Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004981.1 Hibiscus syriacus cultivar Beakdansim tig00011179_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: 89141
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:18122 original size:25 final size:25
Alignment explanation
Indices: 18094--18150 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
18084 CCTTTTAATG
*
18094 AATATTTAAACTGAAATAATTAAAT
1 AATATTTAAACTAAAATAATTAAAT
***
18119 AATATTTATTTTAAAATAATTAAAT
1 AATATTTAAACTAAAATAATTAAAT
*
18144 AAGATTT
1 AATATTT
18151 TAATTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATATTTAAACTAAAATAATTAAAT
Found at i:21155 original size:140 final size:140
Alignment explanation
Indices: 20903--21183 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
20893 GAATAGTAGC
20903 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
1 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
*
20968 TTAGCAAGGAATGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
66 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
21033 TAGCTTGAAG
131 TAGCTTGAAG
21043 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
1 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
21108 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
66 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
21173 TAGCTTGAAG
131 TAGCTTGAAG
21183 A
1 A
21184 GGTCAAGAAG
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.16
Consensus pattern (140 bp):
AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
TAGCTTGAAG
Found at i:25323 original size:26 final size:26
Alignment explanation
Indices: 25294--25352 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
25284 TAAATGAATA
*
25294 TTTAATTCATAATAACTAAATAAGAT
1 TTTAATTCAAAATAACTAAATAAGAT
* **
25320 TTTATTTCAAAATATTTAAATAAGAT
1 TTTAATTCAAAATAACTAAATAAGAT
25346 TTTAATT
1 TTTAATT
25353 AATTCAGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (26 bp):
TTTAATTCAAAATAACTAAATAAGAT
Found at i:27050 original size:19 final size:19
Alignment explanation
Indices: 27003--27043 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
26993 ATTAAAAACA
27003 AAACATGATGATATGTAAC
1 AAACATGATGATATGTAAC
27022 AAACATGATGATATGTAAC
1 AAACATGATGATATGTAAC
27041 AAA
1 AAA
27044 TGTGATGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (19 bp):
AAACATGATGATATGTAAC
Found at i:27438 original size:2 final size:2
Alignment explanation
Indices: 27431--27459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27421 CAAAACATTA
27431 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 A
27460 CTTATCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27499 original size:12 final size:12
Alignment explanation
Indices: 27470--27506 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
27460 CTTATCTATT
* *
27470 TATCTATCTATC
1 TATCTCTCTCTC
27482 TATCTCTCTCTC
1 TATCTCTCTCTC
27494 TATCTCTCTCTC
1 TATCTCTCTCTC
27506 T
1 T
27507 CTCCATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (12 bp):
TATCTCTCTCTC
Found at i:27503 original size:16 final size:16
Alignment explanation
Indices: 27462--27509 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
27452 TATATATACT
* * *
27462 TATCTATTTATCTATC
1 TATCTATCTCTCTCTC
27478 TATCTATCTCTCTCTC
1 TATCTATCTCTCTCTC
*
27494 TATCTCTCTCTCTCTC
1 TATCTATCTCTCTCTC
27510 CATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATCTCTCTCTC
Found at i:30639 original size:23 final size:23
Alignment explanation
Indices: 30613--30659 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30603 AAGATATGGG
30613 TCTATTTAACAATTTTGAAAAGT
1 TCTATTTAACAATTTTGAAAAGT
30636 TCTATTTAACAATTTTGAAAAGT
1 TCTATTTAACAATTTTGAAAAGT
30659 T
1 T
30660 ATGGGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
TCTATTTAACAATTTTGAAAAGT
Found at i:30747 original size:19 final size:20
Alignment explanation
Indices: 30704--30749 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30694 TGATATGCTG
* *
