Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006178.1 Hibiscus syriacus cultivar Beakdansim tig00014684_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: 68370
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11160 original size:25 final size:25
Alignment explanation
Indices: 11132--11205 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
11122 AAATTAAATG
11132 TTAAACATATGAATAAAATGCATAA
1 TTAAACATATGAATAAAATGCATAA
* *
11157 TT--A-AT-T-AAAAAAAT-TA-AA
1 TTAAACATATGAATAAAATGCATAA
11175 TGTTAAACATATGAATAAAATGCATAA
1 --TTAAACATATGAATAAAATGCATAA
11202 TTAA
1 TTAA
11206 TAAATACATT
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 9 0.25
21 1 0.03
22 3 0.08
23 3 0.08
24 1 0.03
25 13 0.36
26 1 0.03
27 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (25 bp):
TTAAACATATGAATAAAATGCATAA
Found at i:11162 original size:45 final size:45
Alignment explanation
Indices: 11111--11206 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
11101 GATAACAATG
11111 ATTAATTAAAAAAATTAAATGTTAAACATATGAATAAAATGCATA
1 ATTAATTAAAAAAATTAAATGTTAAACATATGAATAAAATGCATA
11156 ATTAATTAAAAAAATTAAATGTTAAACATATGAATAAAATGCATA
1 ATTAATTAAAAAAATTAAATGTTAAACATATGAATAAAATGCATA
11201 ATTAAT
1 ATTAAT
11207 AAATACATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (45 bp):
ATTAATTAAAAAAATTAAATGTTAAACATATGAATAAAATGCATA
Found at i:14275 original size:20 final size:20
Alignment explanation
Indices: 14252--14296 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
14242 TGTAGAGCTG
*
14252 GAGCAGGGAATTCACATGGT
1 GAGCAGGGAATTCACAGGGT
* *
14272 GAGCATGGAATTCACGGGGT
1 GAGCAGGGAATTCACAGGGT
14292 GAGCA
1 GAGCA
14297 AAGAAAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.38, T:0.18
Consensus pattern (20 bp):
GAGCAGGGAATTCACAGGGT
Found at i:14407 original size:32 final size:32
Alignment explanation
Indices: 14361--14442 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
14351 TAGAGGATGT
*
14361 CTCGACGTCTTCTTCATATTGGG-GGTGGAAT-A
1 CTCGGCGTCTTCTTCATA-TGGGAGG-GGAATGA
* * *
14393 CTCGGCGTCTTCTTCACATGGGAGGGGGATGT
1 CTCGGCGTCTTCTTCATATGGGAGGGGAATGA
14425 CTCGGCGTCTTCTTCATA
1 CTCGGCGTCTTCTTCATA
14443 ATAATGCATG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 8 0.19
32 35 0.81
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (32 bp):
CTCGGCGTCTTCTTCATATGGGAGGGGAATGA
Found at i:19877 original size:21 final size:23
Alignment explanation
Indices: 19832--19891 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 23
19822 AGAACTCCAT
19832 GGGGGTATCGGTTCCCCTTCAAA
1 GGGGGTATCGGTTCCCCTTCAAA
* *
19855 GGGGGAATCGG-TCCCTTTC-AA
1 GGGGGTATCGGTTCCCCTTCAAA
*
19876 GGGGGTATCGATTCCC
1 GGGGGTATCGGTTCCC
19892 TCTGCCCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 11 0.34
22 11 0.34
23 10 0.31
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (23 bp):
GGGGGTATCGGTTCCCCTTCAAA
Found at i:19892 original size:22 final size:22
Alignment explanation
Indices: 19832--19892 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
19822 AGAACTCCAT
*
19832 GGGGGTATCGGTTCCCCTTCAAA
1 GGGGGTATC-GTTCCCTTTCAAA
* *
19855 GGGGGAATCGGTCCCTTTC-AA
1 GGGGGTATCGTTCCCTTTCAAA
19876 GGGGGTATCGATTCCCT
1 GGGGGTATCG-TTCCCT
19893 CTGCCCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 11 0.34
22 13 0.41
23 8 0.25
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGTTCCCTTTCAAA
Found at i:21708 original size:23 final size:23
Alignment explanation
Indices: 21679--21743 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
21669 CAACTCGTAT
21679 AAATGCACCGAAGTGCCATGTA-
1 AAATGCACCGAAGTGCCATGTAG
* * **
21701 AAATTGCACCGTAGTGTCGCGTAG
1 AAA-TGCACCGAAGTGCCATGTAG
21725 AAATGCACCGAAGTGCCAT
1 AAATGCACCGAAGTGCCAT
21744 ATAATAATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
22 3 0.09
23 27 0.82
24 3 0.09
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:21752 original size:23 final size:22
Alignment explanation
Indices: 21679--21752 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
21669 CAACTCGTAT
*
21679 AAATGCACCGAAGTGCCATGTA
1 AAATGCACCGAAGTGCCATATA
* * *
21701 AAATTGCACCGTAGTGTCGCGTA-G
1 AAA-TGCACCGAAGTG-C-CATATA
21725 AAATGCACCGAAGTGCCATATA
1 AAATGCACCGAAGTGCCATATA
21747 ATAATG
1 A-AATG
21753 TCCATAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
21 3 0.08
22 5 0.12
23 26 0.65
24 4 0.10
25 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCATATA
Found at i:23189 original size:21 final size:21
Alignment explanation
Indices: 23159--23203 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
23149 TTTTGTTCGT
*
23159 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23180 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23201 TTG
1 TTG
23204 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31613 original size:3 final size:3
