Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001525.1 Hibiscus syriacus cultivar Beakdansim tig00002991_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: 86539
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3040 original size:40 final size:41
Alignment explanation
Indices: 2977--3055 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
2967 ATCACAACGC
2977 GAATATGACTATCACAACACGGAAATGACTATCGCAATGCG
1 GAATATGACTATCACAACACGGAAATGACTATCGCAATGCG
* *
3018 GAAT-TGACTATCGCAACGCGGAAATGACTATCGCAATG
1 GAATATGACTATCACAACACGGAAATGACTATCGCAATG
3056 AGAGAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (41 bp):
GAATATGACTATCACAACACGGAAATGACTATCGCAATGCG
Found at i:3050 original size:20 final size:20
Alignment explanation
Indices: 2971--3053 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
2961 ACGGAAATCA
*
2971 CAACGC-GAATATGACTATCA
1 CAACGCGGAA-ATGACTATCG
*
2991 CAACACGGAAATGACTATCG
1 CAACGCGGAAATGACTATCG
* *
3011 CAATGCGGAATTGACTATCG
1 CAACGCGGAAATGACTATCG
3031 CAACGCGGAAATGACTATCG
1 CAACGCGGAAATGACTATCG
3051 CAA
1 CAA
3054 TGAGAGAATC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 52 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
CAACGCGGAAATGACTATCG
Found at i:3115 original size:34 final size:33
Alignment explanation
Indices: 3027--3122 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
3017 GGAATTGACT
* ** *
3027 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
3061 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3094 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
3123 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3118 original size:20 final size:19
Alignment explanation
Indices: 3060--3128 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
3050 GCAATGAGAG
3060 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3079 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
3093 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
3113 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
3129 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3180 original size:34 final size:34
Alignment explanation
Indices: 3137--3232 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
3127 ATTAGTTTCG
3137 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
3171 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
3204 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
3233 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:3350 original size:13 final size:13
Alignment explanation
Indices: 3334--3368 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3324 CATCAATTAA
3334 ACAAATCAACATT
1 ACAAATCAACATT
* *
3347 ACAAATCATCTTT
1 ACAAATCAACATT
3360 ACAAATCAA
1 ACAAATCAA
3369 TTAAACAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (13 bp):
ACAAATCAACATT
Found at i:5332 original size:20 final size:20
Alignment explanation
Indices: 5309--5415 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
5299 GAAACTTAAA
* *
5309 ATCGCAACGCGAAAATGAAT
1 ATCGCAATGCGAAAATGACT
5329 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
5349 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
5369 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
5389 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
5409 ATCGCAA
1 ATCGCAA
5416 CGAGAGAATC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:5503 original size:20 final size:20
Alignment explanation
Indices: 5480--5585 Score: 125
Period size: 20 Copynumber: 5.6 Consensus size: 20
5470 GTTAAATTTA
5480 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
5500 CATTGCGGTAATCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
5520 CATTGTGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
5536 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
5554 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
5574 CATTGCGATAGT
1 CATTGCGATAGT
5586 AAAACTATTC
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
18 6 0.08
20 54 0.75
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:5530 original size:74 final size:74
Alignment explanation
Indices: 5441--5580 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 74
5431 GCGATTTTCA
*
5441 TTTCGCATTGCGATTCTTTCGTTGCGATAGTTAAATTT-ACATTGCGATAGTCATTTTCGCATTG
1 TTTCGCATTGCGATTCTCTCGTTGCGATAG-TAAATTTCACATTGCGATAGTCATTTTCGCATTG
5505 CGGTAATCAT
65 CGGTAATCAT
* * * * *
5515 TTTCGCATTGTGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGC
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTAAATTTCACATTGCGATAGTCATTTTCGCATTGC
5580 G
66 G
5581 ATAGTAAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 5 0.08
74 54 0.92
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (74 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTAAATTTCACATTGCGATAGTCATTTTCGCATTGC
GGTAATCAT
Found at i:7474 original size:20 final size:20
Alignment explanation
Indices: 7451--7505 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
7441 CTGAAACTTT
7451 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
* *
7471 AAATCGTAACACTAAAATGA
1 AAATCGCAACACGAAAATGA
** *
7491 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
7506 TTTGACTATC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:7618 original size:20 final size:20
Alignment explanation
Indices: 7564--7619 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
7554 GCGATTCTCT
**
7564 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
7584 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
7604 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
7620 CTCGGTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:7980 original size:22 final size:22
Alignment explanation
Indices: 7919--7980 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
7909 TGACCGTGAA
* *
7919 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
7941 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
7959 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
7981 GGATGTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:8198 original size:20 final size:20
Alignment explanation
Indices: 8175--8227 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
8165 CGATAGTCAG
*
8175 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
8195 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
8215 AATCGCATTGCGA
1 ATTCGCATTGCGA
8228 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:8241 original size:21 final size:20
Alignment explanation
Indices: 8215--8269 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
8205 CGATTTACGT
*
8215 AATCGCATTGCGAATTAGGAA
1 AATCGCAATGCGAATTAGG-A
* *
8236 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAA-TTAGGA
8257 AATCGCAATGCGA
1 AATCGCAATGCGA
8270 TAGTCAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGAATTAGGA
Found at i:11216 original size:82 final size:82
Alignment explanation
Indices: 11116--11266 Score: 214
Period size: 82 Copynumber: 1.8 Consensus size: 82
11106 TAAATTTAGC
* * *
11116 GGCGTTTTTATACAAAACGCCATAACAAAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCA
1 GGCGTTTTTAAACAAAACGCCATAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCGCA
11181 ATAGGTTCATCCATAGT
66 ATAGGTTCATCCATAGT
* * * *
11198 GGCGTTTTTTAAAC-AAACGTCGTGACATAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCGC
1 GGCG-TTTTTAAACAAAACGCCATAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCGC
*
11262 TATAG
65 AATAG
11267 ACACGTAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 52 0.87
83 8 0.13
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (82 bp):
GGCGTTTTTAAACAAAACGCCATAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCGCA
ATAGGTTCATCCATAGT
Found at i:11248 original size:41 final size:41
Alignment explanation
Indices: 11110--11298 Score: 136
Period size: 41 Copynumber: 4.6 Consensus size: 41
11100 AATTGGTAAA
* * *
11110 TTTAGCGGCGTTTTTATACAAAACGCCATAACAAAGTAGTAC
1 TTTAGCGGCGTTTTTATAC-AAACGCCGTAACATAGTAGAAC
* * ** *
11152 TTTAGTGGCGTTTTTATACAAACGCCG-CA-ATAGGTTCATC
1 TTTAGCGGCGTTTTTATACAAACGCCGTAACATA-GTAGAAC
** * * * *
11192 CATAGTGGCGTTTTTTAAACAAACGTCGTGACATAGTAGAAC
1 TTTAGCGGCG-TTTTTATACAAACGCCGTAACATAGTAGAAC
* *
11234 TTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT--AA-
1 TTTAGCGGCGTTTTTATACAAACGCCG-TA-ACATA-GTAGAAC
*
11275 TTTAGTGGCGTTTTTATACAAACG
1 TTTAGCGGCGTTTTTATACAAACG
11299 ACGCTATAGA
Statistics
Matches: 115, Mismatches: 25, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
39 2 0.02
40 12 0.10
41 60 0.52
42 33 0.29
43 6 0.05
44 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATACAAACGCCGTAACATAGTAGAAC
Found at i:11289 original size:82 final size:82
Alignment explanation
Indices: 11150--11507 Score: 287
Period size: 82 Copynumber: 4.4 Consensus size: 82
11140 ACAAAGTAGT
* * *** * *
11150 ACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCATCCA--TAGTGGCGTTTTTTAAACA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT-AATTTAGTGGCG-TTTTTAAACA
