Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000452.1 Hibiscus syriacus cultivar Beakdansim tig00000836_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: 57610
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1640 original size:29 final size:30
Alignment explanation
Indices: 1608--1675 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1598 GTAGGATTTT
* *
1608 GAAACAAATG-AAAATTTAGATAATAAAAC
1 GAAACAAAAGTAAAAGTTAGATAATAAAAC
* *
1637 GAAACAAAAGTAATAGTTAGATACTAAAAC
1 GAAACAAAAGTAAAAGTTAGATAATAAAAC
*
1667 GAAATAAAA
1 GAAACAAAA
1676 AATAATAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (30 bp):
GAAACAAAAGTAAAAGTTAGATAATAAAAC
Found at i:1685 original size:31 final size:30
Alignment explanation
Indices: 1623--1693 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
1613 AAATGAAAAT
* * *
1623 TTAGATAATAAAACGAAACAAAAGTAATAG
1 TTAGATACTAAAACGAAAAAAAAATAATAG
1653 TTAGATACTAAAACGAAATAAAAAATAATAG
1 TTAGATACTAAAACGAAA-AAAAAATAATAG
1684 TTCAGATACT
1 TT-AGATACT
1694 CTTAGTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 17 0.47
31 12 0.33
32 7 0.19
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.24
Consensus pattern (30 bp):
TTAGATACTAAAACGAAAAAAAAATAATAG
Found at i:4980 original size:19 final size:21
Alignment explanation
Indices: 4956--4994 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
4946 CTCTTACATT
4956 CATATTC-TATATC-TCATAA
1 CATATTCTTATATCATCATAA
4975 CATATTCTTATATCATCATA
1 CATATTCTTATATCATCATA
4995 TAAGTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (21 bp):
CATATTCTTATATCATCATAA
Found at i:5646 original size:30 final size:32
Alignment explanation
Indices: 5612--5688 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 32
5602 TATCTTATGA
* *
5612 TCATATAATTACAT-ATCTTATATT-ATATTC
1 TCATATAATCACATAATCATATATTCATATTC
* **
5642 TCATATTATCACATAATCATATATTCATATAAA
1 TCATATAATCACATAATCATATATTCATAT-TC
5675 TCATATAA-CACATA
1 TCATATAATCACATA
5689 CAAGAACATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 12 0.32
31 9 0.24
32 10 0.26
33 7 0.18
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.42
Consensus pattern (32 bp):
TCATATAATCACATAATCATATATTCATATTC
Found at i:13025 original size:20 final size:20
Alignment explanation
Indices: 13002--13044 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12992 AATCCACCAC
*
13002 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
13022 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
13042 ATG
1 ATG
13045 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:13467 original size:15 final size:16
Alignment explanation
Indices: 13438--13467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13428 CGAGGAGAGT
13438 CATCCCATCACTCTAC
1 CATCCCATCACTCTAC
13454 CATCCCAT-ACTCTA
1 CATCCCATCACTCTA
13468 GATGAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.47, G:0.00, T:0.27
Consensus pattern (16 bp):
CATCCCATCACTCTAC
Found at i:14011 original size:5 final size:5
Alignment explanation
Indices: 14001--14027 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13991 ACATGCTATG
14001 AATGC AATGC AATGC AATGC AATGC AA
1 AATGC AATGC AATGC AATGC AATGC AA
14028 GGTACCTTGG
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:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
AATGC
Found at i:25427 original size:14 final size:14
Alignment explanation
Indices: 25383--25490 Score: 78
Period size: 14 Copynumber: 7.7 Consensus size: 14
25373 GATTACACCT
*
25383 TAAACC-TAAACTC
1 TAAACCTTAAACCC
