT
Found at i:79040 original size:3 final size:3
Alignment explanation
Indices: 79010--79071 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
79000 TTGTAATATT
* * *
79010 TAA TAAA TAA TATA TAT TAT TAA T-A TAA TAA TAA TAA TAC TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
79056 TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
79072 TTAAGTGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:79354 original size:76 final size:76
Alignment explanation
Indices: 79229--79841 Score: 1010
Period size: 76 Copynumber: 8.0 Consensus size: 76
79219 GGTCTTATGA
* * **
79229 ATGACCCTGAGGGTTTAAAAACATCAAAAAAAAATCCCGAAGGCTTTTTGGAAACATCATGCACT
1 ATGACCCTGAGGCTTTGAAAACATC--AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT
*
79294 GCAGGACTTACAG
64 GTAGGACTTACAG
* * * *
79307 ATGACCCTAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGC
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79372 AGGACTTACAG
66 AGGACTTACAG
* * *
79383 ATAACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAGTGT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79448 AGGACTTACAG
66 AGGACTTACAG
* *
79459 ACGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79524 AGGACTTACAG
66 AGGACTTACAG
*
79535 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79600 AGGACTTACAG
66 AGGACTTACAG
* * * *
79611 ACGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTAT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79676 AGGACTTACAG
66 AGGACTTACAG
*
79687 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79752 AGGACTTACAG
66 AGGACTTACAG
* *
79763 ACGACCCTGAGGCTTTGAGAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
79828 AGGACTTACAG
66 AGGACTTACAG
79839 ATG
1 ATG
79842 TGAGAAATAG
Statistics
Matches: 501, Mismatches: 34, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
76 480 0.96
78 21 0.04
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
AGGACTTACAG
Found at i:80119 original size:165 final size:165
Alignment explanation
Indices: 79845--80167 Score: 531
Period size: 165 Copynumber: 2.0 Consensus size: 165
79835 ACAGATGTGA
* * *
79845 GAAATAGTTTACTAAGTAAGAAACTATGGAAATTGTTTTCTTACTATTCAACAATTTCATTTTCA
1 GAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTATTCAACAATTTCATTTTCA
** *
79910 GAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTTATTATTTTTCAAAATAACATGTTGATT
66 GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGATT
79975 GGGTAACATGCCCCAATCTCAAGATAATACTGTTG
131 GGGTAACATGCCCCAATCTCAAGATAATACTGTTG
* *
80010 GAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTTTTACTTTTCAACAATTTCATTTT-
1 GAAATAGTTTACTAAGT-AAAAAACTAAGGAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
**
80074 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTGAAATAACATGTTGAT
65 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
*
80139 TGGGTAACATGCCCCAATTTCAAGATAAT
130 TGGGTAACATGCCCCAATCTCAAGATAAT
80168 TTTCATTCTT
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
165 105 0.72
166 41 0.28
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (165 bp):
GAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTATTCAACAATTTCATTTTCA
GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGATT
GGGTAACATGCCCCAATCTCAAGATAATACTGTTG
Found at i:85421 original size:12 final size:12
Alignment explanation
Indices: 85402--85430 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
85392 TTCTTTTTCC
85402 TTTT-TGTTTTT
1 TTTTCTGTTTTT
85413 TTTTCTGTTTTT
1 TTTTCTGTTTTT
85425 TTTTCT
1 TTTTCT
85431 TCTTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTCTGTTTTT
Found at i:90984 original size:3 final size:3
Alignment explanation
Indices: 90976--91008 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
90966 TTTATGACTA
*
90976 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
91009 TAAGAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:91809 original size:3 final size:3
Alignment explanation
Indices: 91779--91856 Score: 86
Period size: 3 Copynumber: 25.3 Consensus size: 3
91769 TTGTAATATT
* *
91779 TAA TAAA TAA TATA TAT TAT TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
91825 TAA TAA TAA TAA TAA TTT TAA TAA TAAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T
91857 TTAAGTGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.83
4 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:94040 original size:33 final size:33
Alignment explanation
Indices: 93994--94057 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
93984 TGTGTTGGAA
* *
93994 CTTTTTCCTGAATAGGGAAGTACCAACCTTTGC
1 CTTTTTCCCGAATAGGGAAGTACCAAACTTTGC
94027 CTTTTTCCCGAATAGGGAAGTACCAAACTTT
1 CTTTTTCCCGAATAGGGAAGTACCAAACTTT
94058 TTTTTCCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (33 bp):
CTTTTTCCCGAATAGGGAAGTACCAAACTTTGC
Found at i:99537 original size:2 final size:2
Alignment explanation
Indices: 99530--99567 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
99520 TTTGGTGTGC
99530 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
99568 TGTTAAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105053 original size:12 final size:12
Alignment explanation
Indices: 105036--105067 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
105026 TGAAAGATAC
105036 GATGGTGACGGA
1 GATGGTGACGGA
105048 GATGGTGACGGA
1 GATGGTGACGGA
105060 GATGGTGA
1 GATGGTGA
105068 TGGTGGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.06, G:0.50, T:0.19
Consensus pattern (12 bp):
GATGGTGACGGA
Found at i:105958 original size:37 final size:38
Alignment explanation
Indices: 105883--105964 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 38
105873 TTCATTTATC
105883 AAAATTTTTATTATTTTAGTAATTAATTATTTTATTTA
1 AAAATTTTTATTATTTTAGTAATTAATTATTTTATTTA
* *
105921 AAAATTTTGTATTATTTTA-TTATT-ATTTTTTTATTTA
1 AAAATTTT-TATTATTTTAGTAATTAATTATTTTATTTA
*
105958 AACATTT
1 AAAATTT
105965 GAAAGTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 18 0.45
38 12 0.30
39 10 0.25
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (38 bp):
AAAATTTTTATTATTTTAGTAATTAATTATTTTATTTA
Found at i:110720 original size:3 final size:3
Alignment explanation
Indices: 110712--110761 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
110702 AAACTATGTT
110712 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
110758 ATA A
1 ATA A
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.