Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009068.1 Hibiscus syriacus cultivar Beakdansim tig00112495_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: 670922
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:531045 original size:28 final size:28
Alignment explanation
Indices: 530983--531046 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
530973 ATATGAAATG
* *
530983 ATATATGAATATGCAATACATGATACAT
1 ATATATGAATATGAAATACATGATACAC
* *
531011 GTGATATG-ATATGAAATACATGGTTACAC
1 AT-ATATGAATATGAAATACAT-GATACAC
531040 ATATATG
1 ATATATG
531047 TGGTATGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (28 bp):
ATATATGAATATGAAATACATGATACAC
Found at i:532091 original size:39 final size:35
Alignment explanation
Indices: 532023--532106 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
532013 TAAAAATAAT
*
532023 AATTATTATATATATATAATATTTAATTTAATTTA
1 AATTAATATATATATATAATATTTAATTTAATTTA
*
532058 AATTAATATATATATATATATATTT-ATAT-ATTTA
1 AATTAATATATATATATA-ATATTTAATTTAATTTA
*
532092 ATTTAA-ATATATATA
1 AATTAATATATATATA
532107 ACGGGCTCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 9 0.20
34 10 0.22
35 20 0.44
36 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
AATTAATATATATATATAATATTTAATTTAATTTA
Found at i:534570 original size:2 final size:2
Alignment explanation
Indices: 534563--534592 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
534553 CATTACAATT
534563 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
534593 GAATGATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:534996 original size:18 final size:17
Alignment explanation
Indices: 534949--534997 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
534939 TTTAGTTCAC
*
534949 AAAATATAAGATTACCG
1 AAAAAATAAGATTACCG
*
534966 AAAAAATAGGATTACCG
1 AAAAAATAAGATTACCG
**
534983 ACAGGAATAAGATTA
1 A-AAAAATAAGATTA
534998 TTGTGAATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.20
Consensus pattern (17 bp):
AAAAAATAAGATTACCG
Found at i:543578 original size:24 final size:24
Alignment explanation
Indices: 543527--543581 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
543517 TTATTTGAAA
*
543527 AAAAGAAATAAAAGTTTAAGGGTC
1 AAAAGAAATAAAAGTTTAAGGATC
543551 AAAAGAGAA-AAAAGTTTAAAGGAT-
1 AAAAGA-AATAAAAGTTT-AAGGATC
543575 AAAAGAA
1 AAAAGAA
543582 CTTTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 20 0.71
25 7 0.25
ACGTcount: A:0.62, C:0.02, G:0.20, T:0.16
Consensus pattern (24 bp):
AAAAGAAATAAAAGTTTAAGGATC
Found at i:553391 original size:34 final size:34
Alignment explanation
Indices: 553342--553424 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
553332 GTGAATGAAA
* *
553342 TTTGAGA-TTAGAGTTACGAATTTGAGTATTATGT
1 TTTGAGATTTA-AGTTACGAATTCGAGTATTATGC
* * *
553376 TTTGATATTTAAGTTATGGATTCGAGTATTATGC
1 TTTGAGATTTAAGTTACGAATTCGAGTATTATGC
553410 TTTGAGATTTAAGTT
1 TTTGAGATTTAAGTT
553425 TTGATTTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 39 0.93
35 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.47
Consensus pattern (34 bp):
TTTGAGATTTAAGTTACGAATTCGAGTATTATGC
Found at i:559854 original size:23 final size:23
Alignment explanation
Indices: 559782--559858 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
559772 ATAACAGTGT
*
559782 ATCGATGCA-TCCTTGAATGTGC
1 ATCGATGCACACCTTGAATGTGC
* * *
559804 ATCGAT--ACACCATGAAGGTGG
1 ATCGATGCACACCTTGAATGTGC
*
559825 A-CTGATGCACGCCTTGAATGTGC
1 ATC-GATGCACACCTTGAATGTGC
559848 ATCGATGCACA
1 ATCGATGCACA
559859 AGGCCGTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 6 0.15
23 19 0.46
24 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (23 bp):
ATCGATGCACACCTTGAATGTGC
Found at i:561445 original size:36 final size:36
Alignment explanation
Indices: 561405--561507 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
561395 ACGGTGCTGG
561405 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
561441 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
561477 ACATTGATACAAGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
561508 ATACTCAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:569523 original size:36 final size:36
Alignment explanation
Indices: 569483--569585 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
569473 ACGGTGCTGG
569483 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
569519 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
