Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004625.1 Hibiscus syriacus cultivar Beakdansim tig00010350_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: 64976
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1237 original size:199 final size:200
Alignment explanation
Indices: 910--1620 Score: 793
Period size: 199 Copynumber: 3.6 Consensus size: 200
900 ATCTGCAATA
* * * ** * *
910 AAAACTATCGAGTTCGATTCCATT---CTCGAGGGTGTATCAACCGCATGGTAGCAACGAGGAAC
1 AAAACTTTCGAGTTCGATTACATTCAGCTCGATGGCATATCAACCACATAGTAGCAACGAGGAAC
* * * * * * *
972 TACTTTC-GATGAAGTTTAAACCGAGGTCTTTAACTCAAAAAGAATACCTAGGTTGGTTGTGATT
66 TACTTTCGGTTGAAGTTTAAACAGAGGTCTTTAAGTCAAGAAGAAGACCAAGGTTGGTTGCGATT
* * * **
1036 TAGTAATAAGGAACTATCTCCCAGCCGAATTTACTGCATAGCTCAAGGC-A-AAGGGATATCTGT
131 TAGCAACAAAGAACTATCTCCCAGCCGAATTTACTATATAGCTCAAGGCGAGAAGGGATATCTGT
1099 CAACG
196 CAACG
* * * ** * *
1104 AAAACTTTCGAGTTTGATTTCATTCAGCTCGATGGCATATCAGCCGTATGGTAGCAACGAGGAAT
1 AAAACTTTCGAGTTCGATTACATTCAGCTCGATGGCATATCAACCACATAGTAGCAACGAGGAAC
* * *
1169 TACTTTTCGGTTGAAGCTTAAACAGAGGTCTTTAAGTTAAGAAGAAGACCAAGGTTGGCTGCGAT
66 TAC-TTTCGGTTGAAGTTTAAACAGAGGTCTTTAAGTCAAGAAGAAGACCAAGGTTGGTTGCGAT
* *
1234 TTAGCAACAAAGAACTATCTCCCAGTCG--TTTACAATATAGCTCAAGGCGAGAA-GGACTATCT
130 TTAGCAACAAAGAACTATCTCCCAGCCGAATTTACTATATAGCTCAAGGCGAGAAGGGA-TATCT
1296 GTCAACG
194 GTCAACG
* * * * *
1303 AAAACTTTCAAGTTCGATTCCATTCAGCTCGGTGGCATATCAGCCACATAGTAGCAGCGAGGAAC
1 AAAACTTTCGAGTTCGATTACATTCAGCTCGATGGCATATCAACCACATAGTAGCAACGAGGAAC
* * * *
1368 TACTTTCGCTTGAAGTTTAAACTGAGGTCTTTAAGGCAAGAAGAAGACCTAGGTTGGTTGCGATT
66 TACTTTCGGTTGAAGTTTAAACAGAGGTCTTTAAGTCAAGAAGAAGACCAAGGTTGGTTGCGATT
* * * * *
1433 TAGCAACAATGAACTATCTCCCAGCCAAATTTACTATATAACTTAAGGCGAGAAGGGCTATCTGT
131 TAGCAACAAAGAACTATCTCCCAGCCGAATTTACTATATAGCTCAAGGCGAGAAGGGATATCTGT
1498 CAACG
196 CAACG
* * * * * * *
1503 GAAACTTTGGAGTTCGA-TACGTTCAGTTCGAAGGCATATCAACCACATAGTAGCAACAAAGAAC
1 AAAACTTTCGAGTTCGATTACATTCAGCTCGATGGCATATCAACCACATAGTAGCAACGAGGAAC
* * *
1567 TACTTTTCGGTAGAATTTTACACCA-AGGTCTTTAAGTC--G-AGAAGACCAAGGTTG
66 TAC-TTTCGGTTGAAGTTTA-AACAGAGGTCTTTAAGTCAAGAAGAAGACCAAGGTTG
1621 ACTATGATTT
Statistics
Matches: 436, Mismatches: 68, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
194 21 0.05
197 66 0.15
198 88 0.20
199 184 0.42
200 73 0.17
201 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (200 bp):
AAAACTTTCGAGTTCGATTACATTCAGCTCGATGGCATATCAACCACATAGTAGCAACGAGGAAC
TACTTTCGGTTGAAGTTTAAACAGAGGTCTTTAAGTCAAGAAGAAGACCAAGGTTGGTTGCGATT
TAGCAACAAAGAACTATCTCCCAGCCGAATTTACTATATAGCTCAAGGCGAGAAGGGATATCTGT
CAACG
Found at i:2028 original size:37 final size:37
Alignment explanation
Indices: 1983--2199 Score: 239
Period size: 37 Copynumber: 5.8 Consensus size: 37
1973 GTATATATAC
1983 ATATATATATAGTTTT-GAAACATTTTTTCAAAATAT
1 ATATATATATAGTTTTGGAAACATTTTTTCAAAATAT
* * *
2019 ATAATATATAGTATTTTTATGAAACATTTTTTGAAAATAT
1 AT-ATATATA-TAGTTTT-GGAAACATTTTTTCAAAATAT
*
2059 ATATAATATATAGTTTTGGAAAACA-TTTTTCAAAA-AC
1 ATAT-ATATATAGTTTTGG-AAACATTTTTTCAAAATAT
*
2096 ATATA-ATATAGTTTTGGAAA-ATATTTCTTTAAAATAT
1 ATATATATATAGTTTTGGAAACAT-TTT-TTCAAAATAT
**
2133 ATATAATATATAGTTTTGGAAACATTTTTGAAAAATAT
1 ATAT-ATATATAGTTTTGGAAACATTTTTTCAAAATAT
*
2171 ATACATATATAGTTTT-GAAACATTGTTTT
1 ATATATATATAGTTTTGGAAACATT-TTTT
2200 TTAAAAACAT
Statistics
Matches: 155, Mismatches: 12, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
33 1 0.01
34 3 0.02
35 15 0.10
36 17 0.11
37 32 0.21
38 28 0.18
39 31 0.20
40 28 0.18
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATATATAGTTTTGGAAACATTTTTTCAAAATAT
Found at i:2049 original size:39 final size:36
Alignment explanation
Indices: 1983--2194 Score: 225
Period size: 38 Copynumber: 5.7 Consensus size: 36
1973 GTATATATAC
1983 ATATATATATAGTTTT-GAAACATTTTTTCAAAATAT
1 ATATATATATAGTTTTGGAAACA-TTTTTCAAAATAT
* * *
2019 ATAATATATAGTATTTTTATGAAACATTTTTTGAAAATAT
