Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001545.1 Hibiscus syriacus cultivar Beakdansim tig00003034_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: 78070
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:2489 original size:14 final size:14
Alignment explanation
Indices: 2443--2486 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
2433 CGATTGATTT
2443 ATTTTCGTTATTTAA
1 ATTTT-GTTATTTAA
**
2458 ATTTTGTCCTTTAA
1 ATTTTGTTATTTAA
2472 ATTTATGTTATTTAA
1 ATTT-TGTTATTTAA
2487 TTTCTTCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTTGTTATTTAA
Found at i:2813 original size:15 final size:17
Alignment explanation
Indices: 2779--2813 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2769 TAAATTACTT
2779 TTTTTAGATTTAGATCC
1 TTTTTAGATTTAGATCC
2796 TTTTTA-ATTTAG-TCC
1 TTTTTAGATTTAGATCC
2811 TTT
1 TTT
2814 AATTTAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTTTAGATTTAGATCC
Found at i:2957 original size:137 final size:135
Alignment explanation
Indices: 2808--3053 Score: 336
Period size: 136 Copynumber: 1.8 Consensus size: 135
2798 TTTAATTTAG
*
2808 TCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTTAC-TTT-TTCTCAAGGTTCCATTTTAATTA
1 TCCTTTAATTTAGGAGAA-TTTTTATTTGGTCC-T-CGTTTGTGCTCAAGGTTCCATTTTAATT-
* * * *
2871 TTTAATTCAATAA-TCAGTTAAAATGAATTAGGATTAATATTAGAGCCTCCATTTTAGGTTAATT
62 TTCAACTCAATAATTCACTAAAAAT-AATTAGGATTAATATTAGAGCCTCCATTTTAGGTTAATT
2935 TTATAACTAA
126 TTATAACTAA
* *
2945 TCCTTTAATTTAGGAGAATTTTTATTTGGTCCTCGTTTGTGCTCGAGGTTCCATTTTAATTTTCG
1 TCCTTTAATTTAGGAGAATTTTTATTTGGTCCTCGTTTGTGCTCAAGGTTCCATTTTAATTTTCA
* * *
3010 ACTCGATAATTTACTAAAAATAATTTGGATTAATATTAGAGCCT
66 ACTCAATAATTCACTAAAAATAATTAGGATTAATATTAGAGCCT
3054 ATATTTTAAG
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
134 1 0.01
135 35 0.36
136 42 0.44
137 18 0.19
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (135 bp):
TCCTTTAATTTAGGAGAATTTTTATTTGGTCCTCGTTTGTGCTCAAGGTTCCATTTTAATTTTCA
ACTCAATAATTCACTAAAAATAATTAGGATTAATATTAGAGCCTCCATTTTAGGTTAATTTTATA
ACTAA
Found at i:4312 original size:29 final size:29
Alignment explanation
Indices: 4257--4313 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4247 ATTTTAATTT
*
4257 TTAAATATAAAATTTAAATATTCAAAAAC
1 TTAAATATAAAATTTAAATAATCAAAAAC
4286 TTAAATATAAAAATGTTAAA-AAT-AAAAA
1 TTAAATAT-AAAAT-TTAAATAATCAAAAA
4314 TCAAATTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 13 0.52
30 7 0.28
31 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (29 bp):
TTAAATATAAAATTTAAATAATCAAAAAC
Found at i:4591 original size:3 final size:3
Alignment explanation
Indices: 4585--4626 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
4575 AATAAAAACC
4585 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4627 TAATTACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4850 original size:19 final size:18
Alignment explanation
Indices: 4809--4849 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
4799 ATTTCATTTC
4809 TTTTAATTTTTAATAGTAT
1 TTTTAATTTTT-ATAGTAT
4828 TTTTAATTTTT-TAGTAAT
1 TTTTAATTTTTATAGT-AT
4846 TTTT
1 TTTT
4850 TTTGAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTTTTATAGTAT
Found at i:10945 original size:11 final size:11
Alignment explanation
Indices: 10929--10974 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
10919 AACATATTAA
10929 AACAGCTAACT
1 AACAGCTAACT
10940 AACAGCTAACT
1 AACAGCTAACT
*
10951 -ATAGACTAACT
1 AACAG-CTAACT
*
10962 AACAACTAACT
1 AACAGCTAACT
10973 AA
1 AA
10975 TTACAATCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 25 0.83
12 2 0.07
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.20
Consensus pattern (11 bp):
AACAGCTAACT
Found at i:16439 original size:25 final size:25
Alignment explanation
Indices: 16405--16455 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16395 ATTTCCTTTA
16405 GGTTCTATATTTTGTATGGGCATTT
1 GGTTCTATATTTTGTATGGGCATTT
16430 GGTTCTATATTTTGTATGGGCATTT
1 GGTTCTATATTTTGTATGGGCATTT
16455 G
1 G
16456 ATTATCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.25, T:0.51
Consensus pattern (25 bp):
GGTTCTATATTTTGTATGGGCATTT
Found at i:18102 original size:3 final size:3
Alignment explanation
