Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008121.1 Hibiscus syriacus cultivar Beakdansim tig00110674_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: 1116347
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:988509 original size:20 final size:21
Alignment explanation
Indices: 988464--988515 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
988454 CCCAAGCATG
*
988464 GAGTATCAATA-TCATATTAA
1 GAGTATCAATACTCACATTAA
* *
988484 GGGTATCAATACTCACCTT-A
1 GAGTATCAATACTCACATTAA
*
988504 GAGTATAAATAC
1 GAGTATCAATAC
988516 CCTTGATTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (21 bp):
GAGTATCAATACTCACATTAA
Found at i:989887 original size:23 final size:23
Alignment explanation
Indices: 989842--989887 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
989832 ATTAATTGAT
*
989842 TTGATTGATAAAATTAAAAAAAA
1 TTGATTGATAAAATAAAAAAAAA
989865 TTGA-TGATAAAATAAAAAGAAAA
1 TTGATTGATAAAATAAAAA-AAAA
989888 AAAATTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (23 bp):
TTGATTGATAAAATAAAAAAAAA
Found at i:999664 original size:4 final size:4
Alignment explanation
Indices: 999640--999704 Score: 85
Period size: 4 Copynumber: 15.8 Consensus size: 4
999630 TTAAAATTAA
*
999640 AAAT AAAAT ACAAT GAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT -AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
999690 AAAT ACAT AATT AAA
1 AAAT AAAT AAAT AAA
999705 CTTATATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
4 46 0.87
5 7 0.13
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1001103 original size:3 final size:3
Alignment explanation
Indices: 1001095--1001193 Score: 75
Period size: 3 Copynumber: 34.0 Consensus size: 3
1001085 ATGAAAGTGA
* *
1001095 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -GT ATT AA- ATAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * *
1001138 AAGA AAT ACAT -AT TAT AA- AGT GA- AAT AAT AAT AAT AAT AAT AAT
1 AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1001182 AAT AAT AAT AAT
1 AAT AAT AAT AAT
1001194 GTATTATATA
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
2 8 0.10
3 65 0.83
4 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1001205 original size:69 final size:69
Alignment explanation
Indices: 1001095--1001224 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
1001085 ATGAAAGTGA
1001095 AATAATAATAATAATAATAATAATAATAATGTATTAAATATAAAAGAAATACATATTATAAAGTG
1 AATAATAATAATAATAATAATAATAATAATGTATTAAATATAAAAGAAATACATATTATAAAGTG
1001160 AAAT
66 AAAT
* *
1001164 AATAATAATAATAATAATAATAATAATAATGTATTATATATAAAAGAAATGCATATTATAA
1 AATAATAATAATAATAATAATAATAATAATGTATTAAATATAAAAGAAATACATATTATAA
1001225 TGTTGATAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (69 bp):
AATAATAATAATAATAATAATAATAATAATGTATTAAATATAAAAGAAATACATATTATAAAGTG
AAAT
Found at i:1002235 original size:36 final size:36
Alignment explanation
Indices: 1002185--1002355 Score: 121
Period size: 36 Copynumber: 4.4 Consensus size: 36
1002175 TAGTAAACCA
* *
1002185 TCCGTTCTAGTTGAATCGGAAGTGCGGATGCTTCCT
1 TCCGTTCGAGTTGAATCGGAAGTGCAGATGCTTCCT
*
1002221 TCCGTTCGATTTGAATCGGAAGTGCAGATGCTTCTCCGATTCATCCT
1 TCCGTTCGAGTTGAATCGGAAGTGCAGATG------C---T--TCCT
* *
1002268 TCCGTTCGACTTGAATCGGAAGTGTCA-ATGCTTCCC
1 TCCGTTCGAGTTGAATCGGAAGTG-CAGATGCTTCCT
* * * *
1002304 TCAGTTCGACTTGAATCGAAAGTGTC-GATGCTTCCC
1 TCCGTTCGAGTTGAATCGGAAGTG-CAGATGCTTCCT
*
1002340 TCCGTTCGACTTGAAT
1 TCCGTTCGAGTTGAAT
1002356 GGATGCGAAC
Statistics
Matches: 114, Mismatches: 8, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
36 78 0.68
38 1 0.01
41 1 0.01
42 1 0.01
45 1 0.01
47 30 0.26
48 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (36 bp):
TCCGTTCGAGTTGAATCGGAAGTGCAGATGCTTCCT
Found at i:1002318 original size:83 final size:83