*
11213 AACGTCGTGAC-ATAG-TA-GA
64 AACG-C-TG-CTATAGACACGA
*
11232 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGGCGTTTTTATACAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGGCGTTTTTAAACAAA
11297 CGAC-GCTATAGACACGTA
66 CG-CTGCTATAGACACG-A
* * *
11315 A-TTTAGCGGC------ATACAAACGCCGCTATAGACACGTACTTTAGCGGCATTTTTATAA-AA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGGCGTTTTTA-AACAA
* *
11372 ACGCCGCTATAGACACGT
65 ACGCTGCTATAGACACGA
* * * * *
11390 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTGTGTTTAA-
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGGCG-TT-T-TTAAAC
* *
11454 AAACGCTGCTATAGACTCGT
63 AAACGCTGCTATAGACACGA
* *
11474 ACTTTAGCGGCGTTTGTAAACACAAACGCCGCTA
1 ACTTTAGCGGCGTTT-T-TATACAAACGCCGCTA
11508 AAGTTTAAAG
Statistics
Matches: 230, Mismatches: 26, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
75 2 0.01
76 64 0.28
77 1 0.00
79 1 0.00
80 5 0.02
81 2 0.01
82 92 0.40
83 12 0.05
84 34 0.15
85 3 0.01
86 14 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (82 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGGCGTTTTTAAACAAA
CGCTGCTATAGACACGA
Found at i:11304 original size:41 final size:41
Alignment explanation
Indices: 11232--11507 Score: 330
Period size: 41 Copynumber: 6.8 Consensus size: 41
11222 ACATAGTAGA
11232 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
* * *
11273 AATTTAGTGGCGTTTTTATACAAACGACGCTATAGACACGT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
*
11314 AATTTAGCGGC------ATACAAACGCCGCTATAGACACGT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
* *
11349 ACTTTAGCGGCATTTTTATAAAAACGCCGCTATAGACACGT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
* * *
11390 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
* * * * *
11431 ACTTTAGTGGCGTTTGTGTTTAAAAACGCTGCTATAGACTCGT
1 ACTTTAGCGGCGTTT-T-TATACAAACGCCGCTATAGACACGT
* *
11474 ACTTTAGCGGCGTTTGTAAACACAAACGCCGCTA
1 ACTTTAGCGGCGTTT-T-TATACAAACGCCGCTA
11508 AAGTTTAAAG
Statistics
Matches: 206, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.16
41 123 0.60
42 1 0.00
43 49 0.24
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (41 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
Found at i:11346 original size:76 final size:76
Alignment explanation
Indices: 11248--11484 Score: 296
Period size: 76 Copynumber: 3.0 Consensus size: 76
11238 GCGGCGTTTT
* *
11248 TATACAAACGCCGCTATAGACACGTAATTTAGTGGCGTTTTTATACAAACGACGCTATAGACACG
1 TATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTTATAAAAACG-CGCTATAGACACG
*
11313 TAATTTAGCGGC
65 TACTTTAGCGGC
* *
11325 -ATACAAACGCCGCTATAGACACGTACTTTAGCGGCATTTTTATAAAAACGCCGCTATAGACACG
1 TATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTTATAAAAACG-CGCTATAGACACG
*
11389 TACTTTAGTGGC
65 TACTTTAGCGGC
* *
11401 ATTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTGTGTTTAAAAACGCTGCTAT
1 -----TATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTT-T-TATAAAAACGC-GCTAT
*
11466 AGACTCGTACTTTAGCGGC
58 AGACACGTACTTTAGCGGC
11485 GTTTGTAAAC
Statistics
Matches: 138, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
76 69 0.50
82 36 0.26
83 2 0.01
84 31 0.22
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (76 bp):
TATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTTATAAAAACGCGCTATAGACACGT
ACTTTAGCGGC
Found at i:11929 original size:19 final size:20
Alignment explanation
Indices: 11905--11943 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
11895 AAATTGATTG
*
11905 TTGGTTTTGCTCTTG-TTGA
1 TTGGTTTCGCTCTTGCTTGA
11924 TTGGTTTCGCTCTTGCTTGA
1 TTGGTTTCGCTCTTGCTTGA
11944 GTGTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.05, C:0.15, G:0.26, T:0.54
Consensus pattern (20 bp):
TTGGTTTCGCTCTTGCTTGA
Found at i:14538 original size:23 final size:23
Alignment explanation
Indices: 14520--14580 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
14510 TCTATAGTAC
14520 GGTGTC-AT-TTATTTTTATAGT
1 GGTGTCAATATTATTTTTATAGT
* *
14541 GGTGTCAATATTA-TTTTAAAGG
1 GGTGTCAATATTATTTTTATAGT
*
14563 GGTGTCAATTTTATTTTT
1 GGTGTCAATATTATTTTT
14581 CATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 21 0.62
23 7 0.21
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (23 bp):
GGTGTCAATATTATTTTTATAGT
Found at i:15892 original size:21 final size:21
Alignment explanation
Indices: 15863--15919 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
15853 TGATTTATTA
*
15863 TTATAGATTTTAAGTATCTTG