Indices: 18094--18121 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18084 TTTTCTTCCT
18094 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
18122 TGTATTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:20757 original size:21 final size:20
Alignment explanation
Indices: 20671--20828 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
20661 AAATGACCAA
**
20671 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
20690 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
20710 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
20730 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
20751 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
20772 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
20792 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
20813 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
20829 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:20870 original size:20 final size:20
Alignment explanation
Indices: 20796--20988 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
20786 GATTTTCCAG
* ** *
20796 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
20816 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
20836 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20856 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20876 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20896 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20916 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
20936 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
20957 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
20977 AATCGCAACGCG
1 AATCGCAACGCG
20989 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:21407 original size:33 final size:33
Alignment explanation
Indices: 21368--21438 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
21358 TTCACTTAGA
21368 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
21401 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
21434 TTTCA
1 TTTCA
21439 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:21542 original size:21 final size:21
Alignment explanation
Indices: 21518--21594 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
21508 TGCAGAAGAG
*
21518 TCGCAATGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
21539 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
21559 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
21581 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
21595 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.20
21 28 0.61
22 9 0.20
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:21598 original size:14 final size:14
Alignment explanation
Indices: 21579--21635 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21569 GAAAAATGAA
21579 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
21593 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21612 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21626 AATCGCAACG
1 AATCGCAACG
21636 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21610 original size:33 final size:33
Alignment explanation
Indices: 21572--21649 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
21562 GCAACGAGAA
21572 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
21605 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
21638 AAACCAAAATCG
1 AAATGAAAATCG
21650 TATTGCGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:21694 original size:33 final size:33
Alignment explanation
Indices: 21652--21733 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
21642 CAAAATCGTA
21652 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
* *
21685 TTGCGATTTTCATTTCGCGTTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
21718 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
21734 TCTCGTTGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
Found at i:21736 original size:21 final size:21
Alignment explanation
Indices: 21710--21774 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
21700 CGCGTTGCGA
*
21710 TTCTCTTGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
21731 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
21751 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
