Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005948.1 Hibiscus syriacus cultivar Beakdansim tig00013963_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: 91301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4606 original size:21 final size:20
Alignment explanation
Indices: 4582--4659 Score: 93
Period size: 21 Copynumber: 3.8 Consensus size: 20
4572 CTTTCTTTTG
4582 AGGGATCGATCCTTTTCACCA
1 AGGGATCGATCCTTTTCA-CA
* * *
4603 AGGGATTGATCCTTTTGAAA
1 AGGGATCGATCCTTTTCACA
*
4623 AGGGATCGATCCTTTTTCTCA
1 AGGGATCGATCC-TTTTCACA
*
4644 AGGGATCGATCATTTT
1 AGGGATCGATCCTTTT
4660 TAAAGGTGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.33
21 32 0.67
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
AGGGATCGATCCTTTTCACA
Found at i:4646 original size:41 final size:41
Alignment explanation
Indices: 4582--4659 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
4572 CTTTCTTTTG
* *
4582 AGGGATCGATCCTTTTCACCAAGGGATTGATCCTTTTGAAA
1 AGGGATCGATCCTTTTCACCAAGGGATCGATCATTTTGAAA
*
4623 AGGGATCGATCCTTTTTC-TCAAGGGATCGATCATTTT
1 AGGGATCGATCC-TTTTCACCAAGGGATCGATCATTTT
4660 TAAAGGTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 28 0.85
42 5 0.15
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (41 bp):
AGGGATCGATCCTTTTCACCAAGGGATCGATCATTTTGAAA
Found at i:11627 original size:27 final size:26
Alignment explanation
Indices: 11590--11640 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
11580 ATCTGCTTGG
**
11590 TTATTATTAATTTAGTAAAAAAATAA
1 TTATTATTAATTTACAAAAAAAATAA
11616 TTATTAATTAATTTACAAAAAAAAT
1 TTATT-ATTAATTTACAAAAAAAAT
11641 TCCTGATGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TTATTATTAATTTACAAAAAAAATAA
Found at i:11933 original size:77 final size:77
Alignment explanation
Indices: 11797--11945 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 77
11787 CAGTTGACTA
* * * * * *
11797 ACGATTTACATCAACTGAAGATGTTTTTTGACCCAAAATAAAACGTTGAGTGGTCAAATGTGTCA
1 ACGATTTACATCAACCGAAGATGTTTTCTAACCCAAAATAAAACGTTGAATGATAAAATGTGTCA
11862 AAAAAAATAAAG
66 AAAAAAATAAAG
* * * *
11874 ACGATTTCCATCCACCGATGATGTTTTCTAACTCAAAATAAAACGTTGAATGATAAAATGTGTCA
1 ACGATTTACATCAACCGAAGATGTTTTCTAACCCAAAATAAAACGTTGAATGATAAAATGTGTCA
11939 AAAAAAA
66 AAAAAAA
11946 CAATACAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (77 bp):
ACGATTTACATCAACCGAAGATGTTTTCTAACCCAAAATAAAACGTTGAATGATAAAATGTGTCA
AAAAAAATAAAG
Found at i:15596 original size:19 final size:19
Alignment explanation
Indices: 15575--15610 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15565 AATATATTTA
15575 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
15593 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
15611 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:16190 original size:13 final size:13
Alignment explanation
Indices: 16172--16200 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16162 CCACCGTACT
16172 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
16185 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
16198 CCG
1 CCG
16201 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:16961 original size:3 final size:3
Alignment explanation
Indices: 16953--17086 Score: 232
Period size: 3 Copynumber: 44.7 Consensus size: 3
16943 TTAATATATT
* * *
16953 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
17001 TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17049 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17087 TGGATAAAAA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 123 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18393 original size:113 final size:113
Alignment explanation
Indices: 17381--18389 Score: 1640
Period size: 113 Copynumber: 8.9 Consensus size: 113
17371 GATATCAAAC
**
17381 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * *
17446 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAA
66 -ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGC-A
* * *
17496 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
17561 ATGAACTTTCTCTGGAAAATATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
17609 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
17674 ATGGACTTTTTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
17722 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
17787 ATGAACTTTCTCTGAAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
17835 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
17900 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
17948 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
18013 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAACA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
18061 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
18126 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
18174 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
18239 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
18287 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
18352 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATG
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATG
18390 AATTTGAATC
Statistics
Matches: 839, Mismatches: 55, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
113 742 0.88
114 35 0.04
115 62 0.07
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
Found at i:19028 original size:52 final size:52
Alignment explanation
Indices: 18950--19664 Score: 1313
Period size: 52 Copynumber: 13.7 Consensus size: 52
18940 CACTTCTTCG
* * *
18950 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19002 GATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
19054 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19106 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19158 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
19210 GATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
19262 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19314 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
19366 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19418 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
19470 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19523 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
19575 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
19627 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
19665 TGAGCACATA
Statistics
Matches: 644, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
52 593 0.92
53 51 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:20615 original size:1 final size:1
Alignment explanation
Indices: 20604--20647 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
20594 CCTTGACCCC
* * *
20604 TTTTTTCTTTTTCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20648 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:32047 original size:19 final size:19
Alignment explanation
Indices: 32026--32061 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
32016 AATATATTTA
32026 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
32044 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
32062 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:32639 original size:13 final size:13
Alignment explanation
Indices: 32621--32649 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32611 CCACCGTACT
32621 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
32634 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
32647 CCG
1 CCG
32650 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:33407 original size:3 final size:3
Alignment explanation
Indices: 33399--33549 Score: 265
Period size: 3 Copynumber: 51.7 Consensus size: 3
33389 ATTTAATATT
*