569555 ACATTGATACAAGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
569586 ATACTCAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:574820 original size:19 final size:19
Alignment explanation
Indices: 574786--574822 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
574776 TTGAAGATTG
574786 TTGATAAAAATAACATTAT
1 TTGATAAAAATAACATTAT
574805 TTGAGTAAAAAT-ACATTA
1 TTGA-TAAAAATAACATTA
574823 CGTAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
TTGATAAAAATAACATTAT
Found at i:583804 original size:21 final size:21
Alignment explanation
Indices: 583778--583818 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
583768 AAATAATTAA
583778 AATTAGACTAA-TAAAAATAAT
1 AATTAGA-TAATTAAAAATAAT
583799 AATTAGATAATTTAAAAATA
1 AATTAGATAA-TTAAAAATA
583819 TTTGAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
AATTAGATAATTAAAAATAAT
Found at i:587524 original size:31 final size:30
Alignment explanation
Indices: 587486--587607 Score: 111
Period size: 31 Copynumber: 4.0 Consensus size: 30
587476 AGTCGAAGGT
587486 TTACCTATGTTCTACGGAACATATGGACGAA
1 TTACCTATGTTCTACGGAACATATGGAC-AA
* * *
587517 TTACCTATG-TCTTTCGGGACATATGGACAG
1 TTACCTATGTTC-TACGGAACATATGGACAA
* * *
587547 TATACCTATGTTCTAAGGAGCATATGGACATT
1 T-TACCTATGTTCTACGGAACATATGGACA-A
* * * *
587579 TTACCTAGGTTCTTCGGGACCTATGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
587608 GTTTTCGAGG
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 4 0.05
31 66 0.90
32 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTACGGAACATATGGACAA
Found at i:587584 original size:62 final size:62
Alignment explanation
Indices: 587487--587609 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
587477 GTCGAAGGTT
* *
587487 TACCTATGTTCTACGGAACATATGGACGAATTACCTATG-TCTTTCGGGACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACGAATTACCTAGGTTC-TTCGGGACATATGGACAGTA
* * *
587549 TACCTATGTTCTAAGGAGCATATGGAC-ATTTTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACGA-ATTACCTAGGTTCTTCGGGACATATGGACAGT
587610 TTTCGAGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 1 0.02
62 51 0.94
63 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACGAATTACCTAGGTTCTTCGGGACATATGGACAGTA
Found at i:588891 original size:19 final size:22
Alignment explanation
Indices: 588853--588897 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
588843 AAATTTCAAA
*
588853 ATTTATTAATAAATTTAATAGT
1 ATTTATTAATAAATTTAATAAT
588875 ATTTATT-AT-AA-TTAATAAT
1 ATTTATTAATAAATTTAATAAT
588894 ATTT
1 ATTT
588898 TTAGTAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 2 0.09
22 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTATTAATAAATTTAATAAT
Found at i:589177 original size:19 final size:19
Alignment explanation
Indices: 589153--589193 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
589143 AATAATAGCT
*
589153 TTAATAGTATTTATTA-TAA
1 TTAATAATATTT-TTAGTAA
589172 TTAATAATATTTTTAGTAA
1 TTAATAATATTTTTAGTAA
589191 TTA
1 TTA
589194 TTTTAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATAATATTTTTAGTAA
Found at i:591730 original size:36 final size:36
Alignment explanation
Indices: 591649--591793 Score: 206
Period size: 36 Copynumber: 4.1 Consensus size: 36
591639 AGATGAACAA
*
591649 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCTTC
*
591684 TTGAATCGAAAGTGAC-GATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTCTTC
*
591720 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATT-
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTC-TTC
* *
591756 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCTTC
591792 TT
1 TT
591794 ATTCACCTTC
Statistics
Matches: 100, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
35 33 0.33
36 65 0.65
37 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCTTC
Found at i:591790 original size:72 final size:71
Alignment explanation
Indices: 591649--591793 Score: 247
Period size: 72 Copynumber: 2.0 Consensus size: 71
591639 AGATGAACAA
*
591649 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGACGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGACGATGCTTCCTTTCG
591714 TTCTTC
66 TTCTTC
*
591720 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAATCGAAAGTG-CTGATGCTTCCTTT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-CTTGAATCGAAAGTGAC-GATGCTTCCTTT
591784 CGTTCTTC
64 CGTTCTTC
591792 TT
1 TT
591794 ATTCACCTTC
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 34 0.49
