Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009082.1 Hibiscus syriacus cultivar Beakdansim tig00112524_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: 119442
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:201 original size:16 final size:16
Alignment explanation
Indices: 152--211 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
142 CGAGGCGAGC
*
152 AATGAGCATCGAGCTT
1 AATGAGCAACGAGCTT
* * *
168 AACGAGTAACGAGTTT
1 AATGAGCAACGAGCTT
*
184 AATGAGCAACAAGCTT
1 AATGAGCAACGAGCTT
*
200 AAAGAGCAACGA
1 AATGAGCAACGA
212 TTCGAGCAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (16 bp):
AATGAGCAACGAGCTT
Found at i:3940 original size:24 final size:25
Alignment explanation
Indices: 3908--3954 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3898 CTATTCTTTC
3908 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
3932 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
3955 TTTTGAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:4712 original size:2 final size:2
Alignment explanation
Indices: 4705--4746 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4695 GATACAACTA
4705 AT AT 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 AT AT
4747 TTGTACAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14557 original size:16 final size:16
Alignment explanation
Indices: 14533--14586 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
14523 TATATCTGCA
* *
14533 AAAAAATTAAATAAGT
1 AAAATATTAAATAAAT
14549 AAAATATTAAATAAAT
1 AAAATATTAAATAAAT
*
14565 TAAATATTAAATAAAT
1 AAAATATTAAATAAAT
*
14581 TAAATA
1 AAAATA
14587 CAAAATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:14566 original size:9 final size:9
Alignment explanation
Indices: 14536--14586 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
14526 ATCTGCAAAA
14536 AAATTAAAT
1 AAATTAAAT
*
14545 -AAGTAAA-
1 AAATTAAAT
*
14552 ATATTAAAT
1 AAATTAAAT
14561 AAATTAAAT
1 AAATTAAAT
14570 --ATTAAAT
1 AAATTAAAT
14577 AAATTAAAT
1 AAATTAAAT
14586 A
1 A
14587 CAAAATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 16 0.47
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:14582 original size:25 final size:24
Alignment explanation
Indices: 14536--14600 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
14526 ATCTGCAAAA
* *
14536 AAATTAAATAAGTAAAATATTAAAT
1 AAATTAAAT-ATTAAAAAATTAAAT
14561 AAATTAAATATTAAATAAATTAAAT
1 AAATTAAATATTAAA-AAATTAAAT
*
14586 ACA--AAATATTAAAAA
1 AAATTAAATATTAAAAA
14601 TATATTTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.06
23 10 0.28
24 5 0.14
25 19 0.53
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATTAAATATTAAAAAATTAAAT
Found at i:14592 original size:16 final size:16
Alignment explanation
Indices: 14557--14593 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
14547 GTAAAATATT
**
14557 AAATAAATTAAATATT
1 AAATAAATTAAATACA
14573 AAATAAATTAAATACA
1 AAATAAATTAAATACA
14589 AAATA
1 AAATA
14594 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAATTAAATACA
Found at i:15000 original size:29 final size:29
Alignment explanation