33399 TAA TAA TAA -AA TAA TAA TAA TAA T-A TAA TAT TAA TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33443 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33491 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33539 TAA TAA TAA TA
1 TAA TAA TAA TA
33550 TGGATAAAAA
Statistics
Matches: 142, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
2 8 0.06
3 134 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:36221 original size:29 final size:29
Alignment explanation
Indices: 36179--36253 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
36169 AACCCAACCA
**
36179 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
36208 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
36237 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
36254 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:36259 original size:29 final size:29
Alignment explanation
Indices: 36180--36267 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
36170 ACCCAACCAT
* * ****
36180 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
36209 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
36238 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
36267 A
1 A
36268 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:36542 original size:29 final size:29
Alignment explanation
Indices: 36485--36566 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
36475 AGGGGATGTT
* * **
36485 GCCGCGAGTGCATGGCGACCTCCTTGGTC
1 GCCGAGAGTGCATGGCGACCTACGAGGTC
* * *
36514 GCCGGGCGTGCATGGCGACCTAGGAGGTC
1 GCCGAGAGTGCATGGCGACCTACGAGGTC
*
36543 GCTGAGAGTGCATGGCGACCTACG
1 GCCGAGAGTGCATGGCGACCTACG
36567 GCCACTGTTG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.17
Consensus pattern (29 bp):
GCCGAGAGTGCATGGCGACCTACGAGGTC
Found at i:43638 original size:13 final size:13
Alignment explanation
Indices: 43620--43675 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
43610 TAAAATGTTA
43620 TATATATGTTTAG
1 TATATATGTTTAG
*
43633 TATATATG---GG
1 TATATATGTTTAG
* *
43643 TTTAT-TGTTAAG
1 TATATATGTTTAG
43655 TATATATGTTTAG
1 TATATATGTTTAG
43668 TATATATG
1 TATATATG
43676 GGTTTCTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 2 0.06
10 5 0.15
12 5 0.15
13 22 0.65
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (13 bp):
TATATATGTTTAG
Found at i:43665 original size:20 final size:21
Alignment explanation
Indices: 43626--43666 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
43616 GTTATATATA
*
43626 TGTTTAGTATATATGGGTTTAT
1 TGTTAAGTATATAT-GGTTTAT
43648 TGTTAAGTATATAT-GTTTA
1 TGTTAAGTATATATGGTTTA
43667 GTATATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TGTTAAGTATATATGGTTTAT
Found at i:43948 original size:107 final size:108
Alignment explanation
Indices: 43745--43998 Score: 429
Period size: 107 Copynumber: 2.4 Consensus size: 108
43735 GGTTTACTGC
* * ***
43745 TTACTAATTGCACGAATGAGAAATTATTTAATATATATGTTTAGAAACCCCTAAAAACCTTGTTG
1 TTACTAATTGCACGAATGAGAAATTGTTTAATATATATGTTTAGAAAACCCTAAAAACCTTACCG
43810 ATTGTTTACTAATTGTGTAATATATATGTTTGATGATATATGT
66 ATTGTTTACTAATTGTGTAATATATATGTTTGATGATATATGT
* *
43853 TTACTGATTGCACGAATGATAAATTGTTTAATATATATGTTTA-AAAACCCTAAAAACCTTACCG
1 TTACTAATTGCACGAATGAGAAATTGTTTAATATATATGTTTAGAAAACCCTAAAAACCTTACCG
*
43917 ATTGTTTACTAATTGTGTAATATATATGTTTGCTGATATATGT
66 ATTGTTTACTAATTGTGTAATATATATGTTTGATGATATATGT
43960 TTACTAATTGCACGAATGAGAAATTGTTTAATATATATG
1 TTACTAATTGCACGAATGAGAAATTGTTTAATATATATG
43999 ATTACTGATT
Statistics
Matches: 136, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
107 96 0.71
108 40 0.29
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (108 bp):
TTACTAATTGCACGAATGAGAAATTGTTTAATATATATGTTTAGAAAACCCTAAAAACCTTACCG
ATTGTTTACTAATTGTGTAATATATATGTTTGATGATATATGT
Found at i:44077 original size:15 final size:15
Alignment explanation
Indices: 44056--44112 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
44046 TTTATTAATG
44056 ATATGTTTACTGATT
1 ATATGTTTACTGATT
* *
44071 ATTTGTTTACTGGTT