72 36 0.51
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGACGATGCTTCCTTTCG
TTCTTC
Found at i:594764 original size:2 final size:2
Alignment explanation
Indices: 594757--594789 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
594747 CTTTTTAAAA
594757 AT AT 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 AT AT A
594790 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:594838 original size:24 final size:24
Alignment explanation
Indices: 594789--594838 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
594779 ATATATATAT
* *
594789 AATTTTTAAAATTTTAAAGAAATA
1 AATTTATAAAATTATAAAGAAATA
* *
594813 AATTTATAAAATTATAAGGAAGTA
1 AATTTATAAAATTATAAAGAAATA
594837 AA
1 AA
594839 AATATATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (24 bp):
AATTTATAAAATTATAAAGAAATA
Found at i:594922 original size:2 final size:2
Alignment explanation
Indices: 594915--594942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
594905 AGTCAAACTA
594915 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
594943 TTATTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:596278 original size:14 final size:14
Alignment explanation
Indices: 596261--596290 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
596251 ATTATTTTAA
596261 AATTATAATTCATT
1 AATTATAATTCATT
*
596275 AATTATAATTTATT
1 AATTATAATTCATT
596289 AA
1 AA
596291 CTGTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATAATTCATT
Found at i:601450 original size:26 final size:26
Alignment explanation
Indices: 601387--601453 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
601377 GCGACGAAGT
*
601387 CTTCTAGAAACCGCCGCTAACTGGAC
1 CTTCTAGAAACTGCCGCTAACTGGAC
*
601413 CTTCTAGAAACTGCCGCTGACTGGAC
1 CTTCTAGAAACTGCCGCTAACTGGAC
601439 CTTCTAGAAACTGCC
1 CTTCTAGAAACTGCC
601454 ACGTCAGACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (26 bp):
CTTCTAGAAACTGCCGCTAACTGGAC
Found at i:603120 original size:18 final size:18
Alignment explanation
Indices: 603099--603139 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
603089 TTCGTCCCGA
*
603099 AGGACCACTATGTCCCAT
1 AGGACCACTACGTCCCAT
*
603117 AGGACCACTACGTCCCGT
1 AGGACCACTACGTCCCAT
603135 AGGAC
1 AGGAC
603140 TACGTCCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (18 bp):
AGGACCACTACGTCCCAT
Found at i:603143 original size:15 final size:15
Alignment explanation
Indices: 603123--603155 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
603113 CCATAGGACC
*
603123 ACTACGTCCCGTAGG
1 ACTACGTCCCGAAGG
603138 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
603153 ACT
1 ACT
603156 TCTCCTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:603384 original size:29 final size:29
Alignment explanation
Indices: 603341--603420 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
603331 TTTTATATGT
603341 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
603369 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
603398 TCATGTAGCTCATGTCATTTCTC
1 TCATGTAGCTCATGTCATTTCTC
603421 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:604579 original size:64 final size:62
Alignment explanation
Indices: 604508--604664 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 62
604498 TAATGAAGGT
* **
604508 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGCATTCGATG-TTGTATTATTAATGG
1 ATGCATCGATGCACTACT-ATGCATCGATGCACT-AAATGCATTCGATGTTTGTATT-TTAA-AA
604571 G
62 G
* * *
604572 ATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACTAC-TATGCATCGATGCACTAAATGCATTCGATGTTTGTATTTTAAAAG
604635 AGTGCATCGATGCACTACCTATGCATCGAT
1 A-TGCATCGATGCACTA-CTATGCATCGAT
604665 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.02
64 70 0.86
65 9 0.11
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTATGCATCGATGCACTAAATGCATTCGATGTTTGTATTTTAAAAG
Found at i:608111 original size:18 final size:18
Alignment explanation
Indices: 608087--608135 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
608077 GTTCAGTATT
608087 CGTCCCGAAGGACCACTA
1 CGTCCCGAAGGACCACTA
* *
608105 TGTCCCGTAGGACCACTA
1 CGTCCCGAAGGACCACTA
608123 CGTCCCGAAGGAC
1 CGTCCCGAAGGAC
608136 TTCTCCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.14
Consensus pattern (18 bp):
CGTCCCGAAGGACCACTA
Found at i:608365 original size:29 final size:29
Alignment explanation
Indices: 608322--608401 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
608312 TTTTATATGT