1 AT-ATATATA-TAGTTTT-GGAAACA-TTTTTCAAAATAT
*
2059 ATATAATATATAGTTTTGGAAAACATTTTTCAAAA-AC
1 ATAT-ATATATAGTTTTGG-AAACATTTTTCAAAATAT
* *
2096 ATATA-ATATAGTTTTGGAAAATATTTCTTTAAAATAT
1 ATATATATATAGTTTTGG-AAACATTT-TTCAAAATAT
*
2133 ATATAATATATAGTTTTGGAAACATTTTTGAAAAATAT
1 ATAT-ATATATAGTTTTGGAAACATTTTT-CAAAATAT
*
2171 ATACATATATAGTTTT-GAAACATT
1 ATATATATATAGTTTTGGAAACATT
2195 GTTTTTTAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
35 20 0.13
36 17 0.11
37 31 0.20
38 34 0.22
39 25 0.16
40 26 0.17
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATATATATAGTTTTGGAAACATTTTTCAAAATAT
Found at i:2239 original size:36 final size:38
Alignment explanation
Indices: 2195--2268 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
2185 TTGAAACATT
* *
2195 GTTTTTT-AAAAA-CATTTTGAAAGCATATAATATATA
1 GTTTTTTAAAAAATAATTTTGAAACCATATAATATATA
*
2231 GTTTTTTAAAAAATAATTTTTAAACCATATAATATATA
1 GTTTTTTAAAAAATAATTTTGAAACCATATAATATATA
2269 ATTTGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 7 0.21
37 5 0.15
38 21 0.64
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (38 bp):
GTTTTTTAAAAAATAATTTTGAAACCATATAATATATA
Found at i:2403 original size:5 final size:5
Alignment explanation
Indices: 2393--2430 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
2383 TAGTTTTTAT
2393 TATTA TATTA TATTA TATTA TATT- TATT- TATT- TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T
2431 TTTTAATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:2406 original size:10 final size:9
Alignment explanation
Indices: 2388--2435 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
2378 TTATATAGTT
2388 TTTATTAT-
1 TTTATTATA
*
2396 TATATTATA
1 TTTATTATA
2405 TTATATTATA
1 TT-TATTATA
2415 TTTATT-TA
1 TTTATTATA
*
2423 TTTATTATT
1 TTTATTATA
2432 TTTA
1 TTTA
2436 ATCTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 15 0.44
9 10 0.29
10 9 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATTATA
Found at i:2411 original size:15 final size:14
Alignment explanation
Indices: 2392--2435 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
2382 ATAGTTTTTA
2392 TTATTATATTATAT
1 TTATTATATTATAT
2406 TATATTATATT-TAT
1 T-TATTATATTATAT
*
2420 TTATT-TATTATTT
1 TTATTATATTATAT
2433 TTA
1 TTA
2436 ATCTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.15
13 9 0.33
14 5 0.19
15 9 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATATTATAT
Found at i:4662 original size:60 final size:62
Alignment explanation
Indices: 4571--4711 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 62
4561 TAAAATTTTC
* * * **
4571 CAATTTCATCCCTAAACTATGACTTTAATTCTGAATT-AT-TCCTTTAAC-TTTTGAACATTT
1 CAATTTCATCCCCAAACTATGACCTTAATTCTAAATTGATCTCC-CAAACTTTTTGAACATTT
* *
4631 CAATTTCATCCCCAAACTACT-ACCTTCATTCTAAATTGGTCTCCCAAACTTTTTGAACATTT
1 CAATTTCATCCCCAAACTA-TGACCTTAATTCTAAATTGATCTCCCAAACTTTTTGAACATTT
* *
4693 TAACTTCAT-CCCAAACTAT
1 CAATTTCATCCCCAAACTAT
4712 ATGTATATAC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
60 32 0.47
61 14 0.21
62 22 0.32
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (62 bp):
CAATTTCATCCCCAAACTATGACCTTAATTCTAAATTGATCTCCCAAACTTTTTGAACATTT
Found at i:8298 original size:19 final size:20
Alignment explanation
Indices: 8273--8331 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
8263 ACTATCGCAT
*
8273 TGCGATTTTCTAAAATCGCG
1 TGCGATTTTCCAAAATCGCG
*
8293 -GCGATTTTCCAAATTCGCG
1 TGCGATTTTCCAAAATCGCG
**
8312 TTGCGATTTTAGAAAATCGC
1 -TGCGATTTTCCAAAATCGC
8332 AATGCGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (20 bp):
TGCGATTTTCCAAAATCGCG
Found at i:8319 original size:21 final size:21
Alignment explanation
Indices: 8266--8331 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
8256 GATTTTGACT
* *
8266 ATCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGATTTTCCAAA
8287 ATCGCG--GCGATTTTCCAAA
1 ATCGCGTTGCGATTTTCCAAA
* **
8306 TTCGCGTTGCGATTTTAGAAA
1 ATCGCGTTGCGATTTTCCAAA
8327 ATCGC