Indices: 14954--15032 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
14944 TACTGCTAAA
* * *
14954 GATATTAGATCGAAAAATATAATCTGATC
1 GATATTACATCGATAAATATAACCTGATC
* *
14983 GGTATTATATCGATAAATATAACCTGATC
1 GATATTACATCGATAAATATAACCTGATC
* *
15012 GATGTTACATCAATAAATATA
1 GATATTACATCGATAAATATA
15033 TCGATCACCG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
GATATTACATCGATAAATATAACCTGATC
Found at i:38917 original size:21 final size:21
Alignment explanation
Indices: 38893--38942 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
38883 TAACAAAATT
38893 AAATTCGAATCGTAATTCTAA
1 AAATTCGAATCGTAATTCTAA
38914 AAATTCGAATCGTAATTCTAA
1 AAATTCGAATCGTAATTCTAA
38935 AAATTCGA
1 AAATTCGA
38943 CTAAGGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (21 bp):
AAATTCGAATCGTAATTCTAA
Found at i:39311 original size:50 final size:51
Alignment explanation
Indices: 39233--39333 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 51
39223 AAAAATAACC
* *
39233 ATCCTAGTCCTTGAAAAATAATAATTCTCAACCTTAAATCACTTAACTTTT
1 ATCCTAGTCATTGAAAAATAATAATTCTCAACCTTAAAGCACTTAACTTTT
*
39284 ATCCTAGTTATTG-AAAATAATAATTCTCAACCTTAAAGCACTTAACTTTT
1 ATCCTAGTCATTGAAAAATAATAATTCTCAACCTTAAAGCACTTAACTTTT
39334 CACAATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 36 0.77
51 11 0.23
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (51 bp):
ATCCTAGTCATTGAAAAATAATAATTCTCAACCTTAAAGCACTTAACTTTT
Found at i:43790 original size:22 final size:23
Alignment explanation
Indices: 43765--43808 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
43755 AATTAAGTTT
43765 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
43787 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
43809 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:51757 original size:17 final size:18
Alignment explanation
Indices: 51719--51757 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
51709 TTTTAACATT
*
51719 TTGAATATTTTGGAATGT
1 TTGAATATTTTGGAATGA
*
51737 TTGAAT-TTTTGGATTGA
1 TTGAATATTTTGGAATGA
51754 TTGA
1 TTGA
51758 CTTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGAATATTTTGGAATGA
Found at i:54352 original size:34 final size:34
Alignment explanation
Indices: 54312--54424 Score: 115
Period size: 34 Copynumber: 3.3 Consensus size: 34
54302 GTCAATTTAA
*
54312 AAAGATATTTGTTATCTTTTTAAATTTGAATATT
1 AAAGATATTTATTATCTTTTTAAATTTGAATATT
* * *
54346 AAAGATAATTATATAT-TTTTGTATATTTCAA-ATT
1 AAAGATATTTAT-TATCTTTT-TAAATTTGAATATT
* *
54380 AAA-ATATATTATTATCTATTTAAAGTTGAATATT
1 AAAGATAT-TTATTATCTTTTTAAATTTGAATATT
54414 AAAAGATATTT
1 -AAAGATATTT
54425 GGTTGGGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
33 13 0.21
34 30 0.48
35 16 0.25
36 4 0.06
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (34 bp):
AAAGATATTTATTATCTTTTTAAATTTGAATATT
Found at i:55300 original size:2 final size:2
Alignment explanation
Indices: 55293--55322 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55283 CCAAAATTTA
55293 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
55323 TTAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56353 original size:19 final size:19