Alignment explanation
Indices: 31607--31641 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
31597 AAAGTTTCAT
31607 ATA ATA ATA ATA ATCA ATA ATCA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA
31642 GTTAGGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:32046 original size:21 final size:22
Alignment explanation
Indices: 32020--32062 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
32010 CCAATACAAG
32020 GAGTATCGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
*
32041 GAGTATCGGTACTTCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
32063 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:33004 original size:18 final size:18
Alignment explanation
Indices: 32981--33016 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32971 ATAATCAATA
32981 CTAAATACTAAGTAACAG
1 CTAAATACTAAGTAACAG
32999 CTAAATACTAAGTAACAG
1 CTAAATACTAAGTAACAG
33017 TAACAATTAG
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:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (18 bp):
CTAAATACTAAGTAACAG
Found at i:35536 original size:18 final size:18
Alignment explanation
Indices: 35513--35589 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
35503 ACCGGTCACA
35513 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
35531 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
*
35549 -----ACCCGACCCGTTG
1 ACCCGACCCGACCCGTTT
35562 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
35580 ACCCGACCCG
1 ACCCGACCCG
35590 TTGACCCGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.17, C:0.51, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:35553 original size:31 final size:31
Alignment explanation
Indices: 35518--35615 Score: 178
Period size: 31 Copynumber: 3.2 Consensus size: 31
35508 TCACAACCCG
*
35518 ACCCGACCCGTTTACCCGACCCGACCCGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
35549 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
*
35580 ACCCGACCCGTTGACCCGACCCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
35611 ACCCG
1 ACCCG
35616 TTGACCGTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.16, C:0.49, G:0.19, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCGTTT
Found at i:35601 original size:18 final size:18
Alignment explanation
Indices: 35513--35615 Score: 109
Period size: 18 Copynumber: 6.3 Consensus size: 18
35503 ACCGGTCACA
*
35513 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
35531 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
35548 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
35562 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
35579 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
35593 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
35611 ACCCG
1 ACCCG
35616 TTGACCGTTG
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
13 24 0.34
18 47 0.66
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:35613 original size:8 final size:8
Alignment explanation
Indices: 35602--35643 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
35592 GACCCGACCC
35602 GACCCGTT
1 GACCCGTT
35610 GACCCGTT
1 GACCCGTT
35618 GA-CCGTT
1 GACCCGTT
35625 GACCCGTT
1 GACCCGTT
35633 GA-CCGTT
1 GACCCGTT
35640 GACC
1 GACC
35644 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:35615 original size:13 final size:13
Alignment explanation
Indices: 35535--35602 Score: 73
Period size: 13 Copynumber: 4.8 Consensus size: 13
35525 CCGTTTACCC
35535 GACCCGACCCGTT
1 GACCCGACCCGTT
*
35548 TACCCGACCCGTT
1 GACCCGACCCGTT
35561 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
*
35579 TACCCGACCCGTT
1 GACCCGACCCGTT
35592 GACCCGACCCG
1 GACCCGACCCG
35603 ACCCGTTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
13 34 0.74
18 12 0.26
ACGTcount: A:0.16, C:0.49, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:35625 original size:7 final size:7
Alignment explanation
Indices: 35605--35644 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
35595 CCGACCCGAC
35605 CCGTTGA
1 CCGTTGA
35612 CCCGTTGA
1 -CCGTTGA
35620 CCGTTGA
1 CCGTTGA
35627 CCCGTTGA
1 -CCGTTGA
35635 CCGTTGA
1 CCGTTGA
35642 CCG
1 CCG
35645 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:35625 original size:15 final size:15
Alignment explanation
Indices: 35605--35643 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
35595 CCGACCCGAC
35605 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
35620 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
35635 CCGTTGACC
1 CCGTTGACC
35644 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:38226 original size:24 final size:24
Alignment explanation
Indices: 38132--38231 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
38122 ATATTTTATC
* *
38132 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