1 ATATGTTTACTGATT
*
44086 ATATG-TT-CTGATA
1 ATATGTTTACTGATT
*
44099 ATATGTTTATTGAT
1 ATATGTTTACTGAT
44113 AGAATATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 9 0.26
14 4 0.12
15 21 0.62
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (15 bp):
ATATGTTTACTGATT
Found at i:44214 original size:17 final size:17
Alignment explanation
Indices: 44174--44215 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
44164 TATGAAATCA
44174 ATGAATATATGTAATGC
1 ATGAATATATGTAATGC
**
44191 ATG--TATATGTTCTGC
1 ATGAATATATGTAATGC
44206 ATGAATATAT
1 ATGAATATAT
44216 AGGTTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (17 bp):
ATGAATATATGTAATGC
Found at i:46805 original size:26 final size:27
Alignment explanation
Indices: 46768--46874 Score: 103
Period size: 26 Copynumber: 3.8 Consensus size: 27
46758 TTTGGTTAAC
* *
46768 TTGTTAATACATATTTTTCATGCATAG
1 TTGTTATTACATATTGTTCATGCATAG
46795 -TGTTATTACATATTGTT-ACTGCAT-G
1 TTGTTATTACATATTGTTCA-TGCATAG
*
46820 TTGTTTTTACATATTGTTCATGCATACTG
1 TTGTTATTACATATTGTTCATGCATA--G
46849 TATACTGTTATTACATATTGTTCATG
1 --T--TGTTATTACATATTGTTCATG
46875 TGTATTGCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
25 2 0.03
26 41 0.62
27 1 0.02
29 1 0.02
31 1 0.02
33 20 0.30
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (27 bp):
TTGTTATTACATATTGTTCATGCATAG
Found at i:46836 original size:13 final size:13
Alignment explanation
Indices: 46768--46837 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
46758 TTTGGTTAAC
*
46768 TTGTTAATACATA
1 TTGTTATTACATA
* *
46781 TTTTTCA-TGCATA
1 TTGTT-ATTACATA
*
46794 GTGTTATTACATA
1 TTGTTATTACATA
* * *
46807 TTGTTACTGCATG
1 TTGTTATTACATA
*
46820 TTGTTTTTACATA
1 TTGTTATTACATA
46833 TTGTT
1 TTGTT
46838 CATGCATACT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTGTTATTACATA
Found at i:46891 original size:33 final size:33
Alignment explanation
Indices: 46811--46899 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
46801 TACATATTGT
* *
46811 TACTGCATGTTGTTTTTACATATTGTTCATGCA
1 TACTGCATATTGTTATTACATATTGTTCATGCA
* * **
46844 TACTGTATACTGTTATTACATATTGTTCATGTG
1 TACTGCATATTGTTATTACATATTGTTCATGCA
*
46877 TATTGCATATTGTTATATACATA
1 TACTGCATATTGTTAT-TACATA
46900 CTATTATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 40 0.87
34 6 0.13
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.48
Consensus pattern (33 bp):
TACTGCATATTGTTATTACATATTGTTCATGCA
Found at i:47740 original size:16 final size:15
Alignment explanation
Indices: 47719--47794 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 15
47709 TTGCAGTTGA
*
47719 ATTTGTTATTGATTGC
1 ATTTGTT-TTGATTGT
*
47735 ATTTGTTTTTTTTATTGT
1 ATTTG---TTTTGATTGT
*
47753 ATTTGTTTTAGATTGG
1 ATTTGTTTT-GATTGT
47769 ATTTGTTTCTGATTGT
1 ATTTGTTT-TGATTGT
47785 ATTTGATTTT
1 ATTTG-TTTT
47795 TATTACAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
15 4 0.08
16 28 0.57
17 4 0.08
18 11 0.22
19 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.17, T:0.64
Consensus pattern (15 bp):
ATTTGTTTTGATTGT
Found at i:49335 original size:32 final size:32
Alignment explanation
Indices: 49277--49337 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
49267 ACATGAATTT
* * *
49277 TTAAATTCTTAAAGAACTTTTTAAAAATTTTA
1 TTAAATTCTTAAAAAACTCTTAAAAAATTTTA
49309 TTAAATTC-TAAAAAACATCTTAAAAAATT
1 TTAAATTCTTAAAAAAC-TCTTAAAAAATT
49338 AAAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (32 bp):
TTAAATTCTTAAAAAACTCTTAAAAAATTTTA
Found at i:49661 original size:40 final size:40
Alignment explanation
Indices: 49612--49697 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
49602 TTTAATTATT
* *
49612 TTATATATCCTTGCTTTTATAGTGTTAAGATAATTTCAAA
1 TTATATATCCTTGCCTTTATAGTGCTAAGATAATTTCAAA
49652 TTATATATCCTTGCCTTTATAGTGCTAAGATAATTTCAAA
1 TTATATATCCTTGCCTTTATAGTGCTAAGATAATTTCAAA
49692 TTATAT
1 TTATAT
49698 GTATATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (40 bp):