21772 TTC
1 TTC
21775 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:23728 original size:19 final size:19
Alignment explanation
Indices: 23686--23858 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
23676 TAGTTTACTT
* *
23686 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
23706 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
23725 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
23744 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
23763 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23782 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
23796 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23815 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
23829 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23848 TCGCAATGCGA
1 TCGCAACGCGA
23859 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 82 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:23799 original size:14 final size:14
Alignment explanation
Indices: 23780--23836 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
23770 GCGAAATGAA
*
23780 AATCGCAACGACAG
1 AATCGCAACGAAAG
23794 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
23811 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
23827 AATCGCAACG
1 AATCGCAACG
23837 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:23807 original size:33 final size:33
Alignment explanation
Indices: 23761--23853 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
23751 GCGAAACCAA
23761 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
23794 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
23827 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
23854 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:23850 original size:52 final size:52
Alignment explanation
Indices: 23720--23858 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
23710 AACGCGAAAT
* * * *
23720 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
23772 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
23824 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
23859 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:23889 original size:14 final size:14
Alignment explanation
Indices: 23870--23928 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
23860 TTTGGTTTCG
23870 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
23884 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
23901 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
23917 CGTTGCGATTTT
1 CGTTGCGATTTT
23929 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:23896 original size:33 final size:33
Alignment explanation
Indices: 23854--23977 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
23844 AAAATCGCAA
*
23854 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
23887 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** * *
23920 TGCGATTTTCATTTCGCGTTGTGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
23953 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
23978 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:23908 original size:19 final size:19
Alignment explanation
Indices: 23854--23912 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
23844 AAAATCGCAA
23854 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
23873 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
23887 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
23906 TGCGATT
1 TGCGATT
23913 CTGTCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:25917 original size:14 final size:14
Alignment explanation
Indices: 25898--25933 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25888 ATTGTTTAAT
25898 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25912 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25926 TGATTTGT
1 TGATTTGT
25934 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26057 original size:20 final size:19
Alignment explanation
Indices: 26040--26138 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
26030 AAAAATGACT
26040 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
26060 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