38156 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
38180 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
38204 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
38228 TGAT
1 TGAT
38232 TTTTGATATC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:38404 original size:2 final size:2
Alignment explanation
Indices: 38397--38445 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38387 GGGATGGGGG
38397 TA TA TA 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
38439 TA TA TA T
1 TA TA TA T
38446 GTTTTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44979 original size:15 final size:15
Alignment explanation
Indices: 44951--44989 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
44941 AATAAACAAA
44951 AAATATTATGATATAAT
1 AAATA-TAT-ATATAAT
*
44968 ATATATATATATAAT
1 AAATATATATATAAT
44983 AAATATA
1 AAATATA
44990 ATAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 3 0.15
17 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATATATATATAAT
Found at i:45158 original size:18 final size:17
Alignment explanation
Indices: 45128--45161 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45118 AAGTAAAAAT
45128 AAAAATAAAATATAATA
1 AAAAATAAAATATAATA
*
45145 AAAAATATACATATAAT
1 AAAAATA-AAATATAAT
45162 GATAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAAATATAATA
Found at i:45769 original size:35 final size:37
Alignment explanation
Indices: 45694--45793 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 37
45684 GTACTTGTGG
* *
45694 ATCCTATCTTTAG-GAGTTTAAAAT-ATAGCAAAATTCT
1 ATCCTAT-TTTAGAGAGTTT-GAATCCTAGCAAAATTCT
* *
45731 ATCCTATTTTAG-GAG-TTGAATCCTAGCATAATTTT
1 ATCCTATTTTAGAGAGTTTGAATCCTAGCAAAATTCT
*
45766 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAGAGAGTTTGAATCCTAG
45794 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
34 3 0.05
35 23 0.42
36 11 0.20
37 18 0.33
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTAGAGAGTTTGAATCCTAGCAAAATTCT
Found at i:46657 original size:109 final size:107
Alignment explanation
Indices: 46262--47089 Score: 519
Period size: 98 Copynumber: 8.0 Consensus size: 107
46252 TCCGAGTCCA
* * * * ** **
46262 ATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACCGAGAAATTGTTTGTTGACAGTCAGCC
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGA-AAATTGTTTGTTGACAACCAGCC
* * * *
46326 GCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CTA--
64 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-ACG
* * * * * * *
46368 ATATCCTTCG-CTGTGAAGTTGAAATTGACTCTG-AA-CG-AAA-T-CTTGTTGACAATCAGCCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
*
46427 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * *
46468 ATATTCTTCG-C-TGCGAAATTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCGGC
1 ATATCCTCCGTCGTG-G-AGTTGAAATCGGCTCTGAAA-TTGAAAATTGTTTGTTGACAACCAGC
46531 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACG
63 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
** * *
46577 ATATCCTCCGTCGTGGAGTTGAAATC-GCGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCC
1 ATATCCTCCGTCGTGGAGTTGAAATCGGC-TCTGAAATTGAAAA-TTGTTTGTTGACAACCAGCC
*
46641 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAAGTAGCACG
64 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
* * * *
46686 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGCTGACAACCAACCG
1 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATT-GAAAATTGTTTGTTGACAACCAGCCG
* * * *
46751 TCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAAT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * * * ** *
46792 ATATCATTCG-CTGTGAAGTTGAGATTGGCTC------CG-AAATTGCTTGTCGACAGTCAGTCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
* * * * *
46849 -CTCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGT-C-CA
65 TC-CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * ** *
46890 ATATCCTTCG-CTGTGAAGTTGAGATTGGCTC------CG-AAATTGTTTGTCGACAGTCAACCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
* * * * * * *
46947 CCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * * * *
46988 ATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATT-ATTGTTGACAACCAGTCG
1 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAA-TTGAAAATTGTTTGTTGACAACCAGCCG
47052 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
47090 CCAATATCCT
Statistics
Matches: 610, Mismatches: 81, Indels: 63
0.81 0.11 0.08
Matches are distributed among these distances:
97 1 0.00
98 171 0.28
99 3 0.00
100 76 0.12
101 3 0.00
102 3 0.00
103 1 0.00
104 5 0.01
105 49 0.08
106 113 0.19
107 1 0.00
108 9 0.01
109 165 0.27
110 8 0.01
111 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (107 bp):
ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCGT
CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
Found at i:46860 original size:55 final size:55