1 ATCGC
8332 AATGCGAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 17 0.46
21 20 0.54
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCCAAA
Found at i:8337 original size:21 final size:20
Alignment explanation
Indices: 8247--8400 Score: 62
Period size: 21 Copynumber: 7.6 Consensus size: 20
8237 GTTTCAAGAT
* **
8247 TCGCAACGCGATTTTGACTA
1 TCGCAATGCGATTTTGAAAA
* *
8267 TCGCATTGCGATTTTCTAAAA
1 TCGCAATGCGATTTT-GAAAA
* * *
8288 TCGC--GGCGATTTTCCAAAT
1 TCGCAATGCGATTTT-GAAAA
**
8307 TCGCGTTGCGATTTTAGAAAA
1 TCGCAATGCGATTTT-GAAAA
* * *
8328 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGATTTTGAAAA
* **
8348 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTTTGA-A-AA
* * *
8369 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGATTTTGAAAA
*
8389 TCGCAACGCGAT
1 TCGCAATGCGAT
8401 AATACATAAT
Statistics
Matches: 101, Mismatches: 27, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
19 16 0.16
20 42 0.42
21 43 0.43
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTTTGAAAA
Found at i:8350 original size:20 final size:20
Alignment explanation
Indices: 8325--8399 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
8315 CGATTTTAGA
*
8325 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
**
8345 AAATCGCAACGCG-ATAATAC
1 AAATCGCAACGCGAAT-ATGT
*
8365 ATAATCGCAATGCGAATATGT
1 A-AATCGCAACGCGAATATGT
8386 AAATCGCAACGCGA
1 AAATCGCAACGCGA
8400 TAATACATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 27 0.60
21 14 0.31
22 2 0.04
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:8371 original size:41 final size:41
Alignment explanation
Indices: 8326--8411 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
8316 GATTTTAGAA
8326 AATCGCAATGCGAATATGTAAATCGCAACGCGATAATACAT
1 AATCGCAATGCGAATATGTAAATCGCAACGCGATAATACAT
8367 AATCGCAATGCGAATATGTAAATCGCAACGCGATAATACAT
1 AATCGCAATGCGAATATGTAAATCGCAACGCGATAATACAT
8408 AATC
1 AATC
8412 AACGCGATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (41 bp):
AATCGCAATGCGAATATGTAAATCGCAACGCGATAATACAT
Found at i:8623 original size:22 final size:22
Alignment explanation
Indices: 8598--8674 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
8588 TCACTCTCTA
*
8598 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
8620 CGACGAAATCCATCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
8642 CGACGAAATCCGTCCTCATCTC
1 CGACGAAATCCGTCCCCATCTC
* *
8664 TGGCGAAATCC
1 CGACGAAATCC
8675 ATCTATCTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:8945 original size:20 final size:20
Alignment explanation
Indices: 8922--9010 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
8912 GTTTCCAGAT
**
8922 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCAGACTA
**
8942 TCGCATTGCGATTCAGACTA
1 TCGCAACGCGATTCAGACTA
**
8962 TCGCATTGCGATTCAGACTA
1 TCGCAACGCGATTCAGACTA
* *
8982 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCAGACTA
9002 TCGCAACGC
1 TCGCAACGC
9011 TGAATTTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCAGACTA
Found at i:9878 original size:24 final size:24
Alignment explanation
Indices: 9827--9880 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9817 GTATTCGAAA
*
9827 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* * *
9851 TTTGATCTTGTTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
9875 TTTGAT
1 TTTGAT
9881 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:12156 original size:18 final size:18
Alignment explanation
Indices: 12133--12167 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12123 AGAAAAAGGC
*
12133 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
12151 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
12168 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:12477 original size:140 final size:140
Alignment explanation
Indices: 12225--12507 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
12215 GCAAACGTTG