Alignment explanation
Indices: 1002185--1002337 Score: 211
Period size: 83 Copynumber: 1.8 Consensus size: 83
1002175 TAGTAAACCA
* * * * * * *
1002185 TCCGTTCTAGTTGAATCGGAAGTGCGGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTG-CAGA
1 TCCGTTCGACTTGAATCGGAAGTGCGAATGCTTCCCTCAGTTCGACTTGAATCGAAAGTGTC-GA
1002249 TGCTTCTCCGATTCATCCT
65 TGCTTCTCCGATTCATCCT
1002268 TCCGTTCGACTTGAATCGGAAGTGTC-AATGCTTCCCTCAGTTCGACTTGAATCGAAAGTGTCGA
1 TCCGTTCGACTTGAATCGGAAGTG-CGAATGCTTCCCTCAGTTCGACTTGAATCGAAAGTGTCGA
1002332 TGCTTC
65 TGCTTC
1002338 CCTCCGTTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
83 59 0.97
84 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (83 bp):
TCCGTTCGACTTGAATCGGAAGTGCGAATGCTTCCCTCAGTTCGACTTGAATCGAAAGTGTCGAT
GCTTCTCCGATTCATCCT
Found at i:1005411 original size:15 final size:15
Alignment explanation
Indices: 1005391--1005442 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
1005381 ATATTTAGCT
1005391 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
1005406 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
*
1005421 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGTG
1005436 GGGCGGG
1 GGGCGGG
1005443 TAATGTCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.06, C:0.15, G:0.69, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGTG
Found at i:1009006 original size:159 final size:159
Alignment explanation
Indices: 1008706--1009028 Score: 560
Period size: 159 Copynumber: 2.0 Consensus size: 159
1008696 TATCTTGACG
*
1008706 TAAAATCGTCGATTTTGAGTGGATTTTGGGGAAAACTAATCCTTAAAAAAGAAAGGAGAGAACTA
1 TAAAATCGTCGATTTTGAGTGGATTTTAGGGAAAACTAATCCTTAAAAAAGAAAGGAGAGAACTA
*
1008771 GACATTTTGGTAATGATCTTGTTGCGAAAGAAGACTGGTGATTAGTTGTCAGCGATAACAAAAAA
66 AACATTTTGGTAATGATCTTGTTGCGAAAGAAGACTGGTGATTAGTTGTCAGCGATAACAAAAAA
* *
1008836 AAAAGTACAGTGCTAAAAAGTGAATTTTT
131 AAAAGTACAGTGCCAAAAAGTGAATTGTT
1008865 TAAAATCGTCGATTTTGAGTGGATTTTAGGGAAAACTAATCC-TAAAAAAGAAAGGAGAGAACTA
1 TAAAATCGTCGATTTTGAGTGGATTTTAGGGAAAACTAATCCTTAAAAAAGAAAGGAGAGAAC--
*
1008929 TAAACATTTTGGTACTGATCTTGTTGCGAAAGAAGACTGGTGATTAGTTGTCAGCGATAAC-AAA
64 TAAACATTTTGGTAATGATCTTGTTGCGAAAGAAGACTGGTGATTAGTTGTCAGCGATAACAAAA
*
1008993 CAAAAAGTACAGTGCCAAAAAGTGAATTGTT
129 AAAAAAGTACAGTGCCAAAAAGTGAATTGTT
1009024 TAAAA
1 TAAAA
1009029 GTTTAGATTA
Statistics
Matches: 156, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
158 20 0.13
159 77 0.49
160 59 0.38
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (159 bp):
TAAAATCGTCGATTTTGAGTGGATTTTAGGGAAAACTAATCCTTAAAAAAGAAAGGAGAGAACTA
AACATTTTGGTAATGATCTTGTTGCGAAAGAAGACTGGTGATTAGTTGTCAGCGATAACAAAAAA
AAAAGTACAGTGCCAAAAAGTGAATTGTT
Found at i:1014533 original size:29 final size:29
Alignment explanation
Indices: 1014498--1014579 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1014488 AAACTAAATT
*
1014498 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1014527 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1014556 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1014580 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1015893 original size:15 final size:15
Alignment explanation
Indices: 1015870--1015899 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1015860 ACGAGGCTGG
1015870 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1015885 AATTCCAACAATAAC
1 AATTACAACAATAAC
1015900 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1019302 original size:29 final size:29
Alignment explanation
Indices: 1019267--1019348 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1019257 AAACTAAATT
*
1019267 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1019296 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1019325 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1019349 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1023265 original size:2 final size:2