TTATATATCCTTGCCTTTATAGTGCTAAGATAATTTCAAA
Found at i:50792 original size:41 final size:41
Alignment explanation
Indices: 50746--50833 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 41
50736 TTTTAAAACT
50746 AAGCTCGACTCGAATCGAAAACTCGCGA-ACTTAAAATTGTC
1 AAGCTCGACTCGAATCGAAAACTCGC-ATACTTAAAATTGTC
* * * *
50787 AAGCTCGATTCGACTCGAAAACTCGCATGCTTAAAATTTTC
1 AAGCTCGACTCGAATCGAAAACTCGCATACTTAAAATTGTC
50828 AAGCTC
1 AAGCTC
50834 AAGCTCCACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
AAGCTCGACTCGAATCGAAAACTCGCATACTTAAAATTGTC
Found at i:68286 original size:3 final size:3
Alignment explanation
Indices: 68278--68306 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
68268 ACGAATCAGG
68278 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
68307 CCTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:69314 original size:22 final size:21
Alignment explanation
Indices: 69265--69336 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
69255 TACTACTATT
*
69265 ATTATTATTATTTGAAAATGACA
1 ATTATTATTA-TTGAAAAT-ATA
*
69288 TTTATTATTATTGAAAGATATA
1 ATTATTATTATTGAAA-ATATA
*
69310 ATTA-TATCTTTTGAAAATATA
1 ATTATTAT-TATTGAAAATATA
69331 ATTATT
1 ATTATT
69337 TTCAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 12 0.29
22 19 0.45
23 11 0.26
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTATTATTATTGAAAATATA
Found at i:73940 original size:29 final size:29
Alignment explanation
Indices: 73907--73988 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
73897 TGTTAAGGGG
* *
73907 GGCGAATGTGAACTTATAAAATTTCAAGA
1 GGCGAATTTAAACTTATAAAATTTCAAGA
73936 GGCGAATTTAAACTTATAAAATTTCAAGA
1 GGCGAATTTAAACTTATAAAATTTCAAGA
73965 GGCGAATTTAAACTTATAAAATTT
1 GGCGAATTTAAACTTATAAAATTT
73989 TAGGGGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.32
Consensus pattern (29 bp):
GGCGAATTTAAACTTATAAAATTTCAAGA
Found at i:74835 original size:14 final size:13
Alignment explanation
Indices: 74817--74878 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
74807 AATAGTAAGT
74817 AAAAAAATAAATA
1 AAAAAAATAAATA
* *
74830 ATAAAATATATATA
1 A-AAAAAATAAATA
*
74844 AAAAAAA-GAA-A
1 AAAAAAATAAATA
*
74855 AAGAAAATAAATA
1 AAAAAAATAAATA
74868 AAACAAAATAA
1 AAA-AAAATAA
74879 TAATAACAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
11 7 0.19
12 3 0.08
13 9 0.24
14 18 0.49
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:74861 original size:26 final size:25
Alignment explanation
Indices: 74817--74875 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
74807 AATAGTAAGT
* *
74817 AAAAAAATAAATAATAAAATATATATA
1 AAAAAAAGAAATAAGAAAATA-A-ATA
74844 AAAAAAAGAAA-AAGAAAATAAATA
1 AAAAAAAGAAATAAGAAAATAAATA
74868 AAACAAAA
1 AAA-AAAA
74876 TAATAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.21
25 5 0.17
26 8 0.28
27 10 0.34
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (25 bp):
AAAAAAAGAAATAAGAAAATAAATA
Found at i:75167 original size:27 final size:28
Alignment explanation
Indices: 75138--75189 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
75128 AGAGAAAGTA
75138 AAAAAATATA-ATA-ATAATA-AAATAT
1 AAAAAATATACATATATAATATAAATAT
75163 AAAAAATATACATATATAATATAAATA
1 AAAAAATATACATATATAATATAAATA
75190 AGTAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAATATACATATATAATATAAATAT
Found at i:75226 original size:12 final size:12
Alignment explanation
Indices: 75204--75248 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
75194 GAATAAAAGG
75204 AAAATATAATAGT
1 AAAA-ATAATAGT
*
75217 AAAAATAATAAT
1 AAAAATAATAGT
*
75229 AAATATAATAGT
1 AAAAATAATAGT
*
75241 AATAATAA
1 AAAAATAA
75249 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:75867 original size:37 final size:37
Alignment explanation
Indices: 75826--75930 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
75816 GTGCTTGTGG
* * *
75826 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