*
608322 TCATGTA-CTCATGTCATTTCTTTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
608350 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
608379 TCATGTAGCTCATGTCATTTCTC
1 TCATGTAGCTCATGTCATTTCTC
608402 ATATCACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.47
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:609580 original size:19 final size:19
Alignment explanation
Indices: 609556--609603 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
609546 TATTAATGGG
609556 ATGCATCGATGCACT-CCTT
1 ATGCATCGATGCACTACC-T
609575 ATGCATCGATGCACTACCT
1 ATGCATCGATGCACTACCT
*
609594 GTGCATCGAT
1 ATGCATCGAT
609604 ACACCTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTACCT
Found at i:610518 original size:20 final size:20
Alignment explanation
Indices: 610486--610539 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
610476 TTGCATAAAT
610486 CATCAATCAAGTTAGATTTAC
1 CATCAA-CAAGTTAGATTTAC
*
610507 CATCAACAAGTTCGATTTAC
1 CATCAACAAGTTAGATTTAC
610527 CATCAACAAGTTA
1 CATCAACAAGTTA
610540 AAAAATGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (20 bp):
CATCAACAAGTTAGATTTAC
Found at i:620980 original size:5 final size:5
Alignment explanation
Indices: 620970--621161 Score: 327
Period size: 5 Copynumber: 38.2 Consensus size: 5
620960 TCATTTTCTA
620970 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-ATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
621020 ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAAT AATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT -ATAAT ATAAT ATAAT
621070 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
621120 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATCAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT A
621162 CCATGCATTC
Statistics
Matches: 180, Mismatches: 0, Indels: 13
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.01
4 3 0.02
5 162 0.90
6 11 0.06
7 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:635197 original size:2 final size:2
Alignment explanation
Indices: 635190--635214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
635180 TTCAAACATT
635190 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
635215 GAGATATTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:637436 original size:31 final size:31
Alignment explanation
Indices: 637401--637465 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
637391 TCCCTTAAGT
637401 AATGTCAGATGTTCGAATCATGATATGTT-CG
1 AATGTCAGATGTTCGAATCATGATAT-TTGCG
* *
637432 AATGTCAGATGTTTGAATTATGATATTTGCG
1 AATGTCAGATGTTCGAATCATGATATTTGCG
637463 AAT
1 AAT
637466 TGGGGTGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (31 bp):
AATGTCAGATGTTCGAATCATGATATTTGCG
Found at i:642601 original size:11 final size:11
Alignment explanation
Indices: 642585--642617 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
642575 ACGGGACTTG
642585 AAGTTATATGT
1 AAGTTATATGT
642596 AAGTTATATGT
1 AAGTTATATGT
642607 AAGTTATATGT
1 AAGTTATATGT
642618 TAAGCAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (11 bp):
AAGTTATATGT
Found at i:648136 original size:2 final size:2
Alignment explanation
Indices: 648129--648162 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
648119 TATCATTGGA
648129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
648163 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:648166 original size:8 final size:9
Alignment explanation
Indices: 648128--648168 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
648118 ATATCATTGG
648128 AATATATAT
1 AATATATAT
648137 ATATATATAT
1 A-ATATATAT
648147 ATATATATAT
1 A-ATATATAT
648157 AATATA-AT
1 AATATATAT
648165 AATA
1 AATA
648169 ATAATTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 6 0.19
9 6 0.19
10 19 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATATATAT
Found at i:656187 original size:48 final size:51
Alignment explanation
Indices: 656131--656230 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 51
656121 GATGTTGAGT
* *
656131 TAGGTTAGGTTGTG-A-C-GGTGTATGAGTCTCGAATACACAAGCACAAGA
1 TAGGTTAGGTGGTGAAGCAGGTGAATGAGTCTCGAATACACAAGCACAAGA
*
656179 TAGGTTAGGTGGTGACAATGCAGGTGAATGAGTCTCGAATACACGAGCACAA
1 TAGGTTAGGTGGTG--AA-GCAGGTGAATGAGTCTCGAATACACAAGCACAA
656231 ACAAGCTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
48 13 0.30
51 1 0.02
53 1 0.02
54 28 0.65
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (51 bp):