**
25396 TAAA-CTCTAAACTA
1 TAAACCT-TAAACCC
*
25410 TAAACCTTAGACCC
1 TAAACCTTAAACCC
* *
25424 TAAATCTCAAACCC
1 TAAACCTTAAACCC
* *
25438 TAAACCTTAAATCA
1 TAAACCTTAAACCC
*
25452 TAAATCTTAAACCC
1 TAAACCTTAAACCC
*
25466 TAAACC-TAAAGACC
1 TAAACCTTAAA-CCC
25480 TAAACCCTTAA
1 TAAA-CCTTAA
25491 TCTAATTATA
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
12 1 0.01
13 8 0.11
14 57 0.78
15 4 0.05
16 3 0.04
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:25448 original size:7 final size:7
Alignment explanation
Indices: 25379--25490 Score: 54
Period size: 7 Copynumber: 16.0 Consensus size: 7
25369 GTTAGATTAC
25379 ACCTTAA
1 ACCTTAA
25386 ACC-TAA
1 ACCTTAA
25392 A-CTCTAA
1 ACCT-TAA
25399 A-CTCTAA
1 ACCT-TAA
25406 A-CTATAA
1 ACCT-TAA
*
25413 ACCTTAG
1 ACCTTAA
*
25420 ACCCTAA
1 ACCTTAA
* *
25427 ATCTCAA
1 ACCTTAA
*
25434 ACCCTAA
1 ACCTTAA
25441 ACCTTAA
1 ACCTTAA
* *
25448 ATCATAA
1 ACCTTAA
*
25455 ATCTTAA
1 ACCTTAA
*
25462 ACCCTAA
1 ACCTTAA
*
25469 ACCTAAA
1 ACCTTAA
25476 GACC-TAA
1 -ACCTTAA
25483 ACCCTTAA
1 A-CCTTAA
25491 TCTAATTATA
Statistics
Matches: 80, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
5 1 0.01
6 5 0.06
7 66 0.82
8 8 0.10
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (7 bp):
ACCTTAA
Found at i:25455 original size:28 final size:28
Alignment explanation
Indices: 25410--25472 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
25400 CTCTAAACTA
* *
25410 TAAACCTTAGACCCTAAATCTCAAACCC
1 TAAACCTTAAACCATAAATCTCAAACCC
* *
25438 TAAACCTTAAATCATAAATCTTAAACCC
1 TAAACCTTAAACCATAAATCTCAAACCC
25466 TAAACCT
1 TAAACCT
25473 AAAGACCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25
Consensus pattern (28 bp):
TAAACCTTAAACCATAAATCTCAAACCC
Found at i:25483 original size:28 final size:28
Alignment explanation
Indices: 25410--25483 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
25400 CTCTAAACTA
* *
25410 TAAACCTTAGACCCTAAATCTCAAACCC
1 TAAACCTTAAAACCTAAATCTCAAACCC
* * *
25438 TAAACCTTAAATCATAAATCTTAAACCC
1 TAAACCTTAAAACCTAAATCTCAAACCC
25466 TAAACC-TAAAGACCTAAA
1 TAAACCTTAAA-ACCTAAA
25484 CCCTTAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (28 bp):
TAAACCTTAAAACCTAAATCTCAAACCC
Found at i:25572 original size:7 final size:7
Alignment explanation
Indices: 25560--25708 Score: 68
Period size: 7 Copynumber: 21.4 Consensus size: 7
25550 TAGATTAGAT
25560 CCTAAAC
1 CCTAAAC
25567 CCTAAA-
1 CCTAAAC
*
25573 CTTAAAC
1 CCTAAAC
**
25580 TATAAAC
1 CCTAAAC
** *
25587 TATAAGC
1 CCTAAAC
*
25594 CCTAAGC
1 CCTAAAC
*
25601 CCTAAGC
1 CCTAAAC
*
25608 CCTAAGC
1 CCTAAAC
*
25615 CCTAAGC
1 CCTAAAC
**
25622 CCTAAGT
1 CCTAAAC
**
25629 TTTAAAC
1 CCTAAAC
**
25636 CCTAAGT
1 CCTAAAC
* *
25643 CTTAAAT
1 CCTAAAC
*
25650 CCTAAGC
1 CCTAAAC
*
25657 CTTAAAC
1 CCTAAAC
25664 CCTAAAC
1 CCTAAAC
*
25671 CCTAAGC
1 CCTAAAC
*
25678 CTTAAAC
1 CCTAAAC
25685 CCTAAGA-
1 CCTAA-AC
*
25692 CTTAAAC
1 CCTAAAC
25699 CCTAAAC
1 CCTAAAC
25706 CCT
1 CCT
25709 TAATCTAATT
Statistics
Matches: 110, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
6 6 0.05
7 103 0.94
8 1 0.01
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:25615 original size:21 final size:21
Alignment explanation
Indices: 25589--25708 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 21
25579 CTATAAACTA
*
25589 TAAGCCCTAAGCCCTAAGCCC
1 TAAGCCCTAAACCCTAAGCCC
* ***
25610 TAAGCCCTAAGCCCTAAGTTT
1 TAAGCCCTAAACCCTAAGCCC
* ** * **
25631 TAAACCCTAAGTCTTAAATCC
1 TAAGCCCTAAACCCTAAGCCC
* *
25652 TAAGCCTTAAACCCTAAACCC