75863 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
75900 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
75931 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:76979 original size:106 final size:106
Alignment explanation
Indices: 76661--78246 Score: 2242
Period size: 106 Copynumber: 15.0 Consensus size: 106
76651 GCATTATTCC
* * * ** *
76661 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTTGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* ** * * *
76725 ACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
76767 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
76826 TCAGCCG-CCCTTTCGTCGTAAAGTTGAGA-TTGTGTTGTCTTG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGA-ACTTGCGTTGTC-TG
* * * *
76868 G-GTCCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
76932 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
76973 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTATGGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
77038 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
77079 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
77143 CCAACGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGGCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
77184 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATAGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
77249 CCAGTGGTCCCTTCGTCGTGAAGTTCAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
77290 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
77355 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
77396 GAGTCCAATATCCTTCATTGTGAAGTTGCAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
77461 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
77502 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
77567 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
77608 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
77673 CCAGCAGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
77714 GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
77779 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
77820 GAGTCGAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
77885 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
77926 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
77991 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
78032 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
78097 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
78138 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATT-ATTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
78202 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
78243 GAGT
1 GAGT
78247 GGCACGATAT
Statistics
Matches: 1339, Mismatches: 127, Indels: 29
0.90 0.08 0.02
Matches are distributed among these distances:
99 3 0.00
100 73 0.05
101 6 0.00
102 4 0.00
104 3 0.00
105 149 0.11
106 1097 0.82
107 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:79100 original size:22 final size:22
Alignment explanation
Indices: 79072--79126 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
79062 TTGTGTTTTG
*
79072 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
79094 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
79116 TCAAAGGTTTG
1 TCAAAGGTTTG
79127 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:79762 original size:24 final size:24
Alignment explanation
Indices: 79728--79796 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
79718 TTTTTTGTCC
79728 CTTTTTCTTTTTGATTTTTGTTCTTT
1 CTTTTT-TTTTTG-TTTTTGTTCTTT
* *
79754 C-TTTTTTTTTGTTCTTTTTTGTTT
1 CTTTTTTTTTTGTT-TTTGTTCTTT
79778 CTTTTCTTTTTTGTTTTTG
1 CTTTT-TTTTTTGTTTTTG
79797 CCCTTTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 10 0.27
26 10 0.27
ACGTcount: A:0.01, C:0.10, G:0.09, T:0.80
Consensus pattern (24 bp):
CTTTTTTTTTTGTTTTTGTTCTTT