Alignment explanation
Indices: 56331--56369 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
56321 CCAAACAAGG
*
56331 TAATACAACATTCTTATAA
1 TAATACAACATTCTAATAA
* *
56350 TAATTCTACATTCTAATAA
1 TAATACAACATTCTAATAA
56369 T
1 T
56370 GTTATTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATACAACATTCTAATAA
Found at i:57131 original size:21 final size:22
Alignment explanation
Indices: 57093--57138 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
57083 ATTTAAAATT
* *
57093 TAAAATTTTAATTTTTTAATTAA
1 TAAAATTTTAA-TCTTTAAATAA
57116 TAAAATTTTAA-CTTTAAATAA
1 TAAAATTTTAATCTTTAAATAA
57137 TA
1 TA
57139 TATATGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATTTTAATCTTTAAATAA
Found at i:65604 original size:331 final size:331
Alignment explanation
Indices: 65000--65632 Score: 1124
Period size: 331 Copynumber: 1.9 Consensus size: 331
64990 ATAGACCTCG
65000 TATCAATCAATACCATAACATGTTTATCAAACAATAGAAAGGTACCTATTACAATCTCTGGGTCA
1 TATCAATCAATACCATAACATGTTTATCAAACAATAGAAAGGTACCTATTACAATCTCTGGGTCA
** *
65065 TCCCGATCCTCATTGGTCTTGAGATTATACACTCAAGCAGTGGAACGTATCTCTTGTTGAGCAGA
66 TCCCGATCCTCATTGGTCTTGAGATTATACACTCAAGCAGTGGAACACATCTCTTGTTAAGCAGA
* * *
65130 GGACTCTGGCTGATTTCTTCCTCTACCTCTACCTCTTCCCCTTTGGCCTGCAGAAATAGACCTCT
131 GGACTATGACTGATTTCTTCATCTACCTCTACCTCTTCCCCTTTGGCCTGCAGAAATAGACCTCT
* * *
65195 CTAGTTGTGTAGAATCATCGGCTACCCTGAGACAATCCCGAACAAAATGTTCGGTCTCTCCACAT
196 CTAGTTGTGCAGAATCATCGGCTACCCTGAGACAATCCCGAACAAAATGTCCGGTCTCCCCACAT
*
65260 CTAAAATAAGCTCCAGAAATTATCCTACATATCCCTGAATGATTCTTTCCACAATGTGGGCATTG
261 CTAAAACAAGCTCCAGAAATTATCCTACATATCCCTGAATGATTCTTTCCACAATGTGGGCATTG
65325 TCTGAC
326 TCTGAC
65331 TATCAATCAATACCATAACATGTTTATCAAACAATAGAAAGGTACCTATTACAATCGT-TGGGTC
1 TATCAATCAATACCATAACATGTTTATCAAACAATAGAAAGGTACCTATTACAATC-TCTGGGTC
* *
65395 ATCCCGATCCTCATTGGTCTTGAGATTATACACTCGAGCAGTGGAACACATCTCTTGTTAAGTAG
65 ATCCCGATCCTCATTGGTCTTGAGATTATACACTCAAGCAGTGGAACACATCTCTTGTTAAGCAG
*
65460 AGGACTATGACTGATTTCTTCATCTGCCTCTACCTCTTCCCCTTTGGCCTGCAGAAATAGACCTC
130 AGGACTATGACTGATTTCTTCATCTACCTCTACCTCTTCCCCTTTGGCCTGCAGAAATAGACCTC
*
65525 TCTAGTTGTGCAGAATCATCGGCTACCCTGGGACAATCCCGAACAAAATGTCCGGTCTCCCCACA
195 TCTAGTTGTGCAGAATCATCGGCTACCCTGAGACAATCCCGAACAAAATGTCCGGTCTCCCCACA
65590 TCTAAAACAAGCTCCAGAAATTATCCTACATATCCCTGAATGA
260 TCTAAAACAAGCTCCAGAAATTATCCTACATATCCCTGAATGA
65633 GATTACGCTC
Statistics
Matches: 287, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
331 286 1.00
332 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (331 bp):
TATCAATCAATACCATAACATGTTTATCAAACAATAGAAAGGTACCTATTACAATCTCTGGGTCA
TCCCGATCCTCATTGGTCTTGAGATTATACACTCAAGCAGTGGAACACATCTCTTGTTAAGCAGA
GGACTATGACTGATTTCTTCATCTACCTCTACCTCTTCCCCTTTGGCCTGCAGAAATAGACCTCT
CTAGTTGTGCAGAATCATCGGCTACCCTGAGACAATCCCGAACAAAATGTCCGGTCTCCCCACAT
CTAAAACAAGCTCCAGAAATTATCCTACATATCCCTGAATGATTCTTTCCACAATGTGGGCATTG
TCTGAC
Found at i:70893 original size:26 final size:26
Alignment explanation
Indices: 70828--70894 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 26
70818 AGCTCGAGTA
70828 TTGCTGAGCTCGACTCGACTCGAAAAC