Alignment explanation
Indices: 1023258--1023282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1023248 GGGGTTAATC
1023258 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 A
1023283 ACTCTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1025803 original size:60 final size:58
Alignment explanation
Indices: 1025660--1025820 Score: 225
Period size: 60 Copynumber: 2.8 Consensus size: 58
1025650 CAAATATAAT
* *
1025660 TATGTGTTTATTTTTAGGTATCAAGATATTGAGAGATGT-CATAATTACACGTGTAAG
1 TATGTGTTTATTTTTAGGTATCAAGATATTTAGAGATGTACATAATTACACGTGTAAA
* * * *
1025717 TGTGTATTTATTTTTACGTATCAAGATATTTTGAGATGTACATAATTACACATGTGTAAA
1 TATGTGTTTATTTTTAGGTATCAAGATATTTAGAGATGTACATAATTACAC--GTGTAAA
* *
1025777 TATGTGTTTATTTTTAGGTATTAAGATATTTGGAGATGTACATA
1 TATGTGTTTATTTTTAGGTATCAAGATATTTAGAGATGTACATA
1025821 CTTATATCGA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
57 34 0.38
58 11 0.12
60 45 0.50
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (58 bp):
TATGTGTTTATTTTTAGGTATCAAGATATTTAGAGATGTACATAATTACACGTGTAAA
Found at i:1025835 original size:60 final size:59
Alignment explanation
Indices: 1025660--1025841 Score: 219
Period size: 60 Copynumber: 3.1 Consensus size: 59
1025650 CAAATATAAT
*
1025660 TATGTGTTTATTTTTAGGTATCAAGATA-TTGAGAGATGT-CATAATTACACG-TGTAAG
1 TATGTGTTTATTTTTAGGTATCAAGATATTTG-GAGATGTACATAATTACACGATGTAAA
* * * *
1025717 TGTGTATTTATTTTTACGTATCAAGATATTTTGAGATGTACATAATTACAC-ATGTGTAAA
1 TATGTGTTTATTTTTAGGTATCAAGATATTTGGAGATGTACATAATTACACGA--TGTAAA
* * * *
1025777 TATGTGTTTATTTTTAGGTATTAAGATATTTGGAGATGTACATACTTATATCGATGTAAT
1 TATGTGTTTATTTTTAGGTATCAAGATATTTGGAGATGTACATAATTACA-CGATGTAAA
1025837 TATGT
1 TATGT
1025842 ATTAATTACT
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
57 32 0.30
58 13 0.12
60 58 0.55
61 1 0.01
62 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (59 bp):
TATGTGTTTATTTTTAGGTATCAAGATATTTGGAGATGTACATAATTACACGATGTAAA
Found at i:1027046 original size:21 final size:22
Alignment explanation
Indices: 1027016--1027063 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1027006 AAATTTTGGG
*
1027016 TTTT-ATTTTTATAAATATAAT
1 TTTTAATTTTTATAAATAAAAT
*
1027037 TTTTAATTTTTTTAAATAAAAT
1 TTTTAATTTTTATAAATAAAAT
1027059 TTTTA
1 TTTTA
1027064 TAATTACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAATTTTTATAAATAAAAT
Found at i:1029394 original size:27 final size:29
Alignment explanation
Indices: 1029338--1029394 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 29
1029328 GATTCTCTAA
**
1029338 ATAATTTTAATATAATTTTATTTTTCAAT
1 ATAATTTTAATATAATTTTATTTTAAAAT
1029367 ATAA-TTT-ATAT-ATTATTATTTTAAAAT
1 ATAATTTTAATATAATT-TTATTTTAAAAT
1029394 A
1 A
1029395 ATCGTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.12
27 15 0.60
28 3 0.12
29 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
ATAATTTTAATATAATTTTATTTTAAAAT
Found at i:1039484 original size:21 final size:22
Alignment explanation
Indices: 1039442--1039484 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1039432 TCCTAACATT
* * *
1039442 AACTTAAAACCTTTAATTATAA
1 AACTTAAAACCCTAAATCATAA
1039464 AACTT-AAACCCTAAATCATAA
1 AACTTAAAACCCTAAATCATAA
1039485 CCATATTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (22 bp):
AACTTAAAACCCTAAATCATAA
Found at i:1042799 original size:36 final size:36
Alignment explanation
Indices: 1042759--1042840 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
1042749 GTAATTTTTT
**
1042759 TTAAAAAATTGCATACAAAGAAAAATAATAATTGTA
1 TTAAAAAATTAAATACAAAGAAAAATAATAATTGTA
* *
1042795 TTAAAAAA-TAAATACAAAGTAAATTAATAATTGTA
1 TTAAAAAATTAAATACAAAGAAAAATAATAATTGTA
*
1042830 CTAAAAAATTA