Found at i:79764 original size:17 final size:16
Alignment explanation
Indices: 79732--79796 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 16
79722 TTGTCCCTTT
**
79732 TTCTTTTTGATTTTTG
1 TTCTTTTTTTTTTTTG
79748 TTCTTTCTTTTTTTTTG
1 TTCTTT-TTTTTTTTTG
*
79765 TTCTTTTTTGTTTCTT-
1 TTCTTTTTT-TTTTTTG
*
79781 TTCTTTTTTGTTTTTG
1 TTCTTTTTTTTTTTTG
79797 CCCTTTTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 4 0.10
16 18 0.44
17 19 0.46
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTG
Found at i:79771 original size:33 final size:31
Alignment explanation
Indices: 79732--79807 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 31
79722 TTGTCCCTTT
*
79732 TTCTTTTTGATTT-TTGTTCTTTCTTTTTTTTTG
1 TTCTTTTTG-TTTCTT-TTCTTT-TTTGTTTTTG
79765 TTCTTTTTTGTTTCTTTTCTTTTTTGTTTTTG
1 TTC-TTTTTGTTTCTTTTCTTTTTTGTTTTTG
**
79797 CCCTTTTTGTT
1 TTCTTTTTGTT
79808 CTGATTGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 8 0.21
32 10 0.26
33 12 0.32
34 8 0.21
ACGTcount: A:0.01, C:0.12, G:0.09, T:0.78
Consensus pattern (31 bp):
TTCTTTTTGTTTCTTTTCTTTTTTGTTTTTG
Found at i:79786 original size:16 final size:16
Alignment explanation
Indices: 79735--79796 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
79725 TCCCTTTTTC
79735 TTTTTGATTTTTGTTCT
1 TTTTTG-TTTTTGTTCT
*
79752 TTCTTTTTTTTTGTTCT
1 TT-TTTGTTTTTGTTCT
79769 TTTTTGTTTCTT-TTCT
1 TTTTTGTTT-TTGTTCT
79785 TTTTTGTTTTTG
1 TTTTTGTTTTTG
79797 CCCTTTTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.05
16 19 0.47
17 16 0.40
18 3 0.08
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTTTGTTCT
Found at i:83097 original size:19 final size:19
Alignment explanation
Indices: 83064--83100 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
83054 TGCAGATGAT
83064 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
83083 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
83101 TTAGTAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:84257 original size:25 final size:24
Alignment explanation
Indices: 84229--84289 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
84219 ATGAAGAAAG
*
84229 CAAAGATAAAATAGTA-AGTAAAAAA
1 CAAAAATAAAATA-TATA-TAAAAAA
84254 CAAATAATAAAATATATATAAAAAA
1 CAAA-AATAAAATATATATAAAAAA
*
84279 GAAAAATAAAA
1 CAAAAATAAAA
84290 AGAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 9 0.28
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (24 bp):
CAAAAATAAAATATATATAAAAAA
Found at i:84266 original size:26 final size:25
Alignment explanation
Indices: 84234--84326 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
84224 GAAAGCAAAG
84234 ATAAAATAGTAAGTAAAAAACAAATA
1 ATAAAATAGTAA-TAAAAAACAAATA
*
84260 ATAAAATA-TATATAAAAAAGAAA-A
1 ATAAAATAGTA-ATAAAAAACAAATA
*
84284 ATAAAA-AGAAAATAAATAAAACAAATAA
1 ATAAAATAG-TAAT-AA-AAAACAAAT-A
* *
84312 ACAAAATAATAATAA
1 ATAAAATAGTAATAA
84327 CAAAGTACGA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
23 1 0.02
24 9 0.17
25 15 0.28
26 16 0.30
27 2 0.04
28 9 0.17
29 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.18
Consensus pattern (25 bp):
ATAAAATAGTAATAAAAAACAAATA
Found at i:84312 original size:13 final size:12
Alignment explanation
Indices: 84248--84317 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
84238 AATAGTAAGT
84248 AAAAAACAAATA
1 AAAAAACAAATA
* *
84260 ATAAAATATATATA
1 A-AAAA-ACAAATA
*
84274 AAAAAGAAAAATA
1 AAAAA-ACAAATA
*
84287 AAAAGA-AAATA
1 AAAAAACAAATA
84298 AATAAAACAAATA
1 AA-AAAACAAATA
84311 AACAAAA
1 AA-AAAA
84318 TAATAATAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
11 7 0.15
12 5 0.11
13 28 0.61
14 6 0.13
ACGTcount: A:0.79, C:0.04, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAACAAATA
Found at i:84325 original size:24 final size:23
Alignment explanation
Indices: 84250--84326 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 23
84240 TAGTAAGTAA
*
84250 AAAACAAATAATAAAATATATATAAA