1 TTGC-GAGCTCGACTCGACTCGAAAAC
*
70855 TCTGAAATAGAGCTCGACTCGACTCGAAAAC
1 T-TG----CGAGCTCGACTCGACTCGAAAAC
70886 TTGCGAGCT
1 TTGCGAGCT
70895 TAAAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
26 5 0.15
27 1 0.03
28 2 0.06
30 2 0.06
31 23 0.70
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (26 bp):
TTGCGAGCTCGACTCGACTCGAAAAC
Found at i:72079 original size:9 final size:9
Alignment explanation
Indices: 72033--72106 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
72023 TTTATATTTT
72033 TTATATTAA
1 TTATATTAA
72042 TTATA-TATA
1 TTATATTA-A
*
72051 TAATATT--
1 TTATATTAA
**
72058 TTATATTTT
1 TTATATTAA
72067 TTATATTAA
1 TTATATTAA
72076 TTATA-TATA
1 TTATATTA-A
*
72085 TAATATT--
1 TTATATTAA
72092 TTATATTAA
1 TTATATTAA
72101 TTATAT
1 TTATAT
72107 ATAAAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
7 12 0.24
8 4 0.08
9 33 0.65
10 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATTAA
Found at i:72106 original size:34 final size:34
Alignment explanation
Indices: 72009--72098 Score: 180
Period size: 34 Copynumber: 2.6 Consensus size: 34
71999 CCCGATTATA
72009 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
72043 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
72077 TATATATATAATATTTTATATT
1 TATATATATAATATTTTATATT
72099 AATTATATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:72107 original size:25 final size:25
Alignment explanation
Indices: 72009--72118 Score: 110
Period size: 25 Copynumber: 4.7 Consensus size: 25
71999 CCCGATTATA
72009 TATATATATAATATTTTATATT--T
1 TATATATATAATATTTTATATTAAT
* *
72032 T-T-TATATTA-ATTATATATATAA-
1 TATATATATAATATTTTATAT-TAAT
* *
72054 TAT-TTTAT-ATTTTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
72077 TATATATATAATATTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
*
72102 TATATATAAAATATTTT
1 TATATATATAATATTTT
72119 CGGGTTCGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.11
21 7 0.10
22 6 0.08
23 16 0.23
24 4 0.06
25 30 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATATATAATATTTTATATTAAT
Found at i:79808 original size:134 final size:134
Alignment explanation
Indices: 79619--79954 Score: 446
Period size: 134 Copynumber: 2.5 Consensus size: 134
79609 ATAAGGAAAT
* * * * *
79619 CTAGTTATCTAAGGGTGACACTA-CTTCTACGTGATAAGGAGATCTGGTCGGTGGATGACACGGT
1 CTAGTTATCTAAGGTTGACGC-AGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGAT
* * * *
79683 TCCTACGTGATGAGGATGGTTGGCCATCTTTAGAGATGATTATAACACGA-TTCCTACGTGCTAA
65 TCCTACGTGATGAGGATAGTTGGCCATCTTTAGAGATGATGATAACAC-ATTTCCTACATGATAA
*
79747 GGATGA
129 GGACGA
* * * *
79753 CTGGTTATCTAAGGTTGACGCAGCTCCTAAGTGATGAGGAGATCTGGTCGATGGATGCCACGATT
1 CTAGTTATCTAAGGTTGACGCAGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGATT
* *
79818 CCTACGTGATGAGGATAGTTGGCCATCTTTAGGGATGATGATAACACATTTCCTACATGATGAGG
66 CCTACGTGATGAGGATAGTTGGCCATCTTTAGAGATGATGATAACACATTTCCTACATGATAAGG
79883 ACGA
131 ACGA
* * *
79887 CTAGTTATCTAAGGTTGACGC-GACTCCTACGTGATGAGGAGATTTGGTTGGTGGATGATAC-AT
1 CTAGTTATCTAAGGTTGACGCAG-CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGAT
79950 TCCTA
65 TCCTA
79955 AACGATGAGG
Statistics
Matches: 176, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
133 10 0.06
134 166 0.94
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (134 bp):
CTAGTTATCTAAGGTTGACGCAGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGATT
CCTACGTGATGAGGATAGTTGGCCATCTTTAGAGATGATGATAACACATTTCCTACATGATAAGG
ACGA
Found at i:80083 original size:65 final size:64
Alignment explanation
Indices: 79991--80123 Score: 178
Period size: 65 Copynumber: 2.1 Consensus size: 64
79981 AGGGATAATG
* * *
79991 TTTTAAGAGAAACTATCTTAAGAGAGACAAAATTTGTTTCGAGGAAAAC-ATACTCAAAGATGAT
1 TTTTAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGAT-CTCAAAGATGAT
* * * *
80055 TTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGGTCTCAAAGATGAT
1 TTTT-AAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGATGAT
80120 TTTT
1 TTTT
80124 TTTATTCAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 4 0.07
65 55 0.92
66 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (64 bp):
TTTTAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGATGAT
Found at i:85895 original size:685 final size:684
Alignment explanation
Indices: 84586--85955 Score: 2139
Period size: 685 Copynumber: 2.0 Consensus size: 684
84576 AATCTGCAAA
** *
84586 AGTTGAAGGATTGATGATGGAAATAAATATTTATGGAATTTAACGAGTATTTTGAGAAGTTTGAA
1 AGTTGAAGGATTGATGATAAAAATAAATATTTATGAAATTTAACGAGTATTTTGAGAAGTTTGAA
84651 TTTATGATGGGAGTACGACTTAGTTTATTATTGATAAGTATTGATTTCATTTTATAAGTTTTATT
66 TTTATGATGGGAGTACGACTTAGTTTATTATTGATAAGTATTGATTTCATTTTATAAGTTTTATT
* ** ** * *
84716 TTTATTTTATTAGGTTTAAATTATGTTAGTACGATACTAACATATATTTGAATATTTTATGTTAT
131 TTTATATTATTAAATTTAAATTATGACAGTACGATACTAACATATAGTTGAATAATTTATGTTAT
*** * * * * *
84781 TATATGGTGTTGTCAGATCATGATAAACCTAGCAAATCGAGTGATCCGAAAGGAAAGAACAAATC
196 TATATCACGTTATCAAATCATAATAAACCTAACAAATCGAGTGATCCAAAAGGAAAGAACAAATC
* *
84846 ACAAGAGTAAGAAGTATTATATAAAAGTTCAATAGTGAGGCAAAGGTGAGTGCAGTTTACATATT
261 ACAAGAGTAAGAAGTATTATATAAAAGTTCAATAGTGAAGCAAAGGTGAGTGCAATTTACATATT
* * **
84911 TAATTATTCTGATCGAGGGCGACTTGCGATAAGCCAATTTCATATTATTTTTAAAGTATGATTTA
326 TAATTATTCTGATCGAGGACGACTTGCAATAAGCCAACCTCATATTATTTTTAAAGTATGATTTA
* * * * * * *
84976 TTATTTTAGTTGTGTATTATTTCCTTAATATTTTCATAAAGTTTTATGAATGATTTATGGTATGA
391 TTATTTTAATTGTGGATTATTTCCATAATATTTCCATAAAATTTTACGAATGATTTAGGGTATGA
*
85041 ACTACCCAAGTTTATGTTTTACGATGATGAATTAAAATGATTCTGATTTTGATATGTTGATCATT
456 ACTACCCAAGTTTATGTTTTACGACGATGAATTAAAATGATTCTGATTTTGATATGTTGATCATT
* **
85106 AAATGATTATGATATAGTTTAAAAGCCCATTGCATGTTGCATTGAGAGTCATAGGTACAATCGGC
521 AAATGATTATGATATAGTTTAAAAGCCCATTGCATGTTGCATTGAGAGTCACAGGTACAATCAAC
* * * * *
85171 ATGCCATGAGGTGGAGTAATTCTGATTATAAATTGGTATATTTGTATACATTTGTGTAGCACCAT
586 ATGCCATGAGGTAGAGTAATTCTAATTATAAATTGGTATATTTGTATACATATATGTAGAACCAT
*
85236 TGGTGTAGATTATATGATTGCACTTGGAGTGCAT
651 TGGTGCAGATTATATGATTGCACTTGGAGTGCAT
*
85270 AGTTGAAGGGTTGATGATAAAAATAAATATTTATGAAATTTAACGAGTATTTTGAGAAGTTTGAA
1 AGTTGAAGGATTGATGATAAAAATAAATATTTATGAAATTTAACGAGTATTTTGAGAAGTTTGAA
* *
85335 TTTATGATGGGAGTGCGACTTAGTTTATTATTGAGTAAGTATTGATTTCATTTTATAGATTTTTA