30704 GAAATTTATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
30724 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
30743 GAAATTG
1 GAAATTG
30750 GTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:38839 original size:22 final size:21
Alignment explanation
Indices: 38802--38842 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38792 CCATCTCCAT
38802 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
38823 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
38843 ATTCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:39251 original size:31 final size:31
Alignment explanation
Indices: 39164--39237 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
39154 GTGCAAAAAG
*
39164 AAAGAA-AAAGACAAAAAGAAGAAAAATTTCAGA
1 AAAGAAGAAAGA-AAGAA-AAG-AAAATTTCAGA
39197 AAAGAAGAAAGAAAGAAAAGAAAATTTCA-A
1 AAAGAAGAAAGAAAGAAAAGAAAATTTCAGA
39227 AAA-ATAGAAAG
1 AAAGA-AGAAAG
39238 CAAGCCAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 1 0.03
30 10 0.26
31 9 0.24
32 3 0.08
33 10 0.26
34 5 0.13
ACGTcount: A:0.70, C:0.04, G:0.16, T:0.09
Consensus pattern (31 bp):
AAAGAAGAAAGAAAGAAAAGAAAATTTCAGA
Found at i:51039 original size:12 final size:13
Alignment explanation
Indices: 51013--51042 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
51003 CTTTCATCTT
51013 TTTAATTCTTTAA
1 TTTAATTCTTTAA
51026 TTTAATTC-TTAA
1 TTTAATTCTTTAA
51038 TTTAA
1 TTTAA
51043 ATAGTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAATTCTTTAA
Found at i:56304 original size:2 final size:2
Alignment explanation
Indices: 56292--56364 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
56282 TTTTCAATTA
*
56292 TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
56334 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
56365 TTAACATAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:61413 original size:55 final size:55
Alignment explanation
Indices: 61289--61667 Score: 449
Period size: 55 Copynumber: 6.9 Consensus size: 55
61279 ATATACGGAA
* * * ** * * *
61289 ATTCATCAACTCACGATGAATTCCATGGGT-TGCACATATAGTGCCTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * * * * * ** *
61343 ATTCATCAACTCATGATGAATTCCATGAGTTTTCACACAAAGTTCTTGTACATTA
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* *
61398 ACTT-ATCAACCCATGATGAATTCCGTGAATTTGCACACAAAATG-TCTGTACGGTG
1 A-TTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCT-TGTACGGTG
*
61453 ATTTATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * * * *
61508 ATTCATCAACCTATGATGAATTACGTGAATATGCACACAAAGTGCCTATACAGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* *
61563 ATTCATCAACACATGATGAATTCAGTGAATATGCACACAAAGTGCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * *
61618 ATTCATCGACCCATGATGAATTTCGTGAATATGCACACAAAGTGCATGTA
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTA
61668 GTACACATAG
Statistics
Matches: 281, Mismatches: 39, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
54 31 0.11
55 247 0.88
56 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
Found at i:61701 original size:2 final size:2
Alignment explanation
Indices: 61696--61741 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
61686 TATCAATGCA
61696 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
61738 AT AT
1 AT AT
61742 CACTTACCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62079 original size:63 final size:61
Alignment explanation
Indices: 61987--62106 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 61
61977 TGGCTCCATA
*
61987 GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTGTCGATACCAAAATTAGTTG
1 GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTG
* * *
62048 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCTGGTATCGATATCAAAATTA
1 GTATCGATACTA-C-TACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTA
62107 TATTTGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.23
62 1 0.02
63 40 0.75
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (61 bp):
GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTG
Found at i:63965 original size:20 final size:20
Alignment explanation
Indices: 63939--63984 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
63929 TATTTTTTTT
*
63939 CAAAAAAACAAAAAAA-AGG
1 CAAAAAAACAAAAAAAGAGC
63958 CAAAAAAACAAAAAAAGAGC
1 CAAAAAAACAAAAAAAGAGC
63978 CAAAAAA
1 CAAAAAA
63985 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAGAGC
Found at i:71293 original size:15 final size:15
Alignment explanation
Indices: 71261--71294 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
71251 AATTGTTTCG
* *
71261 GCTTGGGCGTTCGTA
1 GCTTGGGCGTCCGCA
71276 GCTTGGGCGTCCGCA
1 GCTTGGGCGTCCGCA
71291 GCTT
1 GCTT
71295 AGGCAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.26, G:0.38, T:0.29
Consensus pattern (15 bp):
GCTTGGGCGTCCGCA
Found at i:75752 original size:23 final size:22
Alignment explanation
Indices: 75722--75764 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
75712 GCAGCTAAAG
75722 TTGGTTAGGGTTAAGGTTTTGTT
1 TTGGTTAGGG-TAAGGTTTTGTT
*
75745 TTGGTTAGGGTATGGTTTTG
1 TTGGTTAGGGTAAGGTTTTG
75765 GGTTTGGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (22 bp):
TTGGTTAGGGTAAGGTTTTGTT
Found at i:75770 original size:23 final size:23
Alignment explanation
Indices: 75722--75771 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
75712 GCAGCTAAAG
*
75722 TTGGTTAGGGTTAAGGTTTTGTT
1 TTGGTTAGGGTTAAGGTTTTGGT
*
75745 TTGGTTAGGG-TATGGTTTTGGGT
1 TTGGTTAGGGTTAAGGTTTT-GGT
75768 TTGG
1 TTGG
75772 GCCTGTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (23 bp):
TTGGTTAGGGTTAAGGTTTTGGT
Found at i:76602 original size:41 final size:41
Alignment explanation
Indices: 76539--76667 Score: 107
Period size: 41 Copynumber: 3.1 Consensus size: 41
76529 CTCATTTGAA
* * * * *
76539 ATCATCATGCCCGAAGGTCTTATGGATGGCCCGAAAGACTT
1 ATCATCATACTCGAAAGACTTATAGATGGCCCGAAAGACTT
* * *
76580 ATCATCTTACTCGAAAGACTTATAGATGACCCG-AAGATTT
1 ATCATCATACTCGAAAGACTTATAGATGGCCCGAAAGACTT
* * * * * *
76620 AAGCATCATGCTGGAAAGAATTATTGATGGCCCGAATGACTT
1 -ATCATCATACTCGAAAGACTTATAGATGGCCCGAAAGACTT
76662 ACTCAT
1 A-TCAT
76668 TAAGAAACCC
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
40 6 0.09
41 53 0.79
42 8 0.12
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
ATCATCATACTCGAAAGACTTATAGATGGCCCGAAAGACTT
Found at i:77001 original size:275 final size:274
Alignment explanation
Indices: 76257--77349 Score: 1528
Period size: 275 Copynumber: 4.0 Consensus size: 274
76247 AAAGGAAATG
* * * * * * * * *
76257 TTGAGAACATCCTGCCCTAATGCCTTATGGATTGCTCGAAGGACTTGTCATCTTGCTTGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
*
76322 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* *
76387 CTTATCAAGAAACCCTTGAAAATAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
131 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
* ** * * * * *
76452 CTTAGTTTCCTTTTTTTTTAAACCTCTTTGGAGAT-ATCACCAAGAAACCCCTGAAAAATTAGGC
196 CTTAGCTTCC---TTTTAAAAACTTCATTGAAAATCATCATCAAGAAACCCCTG-AAAATTAGGC
*
76516 TTATTTTCTAAAACTCAT
257 TTAGTTTCTAAAACTCAT
* * *
76534 TTGAAATCATCATGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTACTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
* * * * *
76599 TTATAGATGACCCGAA-GATTTAAGCATCATGCTGGAAAGAATTATTGATGGCCCGAATGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* *
76663 CTCATTAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
131 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
* *
76728 CTTAGCTTCCTTTTAAAAACTTCATTGAAAATCATCATCAAAAAACCCCTGAAAATCAGGCTTAG
196 CTTAGCTTCCTTTTAAAAACTTCATTGAAAATCATCATCAAGAAACCCCTGAAAATTAGGCTTAG
*
76793 TTTCTAAAAACTTAT
261 TTTCT-AAAACTCAT
76808 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
*
76873 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* * *
76938 CTTATCAAGAAACCCGTGAAAATCAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGG
131 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
* ** * * * *