1 TAAGCCCTAAACCCTAAGCCC
* * *
25673 TAAGCCTTAAACCCTAAGACT
1 TAAGCCCTAAACCCTAAGCCC
*
25694 TAAACCCTAAACCCT
1 TAAGCCCTAAACCCT
25709 TAATCTAATT
Statistics
Matches: 79, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.35, C:0.34, G:0.08, T:0.23
Consensus pattern (21 bp):
TAAGCCCTAAACCCTAAGCCC
Found at i:25654 original size:35 final size:35
Alignment explanation
Indices: 25593--25708 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 35
25583 AAACTATAAG
* * * *
25593 CCCTAAGCCCTAAGCCCTAAGCCCTAAGCCCTAAG
1 CCCTAAACCCTAAGCCTTAAACCCTAAGCCCTAAA
*** * * *
25628 TTTTAAACCCTAAGTCTTAAATCCTAAGCCTTAAA
1 CCCTAAACCCTAAGCCTTAAACCCTAAGCCCTAAA
* *
25663 CCCTAAACCCTAAGCCTTAAACCCTAAGACTTAAA
1 CCCTAAACCCTAAGCCTTAAACCCTAAGCCCTAAA
25698 CCCTAAACCCT
1 CCCTAAACCCT
25709 TAATCTAATT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.34, C:0.35, G:0.08, T:0.22
Consensus pattern (35 bp):
CCCTAAACCCTAAGCCTTAAACCCTAAGCCCTAAA
Found at i:25695 original size:14 final size:14
Alignment explanation
Indices: 25593--25703 Score: 92
Period size: 14 Copynumber: 8.4 Consensus size: 14
25583 AAACTATAAG
* *
25593 CCCTAAGCCCTAAG
1 CCCTAAGCCTTAAA
* *
25607 CCCTAAGCCCTAAG
1 CCCTAAGCCTTAAA
**
25621 CCCTAAGTTTTAAA
1 CCCTAAGCCTTAAA
*
25635 CCCTAAGTCTTAAA
1 CCCTAAGCCTTAAA
*
25649 TCCTAAGCCTTAAA
1 CCCTAAGCCTTAAA
25663 --C----CC-TAAA
1 CCCTAAGCCTTAAA
25670 CCCTAAGCCTTAAA
1 CCCTAAGCCTTAAA
*
25684 CCCTAAGACTTAAA
1 CCCTAAGCCTTAAA
25698 CCCTAA
1 CCCTAA
25704 ACCCTTAATC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
7 4 0.05
8 2 0.02
9 1 0.01
12 1 0.01
13 2 0.02
14 72 0.88
ACGTcount: A:0.35, C:0.34, G:0.08, T:0.23
Consensus pattern (14 bp):
CCCTAAGCCTTAAA
Found at i:27156 original size:16 final size:15
Alignment explanation
Indices: 27131--27162 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
27121 TTCTTGAATA
27131 TTTTTTGAGTTCGAG
1 TTTTTTGAGTTCGAG
27146 TTTTTTCGAGTTCGAG
1 TTTTTT-GAGTTCGAG
27162 T
1 T
27163 CGATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (15 bp):
TTTTTTGAGTTCGAG
Found at i:30241 original size:16 final size:17
Alignment explanation
Indices: 30220--30259 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
30210 TTTGATAAAG
*
30220 AAAAATAT-TGTTATTT
1 AAAAATATATATTATTT
30236 AAAAATATATATTATTT
1 AAAAATATATATTATTT
30253 AAAAATA
1 AAAAATA
30260 AAATAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAAATATATATTATTT
Found at i:31999 original size:17 final size:16
Alignment explanation
Indices: 31964--31996 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31954 TATTTTAAAA
31964 TATTAAAATAATTATT
1 TATTAAAATAATTATT
31980 TATTATAAAT-ATTATT
1 TATTA-AAATAATTATT
31996 T
1 T
31997 TATAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAAAATAATTATT
Found at i:32192 original size:37 final size:33
Alignment explanation
Indices: 32134--32205 Score: 81
Period size: 37 Copynumber: 2.1 Consensus size: 33
32124 TAAGTATCTT
* *
32134 TATTAAAATATAACTAGATTATTATATTAATATTAA
1 TATTAAAATATAAATACATTATTA-A-TAAT-TTAA
*
32170 TATTAAATATATAAATTCATTATTAATAATTTAA
1 TATTAAA-ATATAAATACATTATTAATAATTTAA
32204 TA
1 TA
32206 ATATTATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 6 0.19
35 4 0.12
36 8 0.25
37 14 0.44
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (33 bp):
TATTAAAATATAAATACATTATTAATAATTTAA
Found at i:32607 original size:42 final size:42
Alignment explanation
Indices: 32560--32654 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
32550 TTTCTCCAAC
* * * *