TAGGTTAGGTGGTGAAGCAGGTGAATGAGTCTCGAATACACAAGCACAAGA
Found at i:661619 original size:31 final size:31
Alignment explanation
Indices: 661550--661619 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
661540 TTTTTATAAG
* **
661550 TTATAAAATGATCATTAAATTTATTGAATTA
1 TTATAAAATGATCATTAAATATATTGAACAA
*
661581 TTTTAAAATGATCATTACAATA-ATAT-AACAA
1 TTATAAAATGATCATTA-AATATAT-TGAACAA
661612 TTATAAAA
1 TTATAAAA
661620 ATTTAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (31 bp):
TTATAAAATGATCATTAAATATATTGAACAA
Found at i:661647 original size:31 final size:30
Alignment explanation
Indices: 661612--661697 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
661602 AATATAACAA
*
661612 TTATAAAAATTTAATAAATTTAATAATAATT
1 TTATAAAAATTTGATAAATTTAATAAT-ATT
* * *
661643 TTATAAAAA-ATGATAAATTAAATGACTATT
1 TTATAAAAATTTGATAAATTTAAT-AATATT
*
661673 TTATAAATATTTGATAAATTTAATA
1 TTATAAAAATTTGATAAATTTAATA
661698 GTTTTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 23 0.50
31 23 0.50
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (30 bp):
TTATAAAAATTTGATAAATTTAATAATATT
Found at i:661706 original size:31 final size:30
Alignment explanation
Indices: 661612--661707 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
661602 AATATAACAA
* * *
661612 TTATAAAAATTTAATAAATTTAATAATAATT
1 TTAT-AAAATTTGATAAATTTAATAGTTATT
** * *
661643 TTATAAAAAATGATAAATTAAAT-GACTATT
1 TTATAAAATTTGATAAATTTAATAG-TTATT
*
661673 TTATAAATATTTGATAAATTTAATAGTTTTT
1 TTATAAA-ATTTGATAAATTTAATAGTTATT
661704 TTAT
1 TTAT
661708 TTAAAAATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
30 25 0.50
31 24 0.48
32 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (30 bp):
TTATAAAATTTGATAAATTTAATAGTTATT
Found at i:661761 original size:18 final size:19
Alignment explanation
Indices: 661727--661765 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
661717 AAAAGACAAA
*
661727 TAATTATTTGAATGTAATT
1 TAATGATTTGAATGTAATT
661746 TAATGATTTG-ATGTAATT
1 TAATGATTTGAATGTAATT
661764 TA
1 TA
661766 CACAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
TAATGATTTGAATGTAATT
Found at i:662004 original size:31 final size:31
Alignment explanation
Indices: 661969--662033 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
661959 TTTGATTAAA
* *
661969 TTTTAATAAGAA-TATAATTAATTTATATATT
1 TTTTAATAAAAATTATAATTAATTTAGA-ATT
* *
662000 TTTTATTAAAAATTATAATTATTTTAGAATT
1 TTTTAATAAAAATTATAATTAATTTAGAATT
662031 TTT
1 TTT
662034 ATTTGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTAATAAAAATTATAATTAATTTAGAATT
Found at i:663286 original size:21 final size:22
Alignment explanation
Indices: 663251--663293 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
663241 AGTAAGAATC
*
663251 TTTTTTATTTTTTTATTAAATA
1 TTTTTTATTTCTTTATTAAATA
*
663273 TTTTTTA-TTCTTTATTTAATA
1 TTTTTTATTTCTTTATTAAATA
663294 ATAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTATTTCTTTATTAAATA
Found at i:666688 original size:2 final size:2
Alignment explanation
Indices: 666681--666707 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
666671 GTTTTCTTCT
666681 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
666708 GGGATAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:668529 original size:55 final size:55
Alignment explanation
Indices: 668468--668576 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
668458 AGTTTTGATT
668468 ATCTGTTGTAATTTTTCTAATCCATTAAATATTTCAAATAAAATTCAAAGTGTTG
1 ATCTGTTGTAATTTTTCTAATCCATTAAATATTTCAAATAAAATTCAAAGTGTTG
668523 ATCTGTTGTAATTTTTCTAATCCATTAAATATTTCAAATAAAATTCAAAGTGTT
1 ATCTGTTGTAATTTTTCTAATCCATTAAATATTTCAAATAAAATTCAAAGTGTT
668577 ATATATTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (55 bp):
ATCTGTTGTAATTTTTCTAATCCATTAAATATTTCAAATAAAATTCAAAGTGTTG
Found at i:669373 original size:47 final size:46
Alignment explanation
Indices: 669280--669375 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 46
669270 CACAAAGGGG
* *
669280 TATAGCGCGGGGCAAGGGCCGCGCCTTACCTTTAATTCTGATTTATA
1 TATAGCGCGGGGCAAGGGACGCGCCATACCTTTAA-TCTGATTTATA
*
669327 TATAGCGCGGGGCAGGGGACGCGCCATACCTTTAA-CTGATAATTATA
1 TATAGCGCGGGGCAAGGGACGCGCCATACCTTTAATCTGAT--TTATA
669374 TA
1 TA
669376 AGGTGCGGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
45 5 0.11
47 39 0.89
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (46 bp):
TATAGCGCGGGGCAAGGGACGCGCCATACCTTTAATCTGATTTATA
Done.