Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007698.1 Hibiscus syriacus cultivar Beakdansim tig00109908_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: 347831
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:303115 original size:23 final size:23
Alignment explanation
Indices: 303085--303144 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
303075 ATTGTTCGTG
* *
303085 AACATGTTCGTTTAATGTTCACA
1 AACATGTTCATTTAACGTTCACA
*
303108 AACGTGTTCATTTAACGTTCACA
1 AACATGTTCATTTAACGTTCACA
303131 AACATGTTCATTTA
1 AACATGTTCATTTA
303145 GTATTTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
AACATGTTCATTTAACGTTCACA
Found at i:303701 original size:20 final size:19
Alignment explanation
Indices: 303672--303939 Score: 159
Period size: 20 Copynumber: 13.6 Consensus size: 19
303662 AAATAACCAA
303672 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* * **
303691 CCAATTTCGCAACTCAGTTTT
1 -CAAATTCGCAACGC-GAATT
* *
303712 CAATTTCACAACGCGAATAT
1 CAAATTCGCAACGCGAAT-T
* ** *
303732 GTAAA-TCGCATTGCGATTTT
1 -CAAATTCGCAACGCGA-ATT
*
303752 CCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGA-ATT
*
303773 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ATT
** * *
303793 CAAATTCGCAATACAAAAGT
1 CAAATTCGCAACGC-GAATT
*
303813 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ATT
*
303833 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAA-TT
*
303852 CAAATTCGCAAC-TGAATT
1 CAAATTCGCAACGCGAATT
*
303870 GCAAATTCGCAAC-TGAATTT
1 -CAAATTCGCAACGCGAA-TT
* *
303890 CAAATTCACAAC-TGAATTT
1 CAAATTCGCAACGCGAA-TT
303909 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* *
303928 TAATTTCGCAAC
1 CAAATTCGCAAC
303940 AGGTTTTAGT
Statistics
Matches: 204, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
18 3 0.01
19 79 0.39
20 104 0.51
21 18 0.09
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (19 bp):
CAAATTCGCAACGCGAATT
Found at i:303856 original size:19 final size:19
Alignment explanation
Indices: 303832--303939 Score: 164
Period size: 19 Copynumber: 5.7 Consensus size: 19
303822 AACGCGATAG
303832 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
303851 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
303870 GCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
303889 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
*
303908 TCAAATTCGCAACGCGAATT
1 TCAAATTCGCAAC-TGAATT
*
303928 T-AATTTCGCAAC
1 TCAAATTCGCAAC
303940 AGGTTTTAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 76 0.93
20 6 0.07
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:304708 original size:12 final size:12
Alignment explanation
Indices: 304687--304720 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
304677 ACCATATTTT
*
304687 CAATACCAAACA
1 CAATATCAAACA
304699 CAATATCAAACA
1 CAATATCAAACA
*
304711 CAATCTCAAA
1 CAATATCAAA
304721 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:305082 original size:3 final size:3
Alignment explanation
Indices: 305074--305104 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
305064 ATATAACCTT
*
305074 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
305105 TCCCCGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:307038 original size:64 final size:64
Alignment explanation
Indices: 306953--307112 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 64
306943 TTGTTTAAGG
* * ** *
306953 TGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAA-AGCATTTT
307016 A
64 A
* * * *
307017 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAACGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAAAGCATTTTA
* *
307081 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
307113 ACATTCATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.02
64 73 0.89
65 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAAAGCATTTTA
Found at i:307623 original size:17 final size:19
Alignment explanation
Indices: 307601--307636 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
307591 GATTTACATG
307601 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
307618 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
307637 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:307810 original size:31 final size:30
Alignment explanation
Indices: 307771--307844 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
307761 GTCGAGGGTT
**
307771 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
307801 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
*
307832 TTACCTAGGTTCT
1 TTACCTATGTTCT
307845 TTGGGACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.32
31 21 0.55
32 5 0.13
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:307857 original size:30 final size:30
Alignment explanation
Indices: 307792--307896 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
307782 TTTCGAGACA
* ** * *
307792 TATGGACAGTATACCTATGTTCTAAGGAACA
1 TATGGACAGT-TACCTAGGTTCTTTGGGACC
307823 TATGGACAGTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTACCTAGGTTCTTTGGGACC
* * * **
307853 TATGGATAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCTAGGTTCTTTGGGACC
* *
307883 TCTGGATAGTTACC
1 TATGGACAGTTACC
307897 GGGGTCTGTG
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
30 52 0.84
31 10 0.16
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCTAGGTTCTTTGGGACC
Found at i:307915 original size:29 final size:30
Alignment explanation
Indices: 307849--307920 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
307839 GGTTCTTTGG
* * * *
307849 GACCTATGGATAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTGTAT
*
307879 GACCTCTGGATAGTTACCG-GGGTCTGTGT
1 GACCTCTGGATAGTTACCGAGGGTCTGTAT
307908 GACCTCTGGATAG
1 GACCTCTGGATAG
307921 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTGTAT
Found at i:310810 original size:64 final size:64
Alignment explanation
Indices: 310725--310884 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 64
310715 TTGTTTAAGG
* * ** *
310725 TGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTTT
310788 A
64 A
* * *
310789 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTTA
* **
310853 TGCACCGATGCACAAATAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
310885 ACATTCATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.02
64 73 0.89
65 7 0.09
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTTA
Found at i:311618 original size:30 final size:30
Alignment explanation
Indices: 311563--311648 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
311553 GTCTTTCGAG
* *
311563 ACATATGGACAATATACCTATGTTCTAAGGA
1 ACATATGGACAGT-TACCTAGGTTCTAAGGA
** *
311594 ACATATGGACAGTTACCTAGGTTCTTTGGG
1 ACATATGGACAGTTACCTAGGTTCTAAGGA
* * *
311624 ACCTATGGACAGTTGCCGAGGTTCT
1 ACATATGGACAGTTACCTAGGTTCT
311649 TTATGACCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 35 0.74
31 12 0.26
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (30 bp):
ACATATGGACAGTTACCTAGGTTCTAAGGA
Found at i:311657 original size:30 final size:30
Alignment explanation
Indices: 311597--311671 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
311587 CTAAGGAACA
* *
311597 TATGGACAGTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
311627 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
311657 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
311672 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:314345 original size:15 final size:15
Alignment explanation
Indices: 314325--314357 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
314315 ATGGATATTG
314325 GTTCAAGTTATAGTA
1 GTTCAAGTTATAGTA
314340 GTTCAAGTTATAGTA
1 GTTCAAGTTATAGTA
314355 GTT
1 GTT
314358 GAGTTTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (15 bp):
GTTCAAGTTATAGTA
Found at i:314594 original size:64 final size:64
Alignment explanation
Indices: 314509--314668 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 64
314499 TTGTTTAAGG
* * ** *
314509 TGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTTT
314572 A
64 A
* * *
314573 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTTA
* **
314637 TGCACCGATGCACAAATAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
314669 ACATTCATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.02
64 73 0.89
65 7 0.09
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTTA
Found at i:315179 original size:17 final size:19
Alignment explanation
Indices: 315157--315192 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
315147 GATTTACATG
315157 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
315174 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
315193 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:317506 original size:20 final size:20
Alignment explanation
Indices: 317482--317547 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
317472 ATTGCAAACT
*
317482 GAATTTGACTTTCGCGTTGT
1 GAATTTGACTTTCGCGTTGC
* *
317502 GAATTTGACTATCGCGTAGC
1 GAATTTGACTTTCGCGTTGC
* *
317522 GAATTTAACTTTCGTGTTGC
1 GAATTTGACTTTCGCGTTGC
317542 GAATTT
1 GAATTT
317548 ACCTTCAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:318051 original size:18 final size:18
Alignment explanation
Indices: 318030--318066 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
318020 GTAATTGGAG
318030 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
318048 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
318066 T
1 T
318067 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:318073 original size:24 final size:24
Alignment explanation
Indices: 318022--318074 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
318012 TTTCATATGT
* * *
318022 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
318046 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
318070 AATTT
1 AATTT
318075 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:318429 original size:39 final size:39
Alignment explanation
Indices: 318379--318465 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
318369 TCTGATGCTC
*
318379 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
*
318418 ATCAGAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
318457 ATCAAAATC
1 ATCAAAATC
318466 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:318733 original size:20 final size:20
Alignment explanation
Indices: 318708--318749 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
318698 ACCGAAAATT
* *
318708 GCGTTGTGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
318728 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
318748 GC
1 GC
318750 AACGCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:318934 original size:66 final size:60