32560 CAAACACTAAAAAATATTTT-TCGAAAAACGAATTACTTGAAA
1 CAAACACGAAAAAACATTTTCTCG-AAAACAAATTACGTGAAA
* * *
32602 CAAACAAGAGAAAACATTTTCTTGAAAACAAATTACGTGAAA
1 CAAACACGAAAAAACATTTTCTCGAAAACAAATTACGTGAAA
32644 CAAACACGAAA
1 CAAACACGAAA
32655 TTTCGAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (42 bp):
CAAACACGAAAAAACATTTTCTCGAAAACAAATTACGTGAAA
Found at i:37613 original size:22 final size:24
Alignment explanation
Indices: 37585--37628 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
37575 ATATAAGTAA
37585 TTATAAAAAAT-ATAAT-TTTCAT
1 TTATAAAAAATAATAATATTTCAT
*
37607 TTATAAAATATAATAATATTTC
1 TTATAAAAAATAATAATATTTC
37629 TTAGTACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATAAAAAATAATAATATTTCAT
Found at i:38899 original size:60 final size:60
Alignment explanation
Indices: 38826--38942 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
38816 GCCTCATTTG
* * *
38826 TCCTTCAATTATGATCT-ATATTTTAAATTAGT-CTCTAAACTTTTAAATATTTCAATTTCT
1 TCCTTAAATTATGAT-TGATATTATAAATTAGTCCTC-AAACTTTTAAACATTTCAATTTCT
* * *
38886 TCCTTAAATTATGATTGTTATTATAAATTAGTCCTCAAATTTTTTAACATTTCAATT
1 TCCTTAAATTATGATTGATATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATT
38943 CCATCCCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.92
61 3 0.06
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (60 bp):
TCCTTAAATTATGATTGATATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCT
Found at i:39213 original size:60 final size:60
Alignment explanation
Indices: 39140--39257 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
39130 ATGAAATTGA
* * * * *
39140 GGATGAAATTGAAAGA-TTCAAAAGTTTAAGGATTAATTTAAAATGATAGTTATAATTTGG
1 GGATGAAATTGAAAGATTTCAAAA-ATTAAGAATTAATTTAAAATAAAAATTATAATTTGG
*
39200 GGATGAAATTGAAATATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTT
1 GGATGAAATTGAAAGATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTT
39258 AAAAATAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 44 0.86
61 7 0.14
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (60 bp):
GGATGAAATTGAAAGATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTTGG
Found at i:41624 original size:60 final size:60
Alignment explanation
Indices: 41551--41667 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
41541 GCCTCATTTG
* * *
41551 TCCTTCAATTATGATCT-ATATTTTAAATTAGT-CTCTAAACTTTTAAATATTTCAATTTCT
1 TCCTTAAATTATGAT-TGATATTATAAATTAGTCCTC-AAACTTTTAAACATTTCAATTTCT
* * *
41611 TCCTTAAATTATGATTGTTATTATAAATTAGTCCTCAAATTTTTTAACATTTCAATT
1 TCCTTAAATTATGATTGATATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATT
41668 CCATCCCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.92
61 3 0.06
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (60 bp):
TCCTTAAATTATGATTGATATTATAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCT
Found at i:41938 original size:60 final size:60
Alignment explanation
Indices: 41865--41982 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
41855 ATGAAATTGA
* * * * *
41865 GGATGAAATTGAAAGA-TTCAAAAGTTTAAGGATTAATTTAAAATGATAGTTATAATTTGG
1 GGATGAAATTGAAAGATTTCAAAA-ATTAAGAATTAATTTAAAATAAAAATTATAATTTGG
*
41925 GGATGAAATTGAAATATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTT
1 GGATGAAATTGAAAGATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTT
41983 AAAAATAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 44 0.86
61 7 0.14
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (60 bp):
GGATGAAATTGAAAGATTTCAAAAATTAAGAATTAATTTAAAATAAAAATTATAATTTGG
Found at i:42567 original size:6 final size:6
