Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000939.1 Hibiscus syriacus cultivar Beakdansim tig00001875_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: 54498
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:647 original size:2 final size:2
Alignment explanation
Indices: 640--712 Score: 123
Period size: 2 Copynumber: 37.5 Consensus size: 2
630 ATTATATCTC
*
640 AT AT AT AT -T AT AT AT AT AT AG AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
680 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
713 ATTATATCTA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5931 original size:21 final size:21
Alignment explanation
Indices: 5906--5954 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5896 CAACTATATT
* *
5906 TTTAATTTTA-AATTATTTAGA
1 TTTAATTTGATAA-TATTTAAA
*
5927 TTTAAATTGATAATATTTAAA
1 TTTAATTTGATAATATTTAAA
5948 TTTAATT
1 TTTAATT
5955 CAATTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTAATTTGATAATATTTAAA
Found at i:16236 original size:2 final size:2
Alignment explanation
Indices: 16229--16265 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16219 TTGAATATGT
16229 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16266 GTTCACAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16335 original size:36 final size:36
Alignment explanation
Indices: 16290--16547 Score: 257
Period size: 36 Copynumber: 7.2 Consensus size: 36
16280 TGAAAATACG
*
16290 TATATAATATATATTTTTAAAAACCTTTTGAAAA-T
1 TATATAATATATATTTTTAAAAACATTTTGAAAACT
* **
16325 GAATATAATAT-GGTTTTT-AAAACACTTTTGAAAAC-
1 -TATATAATATATATTTTTAAAAACA-TTTTGAAAACT
* *
16360 TGTATAATATATAGTTTTT-AAAATATTTTAGGAAAA--
1 TATATAATATATA-TTTTTAAAAACATTTT--GAAAACT
*
16396 TATATAATATATGATTTTTAAAATCATTTTGAAAACT
1 TATATAATATAT-ATTTTTAAAAACATTTTGAAAACT
* *
16433 TATATAATATA-ATTTTTGAAAACATTTTTTAAAACT
1 TATATAATATATATTTTTAAAAACA-TTTTGAAAACT
*
16469 TATATAATATATAGTTTTTGAAAACATTTTGAAAACT
1 TATATAATATATA-TTTTTAAAAACATTTTGAAAACT
*
16506 TATAT-ATATATGATTTTTGAAAACATTTTTGAAAA-T
1 TATATAATATAT-ATTTTTAAAAACA-TTTTGAAAACT
16542 TATATA
1 TATATA
16548 GTTTTTAAAA
Statistics
Matches: 190, Mismatches: 16, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
34 13 0.07
35 34 0.18
36 80 0.42
37 51 0.27
38 12 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (36 bp):
TATATAATATATATTTTTAAAAACATTTTGAAAACT
Found at i:16357 original size:73 final size:71
Alignment explanation
Indices: 16290--16547 Score: 287
Period size: 73 Copynumber: 3.6 Consensus size: 71
16280 TGAAAATACG
*
16290 TATATAATATATATTTTTAAAAAC-CTTTTGAAAATGA-AT-ATAATATGGTTTTTAAAACACTT
1 TATATAATATATATTTTTAAAAACATTTTTGAAAAT-ATATAAT-ATATGGTTTTTAAAACA-TT
16352 TTGAAAAC-
63 TTGAAAACT
* * * *
16360 TGTATAATATATAGTTTTT-AAAATATTTTAGGAAAATATATAATATATGATTTTTAAAATCATT
1 TATATAATATATA-TTTTTAAAAACATTTT-TGAAAATATATAATATATGGTTTTTAAAA-CATT
16424 TTGAAAACT
63 TTGAAAACT
* * *
16433 TATATAATATA-ATTTTTGAAAACATTTTTTAAAACTTATATAATATATAGTTTTTGAAAACATT
1 TATATAATATATATTTTTAAAAACATTTTTGAAAA--TATATAATATATGGTTTTT-AAAACATT
16497 TTGAAAACT
63 TTGAAAACT
*
16506 TATAT-ATATATGATTTTTGAAAACATTTTTGAAAATTATATA