26079 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
26093 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
26112 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
26132 ATCGCAA
1 ATCGCAA
26139 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 29 0.41
20 26 0.37
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:26170 original size:53 final size:53
Alignment explanation
Indices: 26040--26157 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
26030 AAAAATGACT
26040 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
26093 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
26146 ATCGCAATGCGA
1 ATCGCAATGCGA
26158 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:26216 original size:53 final size:52
Alignment explanation
Indices: 26153--26370 Score: 293
Period size: 53 Copynumber: 4.1 Consensus size: 52
26143 AGAATCGCAA
26153 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
26206 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
26259 TGCGATTTTCATTTCGCCTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
26317 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
26364 TACGATT
1 TGCGATT
26371 GTAATTTCCG
Statistics
Matches: 154, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
47 7 0.05
49 2 0.01
50 2 0.01
51 3 0.02
52 10 0.06
53 109 0.71
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:26234 original size:72 final size:71
Alignment explanation
Indices: 26147--26356 Score: 255
Period size: 72 Copynumber: 2.9 Consensus size: 71
26137 AACGAGAGAA
* * *
26147 TCGCAATGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCA-TTGCGATTCTCTCGTTGCG
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCG-ATTTGC-ATT-TCGCCTTGCG
26210 ATTTTCATT
63 ATTTTCATT
* * *
26219 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCCTTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCCGATTTGCATTTCGCCTTGCGA
26283 TTTTCATT
64 TTTTCATT
** * *
26291 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-TTCCGATTTGCATTTCGCCTTGCGAT
26356 T
65 T
26357 CTCTCGTTAC
Statistics
Matches: 123, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
70 2 0.02
71 1 0.01
72 94 0.76
73 16 0.13
74 8 0.07
75 2 0.02
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGATTTGCATTTCGCCTTGCGATT
TTCATT
Found at i:26378 original size:33 final size:33
Alignment explanation
Indices: 26224--26370 Score: 170
Period size: 33 Copynumber: 4.2 Consensus size: 33
26214 TCATTTCGCA
26224 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
26258 TTGCGATTTTCATTTCGCCTTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
26294 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
26330 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
26363 TTACGATT
1 TTGCGATT
26371 GTAATTTCCG
Statistics
Matches: 96, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.01
33 30 0.31
34 29 0.30
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.16
39 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:26516 original size:12 final size:12
Alignment explanation
Indices: 26499--26523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26489 TCTTCGGGGA
26499 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26511 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26523 C
1 C
26524 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:26732 original size:24 final size:24
Alignment explanation
Indices: 26698--26744 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26688 CTGAAACATC
26698 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26722 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26745 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27462 original size:20 final size:20
Alignment explanation
Indices: 27434--27622 Score: 211
Period size: 20 Copynumber: 9.4 Consensus size: 20
27424 AAATTTCAGT
* * * *
27434 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
27454 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
27474 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27494 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27514 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27534 GTTGCTATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27554 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