12225 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
12290 TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAACA
66 TTGAACATTGCTATGATCTGTTCAGTTATTATCAACTATTACACATTCATTTGAATATCGCAACA
12355 CGAATTTGAC
131 CGAATTTGAC
*
12365 TATTATGTGTATTTTATGTGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * *
12430 TTGAACATTGTTATGATCTGTTCAGTTATTATCACCTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTATTATCAACTATTACACATTCATTTGAATATCGCAACA
12495 CGAATTTGAC
131 CGAATTTGAC
12505 TAT
1 TAT
12508 CGCAACGGGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTATTATCAACTATTACACATTCATTTGAATATCGCAACA
CGAATTTGAC
Found at i:12503 original size:20 final size:20
Alignment explanation
Indices: 12478--12534 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
12468 TTACACATTC
*
12478 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
12498 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
12518 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
12535 AGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:12609 original size:20 final size:20
Alignment explanation
Indices: 12573--12647 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
12563 GCAACGTGAA
12573 TTGACTTTCGC---GCGATT
1 TTGACTTTCGCATTGCGATT
* *
12590 TTGGCTTTCGTATTGCGATT
1 TTGACTTTCGCATTGCGATT
12610 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
12630 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
12648 AAGTGTACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 9 0.19
20 39 0.81
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:14278 original size:42 final size:42
Alignment explanation
Indices: 14190--14299 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
14180 TTGAATGGTG
* * * *
14190 GGAG-GGACCTCTTCAACCATGACAGGGGCCTCTTGAACAGTG
1 GGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACAGTA
* ** *
14232 GGAGAGGACTTTTGAGGGATGATAGGGGCCTCTTGAA-TGATA
1 GGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACAG-TA
*
14274 GGAGAGGCCTCTTGAACGATGATAGG
1 GGAGAGGACTCTTGAACGATGATAGG
14300 TGAGTCAGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.02
42 50 0.93
43 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.22
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACAGTA
Found at i:14793 original size:20 final size:21
Alignment explanation
Indices: 14768--14812 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
14758 AATAGTTTCT
*
14768 GAAACTT-AAAATCGTAACAC
1 GAAACTTAAAAATCGCAACAC
*
14788 GAAACTTAAAAATCGCAACGC
1 GAAACTTAAAAATCGCAACAC
14809 GAAA
1 GAAA
14813 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (21 bp):
GAAACTTAAAAATCGCAACAC
Found at i:14824 original size:20 final size:20
Alignment explanation
Indices: 14799--14847 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
14789 AAACTTAAAA
14799 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
14819 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
14839 ATCGCAACG
1 ATCGCAACG
14848 GGATAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:14885 original size:19 final size:19
Alignment explanation
Indices: 14775--14909 Score: 64
Period size: 20 Copynumber: 7.1 Consensus size: 19
14765 TCTGAAACTT
* *
14775 AAAATCGTAACACGAAACTTA
1 AAAATCGCAACGCGAAA--TA
*
14796 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCG-AAATA
** *
14816 ACTATCGCAACGCGAAAATG
1 AAAATCGCAACGCG-AAATA
** *
14836 ACTATCGCAACG-G-GAT-
1 AAAATCGCAACGCGAAATA
*
14852 --AATCGCAATGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
14869 AAAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATA
*
14888 AAAATCTCAACGCGAAACTA
1 AAAATCGCAACGCGAAA-TA
14908 AA
1 AA
14910 TTCGCGTTGC
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 2 0.02
17 2 0.02
19 29 0.32
20 33 0.37
21 12 0.13
22 3 0.03
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:14953 original size:19 final size:20
Alignment explanation