1 TATATAATATAT-ATTTTTAAAAACATTTTTGAAAA-TATATA
16548 GTTTTTAAAA
Statistics
Matches: 163, Mismatches: 12, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
70 16 0.10
71 18 0.11
72 47 0.29
73 56 0.34
74 26 0.16
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (71 bp):
TATATAATATATATTTTTAAAAACATTTTTGAAAATATATAATATATGGTTTTTAAAACATTTTG
AAAACT
Found at i:16566 original size:31 final size:32
Alignment explanation
Indices: 16525--16611 Score: 122
Period size: 31 Copynumber: 2.7 Consensus size: 32
16515 ATGATTTTTG
16525 AAAACATTTTTGAAAATTATATAGTTTTT-AA
1 AAAACATTTTTGAAAATTATATAGTTTTTAAA
* * *
16556 AAAACTTTTTTTAAGATTATATAGTTTTTAAA
1 AAAACATTTTTGAAAATTATATAGTTTTTAAA
*
16588 AAAACATTTTTGAAATTTTATATA
1 AAAACATTTTTGAAA-ATTATATA
16612 TAATATATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 26 0.55
32 14 0.30
33 7 0.15
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (32 bp):
AAAACATTTTTGAAAATTATATAGTTTTTAAA
Found at i:16620 original size:42 final size:38
Alignment explanation
Indices: 16571--16670 Score: 128
Period size: 42 Copynumber: 2.5 Consensus size: 38
16561 TTTTTTTAAG
**
16571 ATTATATAGTTTTTAAAAAAACATTTTTGAAATTTTATAT
1 ATTATATAGTTTTTAAAAAAACATTTTT-AAAAATT-TAT
* *
16611 ATAATATATAGTTTTTTAAAAAACCTTTTTAAAAATTTAT
1 AT--TATATAGTTTTTAAAAAAACATTTTTAAAAATTTAT
16651 ATTATATAGTTTTTAAAAAA
1 ATTATATAGTTTTTAAAAAA
16671 TACTTTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
38 17 0.32
40 7 0.13
41 5 0.09
42 24 0.45
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTTAT
Found at i:17349 original size:28 final size:29
Alignment explanation
Indices: 17318--17379 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
17308 AAAAACAAGA
*
17318 AAGCAAATATTCTACACAA-AAAACCCAC
1 AAGCAAATATTATACACAAGAAAACCCAC
17346 AAGCAAATATTATACACAAGAAAACCCAC
1 AAGCAAATATTATACACAAGAAAACCCAC
*
17375 GAGCA
1 AAGCA
17380 CAAGACCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.53, C:0.26, G:0.08, T:0.13
Consensus pattern (29 bp):
AAGCAAATATTATACACAAGAAAACCCAC
Found at i:17930 original size:5 final size:5
Alignment explanation
Indices: 17920--17964 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
17910 CATTTTTATA
* * *
17920 TATTT TATTT TATTT TGTTT TATTT TACTTT TTTTT TGTTT TATT
1 TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATT
17965 AATATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:17956 original size:21 final size:20
Alignment explanation
Indices: 17920--17964 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
17910 CATTTTTATA
17920 TATTTTATTTTATTTTGTTT
1 TATTTTATTTTATTTTGTTT
*
17940 TATTTTACTTTTTTTTTGTTT
1 TATTTTA-TTTTATTTTGTTT
17961 TATT
1 TATT
17965 AATATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (20 bp):
TATTTTATTTTATTTTGTTT
Found at i:18056 original size:15 final size:15
Alignment explanation
Indices: 18037--18078 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
18027 CTACTTTATT
18037 TTTTTTTATTTT-AC
1 TTTTTTTATTTTGAC
*
18051 TATTTTTCATTTTGAC
1 T-TTTTTTATTTTGAC
18067 TTTTTATTATTT
1 TTTTT-TTATTT