77003 CTTAGCTTTCTTTTTTTTAAAC-TCTTTGGAGATAATCATCAAGAAACCCCTGAAAATTAGGCTT
196 CTTAGC-TTC-CTTTTAAAAACTTCATTGAAAATCATCATCAAGAAACCCCTGAAAATTAGGCTT
*
77067 AATTTCTAAAACTCAT
259 AGTTTCTAAAACTCAT
* * * * *
77083 TTGAAATCATTCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAGAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
* * * *
77148 TTATAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGATTTACTGATTGCCCTAAGGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* *
77213 CTCATTAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGTAACCCCTAAAAATTAG
131 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCT-AAAATTAG
* * * * *
77278 GCTTCGTTTCCTTTTAAAAAATTCATTGAAAATCATAATCAGGAAACCCCTGAAAA-TAGGCTTA
195 GCTTAGCTTCCTTTTAAAAACTTCATTGAAAATCATCATCAAGAAACCCCTGAAAATTAGGCTTA
77342 GTTTCTAA
260 GTTTCTAA
77350 GTTGTTAATG
Statistics
Matches: 725, Mismatches: 84, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
273 33 0.05
274 123 0.17
275 320 0.44
276 172 0.24
277 77 0.11
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (274 bp):
TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
CTTAGCTTCCTTTTAAAAACTTCATTGAAAATCATCATCAAGAAACCCCTGAAAATTAGGCTTAG
TTTCTAAAACTCAT
Found at i:77007 original size:38 final size:40
Alignment explanation
Indices: 76934--77014 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 40
76924 GCCCAAAGGA
*
76934 CTTACTTATCAAGAAACCCGTGAAAATCAAGCTTAG-TTT
1 CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
* * * *
76973 CTTAGTTATCAAGGAACCCCT-AAAATTAGGCTTAGCTTT
1 CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
77012 CTT
1 CTT
77015 TTTTTTAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 12 0.33
39 24 0.67
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (40 bp):
CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
Found at i:77305 original size:551 final size:550
Alignment explanation
Indices: 76257--77349 Score: 1773
Period size: 551 Copynumber: 2.0 Consensus size: 550
76247 AAAGGAAATG
* * * * * * * *
76257 TTGAGAACATCCTGCCCTAATGCCTTATGGATTGCTCGAAGGACTTGTCATCTTGCTTGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
* *
76322 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
* *
76387 CTTATCAAGAAACCCTTGAAAATAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGG
131 CTTATCAAGAAACCCGTGAAAATAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGG
76452 CTTAGTTTCCTTTTTTTTTAAACCTCTTTGGAGATATCACCAAGAAACCCCTGAAAAATTAGGCT
196 CTTAGTTTCCTTTTTTTTTAAACCTCTTTGGAGATATCACCAAGAAACCCCTGAAAAATTAGGCT
* *
76517 TATTTTCTAAAACTCATTTGAAATCATCATGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTAT
261 TAATTTCTAAAACTCATTTGAAATCATCATACCCGAAGGTCTTATGGATGGCCCGAAAGACTTAT
* * * *
76582 CATCTTACTCGAAAGACTTATAGATGACCCGAAGATTTAAGCATCATGCTGGAAAGAATTATTGA
326 CATCTTACTCGAAAGACTTATAAATGACCCAAAGATTTAAGCATCATGCTCGAAAGAATTACTGA
*
76647 TGGCCCGAATGACTTACTCATTAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAGTTGTCAAGG
391 TGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAGTTGTCAAGG
* *
76712 AACCCCTAAAATTAGGCTTAGCTTCCTTTTAAAAACTTCATTGAAAATCATCATCAAAAAACCCC
456 AACCCCTAAAATTAGGCTTAGCTTCCTTTTAAAAAATTCATTGAAAATCATAATCAAAAAACCCC
76777 TGAAAATCAGGCTTAGTTTCTAAAAACTTAT
521 TGAAAAT-AGGCTTAGTTTCTAAAAACTTAT
*
76808 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
76873 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
66 TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
*
76938 CTTATCAAGAAACCCGTGAAAATCAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGG
131 CTTATCAAGAAACCCGTGAAAATAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGG
*
77003 CTTAGCTTT-C-TTTTTTTTAAA-CTCTTTGGAGATAATCATCAAGAAACCCCTG-AAAATTAGG
196 CTTAG-TTTCCTTTTTTTTTAAACCTCTTTGGAGAT-ATCACCAAGAAACCCCTGAAAAATTAGG
*
77064 CTTAATTTCTAAAACTCATTTGAAATCATTC-TACCCGAAGGTCTTATGGATGGCCCGAAGGACT
259 CTTAATTTCTAAAACTCATTTGAAATCA-TCATACCCGAAGGTCTTATGGATGGCCCGAAAGACT
* * *
77128 TATCATCTTGCTCGAGAGACTTATAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGATTTA
323 TATCATCTTACTCGAAAGACTTATAAATGACCCAAA-GATTTAAGCATCATGCTCGAAAGAATTA
* * *
77193 CTGATTGCCCTAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTC
387 CTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAGTTGTC
* * * **
77258 AAGTAACCCCTAAAAATTAGGCTTCGTTTCCTTTTAAAAAATTCATTGAAAATCATAATCAGGAA
452 AAGGAACCCCT-AAAATTAGGCTTAGCTTCCTTTTAAAAAATTCATTGAAAATCATAATCAAAAA
77323 ACCCCTGAAAATAGGCTTAGTTTCTAA
516 ACCCCTGAAAATAGGCTTAGTTTCTAA
77350 GTTGTTAATG
Statistics
Matches: 501, Mismatches: 36, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
549 111 0.22
550 141 0.28
551 246 0.49
552 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (550 bp):
TTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGAC
TTATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
CTTATCAAGAAACCCGTGAAAATAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGG
CTTAGTTTCCTTTTTTTTTAAACCTCTTTGGAGATATCACCAAGAAACCCCTGAAAAATTAGGCT
TAATTTCTAAAACTCATTTGAAATCATCATACCCGAAGGTCTTATGGATGGCCCGAAAGACTTAT
CATCTTACTCGAAAGACTTATAAATGACCCAAAGATTTAAGCATCATGCTCGAAAGAATTACTGA
TGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAGTTGTCAAGG
AACCCCTAAAATTAGGCTTAGCTTCCTTTTAAAAAATTCATTGAAAATCATAATCAAAAAACCCC
TGAAAATAGGCTTAGTTTCTAAAAACTTAT
Found at i:77395 original size:98 final size:97
Alignment explanation
Indices: 77214--77643 Score: 623
Period size: 98 Copynumber: 4.4 Consensus size: 97
77204 AAGGACTTAC
* * *
77214 TCATTAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGTAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAG-AACCCCTAAAAATTAGG
* * *
77279 CTTCGTTTCCTTTTAAAAAATTCATTGAAAATCA
65 CTTAGCTTCCTTTT-AAAAACTCATTGAAAATCA
* * * *
77313 TAATCAGGAAACCCCTGAAAAT-AGGCTTAGTTTCTAAGTTGTTAATGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAA-GAACCCCTAAAAATTAGG
* *
77377 CTTAGCTTCCTTTGAAAAACTCATTGAAAATCT
65 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * *
77410 TCATCACA-AAACCCCTGAAACTCAGGCTTAGTTTTTTAGTTGTCAAGGAACCCCTAAATATTAG
1 TCATCA-AGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAA-GAACCCCTAAAAATTAG
77474 GCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
64 GCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
77508 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAAGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTC-AAGAACCCCTAAAAATTAGG
*
77573 CTTAGC-TCCTTTTAAAAACTCATTGAAAATAA
65 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
*
77605 TCATCAAGAAACCCCTGAAAAATCATGCTTAGTTTCTTA
1 TCATCAAGAAACCCCTG-AAAATCAGGCTTAGTTTCTTA
77644 AAAACTCATT
Statistics
Matches: 298, Mismatches: 27, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
97 78 0.26
98 199 0.67
99 21 0.07
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (97 bp):
TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAGAACCCCTAAAAATTAGGC
TTAGCTTCCTTTTAAAAACTCATTGAAAATCA
Found at i:77673 original size:54 final size:55
Alignment explanation
Indices: 77556--77695 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 55
77546 GTTGTCAAAG
* *
77556 AACCCCTAAAAATTAGGCTTAGCTCCTTTTAAAAACTCATTGAAAATAATCATCAAGA
1 AACCCCTAAAAATCAGGCTTAGCT--TCTTAAAAACTCATTG-AAATAATCATCAAGA
* *
77614 AACCCCTGAAAAATCATGCTTAGTTTCTTAAAAACTCATTTG-AA-AA-CATCAAGA
1 AACCCCT-AAAAATCAGGCTTAGCTTCTTAAAAACTCA-TTGAAATAATCATCAAGA
*
77668 AACCCCTAAAAATTAGGCTTAGCTTCTT
1 AACCCCTAAAAATCAGGCTTAGCTTCTT
77696 TTGAAAATTG
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
53 18 0.25
54 15 0.21
55 2 0.03
56 2 0.03
57 12 0.16
58 10 0.14
59 14 0.19
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (55 bp):
AACCCCTAAAAATCAGGCTTAGCTTCTTAAAAACTCATTGAAATAATCATCAAGA
Found at i:79047 original size:32 final size:32
Alignment explanation
Indices: 79011--79076 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
79001 ATGTCGTATG
*
79011 ATAAAACTACCCGAATAAAATTATGTTTTTTA
1 ATAAAACTACCCAAATAAAATTATGTTTTTTA
*
79043 ATAAAACTACCCAAATAAAGTTATGTTTTTTA
1 ATAAAACTACCCAAATAAAATTATGTTTTTTA
79075 AT
1 AT
