Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004088.1 Hibiscus syriacus cultivar Beakdansim tig00008944_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: 70801
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1287 original size:19 final size:20
Alignment explanation
Indices: 1249--1299 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1239 GAAACCCCTT
1249 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1269 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1288 TGAAGATACATG
1 TGAAAATACATG
1300 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4772 original size:81 final size:81
Alignment explanation
Indices: 4669--5240 Score: 707
Period size: 81 Copynumber: 7.2 Consensus size: 81
4659 ATTGCATATT
* * ** * * *
4669 TTGACAC-TTTCCTATCAAATGCACAGCTAATCCATTATTCTCTTACTCAACAGTGTTTAACCGT
1 TTGACACATTT-CTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGT
* *
4733 ACATCTAACTTGCATAA
65 TCATCTAACTGGCATAA
* * *
4750 TTGACACATTTCTGTCAAATGCATAGTTAGGCCATTATTCTTTTATTCAACAGTATTTAACC-TT
1 TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
*
4814 CAATATAACTGGCATAA
66 C-ATCTAACTGGCATAA
* * * * **
4831 TTGACACTTTTATGTCAAATGGACAATTAGGCCATTATTCTTTTACTCAATAGTATTTAACCGTT
1 TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
4896 CATCTAACTGGCATAA
66 CATCTAACTGGCATAA
* *
4912 TTGACACCTTTCTGTCAAATGCAC----A----ATTATTCTTTTACTCAACGGTATTTAACCATT
1 TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
4969 CATCTAACTGGCATAA
66 CATCTAACTGGCATAA
* * *
4985 TTGAAACTTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
1 TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
*
5050 CATCTAACAGGCATAA
66 CATCTAACTGGCATAA
* * * *
5066 TTGACATC-TTTCTGTCAAATGCATAGTTAGGCCATTATTATTTTACTCAACGGTATTTAATCAT
1 TTGACA-CATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGT
*
5130 TTATCTAACTGGCATAA
65 TCATCTAACTGGCATAA
* * * **
5147 TTGACACATTTATGTCAATTGCACAGTTAGGCCATTATTCTTTTATTCAACGGTATTTAGTCGTT
1 TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
**
5212 CATCTAACTTACATAA
66 CATCTAACTGGCATAA
5228 TTGACACATTTCT
1 TTGACACATTTCT
5241 TCCAATTACA
Statistics
Matches: 429, Mismatches: 49, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
73 66 0.15
77 2 0.00
80 3 0.01
81 351 0.82
82 7 0.02
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (81 bp):
TTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTT
CATCTAACTGGCATAA
Found at i:5113 original size:235 final size:237
Alignment explanation
Indices: 4701--5260 Score: 716
Period size: 235 Copynumber: 2.3 Consensus size: 237
4691 ACAGCTAATC
* * * *
4701 CATTATTCTCTTACTCAACAGTGTTTAACCGTACATCTAACTTGCATAATTGACACATTTCTGTC
1 CATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGTC
* * *
4766 AAATGCATAGTTAGGCCATTATTCTTTTATTCAACAGTATTTAACCTTCAATATAACTGGCATAA
66 AATTGCATAGTTAGGCCATTATTCTTTTACTCAACAGTATTTAACCTTCAATATAACAGGCATAA
* * * *
4831 TTGACACTTTTATGTCAAATGGACAATTAGGCCATTATTCTTTTACTCAATAGTATTTAACCGTT
131 TTGACACTTTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCATT
* *
4896 CATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC-A
196 CATCTAACTGGCATAATTGACACATTTATGTCAAATGCACTA
* * * *
4937 -ATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGAAACTTTTCTGTC
1 CATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGTC
* * *
5001 AATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTC-ATCTAACAGGCATA
66 AATTGCATAGTTAGGCCATTATTCTTTTACTCAACAGTATTTAACC-TTCAATATAACAGGCATA
* * * * *
5065 ATTGACA-TCTTTCTGTCAAATGCATAGTTAGGCCATTATTATTTTACTCAACGGTATTTAATCA
130 ATTGACACT-TTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCA
* *
5129 TTTATCTAACTGGCATAATTGACACATTTATGTCAATTGCACAGTTA
194 TTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCAC---TA
* ** *
5176 GGCCATTATTCTTTTATTCAACGGTATTTAGTCGTTCATCTAACTTACATAATTGACACATTTCT
1 ---CATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTGCATAATTGACACATTTCT
*
5241 -TCCAATTACATAGTTAGGCC
63 GT-CAATTGCATAGTTAGGCC
5261 TCAAAGGGAC
Statistics
Matches: 276, Mismatches: 37, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
234 1 0.00
235 201 0.73
236 3 0.01
239 1 0.00
242 1 0.00
243 69 0.25
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (237 bp):
CATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGTC
AATTGCATAGTTAGGCCATTATTCTTTTACTCAACAGTATTTAACCTTCAATATAACAGGCATAA
TTGACACTTTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCATT
CATCTAACTGGCATAATTGACACATTTATGTCAAATGCACTA
Found at i:5430 original size:67 final size:67
Alignment explanation
Indices: 5210--5464 Score: 359
Period size: 68 Copynumber: 3.8 Consensus size: 67
5200 TATTTAGTCG
** * * * * * *
5210 TTCATCTAACTTACATAATTGACACATTTCTTCCAATTACATAGTTAGGCCTCAAAGGGACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTT-CATTTGCACAGTTAGGCCTCAAAGGCACTTAG
5275 CCT
65 CCT
*
5278 TTCATCTAACTGGAATAAATGACACCTTTCTTTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTC-TTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
5343 CCT
65 CCT
* *
5346 TTCATCTAACTGCCATAAATGACACCTTTCTGTCATTTGCACAGTTA-GCCTCATAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCT-TCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
5410 CCT
65 CCT
*
5413 TTCATCTAACTGGCATAAATGACATCTTTCTATCATTTGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCT-TCATTTGCACAGTTAGGCCT
5465 ATAATGTTTA
Statistics
Matches: 169, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
67 64 0.38
68 103 0.61
69 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (67 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTTCATTTGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:5453 original size:135 final size:136
Alignment explanation
Indices: 5210--5464 Score: 379
Period size: 135 Copynumber: 1.9 Consensus size: 136
5200 TATTTAGTCG
* * * *
5210 TTCATCTAACTTACATAATTGACACATTTCTTCCAATTACATAGTTAGGCCTCAAAGGGACTTAG
1 TTCATCTAACTGACATAAATGACACATTTCTTCCAATTACACAGTTAGGCCTCAAAGGCACTTAG
*
5275 CCTTTCATCTAACTGGAATAAATGACACCTTTCTTTCATTTGCACAGTTAGGCCTCAAAGGCACT
66 CCTTTCATCTAACTGGAATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACT
5340 TAGCCT
131 TAGCCT
* * * * *
5346 TTCATCTAACTGCCATAAATGACACCTTTCTGT-CATTTGCACAGTTA-GCCTCATAGGCACTTA
1 TTCATCTAACTGACATAAATGACACATTTCT-TCCAATTACACAGTTAGGCCTCAAAGGCACTTA
* *
5409 GCCTTTCATCTAACTGGCATAAATGACATCTTTCTATCATTTGCACAGTTAGGCCT
65 GCCTTTCATCTAACTGGAATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCT
5465 ATAATGTTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
135 67 0.63
136 38 0.36
137 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (136 bp):
TTCATCTAACTGACATAAATGACACATTTCTTCCAATTACACAGTTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACTGGAATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:9699 original size:31 final size:31
Alignment explanation
Indices: 9656--9720 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
9646 GTCCCGAATG
*
9656 ACCTATCCATATGTCCTGAAGGACATACGTA
1 ACCTATCCATATGTCCCGAAGGACATACGTA
* *
9687 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTATCCATATGTCCCGAAGGACATACGTA
9718 ACC
1 ACC
9721 CTCGACTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (31 bp):
ACCTATCCATATGTCCCGAAGGACATACGTA
Found at i:12698 original size:81 final size:81
Alignment explanation
Indices: 12559--13165 Score: 749
Period size: 81 Copynumber: 7.5 Consensus size: 81
12549 GTTTTTCACT
* * * * * * * ** * *
12559 TAACTTGCATATTTGACAATTTCCTGTCAAATGTAAAGCTAATCCATTATTCTCTTACTCAACAG
1 TAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
* * *
12624 TGTTTAACCGTACATC
66 TATTTAACCATTCATC
* * *
12640 TAACTGGCATAATTGACACTTTTCTGTTAAATGCACAGTTAGACCATTATCCTTTTACTCAACGG
1 TAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
**
12705 TA-TTAACTGTTCATC
66 TATTTAACCATTCATC
*
12720 TAACTAGCATAATTGACA-TATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACG
1 TAACTGGCATAATTGACACT-TTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACG
*
12784 TTATTTAACCATTCATC
65 GTATTTAACCATTCATC
* * * * *
12801 TAACTGGCATAATTGACACTTTTTCTATTAAATACACAATTAGGCCATTATTCTTTTACTCAATG
1 TAACTGGCATAATTGACAC-TTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACG
* *
12866 GTATTTAGCCTTTCATC
65 GTATTTAACCATTCATC
* *
12883 TAACTGGCATAATTGACACTTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGG
1 TAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
*
12948 TATTTATCCATTCATC
66 TATTTAACCATTCATC
* * * *
12964 TAACAGGCATAATTGACA--TTTATGTCAAATGCATAGTTAGGCCATTATTCTTTTGCTCAACGG
1 TAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
*
13027 TATTTAACTATTCATC
66 TATTTAACCATTCATC
* * *
13043 TAACTGGCATAATTGACACATTTCTGT-AAATTGCACAGTTAGGTCATTATTCTTTTACTCAATG
1 TAACTGGCATAATTGACACTTTTCTGTCAAA-TGCACAGTTAGGCCATTATTCTTTTACTCAACG
* *