Alignment explanation
Indices: 46798--46967 Score: 170
Period size: 55 Copynumber: 3.3 Consensus size: 55
46788 TCCAATATCA
*
46798 TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGTCGCTCC
1 TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAATCGCTCC
* *
46853 TTCGCTGTGAAGTTGAGCTT-G-T--G---TTGTCTTG--G---GTCCAAT--ATCC
1 TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTG-CTTGTCGACAGT-CAATCGCTCC
* * *
46896 TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGTTTGTCGACAGTCAACCGCCCC
1 TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAATCGCTCC
46951 TTCGCTGTGAAGTTGAG
1 TTCGCTGTGAAGTTGAG
46968 CTTGTGCTGT
Statistics
Matches: 91, Mismatches: 8, Indels: 32
0.69 0.06 0.24
Matches are distributed among these distances:
43 22 0.24
44 3 0.03
45 4 0.04
47 2 0.02
48 3 0.03
49 7 0.08
50 3 0.03
51 2 0.02
53 4 0.04
54 3 0.03
55 38 0.42
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.33
Consensus pattern (55 bp):
TTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAATCGCTCC
Found at i:46898 original size:43 final size:43
Alignment explanation
Indices: 46850--47009 Score: 126
Period size: 43 Copynumber: 3.4 Consensus size: 43
46840 AGTCAGTCGC
46850 TCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATA
1 TCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATA
* **
46893 TCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGT-TTGTCGACAGT-CAACCGC
1 TCCTTCGCTGTGAAGTTGAGCTT-G-T--G---TTGTCTTG--G---GTCCAA--TA
* *
46948 CCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATA
1 TCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATA
*
46991 TCCTTCGCCGTGAAGTTGA
1 TCCTTCGCTGTGAAGTTGA
47010 AATTGGCCCT
Statistics
Matches: 91, Mismatches: 10, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
43 39 0.43
44 3 0.03
45 4 0.04
47 2 0.02
48 3 0.03
49 6 0.07
50 4 0.04
51 2 0.02
53 4 0.04
54 3 0.03
55 21 0.23
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (43 bp):
TCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATA
Found at i:47765 original size:63 final size:65
Alignment explanation
Indices: 47649--47812 Score: 287
Period size: 63 Copynumber: 2.6 Consensus size: 65
47639 GACAAAATTT
47649 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
47714 TGTTTCAAGAGAAACTATCTCAAGAG-G-CGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
47777 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
47813 TTGTTTCGAG
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
63 60 0.65
64 2 0.02
65 31 0.33
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:47828 original size:37 final size:37
Alignment explanation
Indices: 47777--48187 Score: 226
Period size: 37 Copynumber: 11.9 Consensus size: 37
47767 TCAATGTTTA
* *
47777 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
47814 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
47850 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
47878 ATGTTTTAAGAGAAACTGTCTCAATG-GAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
*
47916 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
47952 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
47980 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* * *
48018 TGTTTCAAGGGAAACTATCTCAAGATAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
48054 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
48082 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
48120 TGTTTAAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
48156 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
48188 TGGTGAGCAC
Statistics
Matches: 277, Mismatches: 56, Indels: 82
0.67 0.13 0.20
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 38 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 83 0.30
37 113 0.41
38 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:48165 original size:36 final size:36
Alignment explanation
Indices: 48083--48187 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
48073 TCAATGTTTA
* * * * *
48083 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTAAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
48120 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
48156 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAA
48188 TGGTGAGCAC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 38 0.60
37 25 0.40
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (36 bp):
TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:48169 original size:102 final size:102
Alignment explanation
Indices: 47714--48152 Score: 738
Period size: 102 Copynumber: 4.3 Consensus size: 102
47704 TCAATGTTTA
* *
47714 TGTTTCAAGAGAAACTATCTCAAGAG-G-CGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
47777 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