Alignment explanation
Indices: 42530--42565 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
42520 ATATTCTTCT
* *
42530 CCACTA CCACTA CCACTA CCACTA TCACTA TCACTA
1 CCACTA CCACTA CCACTA CCACTA CCACTA CCACTA
42566 TCGCATCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (6 bp):
CCACTA
Found at i:46937 original size:22 final size:22
Alignment explanation
Indices: 46912--46957 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
46902 GTTTACAAAT
* *
46912 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTACTAC
46934 AGGGAACCGATTCCCCTACTAC
1 AGGGAACCGATTCCCCTACTAC
46956 AG
1 AG
46958 TACTGCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTACTAC
Found at i:46972 original size:11 final size:11
Alignment explanation
Indices: 46952--46994 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
46942 GATTCCCCTA
46952 CTACAGTACTG
1 CTACAGTACTG
*
46963 CTACAATACTG
1 CTACAGTACTG
*
46974 CTACAGTACCG
1 CTACAGTACTG
46985 CTACAGTACT
1 CTACAGTACT
46995 TCCGTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (11 bp):
CTACAGTACTG
Found at i:47549 original size:21 final size:21
Alignment explanation
Indices: 47492--47555 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
47482 ATATGAAATT
* *
47492 TTGTCCCGAATGACCTGTGAA
1 TTGTCCCGAAAGACCTATGAA
*
47513 TATGTCCCGAAAGACCTATGAG
1 T-TGTCCCGAAAGACCTATGAA
* *
47535 TTGTCCTGAAGGACCTATGAA
1 TTGTCCCGAAAGACCTATGAA
47556 ACCTTCAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAAGACCTATGAA
Found at i:48574 original size:19 final size:19
Alignment explanation
Indices: 48525--48566 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
48515 CACGTTTGGA
48525 AGAAGAGAA-AAGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
48545 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
48564 AGA
1 AGA
48567 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:53841 original size:11 final size:11
Alignment explanation
Indices: 53825--53859 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
53815 ACCGATTCCC
53825 CTGCTACAGTA
1 CTGCTACAGTA
53836 CTGCTACAGTA
1 CTGCTACAGTA
53847 CTGCTACAGTA
1 CTGCTACAGTA
53858 CT
1 CT
53860 TCCGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:54407 original size:21 final size:21
Alignment explanation
Indices: 54358--54421 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
54348 ATATGAAATT
*
54358 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
54379 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
54401 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
54422 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:55436 original size:19 final size:19
Alignment explanation
Indices: 55387--55428 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
55377 CACGTTTGGA
55387 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
55407 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
55426 AGA
1 AGA
55429 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:56498 original size:30 final size:31
Alignment explanation
Indices: 56433--56499 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
56423 TATTTTTAGC
*
56433 TTTACATTCTTTTTTATTAAATTTTATTCACT
1 TTTA-ATTCTTTTTTATTAAATTTAATTCACT
* * *
56465 TTTAATTCTTTTTT-TTATATTTAATTGATT
1 TTTAATTCTTTTTTATTAAATTTAATTCACT
56495 TTTAA
1 TTTAA
56500 ATATATGAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 17 0.55
31 10 0.32
32 4 0.13
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTAATTCTTTTTTATTAAATTTAATTCACT
Done.