18079 GTTTTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTTATTTTGAC
Found at i:18100 original size:35 final size:36
Alignment explanation
Indices: 18045--18122 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
18035 TTTTTTTTTA
*
18045 TTTTACTATTTTTCATTTTGA-CTTTTTATTATTTG
1 TTTTTCTATTTTTCATTTTGATCTTTTTATTATTTG
*
18080 TTTTTCTATTTTTC-TATTTGATTTTTTTATTATTTG
1 TTTTTCTATTTTTCAT-TTTGATCTTTTTATTATTTG
18116 TTTTTCT
1 TTTTTCT
18123 TACATGTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 1 0.03
35 18 0.46
36 20 0.51
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (36 bp):
TTTTTCTATTTTTCATTTTGATCTTTTTATTATTTG
Found at i:18161 original size:2 final size:2
Alignment explanation
Indices: 18156--18185 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18146 TCTTTTTTTA
18156 AT 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 AT
18186 TATCTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18275 original size:10 final size:11
Alignment explanation
Indices: 18250--18275 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18240 ACTCCATTAC
18250 TTTTTCCTTTA
1 TTTTTCCTTTA
18261 TTTTTCCTTTA
1 TTTTTCCTTTA
18272 TTTT
1 TTTT
18276 GTTTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCCTTTA
Found at i:18286 original size:15 final size:14
Alignment explanation
Indices: 18268--18328 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 14
18258 TTATTTTTCC
18268 TTTATTTTGTTTTT
1 TTTATTTTGTTTTT
*
18282 GTTTA--TTGCTTTT
1 -TTTATTTTGTTTTT
* *
18295 TTTATTTTGTATGT
1 TTTATTTTGTTTTT
*
18309 TTTATTTTTGTTTAT
1 TTTA-TTTTGTTTTT
18324 TTTAT
1 TTTAT
18329 CAGTCTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.11
13 7 0.19
14 10 0.27
15 16 0.43
ACGTcount: A:0.11, C:0.02, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTATTTTGTTTTT
Found at i:18356 original size:19 final size:18
Alignment explanation
Indices: 18319--18379 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
18309 TTTATTTTTG
*
18319 TTTATTTTATCA-GTCTA
1 TTTATTTTATCATTTCTA
*
18336 TTTATTTTGTTCATTTCTA
1 TTTATTTT-ATCATTTCTA
18355 TTTTATTTTATCATTT-T-
1 -TTTATTTTATCATTTCTA
18372 TTTATTTT
1 TTTATTTT
18380 TTTATGTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.21
17 8 0.21
18 4 0.11
19 10 0.26
20 8 0.21
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTATTTTATCATTTCTA
Found at i:25816 original size:84 final size:85
Alignment explanation
Indices: 25653--25817 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 85
25643 CTCGTTGAGT
* * * * * * *
25653 TCATTGATTAAAATAAGTATTCTTCTTCTTTAAAGTTCCAATTTCGAACAACTGTATCTGCAAAG
1 TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAACTGTATCAGCAAAA
* *
25718 TGTGGATGTATCAATTAAAC
66 AGTGGACGTATCAATTAAAC
* *
25738 TCATTAATTAAAAGAAATATTCTTCTTCTTT-AAGTTCAAAGTTCGAACAATTGTGTCAGCAAAA
1 TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAACTGTATCAGCAAAA
*
25802 AGTGTACGTATCAATT
66 AGTGGACGTATCAATT
25818 GATAAGAAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 40 0.59
85 28 0.41
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (85 bp):
TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAACTGTATCAGCAAAA
AGTGGACGTATCAATTAAAC
Found at i:29168 original size:20 final size:20
Alignment explanation
Indices: 29143--29181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29133 TGTGGCGGCG
*
29143 GACGGCTGACGGCGGCAGCA
1 GACGGCGGACGGCGGCAGCA
*
29163 GACGGCGGGCGGCGGCAGC
1 GACGGCGGACGGCGGCAGC
29182 GGCCAGCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.31, G:0.51, T:0.03
Consensus pattern (20 bp):
GACGGCGGACGGCGGCAGCA
Found at i:29190 original size:20 final size:20
Alignment explanation
Indices: 29152--29192 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29142 GGACGGCTGA
*
29152 CGGCGGCAGCAGACGGCGGG
1 CGGCGGCAGCAGACAGCGGG
* *
29172 CGGCGGCAGCGGCCAGCGGG
1 CGGCGGCAGCAGACAGCGGG
29192 C
1 C
29193 AACAGACGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.34, G:0.54, T:0.00
Consensus pattern (20 bp):
CGGCGGCAGCAGACAGCGGG
Found at i:35004 original size:69 final size:69
Alignment explanation
Indices: 34922--35052 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 69
34912 AATTTCACGT
* * **
34922 TCCCTGTCTCGTTC-ACGATCACTCTCGTGCCTTCTTGACCTGCTACTGCTTCTCTCTCTCCTCT
1 TCCCTCTCCCGTTCTAC-ATCACTCTCGTGCCTTCTCAACCTGCTACTGCTTCTCTCTCTCCTCT
34986 CCCTC
65 CCCTC
* * * *
34991 TCCCTCTCCCGTTCTTCCTCCCTTTCGTGCCTTCTCAACCTGCTACTGCTTCTCTCTCTCCT
1 TCCCTCTCCCGTTCTACATCACTCTCGTGCCTTCTCAACCTGCTACTGCTTCTCTCTCTCCT
35053 TTCTTCCTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 52 0.98
70 1 0.02
ACGTcount: A:0.06, C:0.45, G:0.10, T:0.39
Consensus pattern (69 bp):
TCCCTCTCCCGTTCTACATCACTCTCGTGCCTTCTCAACCTGCTACTGCTTCTCTCTCTCCTCTC
CCTC
Found at i:35154 original size:33 final size:33
Alignment explanation
Indices: 35042--35154 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
35032 GCTACTGCTT
*
35042 CTCTCTCTCCTTTCTTCCTCCCTTTCCCTTTCC
1 CTCTCTCTCCTCTCTTCCTCCCTTTCCCTTTCC
* * *
35075 CTTTCCCTCCTCTCCCTATCCTTCTCTTTCTCCTTATCC
1 CTCTCTCTCCTCT--CT-TCC-TCCCTTTC-CCTT-TCC
* *
35114 CTATCTCTCCTCTCTCTCC-CCCTTTCCATTTCC
1 CTCTCTCTCCTCTCT-TCCTCCCTTTCCCTTTCC
35147 CTCTCTCT
1 CTCTCTCT
35155 AATGCTCCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
33 20 0.31
34 3 0.05
35 8 0.12
36 3 0.05
37 12 0.19
38 4 0.06
39 14 0.22
ACGTcount: A:0.04, C:0.50, G:0.00, T:0.46
Consensus pattern (33 bp):
CTCTCTCTCCTCTCTTCCTCCCTTTCCCTTTCC
Found at i:35265 original size:57 final size:57
Alignment explanation
Indices: 35194--35316 Score: 201
Period size: 57 Copynumber: 2.2 Consensus size: 57
35184 CTCTCTCCCT
* *
35194 ATCGCGGCTGCTTCTATGGCGTTCCTTATCACGGTCTCGCCTCTCCTCACCGTCCTC
1 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
**
35251 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCGTCGTCCTC
1 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
*
35308 GTCGCGGCT
1 ATCGCGGCT
35317 GCCTCTCGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.08, C:0.40, G:0.20, T:0.32
Consensus pattern (57 bp):
ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
Found at i:36169 original size:33 final size:33
Alignment explanation
Indices: 36127--36215 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
36117 AACACGTTGG
*