1 TTAAAAAATTA
1042841 CAAAGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 30 0.75
36 10 0.25
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (36 bp):
TTAAAAAATTAAATACAAAGAAAAATAATAATTGTA
Found at i:1042851 original size:32 final size:33
Alignment explanation
Indices: 1042771--1042851 Score: 110
Period size: 35 Copynumber: 2.4 Consensus size: 33
1042761 AAAAAATTGC
* *
1042771 ATACAAAGAAAAATAATAATTGTATTAAAAAAT
1 ATACAAAGAAAATTAATAATTGTACTAAAAAAT
*
1042804 AAATACAAAGTAAATTAATAATTGTACTAAAAAAT
1 --ATACAAAGAAAATTAATAATTGTACTAAAAAAT
1042839 -TACAAAGAAAATT
1 ATACAAAGAAAATT
1042852 TATTTATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 12 0.29
35 30 0.71
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (33 bp):
ATACAAAGAAAATTAATAATTGTACTAAAAAAT
Found at i:1050639 original size:60 final size:60
Alignment explanation
Indices: 1050570--1050725 Score: 188
Period size: 60 Copynumber: 2.6 Consensus size: 60
1050560 AGTCACTGAT
* * * * *
1050570 TATTAAAAGTTATAAAATGATCATTCGATTATATAATGTTGTTTTTTTGAGTCCCTCAAC
1 TATTAAAAGTTATAAAATGATCATCCGATTATATAATGATGCTTTGTTGAGCCCCTCAAC
* * ** *
1050630 TATTAAAAGTTATAAAATGGTCCTCCGATTATATGGTGATGCTTTGTTGAGCCCCTCGAC
1 TATTAAAAGTTATAAAATGATCATCCGATTATATAATGATGCTTTGTTGAGCCCCTCAAC
* * *
1050690 TATTAAAAGTTACAAAATGATCACCCAATTAT-TAAT
1 TATTAAAAGTTATAAAATGATCATCCGATTATATAAT
1050726 ATATTCCAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 2 0.03
60 77 0.97
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (60 bp):
TATTAAAAGTTATAAAATGATCATCCGATTATATAATGATGCTTTGTTGAGCCCCTCAAC
Found at i:1052498 original size:2 final size:2
Alignment explanation
Indices: 1052491--1052516 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1052481 ATTTTATTAA
1052491 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
1052517 TACAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1057788 original size:29 final size:28
Alignment explanation
Indices: 1057755--1057987 Score: 252
Period size: 29 Copynumber: 8.0 Consensus size: 28
1057745 TCCTAAGCAA
* *
1057755 AATCAGGATGGGAAATAAATCCCATGCAG
1 AATCAGGACGGGATAT-AATCCCATGCAG
*
1057784 AATCAGGACGGGGATATAATCTCATGCAG
1 AATCAGGAC-GGGATATAATCCCATGCAG
* * * *
1057813 AATCAAGAAGATGATATAATCCCATGTAG
1 AATCAGGACG-GGATATAATCCCATGCAG
1057842 AATCAGGACGAGGATATAATCCCATGCAG
1 AATCAGGACG-GGATATAATCCCATGCAG
* *
1057871 AATCAAGACGGAGA-ATAAATCCCATGCAA
1 AATCAGGACGG-GATAT-AATCCCATGCAG
*
1057900 AATCAGGACGAGGATATAATCCTATGCAG
1 AATCAGGACG-GGATATAATCCCATGCAG
* *
1057929 AATCAGGACGGAGATATAATCCAATGCAA
1 AATCAGGACGG-GATATAATCCCATGCAG
* *
1057958 AATCATGATAGGGATATAATCCCATGCAG
1 AATCAGGA-CGGGATATAATCCCATGCAG
1057987 A
1 A
1057988 TGACAGAAAA
Statistics
Matches: 173, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
28 5 0.03
29 157 0.91
30 11 0.06
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (28 bp):
AATCAGGACGGGATATAATCCCATGCAG
Found at i:1057837 original size:58 final size:58
Alignment explanation
Indices: 1057772--1057987 Score: 285
Period size: 58 Copynumber: 3.7 Consensus size: 58
1057762 ATGGGAAATA
* * * *
1057772 AATCCCATGCAGAATCAGGACGGGGATATAATCTCATGCAGAATCAAGA-AGATGATAT
1 AATCCCATGCAAAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGA-GATAT
* *
1057830 AATCCCATGTAGAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGA-AT
1 AATCCCATGCAAAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATAT
* *
1057887 AAATCCCATGCAAAATCAGGACGAGGATATAATCCTATGCAGAATCAGGACGGAGATAT
1 -AATCCCATGCAAAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATAT
* * *
1057946 AATCCAATGCAAAATCATGA-TAGGGATATAATCCCATGCAGA
1 AATCCCATGCAAAATCAGGACGA-GGATATAATCCCATGCAGA
1057988 TGACAGAAAA
Statistics
Matches: 142, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.02