Alignment explanation
Indices: 318854--318993 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
318844 TTTTAGAAAC
*
318854 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
318919 A
60 A
* * **
318920 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
318980 AACAAATCAACTTT
1 AACAAATCAACTTT
318994 CAATATAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.30
62 3 0.04
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:320440 original size:21 final size:21
Alignment explanation
Indices: 320369--320471 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
320359 GGCGGGACCA
* *
320369 CTTGAACGATGATAGAG-GCCT
1 CTTGAATGATGAGAG-GTGCCT
* * * *
320390 CTTGAACGGTGAGAGGGGCTT
1 CTTGAATGATGAGAGGTGCCT
320411 CTTTG-ATGATGAGAGGTGCCT
1 C-TTGAATGATGAGAGGTGCCT
*
320432 CTTGAATGAT-AGGAGGCGCCT
1 CTTGAATGATGA-GAGGTGCCT
* *
320453 CATGAATGATGATAGGTGC
1 CTTGAATGATGAGAGGTGC
320472 ATCGGGCTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
20 5 0.08
21 57 0.86
22 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (21 bp):
CTTGAATGATGAGAGGTGCCT
Found at i:322451 original size:20 final size:20
Alignment explanation
Indices: 322417--322463 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
322407 AATCGCAACG
322417 CGATTTT-AGTTTCGCGTTA
1 CGATTTTCAGTTTCGCGTTA
*
322436 CGATTTTCATTTTCGCGTTA
1 CGATTTTCAGTTTCGCGTTA
*
322456 TGATTTTC
1 CGATTTTC
322464 GTGTTGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTA
Found at i:322760 original size:22 final size:22
Alignment explanation
Indices: 322726--322783 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
322716 TCTGAGAGAT
*
322726 GGAAAT-A-GACGGATTTTGTC
1 GGAAATGAGGACGGATTTCGTC
322746 GGAAATGAGGACGGATTTCGTC
1 GGAAATGAGGACGGATTTCGTC
* *
322768 GGAGATGGGGACGGAT
1 GGAAATGAGGACGGAT
322784 GTCGCCGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 26 0.79
ACGTcount: A:0.28, C:0.10, G:0.40, T:0.22
Consensus pattern (22 bp):
GGAAATGAGGACGGATTTCGTC
Found at i:322936 original size:20 final size:20
Alignment explanation
Indices: 322911--323115 Score: 148
Period size: 20 Copynumber: 10.2 Consensus size: 20
322901 GCGTAAAAAC
*
322911 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
322931 ATTTGACTATTGCGTTACGA
1 ATTTGACTATCGCGTTGCGA
322951 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
** *
322971 ATTTGACT-TCTATGTTGTGA
1 ATTTGACTATC-GCGTTGCGA
*
322991 ATTTGACTATCGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
** ***
323011 ATTTTGAAAATCGCAACGCGA
1 A-TTTGACTATCGCGTTGCGA
*
323032 ATTTGACTATCTCGTTGCGAA
1 ATTTGACTATCGCGTTGCG-A
* * * *
323053 ATTGGA-AATTGGGTTGCGAA
1 ATTTGACTATCGCGTTGCG-A
* * * *
323073 ATTGGAAT-TTGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
*
323092 ATTTGA-GATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
323111 ATTTG
1 ATTTG
323116 TTGGTCATTT
Statistics
Matches: 145, Mismatches: 34, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
19 22 0.15
20 101 0.70
21 22 0.15
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:332679 original size:19 final size:20
Alignment explanation
Indices: 332634--332677 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
332624 ATCATCCAAT
*
332634 TTTTTAAACCTCATACCGGA
1 TTTTTAAACCTCAGACCGGA
332654 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCTCAGACCGGA
332674 TTTT
1 TTTT
332678 AATCCGGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTTAAACCTCAGACCGGA
Found at i:333612 original size:16 final size:18
Alignment explanation
Indices: 333591--333623 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
333581 CATAATAAGA
333591 ATTATGA-AT-ATTTTTT
1 ATTATGAGATCATTTTTT
333607 ATTATGAGATCATTTTT
1 ATTATGAGATCATTTTT
333624 CGTATCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTATGAGATCATTTTTT
Found at i:337012 original size:18 final size:18
Alignment explanation
Indices: 336989--337025 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
336979 GTGTTGAGAC
336989 TAAACTACCCATGAAATT
1 TAAACTACCCATGAAATT
337007 TAAACTACCCATGAAATT
1 TAAACTACCCATGAAATT
337025 T
1 T
337026 GGGACCGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAACTACCCATGAAATT
Found at i:337351 original size:3 final size:3
Alignment explanation
Indices: 337343--337377 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
337333 TTTATTTTAC
337343 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
337378 GAGAAAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:337639 original size:20 final size:20
Alignment explanation
Indices: 337614--337667 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
337604 AATTGGGAAA
337614 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
337634 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
337654 ATCGCAATGCGATA
1 ATCGCAATGCGATA
337668 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:338263 original size:19 final size:19
Alignment explanation
Indices: 338225--338291 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
338215 TTCGAGAATG
338225 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
338245 ACTATCGCAATGCGAAATA
1 AAAATCGCAACGCGAAATA
**
338264 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
338283 AAAATCGCA
1 AAAATCGCA
338292 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:338328 original size:14 final size:14