36127 GCATCCGAGGCCATCCGACCGAGCTATGCGAGA
1 GCATCCGAGGACATCCGACCGAGCTATGCGAGA
* *
36160 GCATCCGAGGTCATCCGACCGAGCTATGCTAGA
1 GCATCCGAGGACATCCGACCGAGCTATGCGAGA
*
36193 GCATCCGAGGATATCCGACCGAG
1 GCATCCGAGGACATCCGACCGAG
36216 GCCATCCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.25, C:0.31, G:0.29, T:0.15
Consensus pattern (33 bp):
GCATCCGAGGACATCCGACCGAGCTATGCGAGA
Found at i:36281 original size:80 final size:80
Alignment explanation
Indices: 36131--36281 Score: 214
Period size: 80 Copynumber: 1.9 Consensus size: 80
36121 CGTTGGGCAT
* * *
36131 CCGAGGCCATCCGACCGAGCTATGCGAGAGCATCCGAGGTCATCCGACCGAGCTATGCTAGAGCA
1 CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGAGGTCAGCCGACCGAGCTATGCGAGAGCA
*
36196 TCCGAGGATATCCGA
66 GCCGAGGATATCCGA
* * * *
36211 CCGAGGCCATCCGAACGAGCTATGCGGGGGCATCCGATGG-CAGCCGAGCGAGCTATGCGAGGGC
1 CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGA-GGTCAGCCGACCGAGCTATGCGAGAGC
36275 AGCCGAG
65 AGCCGAG
36282 CGAGGGTAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 60 0.97
81 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.34, T:0.13
Consensus pattern (80 bp):
CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGAGGTCAGCCGACCGAGCTATGCGAGAGCA
GCCGAGGATATCCGA
Found at i:36322 original size:29 final size:29
Alignment explanation
Indices: 36289--36403 Score: 196
Period size: 29 Copynumber: 4.0 Consensus size: 29
36279 GAGCGAGGGT
36289 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
36318 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
36347 AGGTCGCCCGGAGTGCATGGCGACCTATA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
36376 AGGTCGCCTGGAAG-GCATGGCGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
36404 GGCCAACACT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
29 80 0.98
30 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:38656 original size:29 final size:29
Alignment explanation
Indices: 38601--38656 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
38591 AAAATATGCG
*
38601 ATGACATAGATTATTTTATTATTTTTATT
1 ATGACATAGATTATTTTATTATATTTATT
38630 ATGACATA-ATGT-TTTTATTAATATTTA
1 ATGACATAGAT-TATTTTATT-ATATTTA
38657 ATGTCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (29 bp):
ATGACATAGATTATTTTATTATATTTATT
Found at i:40877 original size:14 final size:14
Alignment explanation
Indices: 40858--40905 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
40848 ACCAAAATAT
40858 TTTTAATTCCTCCA
1 TTTTAATTCCTCCA
* **
40872 TTTTAATTCTTATA
1 TTTTAATTCCTCCA
40886 TTTTTAATTCCTCCA
1 -TTTTAATTCCTCCA
40901 TTTTA
1 TTTTA
40906 GGGTAAATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATTCCTCCA
Found at i:40903 original size:15 final size:15
Alignment explanation
Indices: 40856--40904 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
40846 CCACCAAAAT
40856 ATTTTTAATTCCTCC
1 ATTTTTAATTCCTCC
* **
40871 A-TTTTAATTCTTAT
1 ATTTTTAATTCCTCC
40885 ATTTTTAATTCCTCC
1 ATTTTTAATTCCTCC
40900 ATTTT
1 ATTTT
40905 AGGGTAAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAATTCCTCC
Found at i:51934 original size:31 final size:31
Alignment explanation