1 TTATGGATTTTAAGTATCTTG
* * *
15884 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTTAAGTATCTTG
*
15905 TTATGGATGTTAAGT
1 TTATGGATTTTAAGT
15920 TTATTGGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.51
Consensus pattern (21 bp):
TTATGGATTTTAAGTATCTTG
Found at i:16104 original size:44 final size:44
Alignment explanation
Indices: 16056--16154 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
16046 TTTTACATTC
* *
16056 ACAAATGCCACTATATGACATA-ACATTTAGCGGCGTTTTTGGGA
1 ACAAACGCCACTATATGACA-AGACATTTAGCGGAGTTTTTGGGA
* * *
16100 ACAAACGCCGCTATATGCCAAGACATTTAGCGGAGTTTTT-GGC
1 ACAAACGCCACTATATGACAAGACATTTAGCGGAGTTTTTGGGA
16143 ACAAAACGCCAC
1 AC-AAACGCCAC
16155 AAAAGAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 5 0.11
44 42 0.89
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (44 bp):
ACAAACGCCACTATATGACAAGACATTTAGCGGAGTTTTTGGGA
Found at i:16295 original size:42 final size:42
Alignment explanation
Indices: 16170--16326 Score: 190
Period size: 43 Copynumber: 3.7 Consensus size: 42
16160 AAAAGATAAA
* * *
16170 TAGCGGCGTTTG-GAAAATACGCCGCTAAATATCATAACATT
1 TAGCGGCGTTTGTAAAAAAACGCCGCTAAATATCATAACCTT
* *
16211 TAGCGGCGTTTGTAATAAAAACGCCGTTAAATATCATTACCTT
1 TAGCGGCGTTTGTAA-AAAAACGCCGCTAAATATCATAACCTT
* * *
16254 TAGCGGCGTTTGTAAAAAAACGCCGCTAAAAAACATCACCTT
1 TAGCGGCGTTTGTAAAAAAACGCCGCTAAATATCATAACCTT
*
16296 CAGCGGCGTTTGTGAACAAAAAACGCCGCTA
1 TAGCGGCGTTTGT--A-AAAAAACGCCGCTA
16327 CCTTTTGCGA
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 12 0.12
42 36 0.36
43 38 0.38
44 1 0.01
45 14 0.14
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTGTAAAAAAACGCCGCTAAATATCATAACCTT
Found at i:20052 original size:12 final size:12
Alignment explanation
Indices: 20016--20055 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
20006 TTTTCTCTAA
*
20016 TTCTGTTCTGAT
1 TTCTGCTCTGAT
*
20028 CTCTGCTCTGAT
1 TTCTGCTCTGAT
20040 TTCTGCTCTGAT
1 TTCTGCTCTGAT
20052 TTCT
1 TTCT
20056 TATATCTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.07, C:0.25, G:0.15, T:0.53
Consensus pattern (12 bp):
TTCTGCTCTGAT
Found at i:22082 original size:38 final size:38
Alignment explanation
Indices: 22036--22113 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
22026 CAACAAACGC
* *
22036 CGCTAAAACTCATATTTTAGTGACGTTTATTTGACAAA
1 CGCTAAAACTCAAACTTTAGTGACGTTTATTTGACAAA
22074 CGCTAAAACTCAAACTTTAGTGACGTTTATTTGACAAA
1 CGCTAAAACTCAAACTTTAGTGACGTTTATTTGACAAA
22112 CG
1 CG
22114 ACGCTAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (38 bp):
CGCTAAAACTCAAACTTTAGTGACGTTTATTTGACAAA
Found at i:22153 original size:42 final size:41
Alignment explanation
Indices: 22087--22204 Score: 105
Period size: 42 Copynumber: 2.8 Consensus size: 41
22077 TAAAACTCAA
* ** *
22087 ACTTTAGTGACGTTTATTTGACAAACGACGCTAA-AGACT-AGT
1 ACTTTAGTGGCGTTT-TTAAACAAACGACGC-AATAGAATCA-T
* *
22129 ACTTTCGTGGCGTTTTTTAAACAAACGCCGCAATAGAATCAT
1 ACTTTAGTGGCG-TTTTTAAACAAACGACGCAATAGAATCAT
* **
22171 TCTTTAGTGGCGTTTTTAAACAAACTTCGCAATA
1 ACTTTAGTGGCGTTTTTAAACAAACGACGCAATA
22205 AGATAAATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 22 0.35
42 37 0.59
43 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTAAACAAACGACGCAATAGAATCAT
Found at i:22268 original size:40 final size:40
Alignment explanation
Indices: 22224--22348 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 40
22214 TATTGCAGCG
22224 TTTTTGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCT
1 TTTTTGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCT
* *
22264 TTTTTGACAAATGCCACTAAAACCT-GATACTTTAGTGGCGT
1 TTTTTGACAAACGCCGCTAAAACCTAG-TACTTTAGTGGC-T
** * * * *
22305 TTTAAGCAAAAACTCCGCTAAAAACTCA-TACTTTAATGGCT
1 TTTTTG-ACAAACGCCGCTAAAACCT-AGTACTTTAGTGGCT
22346 TTT
1 TTT
22349 AATGATTCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 35 0.50
41 9 0.13
42 25 0.36
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (40 bp):
TTTTTGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCT
Found at i:30429 original size:27 final size:27
Alignment explanation
Indices: 30378--30430 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
30368 ATATTTTATC
* *
30378 TAAAATTTAAAGGACAATTTGATATTA
1 TAAAATTTAAAGGACAAATTAATATTA
**
30405 TAAAATTTAAAGGTTAAATTAATATT
1 TAAAATTTAAAGGACAAATTAATATT
30431 TTATCTAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (27 bp):
TAAAATTTAAAGGACAAATTAATATTA
Found at i:32314 original size:85 final size:85
Alignment explanation