58 135 0.95
59 4 0.03
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (58 bp):
AATCCCATGCAAAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATAT
Found at i:1060499 original size:17 final size:17
Alignment explanation
Indices: 1060477--1060513 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1060467 GAATATGATC
1060477 TGAAAATGATTATAATA
1 TGAAAATGATTATAATA
*
1060494 TGAAAATGATTATGATA
1 TGAAAATGATTATAATA
1060511 TGA
1 TGA
1060514 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (17 bp):
TGAAAATGATTATAATA
Found at i:1064510 original size:18 final size:19
Alignment explanation
Indices: 1064487--1064523 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1064477 TTTATTAAAA
*
1064487 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
1064505 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
1064524 TTAAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.35, G:0.16, T:0.03
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:1064660 original size:5 final size:5
Alignment explanation
Indices: 1064650--1064676 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1064640 TTTGGTAAAA
1064650 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
1064677 TACACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:1064981 original size:19 final size:21
Alignment explanation
Indices: 1064922--1065020 Score: 98
Period size: 19 Copynumber: 4.8 Consensus size: 21
1064912 TTTATTTTAT
*
1064922 ATTATTAAAATATATTAGTTA
1 ATTATTAAAATATATTAATTA
**
1064943 ATTATTAAAATATAAAAATT-
1 ATTATTAAAATATATTAATTA
*
1064963 GTTA-TAAAATATATTAATTTA
1 ATTATTAAAATATATTAA-TTA
* *
1064984 ATTATTTAAAATATAATAAATA
1 ATTA-TTAAAATATATTAATTA
1065006 ATTA-T-AAATATATTA
1 ATTATTAAAATATATTA
1065021 TTATAAAATG
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
19 20 0.31
20 6 0.09
21 20 0.31
22 6 0.09
23 12 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTATTAAAATATATTAATTA
Found at i:1065015 original size:42 final size:40
Alignment explanation
Indices: 1064925--1065020 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 40
1064915 ATTTTATATT
*
1064925 ATTA-AAATATATT-AGTTAATTATTAAAATATAAAAATT
1 ATTATAAATATATTAAGTTAATTATTAAAATATAAAAATA
* *
1064963 GTTATAAAATATATTAATTTAATTATTTAAAATATAATAAATA
1 ATTAT-AAATATATTAAGTTAATTA-TTAAAATATAA-AAATA
1065006 ATTATAAATATATTA
1 ATTATAAATATATTA
1065021 TTATAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 3 0.06
40 9 0.18
41 8 0.16
42 21 0.43
43 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (40 bp):
ATTATAAATATATTAAGTTAATTATTAAAATATAAAAATA
Found at i:1070414 original size:21 final size:21
Alignment explanation
Indices: 1070390--1070432 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1070380 TATTTAAATT
*
1070390 AATTAATATATACCAAACATA
1 AATTAATAAATACCAAACATA
* *
1070411 AATTTATAAATATCAAACATA
1 AATTAATAAATACCAAACATA
1070432 A
1 A
1070433 TATCAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATACCAAACATA
Found at i:1070628 original size:23 final size:23
Alignment explanation
Indices: 1070600--1070684 Score: 152
Period size: 23 Copynumber: 3.7 Consensus size: 23
1070590 ATTTTAAAAA
*
1070600 TTAAAATGAAATATTTATTTATT
1 TTAAAATAAAATATTTATTTATT
*
1070623 TTAAAATAAAATATTTAGTTATT
1 TTAAAATAAAATATTTATTTATT
1070646 TTAAAATAAAATATTTATTTATT
1 TTAAAATAAAATATTTATTTATT
1070669 TTAAAATAAAATATTT
1 TTAAAATAAAATATTT
1070685 TTTCTAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATAAAATATTTATTTATT
Found at i:1070632 original size:46 final size:45
Alignment explanation
Indices: 1070582--1070684 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 45
1070572 ACATTAATTG
*
1070582 ATAAATACATTTTA-AAAATTAAAATGAAATATTTATTTATTTTAAA
1 ATAAA-ACA-TTTAGAAAATTAAAATAAAATATTTATTTATTTTAAA
* * **
