Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007729.1 Hibiscus syriacus cultivar Beakdansim tig00109980_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: 1111098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1081242 original size:34 final size:35
Alignment explanation
Indices: 1081199--1081265 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1081189 ATGTGCAGGG
1081199 GAACAGATTCCCCCT-GGGGGCATCGATTCCCCGA
1 GAACAGATTCCCCCTGGGGGGCATCGATTCCCCGA
*
1081233 GAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GAACAGATTCCCCCTGGGGGGCATCGATTCCCC
1081266 CTTAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.19
Consensus pattern (35 bp):
GAACAGATTCCCCCTGGGGGGCATCGATTCCCCGA
Found at i:1082161 original size:38 final size:38
Alignment explanation
Indices: 1082105--1082200 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
1082095 TATAAGACAT
* * *
1082105 ATGATAGGTCCTACGGGACACAGATTACAT-CTTTCGAG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTT-GAG
* *
1082143 ATGACAGGTCTTTCGGGACACAGATGACATCCTTTGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTTGAG
*
1082181 ATGATAGGTCCTTCGGGACA
1 ATGACAGGTCCTTCGGGACA
1082201 TAATTTATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 46 0.92
39 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTTGAG
Found at i:1086163 original size:18 final size:17
Alignment explanation
Indices: 1086142--1086175 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1086132 CCTCCAATAA
1086142 AATGATGTTAATATATAT
1 AATGATGTTAAT-TATAT
*
1086160 AATGTTGTTAATTATA
1 AATGATGTTAATTATA
1086176 AACCAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
AATGATGTTAATTATAT
Found at i:1097829 original size:20 final size:20
Alignment explanation
Indices: 1097735--1098103 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1097725 GATTTTCCAT
* ** *
1097735 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1097755 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1097775 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1097795 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1097815 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1097835 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1097855 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1097875 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1097895 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1097915 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1097935 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1097955 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1097975 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1097995 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1098015 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1098035 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1098055 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1098075 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1098095 AATCACAAC
1 AATCGCAAC
1098104 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1098822 original size:24 final size:23
Alignment explanation
Indices: 1098783--1098828 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1098773 AAATTTGGTC
1098783 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
1098807 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
1098829 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:1099019 original size:12 final size:12
Alignment explanation
Indices: 1099002--1099026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1098992 ATATAATCCT
1099002 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1099014 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1099026 G
1 G
1099027 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1101296 original size:19 final size:19
Alignment explanation
Indices: 1101274--1101564 Score: 374
Period size: 19 Copynumber: 16.4 Consensus size: 19
1101264 CGGAAAATAC
*
1101274 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1101293 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1101307 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1101327 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1101341 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101360 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1101378 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1101392 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1101411 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101430 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101449 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101468 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101487 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1101505 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1101519 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1101557 AATCGCAA
1 AATCGCAA
1101565 CGAGATAATC
Statistics
Matches: 243, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 3 0.01
16 21 0.09
17 3 0.01
18 20 0.08
19 145 0.60
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1101394 original size:51 final size:55
Alignment explanation
Indices: 1101302--1101586 Score: 361
Period size: 51 Copynumber: 5.4 Consensus size: 55
1101292 AAATCCCAAC
*
1101302 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGA-G-AATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
*
1101355 ATGAAAATCGCAATGCGAAATG-AAATCGCAA-CGACA-G-AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
*
1101406 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAA
1101463 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATGAAATCGCAATGCGAA
1101517 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAA
*
1101567 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
1101587 TATAAACGCA
Statistics
Matches: 219, Mismatches: 4, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
50 2 0.01
51 85 0.39
52 42 0.19
53 17 0.08
54 9 0.04
55 1 0.00
56 9 0.04
57 54 0.25
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
Found at i:1101424 original size:70 final size:73
Alignment explanation
Indices: 1101274--1101586 Score: 330
Period size: 70 Copynumber: 4.5 Consensus size: 73
1101264 CGGAAAATAC
* *
1101274 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAA-GC-GAAATG-AAATCGCA
*
1101334 A--CG--A-GAG
62 ATGCGAAATGAA
*
1101341 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA-CGACA-G-AATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAGCGAAATGAAATCGCAATGC
*
1101403 GAAATTAA
66 GAAATGAA
1101411 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAA-GCGAAATG-AAATCGCAA
1101476 TGCGAAATGAA
63 TGCGAAATGAA
1101487 AATCGCAATGCGAAATG-AAATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA-GCGAAATG-AAATCGCAAT
1101547 GCGAAATGAA