27574 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
27594 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
27614 GTTGCGATT
1 GTTGCGATT
27623 CTGGAAAATC
Statistics
Matches: 147, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.01
20 143 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:29098 original size:9 final size:9
Alignment explanation
Indices: 29084--29294 Score: 71
Period size: 9 Copynumber: 22.4 Consensus size: 9
29074 TGTTAGATAA
29084 AAAATAAAT
1 AAAATAAAT
29093 AAAATAAAT
1 AAAATAAAT
*
29102 AAAATGAAT
1 AAAATAAAT
29111 AAAA-AATCTAT
1 AAAATAA---AT
29122 AATAAT-AAT
1 AA-AATAAAT
*
29131 AATAATAAGGAG
1 AA-AATAA--AT
29143 AAAATAAA-
1 AAAATAAAT
29151 AAAATAAAAACT
1 AAAAT--AAA-T
29163 AAAA-AAA-
1 AAAATAAAT
29170 AGAAATAAAT
1 A-AAATAAAT
*
29180 AAAACAAAT
1 AAAATAAAT
*
29189 AAGAATAAAC
1 AA-AATAAAT
*
29199 AAAA-AAAC
1 AAAATAAAT
*
29207 AAAACAAAT
1 AAAATAAAT
*
29216 ACGAAT-AAT
1 A-AAATAAAT
29225 AATAAT-AAT
1 AA-AATAAAT
**
29234 AATAATAGTT
1 AA-AATAAAT
* *
29244 ATAATAATAA
1 AAAATAA-AT
*
29254 AAAATGAAT
1 AAAATAAAT
29263 AAAATAAA-
1 AAAATAAAT
*
29271 ATAATAAAT
1 AAAATAAAT
*
29280 ATATATAAAAT
1 A-AAAT-AAAT
29291 AAAA
1 AAAA
29295 AATAATGATA
Statistics
Matches: 154, Mismatches: 24, Indels: 47
0.68 0.11 0.21
Matches are distributed among these distances:
7 1 0.01
8 24 0.16
9 80 0.52
10 25 0.16
11 14 0.09
12 10 0.06
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:29156 original size:8 final size:8
Alignment explanation
Indices: 29143--29216 Score: 53
Period size: 8 Copynumber: 8.8 Consensus size: 8
29133 TAATAAGGAG
29143 AAAATAAA
1 AAAATAAA
29151 AAAAT-AA
1 AAAATAAA
*
29158 AAACTAAA
1 AAAATAAA
29166 AAAA-AGAA
1 AAAATA-AA
29174 ATAAATAAA
1 A-AAATAAA
29183 ACAAATAAGA
1 A-AAATAA-A
*
29193 ATAAACAAA
1 A-AAATAAA
*
29202 AAAACAAA
1 AAAATAAA
29210 ACAAATA
1 A-AAATA
29217 CGAATAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 7 0.13
8 21 0.39
9 18 0.33
10 8 0.15
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:29227 original size:3 final size:3
Alignment explanation
Indices: 29219--29307 Score: 68
Period size: 3 Copynumber: 31.3 Consensus size: 3
29209 AACAAATACG
* *
29219 AAT AAT AAT AAT AAT AAT AAT AGT TAT AAT AAT AA- AA- AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
29263 AA- AAT AA- AAT AAT AA- ATAT ATAT AA- AAT AA- AA- AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT
29304 AAT A
1 AAT A
29308 TATATATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
2 15 0.21
3 49 0.68
4 8 0.11
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29310 original size:2 final size:2
Alignment explanation
Indices: 29305--29339 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29295 AATAATGATA
29305 AT 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 AT A
29340 ATAGAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29313 original size:31 final size:32
Alignment explanation
Indices: 29246--29317 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
29236 TAATAGTTAT
*
29246 AATA-ATAAAAAATGAATAAAATAAAATAATA
1 AATATATATAAAATGAATAAAATAAAATAATA
*
29277 AATATATATAAAAT-AA-AAAATAATGATAATA
1 AATATATATAAAATGAATAAAATAA-AATAATA
*
29308 TATATATATA
1 AATATATATA
29318 TATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 7 0.19
31 21 0.58
32 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (32 bp):
AATATATATAAAATGAATAAAATAAAATAATA
Found at i:29321 original size:39 final size:37
Alignment explanation
Indices: 29219--29325 Score: 103
Period size: 39 Copynumber: 2.8 Consensus size: 37
29209 AACAAATACG
29219 AATAATAATAATAATA-ATAATAGT-TATAATAATAAAA
1 AATAAT-ATAATAATATATAATA-TATATAATAATAAAA
* *
29256 AATGAATAAAATAAAATAATAAATATATATAA-AATAAAA
1 AAT-AATATAATAATAT-AT-AATATATATAATAATAAAA
29295 AATAATGATAATATATATATATATATATATA
1 AATAAT-ATAATA-ATATATA-ATATATATA
29326 TATATATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
37 10 0.17
38 7 0.12
39 29 0.50
40 12 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (37 bp):
AATAATATAATAATATATAATATATATAATAATAAAA
Found at i:31352 original size:65 final size:65
Alignment explanation