79077 TTGTTGGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (32 bp):
ATAAAACTACCCAAATAAAATTATGTTTTTTA
Found at i:84536 original size:21 final size:21
Alignment explanation
Indices: 84510--84552 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
84500 ACCAAACTAA
*
84510 TAAATTATTAAATTAATATAT
1 TAAATTAATAAATTAATATAT
*
84531 TAAATTAATAATTTAATATAT
1 TAAATTAATAAATTAATATAT
84552 T
1 T
84553 TCTTATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTAATAAATTAATATAT
Found at i:84546 original size:13 final size:13
Alignment explanation
Indices: 84515--84540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84505 ACTAATAAAT
84515 TATTAAATTAATA
1 TATTAAATTAATA
84528 TATTAAATTAATA
1 TATTAAATTAATA
84541 ATTTAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:85047 original size:60 final size:60
Alignment explanation
Indices: 84950--85126 Score: 318
Period size: 60 Copynumber: 3.0 Consensus size: 60
84940 CCCTCTTGAT
84950 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
* * *
85010 AGCAAGATAACAAAAGCCATCCTCTCGTGCAAAAGCCTTAAATCAGCTCAATTGAATTAG
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
*
85070 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCTTTAAATCAGCTCAATTGAAT
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAAT
85127 CAAAACGGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 110 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (60 bp):
AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
Found at i:85417 original size:24 final size:21
Alignment explanation
Indices: 85390--85440 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 21
85380 TCCTTATCTT
85390 AAAAATTAAAGTTTTTCTATAGA
1 AAAAATTAAAGTTTTT-TA-AGA
*
85413 GAAAAATTGAAGTTTTTTAAGA
1 -AAAAATTAAAGTTTTTTAAGA
85435 AAAAAT
1 AAAAAT
85441 AAATATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 2 0.08
24 15 0.58
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAGTTTTTTAAGA
Found at i:86884 original size:35 final size:35
Alignment explanation
Indices: 86838--86968 Score: 118
Period size: 36 Copynumber: 3.7 Consensus size: 35
86828 TCTTAGGTCC
* ** *
86838 ATAAGAAATTACCAGCTGATTTGTGCTGAACCTAT
1 ATAAGGAATTACCAGCTGATCAGTGTTGAACCTAT
** *
86873 ATAAGGAATTACCAGCTTGATCAGAATTGAACCTGAA
1 ATAAGGAATTACCAGC-TGATCAGTGTTGAACCT-AT
* * *
86910 ATAAGGAATTACCAGTTGATCGGTGTTGAACCTGT
1 ATAAGGAATTACCAGCTGATCAGTGTTGAACCTAT
** *
86945 ATAAACAATTATCAGCTTGATCAG
1 ATAAGGAATTACCAGC-TGATCAG
86969 AACTGAACCT
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
35 27 0.36
36 32 0.43
37 16 0.21
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTGATCAGTGTTGAACCTAT
Found at i:86929 original size:36 final size:37
Alignment explanation
Indices: 86864--86979 Score: 139
Period size: 36 Copynumber: 3.2 Consensus size: 37
86854 TGATTTGTGC
86864 TGAACCT-ATATAAGGAATTACCAGCTTGATCAGAAT
1 TGAACCTGATATAAGGAATTACCAGCTTGATCAGAAT
* * **
86900 TGAACCTGAAATAAGGAATTACCAG-TTGATCGGTGT
1 TGAACCTGATATAAGGAATTACCAGCTTGATCAGAAT
** * *
86936 TGAACCTG-TATAAACAATTATCAGCTTGATCAGAAC
1 TGAACCTGATATAAGGAATTACCAGCTTGATCAGAAT
86972 TGAACCTG
1 TGAACCTG
86980 TAGAGACTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 12 0.18
36 38 0.58
37 16 0.24
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (37 bp):
TGAACCTGATATAAGGAATTACCAGCTTGATCAGAAT
Found at i:86955 original size:72 final size:72
Alignment explanation
Indices: 86838--86979 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 72
86828 TCTTAGGTCC
** ** *
86838 ATAAGAAATTACCAGCTGATTTGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAATTGA
1 ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
86903 ACCTGAA
66 ACCTGAA
* * * * *
86910 ATAAGGAATTACCAGTTGATCGGTGTTGAACCTGTATAAACAATTATCAGCTTGATCAGAACTGA
1 ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
86975 ACCTG
66 ACCTG
86980 TAGAGACTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (72 bp):
ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
ACCTGAA
Done.