Indices: 32171--32343 Score: 328
Period size: 85 Copynumber: 2.0 Consensus size: 85
32161 TCGTATGTCA
32171 GTACGCTAAATAAATATGATCGTCAAATCTTATATTTTAACTATGATTGATAACTTTGGCCTTTC
1 GTACGCTAAATAAATATGATCGTCAAATCTTATATTTTAACTATGATTGATAACTTTGGCCTTTC
32236 AGATGTCTTGTCGATGCACT
66 AGATGTCTTGTCGATGCACT
32256 GTACGCTAAATAAATATGATCGTCAAATCTTATATTTTAACTATGATTGATAACTTTGGCCTTTC
1 GTACGCTAAATAAATATGATCGTCAAATCTTATATTTTAACTATGATTGATAACTTTGGCCTTTC
* *
32321 AGGTGTCTTGTTGATGCACT
66 AGATGTCTTGTCGATGCACT
32341 GTA
1 GTA
32344 AATTTAGACT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (85 bp):
GTACGCTAAATAAATATGATCGTCAAATCTTATATTTTAACTATGATTGATAACTTTGGCCTTTC
AGATGTCTTGTCGATGCACT
Found at i:33513 original size:11 final size:11
Alignment explanation
Indices: 33453--33573 Score: 66
Period size: 11 Copynumber: 11.7 Consensus size: 11
33443 AAAATTACAT
33453 TATTAAAAATA
1 TATTAAAAATA
*
33464 AATTAAAAATA
1 TATTAAAAATA
** ***
33475 CGTTATTGATA
1 TATTAAAAATA
33486 -ATTATAAAAT-
1 TATTA-AAAATA
33496 T-TTAAAAATA
1 TATTAAAAATA
33506 TATTAAAAAT-
1 TATTAAAAATA
33516 TA-TATAAAAT-
1 TATTA-AAAATA
33526 T-TTAAAAATA
1 TATTAAAAATA
33536 TATTAAAAAT-
1 TATTAAAAATA
*
33546 T-CTATAAAAT-
1 TATTA-AAAATA
33556 T-TTAAAAATA
1 TATTAAAAATA
*
33566 TAATAAAA
1 TATTAAAA
33574 TAAAAATATG
Statistics
Matches: 86, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
9 19 0.22
10 28 0.33
11 39 0.45
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:33524 original size:30 final size:30
Alignment explanation
Indices: 33488--33573 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
33478 TATTGATAAT
33488 TATAAAATTTTAAAAATATATTAAAAATTA
1 TATAAAATTTTAAAAATATATTAAAAATTA
*
33518 TATAAAATTTTAAAAATATATTAAAAATTC
1 TATAAAATTTTAAAAATATATTAAAAATTA
*
33548 TATAAAATTTTAAAAATATAATAAAA
1 TATAAAATTTTAAAAATATATTAAAA
33574 TAAAAATATG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (30 bp):
TATAAAATTTTAAAAATATATTAAAAATTA
Found at i:33530 original size:19 final size:18
Alignment explanation
Indices: 33488--33574 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 18
33478 TATTGATAAT
33488 TATAAAATTTTAAAAATA
1 TATAAAATTTTAAAAATA
*
33506 TATTAAAAATTATATAAAAT-
1 TA-T-AAAATTTTA-AAAATA
* *
33526 TTTAAAAATATATTAAAAATTC
1 TAT-AAAAT-T-TTAAAAA-TA
33548 TATAAAATTTTAAAAATA
1 TATAAAATTTTAAAAATA
33566 TAATAAAAT
1 T-ATAAAAT
33575 AAAAATATGA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
18 4 0.07
19 22 0.39
20 15 0.27
21 13 0.23
22 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAAATTTTAAAAATA
Found at i:34045 original size:7 final size:7
Alignment explanation
Indices: 34033--34071 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
34023 TAATGAGCCT
34033 TAAACCC
1 TAAACCC
34040 TAAACCC
1 TAAACCC
**
34047 TAAATAC
1 TAAACCC
34054 TAAACCC
1 TAAACCC
34061 TAAACCC
1 TAAACCC
34068 TAAA
1 TAAA
34072 ATCTTAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:36310 original size:11 final size:11
Alignment explanation
Indices: 36294--36338 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
36284 CGCGGTGAGC
36294 ATTCGAGCTTG
1 ATTCGAGCTTG
36305 ATTCGAGCTTG
1 ATTCGAGCTTG
* * *
36316 AATCGAGTTTA
1 ATTCGAGCTTG
36327 ATTCGAGCTTG
1 ATTCGAGCTTG
36338 A
1 A
36339 ATTAAGCTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (11 bp):
ATTCGAGCTTG
Found at i:36321 original size:22 final size:22
Alignment explanation
Indices: 36296--36340 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
36286 CGGTGAGCAT
*
36296 TCGAGCTTGATTCGAGCTTGAA
1 TCGAGCTTAATTCGAGCTTGAA
*
36318 TCGAGTTTAATTCGAGCTTGAA
1 TCGAGCTTAATTCGAGCTTGAA
36340 T
1 T
36341 TAAGCTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (22 bp):
TCGAGCTTAATTCGAGCTTGAA
Found at i:41182 original size:22 final size:23
Alignment explanation
Indices: 41157--41206 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
41147 CATTTAAGTT
*
41157 CAAAACATCCAATTCAAAC-ATC
1 CAAAACATCAAATTCAAACAATC
*
41179 CAAATCATCAAATTCAAACAATC
1 CAAAACATCAAATTCAAACAATC
41202 CAAAA
1 CAAAA
41207 ACATGTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (23 bp):
CAAAACATCAAATTCAAACAATC
Found at i:42742 original size:22 final size:25
Alignment explanation
Indices: 42712--42759 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
42702 ATTAAAACAA
42712 TAATATTCGAAAAT-C-ATTTTTTT
1 TAATATTCGAAAATCCAATTTTTTT
*
42735 TAAT-TTCGAAATTCCAATTTTTTT
1 TAATATTCGAAAATCCAATTTTTTT
42759 T
1 T
42760 TGAAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (25 bp):