Indices: 14910--14962 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
14900 CGAAACTAAA
*
14910 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
*
14930 TTCGCATTGCGATTTTTA-T
1 TTCGCATTGCGATTTTCATT
14949 TTCGCATTGCGATT
1 TTCGCATTGCGATT
14963 ATCCCGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:14996 original size:20 final size:20
Alignment explanation
Indices: 14967--15015 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
14957 GCGATTATCC
*
14967 CGTTGAGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
14987 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
15007 CGTTGCGAT
1 CGTTGCGAT
15016 TTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:15037 original size:22 final size:20
Alignment explanation
Indices: 15002--15047 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
14992 CGATAGTCAT
*
15002 TTTCGCGTTGCGATTTTTTAAG
1 TTTCGCGTTACGA--TTTTAAG
*
15024 TTTCGTGTTACGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
15044 TTTC
1 TTTC
15048 AAAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.15, C:0.13, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTACGATTTTAAG
Found at i:16947 original size:20 final size:20
Alignment explanation
Indices: 16924--16979 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
16914 TCTGAAACTT
* *
16924 AAAATTGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
16944 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
16964 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
16980 TTTGCCTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:17391 original size:19 final size:19
Alignment explanation
Indices: 17358--17394 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17348 ATGACCAACA
*
17358 AAATCGCAATACGATCTCT
1 AAATCGCAACACGATCTCT
*
17377 AAATCGCAACGCGATCTC
1 AAATCGCAACACGATCTC
17395 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:17558 original size:19 final size:19
Alignment explanation
Indices: 17534--17570 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17524 TGCGATACTG
* *
17534 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGCGATTTA
17553 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
17571 TATTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:19083 original size:27 final size:27
Alignment explanation
Indices: 19053--19112 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
19043 TCAACTCGAA
**
19053 TCGACTTCGAATTTTAATTTCATAAAT
1 TCGACTTAAAATTTTAATTTCATAAAT
*
19080 TCGACTTAAAATTTTAATTTGATAAAT
1 TCGACTTAAAATTTTAATTTCATAAAT
19107 TCGACT
1 TCGACT
19113 AGACTAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.43
Consensus pattern (27 bp):
TCGACTTAAAATTTTAATTTCATAAAT
Found at i:23721 original size:21 final size:21
Alignment explanation
Indices: 23697--23759 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
23687 TAATTTTAGG
23697 TTACTAATATCTTTGAAATCA
1 TTACTAATATCTTTGAAATCA
* **
23718 TTACTATTAAGTTTG------
1 TTACTAATATCTTTGAAATCA
23733 TTACTAATATCTTTGAAATCA
1 TTACTAATATCTTTGAAATCA
23754 TTACTA
1 TTACTA
23760 TTAAGTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 12 0.40
21 18 0.60
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
TTACTAATATCTTTGAAATCA
Found at i:23736 original size:36 final size:36
Alignment explanation
Indices: 23696--23767 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
23686 TTAATTTTAG
23696 GTTACTAATATCTTTGAAATCATTACTATTAAGTTT
1 GTTACTAATATCTTTGAAATCATTACTATTAAGTTT
23732 GTTACTAATATCTTTGAAATCATTACTATTAAGTTT
1 GTTACTAATATCTTTGAAATCATTACTATTAAGTTT
23768 AAGTTTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.47
Consensus pattern (36 bp):
GTTACTAATATCTTTGAAATCATTACTATTAAGTTT
Found at i:36519 original size:17 final size:19
Alignment explanation
Indices: 36491--36539 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
36481 TATTTTGAAA
36491 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