Alignment explanation
Indices: 338309--338397 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
338299 TTTCATTTCG
338309 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
338323 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
338342 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
338356 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
338375 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
338389 CGTTGCGAT
1 CGTTGCGAT
338398 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 30 0.49
16 5 0.08
17 5 0.08
19 21 0.34
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:338334 original size:33 final size:33
Alignment explanation
Indices: 338292--338421 Score: 215
Period size: 33 Copynumber: 3.9 Consensus size: 33
338282 CAAAATCGCA
**
338292 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
**
338325 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
338358 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
338391 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
338422 ATTATCTCGT
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 79 0.84
34 15 0.16
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:340545 original size:21 final size:21
Alignment explanation
Indices: 340486--340546 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
340476 CTCGAGAGTC
340486 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
340507 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
340528 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
340547 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:344802 original size:3 final size:3
Alignment explanation
Indices: 344794--344829 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
344784 CAATATGTAA
344794 AAT AAT AAT AAT AAT AAT AAT ACAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
344830 GAACGAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:345133 original size:47 final size:47
Alignment explanation
Indices: 345063--345439 Score: 317
Period size: 48 Copynumber: 8.3 Consensus size: 47
345053 CCGCTGTCAC
* * *
345063 AGGGAATA-CAAACCTTGGAAAAAGAGATATGTTCCGCTT-CTTCTGA
1 AGGGAATATCAAATCTTGGAAAAAGAGATCTGTTCCACTTAC-TCTGA
* *
345109 AGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAGAGATCTGTTCCACTTACTCTGA
* * * *
345156 AGGGAATGTCAGATC-TGG---TAGA-CT-TGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAAAAAGAGATCTGTTCCACTTACTCTGA
* * *
345197 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGA-AAAAGAGATCTGTTCCACTTACTCTGA
* * * * *
345245 AGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGA-AAAAGAGATCTGTTCCACTTACTCTGA
* * * *
345293 AGGGAATATCAAATCTTTGAGAAGAGAGACCTGTT-C-C--GCTCTGA
1 AGGGAATATCAAATCTTGGA-AAAAGAGATCTGTTCCACTTACTCTGA
* * * *
345337 A--GAATATCAGATC-TGG---CAGA-CT-TGTTCCACTTACTCTAA
1 AGGGAATATCAAATCTTGGAAAAAGAGATCTGTTCCACTTACTCTGA
* *
345376 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGA-AAAAGAGATCTGTTCCACTTACTCTGA
*
345424 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
345440 GGGGGAGTTG
Statistics
Matches: 267, Mismatches: 42, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
35 4 0.01
36 1 0.00
37 4 0.01
39 6 0.02
41 43 0.16
42 17 0.06
43 3 0.01
44 7 0.03
46 18 0.07
47 45 0.17
48 119 0.45
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (47 bp):
AGGGAATATCAAATCTTGGAAAAAGAGATCTGTTCCACTTACTCTGA
Found at i:345360 original size:179 final size:182
Alignment explanation
Indices: 345087--345439 Score: 536
Period size: 179 Copynumber: 1.9 Consensus size: 182
345077 TTGGAAAAAG
*
345087 AGATATGTTCCGCTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACT
1 AGATATGTTCCACTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCAC-TACT
* * *
345152 CTGAAGGGAATGTCAGATCTGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA
65 CTGAA-GGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGA
*
345217 GAAGAGAGACCTGTTCCGCTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
129 GAAGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
* * * * *
345271 AGATTTGTTCCACTTAC-TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTT-C-C-GC
1 AGATATGTTCCACTT-CTTCTGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTAC
345332 TCTGAA-GAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGA
64 TCTGAAGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGA
*
345396 GAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
129 GAAGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCT
345440 GGGGGAGTTG
Statistics
Matches: 156, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
179 97 0.62
181 7 0.04
183 1 0.01
184 37 0.24
185 14 0.09
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (182 bp):
AGATATGTTCCACTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTACTC
TGAAGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGA
AGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
Found at i:346818 original size:16 final size:17
Alignment explanation
Indices: 346797--346830 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
346787 CCCTTATCTA
346797 CGTTTCTGGT-CATTTG
1 CGTTTCTGGTACATTTG
346813 CGTTTCTGGTACATTTG
1 CGTTTCTGGTACATTTG
346830 C
1 C
346831 CCATAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.47
Consensus pattern (17 bp):
CGTTTCTGGTACATTTG
Done.