1 AAAACAAATAA-AAAA-ATA-ATAAT
*
84276 AAAGAAAAATAAAAAGAA-AATAAAT
1 AAA-ACAAATAAAAA-AATAAT-AAT
84301 AAAACAAATAAACAAAATAATAAT
1 AAAACAAATAAA-AAAATAATAAT
84325 AA
1 AA
84327 CAAAGTACGA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
24 17 0.40
25 11 0.26
26 7 0.16
27 8 0.19
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.17
Consensus pattern (23 bp):
AAAACAAATAAAAAAATAATAAT
Found at i:84326 original size:39 final size:39
Alignment explanation
Indices: 84236--84342 Score: 94
Period size: 39 Copynumber: 2.7 Consensus size: 39
84226 AAGCAAAGAT
* * *
84236 AAAATAGTAAGTAAAAA-ACAAATAATAAAATATATATAA
1 AAAATAATAA-TAAAAAGACAAATAATAAAACAAATATAA
* *
84275 AAAAGAAAAATAAAAAGA-AAATAAATAAAACAAATA-AA
1 AAAATAATAATAAAAAGACAAAT-AATAAAACAAATATAA
*
84313 CAAAATAATAATAACAAAGTACGAATAATA
1 -AAAATAATAATAA-AAAG-ACAAATAATA
84343 TATATATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 12 0.22
39 30 0.56
40 4 0.07
41 5 0.09
42 3 0.06
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.18
Consensus pattern (39 bp):
AAAATAATAATAAAAAGACAAATAATAAAACAAATATAA
Found at i:84626 original size:72 final size:72
Alignment explanation
Indices: 84535--84669 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
84525 ATATAACAAA
* * *
84535 ATAAATAATATAAAAATAATA-CAAGAATAATAAAAAGAAAGATAA-AGTAAAAATATATAATAA
1 ATAAAAAATATAAAAATAATATAAAGAAGAATAAAAAGAAA-ATAATAGTAAAAATA-ATAATAA
84598 TAATAAAAT
64 TAATAAAAT
* * * *
84607 ATAAAAAATATACATATAATATAAAGTAGAATAAAAGGAAAATAATAGTAAAAATAATAATAA
1 ATAAAAAATATAAAAATAATATAAAGAAGAATAAAAAGAAAATAATAGTAAAAATAATAATAA
84670 ATATAATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 29 0.54
73 25 0.46
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (72 bp):
ATAAAAAATATAAAAATAATATAAAGAAGAATAAAAAGAAAATAATAGTAAAAATAATAATAATA
ATAAAAT
Found at i:84662 original size:12 final size:12
Alignment explanation
Indices: 84645--84687 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
84635 GAATAAAAGG
84645 AAAATAATAGTA
1 AAAATAATAGTA
*
84657 AAAATAATAATA
1 AAAATAATAGTA
*
84669 AATATAATAGTA
1 AAAATAATAGTA
*
84681 ATAATAA
1 AAAATAA
84688 AAATGTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAATAATAGTA
Found at i:85309 original size:37 final size:36
Alignment explanation
Indices: 85263--85364 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
85253 CTTGTGGATC
* *
85263 CTATCTTTAGGAGTTTAAATCATAGTAGAACTCTAT
1 CTATTTTTAGGAGTTTGAATCATAGTAGAACTCTAT
* * *
85299 ACTATTTTTAGGAGTTTGAATCATAGCAAAATTCTAT
1 -CTATTTTTAGGAGTTTGAATCATAGTAGAACTCTAT
* *
85336 CTTATTTTTATGAGTTTGAATCTTAGTAG
1 C-TATTTTTAGGAGTTTGAATCATAGTAG
85365 GACGAAAATG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (36 bp):
CTATTTTTAGGAGTTTGAATCATAGTAGAACTCTAT
Found at i:90734 original size:44 final size:44
Alignment explanation
Indices: 90601--90863 Score: 250
Period size: 44 Copynumber: 6.0 Consensus size: 44
90591 TCAAGTCACG
* * *
90601 AGTGTCGAAGA-AGGGTACTTAAGTAAAAACCAAGAGTCGGAGTA
1 AGTGTCGGAGATA-GGTACTTAAGTAAAAACCGAGAGTCAGAGTA
* * *
90645 AGTGTCGGGGATAGATATACTTAAGTAAAAACCGAGAGTCGGAGTA
1 AGTGTCGGAGATAG--GTACTTAAGTAAAAACCGAGAGTCAGAGTA
* * *
90691 AATGTCGGAGATAGGTACTCAAGTAAAAACCGAGAATCAGAGTA
1 AGTGTCGGAGATAGGTACTTAAGTAAAAACCGAGAGTCAGAGTA
* * * * * *
90735 AGCGCCGGAGATAGGTGCTTAAGTAAAAATCGAGAG-CAATAATA
1 AGTGTCGGAGATAGGTACTTAAGTAAAAACCGAGAGTC-AGAGTA
* * * * *
90779 AGTGCCGGAGATA-G-A--TAACTAAAAATCGAGAGCCGGAGTA
1 AGTGTCGGAGATAGGTACTTAAGTAAAAACCGAGAGTCAGAGTA
90819 AGTGTCGGAGATAGGTACTTTAAGTAAAAACCGAGAGTTCAGAGT
1 AGTGTCGGAGATAGGTAC-TTAAGTAAAAACCGAGAG-TCAGAGT
90864 TGGGGGTGCT
Statistics
Matches: 178, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
40 31 0.17
41 2 0.01
42 1 0.01
43 2 0.01
44 81 0.46
45 16 0.09
46 45 0.25
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.19
Consensus pattern (44 bp):
AGTGTCGGAGATAGGTACTTAAGTAAAAACCGAGAGTCAGAGTA
Done.