36509 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
36528 CACCGATGCACT
1 CATCGATGCACT
36540 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:42344 original size:24 final size:24
Alignment explanation
Indices: 42317--42397 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
42307 ACACTTAACA
42317 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
42341 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
42363 -TGCACCGATGCA-CACC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
42385 GTGCATCGATGCA
1 GTGCATCGATGCA
42398 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:45232 original size:64 final size:63
Alignment explanation
Indices: 45026--45235 Score: 210
Period size: 65 Copynumber: 3.3 Consensus size: 63
45016 ATTTTCAGAG
* * **
45026 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACC-A-CCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
45089 TT
62 TT
* * * * ** *
45091 TCATGCATCGATGCACTTACCATGCACCGATGCATTGAGGAT-TTTATAAAAACATCGAATGCAT
1 TGATGCATCGATGCAC-CACCATGCATCGATGCACTCTGGATATTT-T-GAAACATCGAATGCAT
45155 T
63 T
* *
45156 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCA-CCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
45220 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
45236 TCTTAGTGCA
Statistics
Matches: 118, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 48 0.41
65 64 0.54
66 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACCACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:45235 original size:17 final size:19
Alignment explanation
Indices: 45207--45255 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
45197 TATTTTGAAA
45207 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
45225 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
45244 CACCGATGCACT
1 CATCGATGCACT
45256 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:47860 original size:3 final size:3
Alignment explanation
Indices: 47852--47891 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
47842 ATTATAATGT
47852 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
47892 TAATTAGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48477 original size:37 final size:37
Alignment explanation
Indices: 48427--48943 Score: 361
Period size: 37 Copynumber: 14.6 Consensus size: 37
48417 CAATTATTTA
*
48427 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * * ** * *
48464 TGTTTCAAGAGAAATTGTCTTAATCGTGACGAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * * *
48501 TGTTTCGAGAGAAACTGTCTAAAGCGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * * ** *
48537 TATTTCAAGGGAAACAATCTC-AG-TTG------TTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* *
48566 ATGTTTTAAGAGAAACTATCTTAAGAGAGACAAAACTT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * ** **
48604 TGTTTTAAGAGAAACTGTCTCAACCGAGATGAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
*
48641 TGTTTCGAGAGAAACTATCTCAAGCA-AGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAG-AGAGACAAAACTT
* * ** *
48677 TGTTTCAAGGGAAACAATCTC-A-ATTG------TTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
*
48706 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACAT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * * * *
48744 TGTTTCAAGAGAGAGTATTTCAAGCGAGACGAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * *
48781 TATTTCGAGAGAAACTATCTCAAGCGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * ** *
48817 TGTTTCAAGGGAAACAATCTC-A-ATTG------TTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
48846 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* *
48884 TGTTTCAAGAGAAACTATCTCAAGCGAGACTAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
*
48921 TGTTTCGAGAGAAACTATCTCAA
1 TGTTTCAAGAGAAACTATCTCAA
48944 TGGTTTATAT
Statistics
Matches: 370, Mismatches: 78, Indels: 64
0.72 0.15 0.12
Matches are distributed among these distances:
29 6 0.02
30 54 0.15