64 GCGAAATGAA
*
1101557 AATCGCAA--CG--A-GATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1101587 TATAAACGCA
Statistics
Matches: 218, Mismatches: 8, Indels: 38
0.83 0.03 0.14
Matches are distributed among these distances:
65 9 0.04
66 9 0.04
67 28 0.13
68 10 0.05
69 3 0.01
70 83 0.38
71 18 0.08
72 4 0.02
73 9 0.04
74 1 0.00
75 9 0.04
76 35 0.16
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (73 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAGCGAAATGAAATCGCAATGC
GAAATGAA
Found at i:1101484 original size:127 final size:127
Alignment explanation
Indices: 1101274--1101586 Score: 458
Period size: 127 Copynumber: 2.6 Consensus size: 127
1101264 CGGAAAATAC
* *
1101274 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
1101334 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAG
*
1101392 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1101457 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAG
*
1101519 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1101579 TGCGAAAT
66 TGCGAAAT
1101587 TATAAACGCA
Statistics
Matches: 178, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
118 24 0.13
120 1 0.01
122 34 0.19
123 17 0.10
124 2 0.01
125 2 0.01
126 1 0.01
127 97 0.54
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (127 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAG
Found at i:1101702 original size:19 final size:19
Alignment explanation
Indices: 1101593--1101694 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1101583 AAATTATAAA
1101593 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1101612 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1101632 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1101648 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1101665 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1101684 CGCATTGCGAT
1 CGCATTGCGAT
1101695 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1101820 original size:14 final size:14
Alignment explanation
Indices: 1101801--1101837 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1101791 CATCAATTAC
1101801 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1101815 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1101829 ACAAATCAA
1 ACAAATCAA
1101838 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1103799 original size:14 final size:14
Alignment explanation
Indices: 1103780--1103836 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1103770 CGCGAAATGA
*
1103780 AATCGCAACGACAG
1 AATCGCAACGAAAG
1103794 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1103811 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1103827 AATCGCAACG
1 AATCGCAACG
1103837 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1103818 original size:19 final size:19
Alignment explanation
Indices: 1103725--1103858 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1103715 TAGTTTACTT
* *
1103725 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1103745 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1103764 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1103782 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1103796 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1103815 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1103829 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1103848 TCGCAATGCGA
1 TCGCAACGCGA
1103859 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
15 1 0.01
16 14 0.15
17 7 0.07
18 9 0.09
19 37 0.39
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1103819 original size:51 final size:47
Alignment explanation
Indices: 1103743--1103836 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
1103733 CGAAACTTAA
1103743 AATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAATCGCAACGACAG
1 AATCGCAACGCGAAACCAAAATCGCAA--CGAAA-G-AATCGCAACGACAG
* **
1103794 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAACG
1 AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACG
1103837 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 10 0.25
48 1 0.03
49 5 0.12
51 24 0.60
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (47 bp):
AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACGACAG
Found at i:1103821 original size:33 final size:33
Alignment explanation
Indices: 1103762--1103853 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1103752 GCGAAACCAA
*
1103762 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1103794 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1103827 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1103854 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 16 0.29
33 40 0.71
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1103876 original size:19 final size:19
Alignment explanation
Indices: 1103854--1103982 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1103844 AAAATCGCAA
1103854 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1103873 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1103887 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1103906 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1103920 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1103939 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1103958 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1103978 TGCGA
1 TGCGA
1103983 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1103896 original size:33 final size:33
Alignment explanation
Indices: 1103854--1103945 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1103844 AAAATCGCAA
1103854 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1103887 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1103920 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1103946 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1104183 original size:92 final size:93
Alignment explanation
Indices: 1104026--1104493 Score: 876
Period size: 92 Copynumber: 5.1 Consensus size: 93
1104016 TTGAATGGAT
1104026 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1104090 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1104118 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1104182 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1104210 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1104274 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1104302 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1104366 AGTTTAGCAGAATTGGCAGC-ACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1104393 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1104457 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1104485 AAATTTACT
1 AAATTTACT
1104494 AAGCAATCTA
Statistics
Matches: 368, Mismatches: 3, Indels: 10
0.97 0.01 0.03
Matches are distributed among these distances:
90 22 0.06
91 71 0.19
92 267 0.73
93 8 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1106204 original size:14 final size:14
Alignment explanation
Indices: 1106185--1106274 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1106175 TTGAAATGAA
1106185 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1106199 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1106216 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1106232 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1106251 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1106265 AATCGCAACG
1 AATCGCAACG
1106275 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1106222 original size:33 final size:33
Alignment explanation
Indices: 1106177--1106291 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1106167 TCTTTTGGTT
1106177 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1106210 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1106243 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1106276 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1106292 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1106223 original size:19 final size:18
Alignment explanation
Indices: 1106184--1106296 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1106174 GTTGAAATGA
1106184 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1106199 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1106216 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1106232 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1106249 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1106265 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1106282 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1106297 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1106327 original size:14 final size:14
Alignment explanation
Indices: 1106308--1106362 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1106298 TTTGGTTTCG
1106308 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1106322 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1106341 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1106355 CGTTGCGA
1 CGTTGCGA
1106363 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1106340 original size:33 final size:33
Alignment explanation
Indices: 1106292--1106362 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1106282 AAAATCGCAA
**
1106292 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1106325 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1106358 TGCGA
1 TGCGA
1106363 CAGTCATTCT
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:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1106370 original size:33 final size:33
Alignment explanation
Indices: 1106303--1106384 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1106293 GCGATTTTGG
***
1106303 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1106336 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1106369 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1106385 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1106389 original size:20 final size:20
Alignment explanation
Indices: 1106315--1106403 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1106305 TCGCGTTGCG
1106315 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1106335 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1106348 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1106368 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1106388 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1106404 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1106524 original size:33 final size:33
Alignment explanation
Indices: 1106482--1106552 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1106472 AATACTAACT
*
1106482 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1106515 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1106548 TGAAA
1 TGAAA
1106553 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1106783 original size:22 final size:22
Alignment explanation
Indices: 1106731--1106783 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1106721 TGGTTGTGAG
**
1106731 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1106753 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1106775 GGATTTCTT
1 GGATTTCTT
1106784 TGCCGTAGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1106954 original size:20 final size:20
Alignment explanation
Indices: 1106929--1107121 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1106919 CTTTAAATAT
1106929 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1106949 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1106971 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1106990 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1107010 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1107030 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1107050 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1107070 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1107090 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1107110 CGCGTTGCGATT
1 CGCGTTGCGATT
1107122 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1107116 original size:60 final size:60
Alignment explanation
Indices: 1106929--1107121 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1106919 CTTTAAATAT
**
1106929 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1106990 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1107050 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1107110 CGCGTTGCGATT
1 CGCGTTGCGATT
1107122 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1107201 original size:19 final size:20
Alignment explanation
Indices: 1107177--1107227 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1107167 AAGAATCGCG
*
1107177 TTGCGATTTTGGAAACTGA-
1 TTGCGATTCTGGAAACTGAT
1107196 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1107216 TTGCGATTCTGG
1 TTGCGATTCTGG
1107228 GATCGCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1111054 original size:61 final size:62
Alignment explanation
Indices: 1110956--1111098 Score: 256
Period size: 61 Copynumber: 2.3 Consensus size: 62
1110946 TTCCTTACCG
1110956 GCAAAAATCTGAGGTGGAAAGCCAAAATAATAGATTGTTGGCTGCATCGGTGATTAAGACCA
1 GCAAAAATCTGAGGTGGAAAGCCAAAATAATAGATTGTTGGCTGCATCGGTGATTAAGACCA
1111018 GCAAAAATCTGA-GTGGAAAGCCAAAAT-ATAGAATTGTTGGCTGCATCGGTGATTAAGACCA
1 GCAAAAATCTGAGGTGGAAAGCCAAAATAATAG-ATTGTTGGCTGCATCGGTGATTAAGACCA
1111079 -CAAAAATCTGAGGTGGAAAG
1 GCAAAAATCTGAGGTGGAAAG
Statistics
Matches: 79, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
60 15 0.19
61 52 0.66
62 12 0.15
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (62 bp):
GCAAAAATCTGAGGTGGAAAGCCAAAATAATAGATTGTTGGCTGCATCGGTGATTAAGACCA
Done.