Indices: 51899--51972 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
51889 GGTTCGTCCG
51899 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
1 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
** * *
51930 ATTTAAGTCTTTAACGTTATCGGTCCGTTCG
1 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
*
51961 ATTTTAGTCCCT
1 ATTTAAGTCCCT
51973 CAATCATGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (31 bp):
ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
Found at i:54042 original size:42 final size:41
Alignment explanation
Indices: 53979--54058 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 41
53969 TTAAATTGAG
*
53979 GCTCCTAATTTTTTAATCTCATATTTTACATT-TATAATGAA
1 GCTCCTAATTTTTCAATCTCATATTTTA-ATTATATAATGAA
*
54020 GCTCCTAACTTTTTCAATCTCATTTTTTAATTATATAAT
1 GCTCCTAA-TTTTTCAATCTCATATTTTAATTATATAAT
54059 TTAGGCCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 11 0.31
42 24 0.69
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.50
Consensus pattern (41 bp):
GCTCCTAATTTTTCAATCTCATATTTTAATTATATAATGAA
Found at i:54144 original size:86 final size:85
Alignment explanation
Indices: 53951--54165 Score: 204
Period size: 86 Copynumber: 2.5 Consensus size: 85
53941 TATATGTCAA
* * * * * * *
53951 CAATCTTACTTTCCACCTTTA-AATTGAGGCTCCTAATTTTTT-AATCTCATATTTTACATTTAT
1 CAATCTTACTTTTCACCTTTATAATTAAGGCCCCTAATTTTTTCAAGCTAACATTTTACATTTAA
*
54014 AATGAAGCTCCTAACTTTTT
66 AATGAAGCCCCTAACTTTTT
* * * * * *
54034 CAATCTCATTTTTTA-ATTATATAATTTAGGCCCCTAATTTTTTCAAGCTAACCTTTTACATTTA
1 CAATCTTACTTTTCACCTT-TATAATTAAGGCCCCTAATTTTTTCAAGCTAACATTTTACATTTA
*
54098 AAATTG-AGTCCCCTAATTTTTT
65 AAA-TGAAG-CCCCTAACTTTTT
* * * *
54120 TAATCTTACTTTTGACCTTTATAATTAAGGTCCTTAATTTTTTCAA
1 CAATCTTACTTTTCACCTTTATAATTAAGGCCCCTAATTTTTTCAA
54166 TCATACTTTT
Statistics
Matches: 104, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
82 2 0.02
83 13 0.12
84 19 0.18
85 20 0.19
86 48 0.46
87 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (85 bp):
CAATCTTACTTTTCACCTTTATAATTAAGGCCCCTAATTTTTTCAAGCTAACATTTTACATTTAA
AATGAAGCCCCTAACTTTTT
Found at i:54158 original size:43 final size:41
Alignment explanation
Indices: 53951--54177 Score: 158
Period size: 43 Copynumber: 5.4 Consensus size: 41
53941 TATATGTCAA
* * *
53951 CAATCTTACTTTCCACCTTTA-AATTGAGGCTCCTAATTTTTT
1 CAATCTTACTTT-TACATTTATAATTAAGG-TCCTAATTTTTT
* * *
53993 -AATCTCATA-TTTTACATTTATAATGAAGCTCCTAACTTTTT
1 CAATCT--TACTTTTACATTTATAATTAAGGTCCTAATTTTTT
* * * *
54034 CAATCTCATTTTTTA-ATTATATAATTTAGGCCCCTAATTTTTT
1 CAATCTTA-CTTTTACATT-TATAATTAAGG-TCCTAATTTTTT
* * * *
54077 CAAGCTAACCTTTTACATTTAAAATTGA-GTCCCCTAATTTTTT
1 CAATCTTA-CTTTTACATTTATAATTAAGGT--CCTAATTTTTT
* *
54120 TAATCTTACTTTTGACCTTTATAATTAAGGTCCTTAATTTTTT
1 CAATCTTACTTTT-ACATTTATAATTAAGGTCC-TAATTTTTT
*
54163 CAATCATACTTTTAC
1 CAATCTTACTTTTAC
54178 TTTTTTATAG
Statistics
Matches: 144, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
40 1 0.01
41 25 0.17
42 36 0.25
43 77 0.53
44 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (41 bp):
CAATCTTACTTTTACATTTATAATTAAGGTCCTAATTTTTT
Done.