66 TTTATGATGGGAGTACGACTTAGTTTATTATTGA-TAAGTATTGATTTCATTTTATA-AGTTTTA
*
85400 TTTTTATATTATTAAATTTAAATTATGACAGTACGATATTAACATATAGTTGAATAATTTATGTT
129 TTTTTATATTATTAAATTTAAATTATGACAGTACGATACTAACATATAGTTGAATAATTTATGTT
* *
85465 ATTTTATCACGTTATCAAATCATAATAAACCTAACGAATCGAGTGATCCAAAAGGAAAGAACAAA
194 ATTATATCACGTTATCAAATCATAATAAACCTAACAAATCGAGTGATCCAAAAGGAAAGAACAAA
* * *
85530 TCACAAGAGTAAGGAGTATTATATAAAAGTTCAATAGTGAAGCAAAGGTGAGTGTAATTTACTTA
259 TCACAAGAGTAAGAAGTATTATATAAAAGTTCAATAGTGAAGCAAAGGTGAGTGCAATTTACATA
* * * *
85595 TTTAATTATTCTGATCGAGGACGATTTGTAATAGGTCAACCTCATATTA-TTTTAAAGTATGATT
324 TTTAATTATTCTGATCGAGGACGACTTGCAATAAGCCAACCTCATATTATTTTTAAAGTATGATT
85659 TATTATTTTAATTGTGGATTATTTCCATAATATTTCCATAAAATTTTACGAATGATTTAGGGTAT
389 TATTATTTTAATTGTGGATTATTTCCATAATATTTCCATAAAATTTTACGAATGATTTAGGGTAT
85724 GAACTACCCAAGTTTATGTTTTACGACGATGAATTAAAATGATTCTGATTTTGATATGTTGATCA
454 GAACTACCCAAGTTTATGTTTTACGACGATGAATTAAAATGATTCTGATTTTGATATGTTGATCA
* * * *
85789 TTAAATGATTATGATATAGTTTAAAAGCCCATTGTATGTTGCATTGAGAGTCGCATGTACAATTA
519 TTAAATGATTATGATATAGTTTAAAAGCCCATTGCATGTTGCATTGAGAGTCACAGGTACAATCA
* * * * *
85854 ACATGTCATGAGGTAGAGTGATTCTAATTCTAATTTGGTATATTTGTGTACATATATGTAGAACC
584 ACATGCCATGAGGTAGAGTAATTCTAATTATAAATTGGTATATTTGTATACATATATGTAGAACC
*
85919 GTTGGTGCAGATTATATGATTGCACTTGGAGTGCAT
649 ATTGGTGCAGATTATATGATTGCACTTGGAGTGCAT
85955 A
1 A
85956 ATCTGATTTG
Statistics
Matches: 620, Mismatches: 64, Indels: 3
0.90 0.09 0.00
Matches are distributed among these distances:
684 94 0.15
685 307 0.50
686 219 0.35
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (684 bp):
AGTTGAAGGATTGATGATAAAAATAAATATTTATGAAATTTAACGAGTATTTTGAGAAGTTTGAA
TTTATGATGGGAGTACGACTTAGTTTATTATTGATAAGTATTGATTTCATTTTATAAGTTTTATT
TTTATATTATTAAATTTAAATTATGACAGTACGATACTAACATATAGTTGAATAATTTATGTTAT
TATATCACGTTATCAAATCATAATAAACCTAACAAATCGAGTGATCCAAAAGGAAAGAACAAATC
ACAAGAGTAAGAAGTATTATATAAAAGTTCAATAGTGAAGCAAAGGTGAGTGCAATTTACATATT
TAATTATTCTGATCGAGGACGACTTGCAATAAGCCAACCTCATATTATTTTTAAAGTATGATTTA
TTATTTTAATTGTGGATTATTTCCATAATATTTCCATAAAATTTTACGAATGATTTAGGGTATGA
ACTACCCAAGTTTATGTTTTACGACGATGAATTAAAATGATTCTGATTTTGATATGTTGATCATT
AAATGATTATGATATAGTTTAAAAGCCCATTGCATGTTGCATTGAGAGTCACAGGTACAATCAAC
ATGCCATGAGGTAGAGTAATTCTAATTATAAATTGGTATATTTGTATACATATATGTAGAACCAT
TGGTGCAGATTATATGATTGCACTTGGAGTGCAT
Found at i:87380 original size:19 final size:20
Alignment explanation
Indices: 87356--87401 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
87346 CAAAATGACC
*
87356 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
87375 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
87395 TAATTTC
1 CAATTTC
87402 TAGCATAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:95044 original size:10 final size:10
Alignment explanation
Indices: 95029--95059 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
95019 CCTTTACAGC
95029 AAAAGTAAAA
1 AAAAGTAAAA
95039 AAAAGTAAAA
1 AAAAGTAAAA
95049 AAAAGTAAAA
1 AAAAGTAAAA
95059 A
1 A
95060 TGAAAGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAGTAAAA
Done.