Indices: 31209--31384 Score: 213
Period size: 65 Copynumber: 2.8 Consensus size: 65
31199 GTGAAGTTGA
* * *
31209 GCTTTGAGTTAGATATCCTTCGTTGTGAAGTTAAAATCCAAGT-AT---T--GTTTCTCCAAATT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-TCATGAGTAAGTTTCACCAAATT
31268 G
65 G
* * *
31269 GTTTTTAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCATGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCATGAGTAAGTTTCACCAAATTG
* *
31334 GCTTTGAGTTGGACATCCTTCGTTGTGAAGTTGAAATTCAATC-TCGAGTAA
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCAT-GAGTAA
31385 ATTGTGTCGC
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 1 0.01
60 38 0.39
63 1 0.01
64 1 0.01
65 57 0.58
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (65 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCATGAGTAAGTTTCACCAAATTG
Found at i:45802 original size:20 final size:20
Alignment explanation
Indices: 45766--45803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45756 CCAGAACCCG
* *
45766 ATGGGGGTATCGGTACCCTT
1 ATGGGGGTAGCGATACCCTT
45786 ATGGGGGTAGCGATACCC
1 ATGGGGGTAGCGATACCC
45804 ATTCAAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (20 bp):
ATGGGGGTAGCGATACCCTT
Found at i:45817 original size:23 final size:23
Alignment explanation
Indices: 45790--45848 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
45780 ACCCTTATGG
*
45790 GGGTAGCGATACCCATTCAAAGA
1 GGGTATCGATACCCATTCAAAGA
45813 GGGTATC-AGTACCCATTCAAAGA
1 GGGTATCGA-TACCCATTCAAAGA
*
45836 GGGAATCGATACC
1 GGGTATCGATACC
45849 TAGTGAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGTATCGATACCCATTCAAAGA
Found at i:48235 original size:65 final size:63
Alignment explanation
Indices: 48112--48320 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 63
48102 TATTCAAAGG
* * *
48112 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATTGAAACGTCGAATGCA
1 CATGCACCGATGCATC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGCA
*
48175 TTC
61 TTT
48178 CATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCA-TCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * * * **
48243 GATGCATCGATGCA-CAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATT
1 CATGCACCGATGCATC--TCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATT
48306 T
63 T
*
48307 CATGCATCGATGCA
1 CATGCACCGATGCA
48321 CACTTGGTGC
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
63 1 0.01
64 41 0.33
65 65 0.52
66 16 0.13
67 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCATCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:48315 original size:64 final size:65
Alignment explanation
Indices: 48161--48322 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
48151 GAATTAATTG
* * * **** *
48161 AAACGTCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
* **
48226 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTC
48290 -
65 A
48290 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
48323 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:54880 original size:21 final size:21
Alignment explanation
Indices: 54856--54919 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
54846 AAAACCGTCC
54856 TCCCGTTCCTCAACATCCTAA
1 TCCCGTTCCTCAACATCCTAA
* *
54877 TCCCGTTCCTCATCAACCTAA
1 TCCCGTTCCTCAACATCCTAA
* *
54898 TCCTGATCCTCAAGC-TCCTAA
1 TCCCGTTCCTCAA-CATCCTAA
54919 T
1 T
54920 GGCTTATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.41, G:0.06, T:0.30
Consensus pattern (21 bp):
TCCCGTTCCTCAACATCCTAA
Found at i:55720 original size:21 final size:21
Alignment explanation
Indices: 55678--55721 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55668 ACTCCGGGAG
*
55678 CTAGTTCTTCTAGAGCTGCTC
1 CTAGTTCTTCTAGAGCTCCTC
* *
55699 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTAGAGCTCCTC
55720 CT
1 CT
55722 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCTAGAGCTCCTC
Found at i:56911 original size:64 final size:65
Alignment explanation
Indices: 56684--56896 Score: 220
Period size: 65 Copynumber: 3.3 Consensus size: 65
56674 TATTCAAAGG
* * * *
56684 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TC-GATAAATTAATT-GAAACATCGAATGC
1 CATGCATCGATGCA-CACTCCATGCATCGATGCACTCAGA-ATATT--TTCAAAACATCGAATGC
*
56746 ATTC