31 4 0.01
32 5 0.01
33 1 0.00
34 3 0.01
35 4 0.01
36 56 0.15
37 232 0.63
38 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
Found at i:48614 original size:140 final size:140
Alignment explanation
Indices: 48359--48943 Score: 927
Period size: 140 Copynumber: 4.2 Consensus size: 140
48349 TTAGGGATAA
* * *
48359 TTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTAT
1 TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
* * * * *
48424 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAATTGTCTTAATC
66 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
*
48489 GTGACGAAAC
131 GAGACGAAAC
* * * * *
48499 TTTGTTTCGAGAGAAACTGTCTAAAGCGAGACAAAATTTATTTCAAGGGAAACAATCTCAGTTGT
1 TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
* * * * *
48564 TTATGTTTTAAGAGAAACTATCTTAAGAGAGACAAAACTTTGTTTTAAGAGAAACTGTCTCAACC
66 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
*
48629 GAGATGAAAC
131 GAGACGAAAC
48639 TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
1 TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
* * * *
48704 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACATTGTTTCAAGAGAGAGTATTTCAAGC
66 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
48769 GAGACGAAAC
131 GAGACGAAAC
* *
48779 TTTATTTCGAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
1 TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
48844 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
66 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
*
48909 GAGACTAAAC
131 GAGACGAAAC
48919 TTTGTTTCGAGAGAAACTATCTCAA
1 TTTGTTTCGAGAGAAACTATCTCAA
48944 TGGTTTATAT
Statistics
Matches: 405, Mismatches: 40, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
140 405 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (140 bp):
TTTGTTTCGAGAGAAACTATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGT
TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGC
GAGACGAAAC
Found at i:48711 original size:103 final size:104
Alignment explanation
Indices: 48604--48803 Score: 240
Period size: 103 Copynumber: 1.9 Consensus size: 104
48594 GACAAAACTT
* * * ** * *
48604 TGTTTTAAGAGAAACTGTCTCAACCGAGATGAAACTTTGTTTCGAGAGAAACTATCTCAAGCAAG
1 TGTTTCAAGAGAAACTATCTCAACAGAGACAAAACATTGTTTCAAGAGAAACTATCTCAAGCAAG
* *
48669 AC-AAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTA
66 ACGAAAATTTATTTCAAGAGAAACAATCTCAATTGTTTA
* * * * *
48707 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACATTGTTTCAAGAGAGAGTATTTCAAGCGAG
1 TGTTTCAAGAGAAACTATCTCAACAGAGACAAAACATTGTTTCAAGAGAAACTATCTCAAGCAAG
* * *
48772 ACGAAACTTTATTTCGAGAGAAACTATCTCAA
66 ACGAAAATTTATTTCAAGAGAAACAATCTCAA
48804 GCGAGACAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
103 55 0.70
104 24 0.30
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (104 bp):
TGTTTCAAGAGAAACTATCTCAACAGAGACAAAACATTGTTTCAAGAGAAACTATCTCAAGCAAG
ACGAAAATTTATTTCAAGAGAAACAATCTCAATTGTTTA
Found at i:48851 original size:103 final size:104
Alignment explanation
Indices: 48744--48951 Score: 301
Period size: 103 Copynumber: 2.0 Consensus size: 104
48734 GACAAAACAT
* * * * * *
48744 TGTTTCAAGAGAGAGTATTTCAAGCGAGACGAAACTTTATTTCGAGAGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACTATCTCAAGCGAG
* *
48809 AC-AAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTA
66 ACTAAAATTTGTTTCAAGAGAAACAATCTCAATGGTTTA
*
48847 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACTATCTCAAGCGAG
* * *
48912 ACTAAACTTTGTTTCGAGAGAAACTATCTCAATGGTTTA
66 ACTAAAATTTGTTTCAAGAGAAACAATCTCAATGGTTTA
48951 T
1 T
48952 ATTTTGTTAG
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
103 60 0.65
104 32 0.35
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (104 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACTATCTCAAGCGAG
ACTAAAATTTGTTTCAAGAGAAACAATCTCAATGGTTTA
Found at i:49126 original size:37 final size:36
Alignment explanation