47814 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
47879 TGTTTTAAGAGAAACTGTCTCAATGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
47916 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
47981 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
48018 TGTTTCAAGGGAAACTATCTCAAGATAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
48083 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
48120 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
48153 GTTTGTTTAA
Statistics
Matches: 317, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
100 24 0.08
101 1 0.00
102 292 0.92
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:49070 original size:22 final size:22
Alignment explanation
Indices: 49045--49095 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
49035 TTGTGTTTGG
49045 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
49067 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
49089 TCAAAGG
1 TCAAAGG
49096 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:49728 original size:20 final size:21
Alignment explanation
Indices: 49705--49763 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
49695 TTTGTCCCCT
*
49705 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
49725 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
**
49746 TTTTTGCTTCTT-TTCTTT
1 TTTTTTATTCTTGTTCTTT
49764 TTTCTTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:49781 original size:22 final size:23
Alignment explanation
Indices: 49738--49780 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
49728 TTTGTTCTTG
*
49738 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
49761 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
49781 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:54321 original size:21 final size:24
Alignment explanation
Indices: 54285--54344 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
54275 ATATATATAT
* *
54285 ATAATAAATATAATAACG-AAAA-A
1 ATAAT-AATGTAATAAAGTAAAATA
*
54308 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAATAAAGTAAAATA
54331 ATAATAATGTAATA
1 ATAATAATGTAATA
54345 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 7 0.23
23 3 0.10
24 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAATAATGTAATAAAGTAAAATA
Found at i:54337 original size:16 final size:16
Alignment explanation
Indices: 54316--54353 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54306 AAAAATAATT
54316 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
54332 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
54348 T-ATAAA
1 TAATAAA
54354 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:55087 original size:35 final size:36
Alignment explanation
Indices: 55043--55111 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
55033 AACATAGCAA
55043 AATTCTATCC-TATTTTAGGAG-TTGAATCCTAACAG
1 AATTCTATCCATATTTTA-GAGTTTGAATCCTAACAG
55078 AATTCTATCCTATATTTTAGAGTTTGAATCCTAA
1 AATTCTATCC-ATATTTTAGAGTTTGAATCCTAA
55112 TAGGACGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 10 0.32
36 3 0.10
37 18 0.58
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (36 bp):
AATTCTATCCATATTTTAGAGTTTGAATCCTAACAG
Found at i:57129 original size:26 final size:26
Alignment explanation
Indices: 57079--57129 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
57069 AGGGCAAACC
*
57079 TATAAAATTTTAAAGAAGAGCGAATT
1 TATAAAATTTTAAAGAAGAGAGAATT
*
57105 TATAAAATTTTAGA-AAGACGAGAAT
1 TATAAAATTTTAAAGAAGA-GAGAAT
57130 ATATTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (26 bp):
TATAAAATTTTAAAGAAGAGAGAATT
Found at i:57793 original size:60 final size:60
Alignment explanation
Indices: 57715--57889 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 60
57705 GTCCCTAAAT
* * * ** *
57715 TATAACTCTCATTTTAAATTAGTTCTTAATTTTTTGAATATTCTAATTTCATCCTCAAAC
1 TATAACTATCATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTCAAAC
* *
57775 TATAACTATCATTATAAATTAGTCCTTAAACTTTTGAACGTTCTAATTTCATCC-CTAAAA
1 TATAACTATCATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTC-AAAC
* ** * * ** * * *
57835 TATGACCCTCTTTCTAAATTAGTCCCCAAACTTTTGAATATTCCAATTTTATCCT
1 TATAACTATCATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCT
57890 TAAATTCATC
Statistics
Matches: 94, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 93 0.99
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
TATAACTATCATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTCAAAC
Found at i:67371 original size:13 final size:13
Alignment explanation
Indices: 67350--67383 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
67340 AATTTTGAGT
*
67350 TTTTTAATTATAA
1 TTTTAAATTATAA
*
67363 TTTTAAATTTTAA
1 TTTTAAATTATAA
67376 TTTTAAAT
1 TTTTAAAT
67384 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAATTATAA
Done.