62 ATTT
* ** *
56750 CATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
56815 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATT
1 CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATT
56878 T
65 T
56879 CATGCATCGATGCACACT
1 CATGCATCGATGCACACT
56897 TGGTGCACCG
Statistics
Matches: 125, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
64 38 0.30
65 65 0.52
66 20 0.16
67 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:59283 original size:20 final size:21
Alignment explanation
Indices: 59244--59283 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
59234 GAAGTTTTAA
* *
59244 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
59265 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
59284 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:61360 original size:20 final size:20
Alignment explanation
Indices: 61335--61387 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
61325 ATATGACTAG
61335 GGGTATCGGTACCTCAAAGA
1 GGGTATCGGTACCTCAAAGA
*
61355 GGGTATCGGTACCTCAAAGG
1 GGGTATCGGTACCTCAAAGA
61375 GGGTATCGGTACC
1 GGGTATCGGTACC
61388 CTTAGGGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGTATCGGTACCTCAAAGA
Found at i:61894 original size:9 final size:9
Alignment explanation
Indices: 61876--62013 Score: 60
Period size: 9 Copynumber: 15.1 Consensus size: 9
61866 TGTTAGATAA
61876 AAAATAAAT
1 AAAATAAAT
*
61885 AAAATGAAT
1 AAAATAAAT
61894 AAAA-AAACT
1 AAAATAAA-T
*
61903 ATAAT-AAT
1 AAAATAAAT
61911 AATAATAAGAAT
1 AA-AAT-A-AAT
61923 AAGGAGA-AAAT
1 AA--A-ATAAAT
61934 AAAA-AAAT
1 AAAATAAAT
61942 AAAA-ACTAA-
1 AAAATA--AAT
*
61951 AAACTAAAT
1 AAAATAAAT
*
61960 CAAAAGAAAT
1 -AAAATAAAT
61970 -AAATAAAT
1 AAAATAAAT
61978 AAAATAAAT
1 AAAATAAAT
61987 AAGAATAAA-
1 AA-AATAAAT
*
61996 CAAA-AAAT
1 AAAATAAAT
*
62004 AAAACAAAT
1 AAAATAAAT
62013 A
1 A
62014 CGAATAATAA
Statistics
Matches: 101, Mismatches: 11, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
7 3 0.03
8 28 0.28
9 41 0.41
10 16 0.16
11 5 0.05
12 6 0.06
13 1 0.01
14 1 0.01
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:61898 original size:10 final size:10
Alignment explanation
Indices: 61875--62006 Score: 51
Period size: 11 Copynumber: 12.9 Consensus size: 10
61865 GTGTTAGATA
61875 AAAAATAAAT
1 AAAAATAAAT
*
61885 -AAAATGAAT
1 AAAAATAAAT
61894 AAAAA-AACTAT
1 AAAAATAA--AT
*
61905 AATAATAATAAT
1 AAAAAT-A-AAT
* **
61917 AAGAATAAGG
1 AAAAATAAAT
61927 AGAAAATAAA-
1 A-AAAATAAAT
*
61937 AAAATAAAAACT
1 AAAA-ATAAA-T
61949 AAAAACTAAAT
1 AAAAA-TAAAT
* *
61960 CAAAAGAAAT
1 AAAAATAAAT
61970 --AAATAAAT
1 AAAAATAAAT
61978 -AAAATAAAT
1 AAAAATAAAT
* *
61987 AAGAATAAACA
1 AAAAATAAA-T
61998 AAAAATAAA
1 AAAAATAAA
62007 ACAAATACGA
Statistics
Matches: 92, Mismatches: 16, Indels: 27
0.68 0.12 0.20
Matches are distributed among these distances:
8 7 0.08
9 20 0.22
10 22 0.24
11 27 0.29
12 14 0.15
13 1 0.01
14 1 0.01
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.17
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:61984 original size:13 final size:12
Alignment explanation
Indices: 61930--61988 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 12
61920 AATAAGGAGA
61930 AAATAAAAAAAT
1 AAATAAAAAAAT
61942 AAA-AACTAAAAACT
1 AAATAA--AAAAA-T
61956 AAATCAAAAGAAAT
1 AAAT-AAAA-AAAT
61970 AAATAAATAAAAT
1 AAATAAA-AAAAT
61983 AAATAA
1 AAATAA
61989 GAATAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.05
12 3 0.08
13 18 0.45
14 12 0.30
15 3 0.08
16 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:62000 original size:36 final size:36
Alignment explanation
Indices: 61930--62013 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
61920 AATAAGGAGA
*
61930 AAATAAAAAAATAAAAACTAAAAACTAAATCAAAAG
1 AAATAAAAAAATAAAAAATAAAAACTAAATCAAAAG
* *
61966 AAATAAATAAATAAAATAAATAAGAA-TAAA-C-AAA-
1 AAATAAAAAAAT-AAA-AAATAAAAACTAAATCAAAAG
62000 AAATAAAACAAATA
1 AAATAAAA-AAATA
62014 CGAATAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
34 8 0.20
35 7 0.17
36 12 0.29
37 7 0.17
38 7 0.17
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.15
Consensus pattern (36 bp):
AAATAAAAAAATAAAAAATAAAAACTAAATCAAAAG
Found at i:62024 original size:3 final size:3
Alignment explanation