TAATATTCGAAAATCCAATTTTTTT
Found at i:43203 original size:21 final size:22
Alignment explanation
Indices: 43142--43214 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
43132 CACAGTAGAG
43142 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * *
43165 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
**
43186 TGTGTCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
43209 TGCATC
1 TGCATC
43215 AGTACATTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 14 0.37
22 2 0.05
23 22 0.58
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:46934 original size:20 final size:21
Alignment explanation
Indices: 46895--46934 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
46885 GAAGCTTTAA
* *
46895 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
46916 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
46935 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:48970 original size:20 final size:21
Alignment explanation
Indices: 48928--48975 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
48918 GCGTGGGGTG
48928 CATCGATGCATAGCCAAGGTA
1 CATCGATGCATAGCCAAGGTA
*
48949 CATCGATGCATAG-CACGGTA
1 CATCGATGCATAGCCAAGGTA
48969 CATCGAT
1 CATCGAT
48976 ACACTATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (21 bp):
CATCGATGCATAGCCAAGGTA
Found at i:54551 original size:29 final size:29
Alignment explanation
Indices: 54519--54575 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
54509 ATTTCAAAAT
54519 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
54548 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
54576 TCAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:54849 original size:22 final size:18
Alignment explanation
Indices: 54804--54839 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54794 TAATTAAATA
54804 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
54822 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
54840 GGCTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:56243 original size:2 final size:2
Alignment explanation
Indices: 56236--56262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56226 TGGGCTTGTA
56236 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 A
56263 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56490 original size:76 final size:76
Alignment explanation
Indices: 56399--57114 Score: 1288
Period size: 76 Copynumber: 9.4 Consensus size: 76
56389 ATGAAATATT
* * * *
56399 GAAATCATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGAAAACATCAAAAAGCTCCC
1 GAAA-CATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCC
56464 GAAGGCTTTTTG
65 GAAGGCTTTTTG
* *
56476 AAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
*
56541 AAGGTTTTTTG
66 AAGGCTTTTTG
* *
56552 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56617 AAGGCTTTTTG
66 AAGGCTTTTTG
56628 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56693 AAGGCTTTTTG
66 AAGGCTTTTTG
*
56704 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTCGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56769 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
56780 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTCGAAAACATCAAAAAGCTTCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56845 AAGGCTTTTTG
66 AAGGCTTTTTG
56856 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56921 AAGGCTTTTTG
66 AAGGCTTTTTG
56932 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
56997 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
57008 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
57073 AAGGCTTTTTG
66 AAGGCTTTTTG
*
57084 GAAACATCATGCACTGTAGGACTTACAGATG
1 GAAACATCATGCACTGCAGGACTTACAGATG
57115 TGGGAAATAG
Statistics
Matches: 620, Mismatches: 19, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 617 1.00
77 3 0.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:57817 original size:22 final size:22
Alignment explanation
Indices: 57792--57846 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
57782 CATAAAGCTT
57792 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
57814 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
57836 TCATCTTTGAA
1 TCATCTTTGAA
57847 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:59265 original size:75 final size:74
Alignment explanation
Indices: 59172--59347 Score: 212
Period size: 74 Copynumber: 2.4 Consensus size: 74
59162 CAGGATGTTG
* *