1070628 ATAAAATATTTAGTTATTTTAAAATAAAATATTTATTTATTTTAAA
1 ATAAAACATTTAG-AAAATTAAAATAAAATATTTATTTATTTTAAA
*
1070674 ATAAAATATTT
1 ATAAAACATTT
1070685 TTTCTAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 4 0.08
45 2 0.04
46 44 0.88
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (45 bp):
ATAAAACATTTAGAAAATTAAAATAAAATATTTATTTATTTTAAA
Found at i:1072255 original size:81 final size:81
Alignment explanation
Indices: 1072120--1072282 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
1072110 GTTCCAAGTC
1072120 GTATAAAATGACATCTTCCTACATTCTTATCGATATTATTATAGAGTACACCGCTAAACTTAATA
1 GTATAAAATGACATCTTCCTACATTCTTATCGATATTATTATAGAGTACACCGCTAAACTTAATA
*
1072185 GTGTGGCCCTCCAATG
66 GTGTGACCCTCCAATG
1072201 GTATAAAATGACATCTTCCTACATTCTTATCGATATTATTATAGAGTACACCGCTAAACTTAATA
1 GTATAAAATGACATCTTCCTACATTCTTATCGATATTATTATAGAGTACACCGCTAAACTTAATA
1072266 GTGTGACCCTCCAATG
66 GTGTGACCCTCCAATG
1072282 G
1 G
1072283 GTGCGATTGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (81 bp):
GTATAAAATGACATCTTCCTACATTCTTATCGATATTATTATAGAGTACACCGCTAAACTTAATA
GTGTGACCCTCCAATG
Found at i:1074795 original size:13 final size:13
Alignment explanation
Indices: 1074777--1074807 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1074767 AGATGACCGA
1074777 TGGTTGGTAGTAT
1 TGGTTGGTAGTAT
1074790 TGGTTGGTAGTAT
1 TGGTTGGTAGTAT
*
1074803 GGGTT
1 TGGTT
1074808 AAATGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.45
Consensus pattern (13 bp):
TGGTTGGTAGTAT
Found at i:1077086 original size:18 final size:19
Alignment explanation
Indices: 1077050--1077086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1077040 TACGGAATGT
1077050 AAGATTATCAGTTAGAATAA
1 AAGATTATCAG-TAGAATAA
1077070 AAGATTATCAG-AGAATA
1 AAGATTATCAGTAGAATA
1077087 TGATTACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (19 bp):
AAGATTATCAGTAGAATAA
Found at i:1086016 original size:16 final size:17
Alignment explanation
Indices: 1085978--1086026 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1085968 TAACTTATCA
1085978 ATAAAATTAAATTAATG
1 ATAAAATTAAATTAATG
* *
1085995 ATAAAATTGATTTAAT-
1 ATAAAATTAAATTAATG
*
1086011 ATAAAAATCAAATTAA
1 AT-AAAATTAAATTAA
1086027 CCGAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAATTAAATTAATG
Found at i:1093361 original size:6 final size:6
Alignment explanation
Indices: 1093350--1093398 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
1093340 GACACGTATT
1093350 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1093398 A
1 A
1093399 TCCGAGCCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1099310 original size:5 final size:5
Alignment explanation
Indices: 1099300--1099363 Score: 92
Period size: 5 Copynumber: 12.8 Consensus size: 5
1099290 ACCACGACCA
* *
1099300 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* *
1099350 CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAG
1099364 ACGGACGGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.20, C:0.36, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:1104281 original size:57 final size:57
Alignment explanation
Indices: 1104193--1104307 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
1104183 AGCCAATTTC
1104193 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1104250 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1104307 T
1 T
1104308 CTATTGCACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
Found at i:1114601 original size:15 final size:16
Alignment explanation
Indices: 1114574--1114603 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1114564 AATTGTTTTT
1114574 TTATAATATAATATAG
1 TTATAATATAATATAG
1114590 TTATAA-ATAATATA
1 TTATAATATAATATA
1114604 TGTTGAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTATAATATAATATAG
Done.