Indices: 62016--62079 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
62006 AACAAATACG
* *
62016 AAT AAT AAT AAT AAT AAT AGT TAT AAT AAT AA- AA- AAT GAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
62059 AAT AAT -AT ATAT ATAT AAT AA
1 AAT AAT AAT A-AT A-AT AAT AA
62080 AAAATTAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 8 0.15
3 34 0.65
4 10 0.19
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62069 original size:29 final size:31
Alignment explanation
Indices: 62037--62114 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 31
62027 TAATAATAGT
62037 TATA-ATAATAAAAAATGAATAAAATAATATA
1 TATATATAATAAAAAATGAATAAAAT-ATATA
* *
62068 TATATATAATAAAAAATTAATGATATATATATA
1 TATATATAATAAAAAATGAAT-A-AAATATATA
62101 TATATATAATAAAA
1 TATATATAATAAAA
62115 TATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 4 0.10
32 15 0.36
33 20 0.48
34 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TATATATAATAAAAAATGAATAAAATATATA
Found at i:62100 original size:33 final size:32
Alignment explanation
Indices: 62021--62120 Score: 123
Period size: 32 Copynumber: 3.1 Consensus size: 32
62011 ATACGAATAA
62021 TAATAATAATAATAGT-TATA-ATAATAAAAAAT
1 TAATAA-AATAATA-TATATATATAATAAAAAAT
*
62053 GAATAAAATAATATATATATATAATAAAAAAT
1 TAATAAAATAATATATATATATAATAAAAAAT
* * *
62085 TAATGATATATATATATATATATAATAAAATAT
1 TAATAAAATA-ATATATATATATAATAAAAAAT
62118 TAA
1 TAA
62121 AAAGGTGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 11 0.18
32 24 0.40
33 24 0.40
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
TAATAAAATAATATATATATATAATAAAAAAT
Found at i:69929 original size:59 final size:59
Alignment explanation
Indices: 69858--70503 Score: 799
Period size: 59 Copynumber: 11.1 Consensus size: 59
69848 GTACACTACT
* * * * **
69858 TTTCATCTAACTTGCATTAGTGGCACCTTTCTACTAAATGCATAGTTAGACATTTAAAT
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * * *
69917 TTTCATCTAACTTGTATTATTGGCACCTTTATACCAAATGCACGGTTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * * * *
69976 ATTCATCTAACTTACATTATTGGTACCTTTCTGCCAAATGCACAATTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* *
70035 TTTCATCTAACTCGCATTATTGGCACATTTCTACCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * * * *
70094 TTTCATCTACCTTGCATTATTGACACCTTTCTATCAAATGAACAGTTAGGCATTTAAAC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * *
70153 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAATTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * * * * *
70212 TTTCA-ATAACTTGCATTATTGGAACCTTTTTTTCCAAATGCATAATTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACC-TTTCTACCAAATGCACAGTTAGGCATTTAACC
* * ** *
70271 TTTCATCTAACTTGCATTATTGGCATCTTTCTTCCAAATGCACAGTTAAACACTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * *
70330 TTTCATCTAACTTGCTTTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * * *
70389 TTTCATATAACTTGCATTATTGGCACCTTTCTGCCAAATGTAAAGTTAGG-------CC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
* * *
70441 TTTCATCTAACTTGCATTATT-GCATCTTTCTACTAAATGCACACTTAGGCA-TTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
70498 TTTCAT
1 TTTCAT
70504 TTTAGAGAAA
Statistics
Matches: 506, Mismatches: 73, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
51 22 0.04
52 22 0.04
57 8 0.02
58 19 0.04
59 417 0.82
60 18 0.04
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAACC
Found at i:76748 original size:18 final size:18
Alignment explanation
Indices: 76725--76781 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
76715 CACGTCGTAC
76725 CCATGTCTCCAGCCGTGA
1 CCATGTCTCCAGCCGTGA
76743 CCATGTCTCCAGCCGTGA
1 CCATGTCTCCAGCCGTGA
* *
76761 CCATTTCTCCAGCAGTGA
1 CCATGTCTCCAGCCGTGA
76779 CCA
1 CCA
76782 AATAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.23
Consensus pattern (18 bp):
CCATGTCTCCAGCCGTGA
Found at i:77336 original size:15 final size:16
Alignment explanation
Indices: 77297--77344 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
77287 TTGTCCGGGT
*
77297 TATTATTAATATTTAA
1 TATTATTATTATTTAA
*
77313 TATTATTATTATTTAT
1 TATTATTATTATTTAA
77329 TA-TATTATTA-TTAA
1 TATTATTATTATTTAA
77343 TA
1 TA
77345 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTATTATTTAA
Done.