59172 TGGGCCTTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCA-AGATACATCAACAGTTCTGA
1 TGGGCTTTCAGCATGCCCCAACATTTGGCTAATA-AA-TATTCAGA-ATACATCAACAGTTCTGA
59235 TTCTGATTGAAA
63 TTCTGATTGAAA
* * * ** *
59247 TGGGCTTTCAGCATGCCCCAGCATTTTGCTGATAAATATTCAGAATATTTCAACATTTCTGATTC
1 TGGGCTTTCAGCATGCCCCAACATTTGGCTAATAAATATTCAGAATACATCAACAGTTCTGATTC
59312 TGATTGAAA
66 TGATTGAAA
* * *
59321 AGGGTTTTCAGCATGCCCCAATATTTG
1 TGGGCTTTCAGCATGCCCCAACATTTG
59348 CTTCTTGTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
74 54 0.63
75 24 0.28
76 8 0.09
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (74 bp):
TGGGCTTTCAGCATGCCCCAACATTTGGCTAATAAATATTCAGAATACATCAACAGTTCTGATTC
TGATTGAAA
Found at i:60473 original size:114 final size:113
Alignment explanation
Indices: 60303--60638 Score: 528
Period size: 114 Copynumber: 2.9 Consensus size: 113
60293 ACGATCATGC
* * * * * *
60303 AATTCATCTTTTAATTCCAATGATTGGTTCTGGGATTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATC-TTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
60368 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
65 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
*
60417 AATTCATCGTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATC-TTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
* * *
60482 GAACACTTCTAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCG
65 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
*
60531 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCATATCAGATAACTCAAA
1 AATTCATCTTT-AAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
* *
60596 GAACACTTCCAGAAGATGATATTGGGTCTCTTTATTTCTACTA
65 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
60639 CGAGAATTTG
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 3 0.01
114 201 0.99
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (113 bp):
AATTCATCTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
Found at i:67306 original size:13 final size:14
Alignment explanation
Indices: 67279--67328 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
67269 ACTTGCAAAA
67279 AAATAAAATAATAT
1 AAATAAAATAATAT
*
67293 AAAT-AAATACTAT
1 AAATAAAATAATAT
67306 AAA-AATAATAATTAT
1 AAATAA-AATAA-TAT
*
67321 ATATAAAA
1 AAATAAAA
67329 AATTTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 12 0.41
14 8 0.28
15 7 0.24
16 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAATAATAT
Found at i:67848 original size:29 final size:29
Alignment explanation
Indices: 67816--67872 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
67806 ATTTCAAAAT
67816 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
67845 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
67873 TCAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:68146 original size:22 final size:18
Alignment explanation
Indices: 68101--68136 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
68091 TAATTAAATA
68101 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
68119 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
68137 GGCTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:68177 original size:13 final size:13
Alignment explanation
Indices: 68159--68186 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
68149 ATAATAATTA
68159 AAAATTAACATAT
1 AAAATTAACATAT
68172 AAAATTAACATAT
1 AAAATTAACATAT
68185 AA
1 AA
68187 CTAAACAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAACATAT
Found at i:71911 original size:17 final size:17
Alignment explanation
Indices: 71868--71913 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
71858 ATTATAATTT
*
71868 AATATAAAACAATTGAA
1 AATATAAAATAATTGAA
71885 AATATAAAATAATTGAA
1 AATATAAAATAATTGAA
71902 AATATAAAATAA
1 AATATAAAATAA
71914 AAACAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (17 bp):
AATATAAAATAATTGAA
Found at i:72074 original size:137 final size:135
Alignment explanation
Indices: 71903--72175 Score: 447
Period size: 137 Copynumber: 2.0 Consensus size: 135
71893 ATAATTGAAA
71903 ATATAAAATAAAAACAAAAGGTGGTCGGACACTACCGTCGGCCACCATCAACCACCGTAAATGGA
1 ATATAAAATAAAAACAAAAGGTGGTCGGACACTACCGTCGGCCACCATCAACCACCGTAAATGGA
* *
71968 GGTCGTTCAGTCCCAAATTTCATGGATTCGGTTAGTCTCGACCCCCTAAATCTAAATTTGATGGT
66 GGTCGTTCAGTCCCAAATTTCATGGA-TCGGTTAGTCTCGACCCCCTAAATCTAAATCTGATAGT
72033 TGTTTC
130 TGTTTC
* * *
72039 ATATAAAATAAAAAGCAAAAGGTGGTCGGACACTACCGTCGGCTATCATCAACCACTGTAAATGG
1 ATATAAAATAAAAA-CAAAAGGTGGTCGGACACTACCGTCGGCCACCATCAACCACCGTAAATGG
* * * *