Indices: 49082--49200 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
49072 TCAAAATGGG
*
49082 AAATTGTCTCAAGTGAGATGAAATTTGTTTTTAAGAA
1 AAATTGTCTCAAGTGAGATAAAATTTG-TTTTAAGAA
* * *
49119 AAATTGTCTCAAGTAAGACAAAATTTGATTTTACGAA
1 AAATTGTCTCAAGTGAGATAAAATTTG-TTTTAAGAA
* * * *
49156 AACA--ATCTCAAGTGAGATCAATTTTGTTTCAAGAAA
1 AA-ATTGTCTCAAGTGAGATAAAATTTGTTTTAAG-AA
49192 AAATTGTCT
1 AAATTGTCT
49201 TTAGCGAGAC
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
35 6 0.09
36 21 0.32
37 37 0.57
38 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (36 bp):
AAATTGTCTCAAGTGAGATAAAATTTGTTTTAAGAA
Found at i:53592 original size:13 final size:13
Alignment explanation
Indices: 53574--53599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53564 TTGGCACCTA
53574 CCGATGGATAAAG
1 CCGATGGATAAAG
53587 CCGATGGATAAAG
1 CCGATGGATAAAG
53600 GTTCGGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
CCGATGGATAAAG
Found at i:56752 original size:3 final size:3
Alignment explanation
Indices: 56744--56816 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
56734 ATTATAATGG
56744 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56792 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
56817 TAGTTAGAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:61867 original size:22 final size:22
Alignment explanation
Indices: 61839--61883 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
61829 ATTTTGAGAC
61839 ATCATTTTTATATTTTAAAAAT
1 ATCATTTTTATATTTTAAAAAT
61861 ATCATTTTTATATTTTAAAAAT
1 ATCATTTTTATATTTTAAAAAT
61883 A
1 A
61884 ATTTCTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
ATCATTTTTATATTTTAAAAAT
Found at i:62825 original size:17 final size:17
Alignment explanation
Indices: 62800--62835 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62790 TGAGCTGGAA
62800 CATTATTTTCTCTCATT
1 CATTATTTTCTCTCATT
* *
62817 CATTCTTTTCTCTCCTT
1 CATTATTTTCTCTCATT
62834 CA
1 CA
62836 CTCCACAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (17 bp):
CATTATTTTCTCTCATT
Found at i:63968 original size:65 final size:64
Alignment explanation
Indices: 63807--63987 Score: 199
Period size: 65 Copynumber: 2.8 Consensus size: 64
63797 TTGGACCCTT
*
63807 AGTGCATCGGTGCACTAAG-AGTGCATTGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCA
1 AGTGCATCGGTGCA-T-AGTAGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCA
63870 G
64 G
** * * * * *
63871 AGTATATCGATGCATGGCTGGTGGATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGGTGCATAG-TAGTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-C
*
63934 TG
63 AG
63936 AGTGCATCGGTGCATAGTATGTGCATCGATGCATGAAATGCATTCGATGTTT
1 AGTGCATCGGTGCATAGTA-GTGCATCGATGCATGAAATGCATTCGATGTTT
63988 AATTTATTCC
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 39 0.41
65 51 0.54
66 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
AGTGCATCGGTGCATAGTAGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAG
Found at i:64025 original size:65 final size:63
Alignment explanation
Indices: 63827--64034 Score: 172
Period size: 65 Copynumber: 3.2 Consensus size: 63
63817 TGCACTAAGA
* * * ** *
63827 GTGCATTGATGCATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTATATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTT--AATTAACCATGAGTGCATCGATGCATGGTTG
* * * * * *
63891 GTGGATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTC-TGAGTGCATCGGTGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTAAT-TAAC-CATGAGTGCATCGATGCATGGT-
63955 T-
62 TG
* *
63956 GTGCATCGATGCATGAAATGCATTCGATGTTTAATTTATTCCATG-GTGCATTGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTAA-TTA-ACCATGAGTGCATCGATGCATGG-TT
64020 G
63 G
*
64021 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
64035 CACTTTGAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
63 1 0.01
64 48 0.42
65 63 0.56
66 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTAATTAACCATGAGTGCATCGATGCATGGTTG
Done.