72104 AGGTTGTTCAGTCTCAAATTTCATGGATCGGTTAGTCTTGACCTCCTAAATCTAAATCTGATAGT
65 AGGTCGTTCAGTCCCAAATTTCATGGATCGGTTAGTCTCGACCCCCTAAATCTAAATCTGATAGT
72169 TGTTTC
130 TGTTTC
72175 A
1 A
72176 CCAGAAAATG
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
136 55 0.43
137 72 0.57
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (135 bp):
ATATAAAATAAAAACAAAAGGTGGTCGGACACTACCGTCGGCCACCATCAACCACCGTAAATGGA
GGTCGTTCAGTCCCAAATTTCATGGATCGGTTAGTCTCGACCCCCTAAATCTAAATCTGATAGTT
GTTTC
Found at i:72456 original size:3 final size:3
Alignment explanation
Indices: 72448--72484 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
72438 TCATACAAAT
72448 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
72485 TTAGAATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:72878 original size:60 final size:60
Alignment explanation
Indices: 72808--72944 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
72798 GATAAAGTAG
* *
72808 ACAAATGGTCCCTTGACTATA-AGATATTATTTTATTGAGTCTCC-CGACT-ATTAAAAGTT
1 ACAAATGGTCCCTTGACTATAGAGA-ATTACTTTATTGAGTC-CCTCGACTAATAAAAAGTT
* * * *
72867 ACAAAGTGGTCCCTCGACTATAGAGAGTTACTTTGTTGAGTCCCTTGACTAATAAAAAGTT
1 ACAAA-TGGTCCCTTGACTATAGAGAATTACTTTATTGAGTCCCTCGACTAATAAAAAGTT
*
72928 ACAAAATGGTCACTTGA
1 AC-AAATGGTCCCTTGA
72945 TTATTCTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 7 0.11
60 32 0.49
61 23 0.35
62 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (60 bp):
ACAAATGGTCCCTTGACTATAGAGAATTACTTTATTGAGTCCCTCGACTAATAAAAAGTT
Found at i:73228 original size:59 final size:59
Alignment explanation
Indices: 73162--73307 Score: 240
Period size: 59 Copynumber: 2.5 Consensus size: 59
73152 ATGACCATTT
* *
73162 TGTAACTTTTAATTGTCGAGTGACTCAACGAAA-CAACTCTCCATAGTTTGGGATTATTG
1 TGTAACTTTTAATAGTCGAGTGACTCAAC-AAAGCAACTCTCCATAGTTTGGGACTATTG
*
73221 TGTAACTTTTAATAGTTGAGTGACTCAACAAAGCAACTCTCCATAGTTTGGGACTATTG
1 TGTAACTTTTAATAGTCGAGTGACTCAACAAAGCAACTCTCCATAGTTTGGGACTATTG
*
73280 TGTAACTTTTAATAGTCGAATGACTCAA
1 TGTAACTTTTAATAGTCGAGTGACTCAA
73308 TAAAATAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 3 0.04
59 78 0.96
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (59 bp):
TGTAACTTTTAATAGTCGAGTGACTCAACAAAGCAACTCTCCATAGTTTGGGACTATTG
Found at i:80247 original size:54 final size:54
Alignment explanation
Indices: 80163--80290 Score: 233
Period size: 54 Copynumber: 2.4 Consensus size: 54
80153 CATACCCATG
80163 GTGCATCGGTGCATC-AGTGTAAAATTCAAATATTTTGACCGTTGGAACACTTA
1 GTGCATCGGTGCATCAAGTGTAAAATTCAAATATTTTGACCGTTGGAACACTTA
80216 GTGCATCGGTGCATCAAGTGTAAAATTCAAATATTTTGACCGTTGGAACACTTA
1 GTGCATCGGTGCATCAAGTGTAAAATTCAAATATTTTGACCGTTGGAACACTTA
80270 GTGCATCGGTGCA-CTAAGTGT
1 GTGCATCGGTGCATC-AAGTGT
80291 GCATCAATGC
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
53 16 0.22
54 57 0.78
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (54 bp):
GTGCATCGGTGCATCAAGTGTAAAATTCAAATATTTTGACCGTTGGAACACTTA
Found at i:80467 original size:20 final size:20
Alignment explanation
Indices: 80442--80479 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
80432 CAATTTATTC
80442 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
80462 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
80480 CCCTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:82373 original size:23 final size:22
Alignment explanation
Indices: 82343--82424 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 22
82333 GCATGGCTTT
82343 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
82365 AGTGCATCGGTGCATC-TTC-ATG
1 -GTGCATCGATGCA-CATTCAAGG
*
82387 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
82410 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
82425 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 2 0.04
23 18 0.38
24 13 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:82435 original size:44 final size:42
Alignment explanation
Indices: 82321--82443 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 42
82311 AAAACTCGAT
* *
82321 GGATGCATCGATGCA-TGGCTT-TGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-G-TTAAGTGTATCGATGCACATTCAA
* * *
82363 GGAGTGCATCGGTGCATCT-TCATGGTGTATCGATGCACATTCAAA
1 GGA-TGCATCGATGCA-CTGTTA-AGTGTATCGATGCACATTC-AA
82408 GGGATGCATCGATGCACTGTTAAGTGTATCGATGCA
1 -GGATGCATCGATGCACTGTTAAGTGTATCGATGCA
82444 TTAAGCACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
42 4 0.06
43 11 0.17
44 32 0.48
45 16 0.24
46 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTTAAGTGTATCGATGCACATTCAA
Done.