13107 GTGTTTAGCCATTCATC
65 GTATTTAACCATTCATC
* *
13124 TAACTGGCATAATTGACACATTTCT-TCCAATTGCACAGTTAG
1 TAACTGGCATAATTGACACTTTTCTGT-CAAATGCACAGTTAG
13166 ACCTCAAAGG
Statistics
Matches: 458, Mismatches: 59, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
79 72 0.16
80 75 0.16
81 236 0.52
82 74 0.16
83 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (81 bp):
TAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
TATTTAACCATTCATC
Found at i:13077 original size:160 final size:160
Alignment explanation
Indices: 12602--13141 Score: 744
Period size: 160 Copynumber: 3.4 Consensus size: 160
12592 TAAAGCTAAT
* * * * *
12602 CCATTATTCTCTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTGACACTTTTCTGT
1 CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACA-TTTTCTGT
* * *
12667 TAAATGCACAGTTAGACCATTATCCTTTTACTCAACGGTA-TTAACTGTTCATCTAACTAGCATA
65 TAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACT-TTCATCTAACTGGCATA
*
12731 ATTGACATATTTCTGTCAAA-TGCACAGTTAGG
129 ATTGACACATTTCTGT-AAATTGCACAGTTAGG
* *
12763 CCATTATTCTTTTACTCAACGTTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTTCTA
1 CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACA--TTTTCTG
* * * *
12828 TTAAATACACAATTAGGCCATTATTCTTTTACTCAATGGTATTTAGCCTTTCATCTAACTGGCAT
64 TTAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTA-ACTTTCATCTAACTGGCAT
* *
12893 AATTGACACTTTTCTGTCAATTGCACAGTTAGG
128 AATTGACACATTTCTGTAAATTGCACAGTTAGG
* * * * *
12926 CCATTATTCTTTTACTTAACGGTATTTATCCATTCATCTAACAGGCATAATTGACA-TTTATGTC
1 CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACATTTTCTGTT
* *
12990 AAATGCATAGTTAGGCCATTATTCTTTTGCTCAACGGTATTTAACTATTCATCTAACTGGCATAA
66 AAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACT-TTCATCTAACTGGCATAA
13055 TTGACACATTTCTGTAAATTGCACAGTTAGG
130 TTGACACATTTCTGTAAATTGCACAGTTAGG
* * * *
13086 TCATTATTCTTTTACTCAATGGTGTTTAGCCATTCATCTAACTGGCATAATTGACA
1 CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACA
13142 CATTTCTTCC
Statistics
Matches: 335, Mismatches: 39, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
159 2 0.01
160 140 0.42
161 50 0.15
162 44 0.13
163 97 0.29
164 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (160 bp):
CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACATTTTCTGTT
AAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACTTTCATCTAACTGGCATAAT
TGACACATTTCTGTAAATTGCACAGTTAGG
Found at i:13438 original size:68 final size:68
Alignment explanation
Indices: 13111--13441 Score: 493
Period size: 68 Copynumber: 4.9 Consensus size: 68
13101 TCAATGGTGT
* * * *
13111 TTAGCCATTCATCTAACTGGCATAATTGACACATTTCT-TCCAATTGCACAGTTAGACCTCAAAG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGT-CATTTGCACAGTTAGGCCTCAAAG
13175 GCAC
65 GCAC
* * *
13179 TTAGCCTTTCATCTAACTGGCATAAATAATACATTTCTGTCATTTGCACAGTTAAGCCTCAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
13244 CAC
66 CAC
* * * * * *
13247 CTAGCCTTTCATCTAACTGGCATAAATGATACTTTTCTATCATTTGCACAGTTCGGCCTTAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
13312 CAC
66 CAC
* * *
13315 TTAGCCTTTTATCTAACTGGCATGAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
13380 CAC
66 CAC
*
13383 TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
13442 ATAATCGTTT
Statistics
Matches: 238, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 237 1.00
69 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (68 bp):
TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
CAC
Found at i:14218 original size:22 final size:22
Alignment explanation
Indices: 14192--14247 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
14182 TCGATACTCT
14192 TACTATGGTATCAAAACTATCA
1 TACTATGGTATCAAAACTATCA
14214 TACTATGGTATCAAAACTATCA
1 TACTATGGTATCAAAACTATCA
14236 TACTATGGTATC
1 TACTATGGTATC
14248 GATACCCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
TACTATGGTATCAAAACTATCA
Found at i:18621 original size:24 final size:24
Alignment explanation
Indices: 18594--18705 Score: 73
Period size: 24 Copynumber: 4.7 Consensus size: 24
18584 TATATCAAAA
*
18594 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
18618 ATCAGATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
18642 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
* * * * *
18665 ATCAGATCAGAATCCAGGTCAGGT
1 ATCAAAACAGAATTCAAGTCAAGT
* *
18689 ATCATAACAAAATTCAA
1 ATCAAAACAGAATTCAA
18706 ATTAGAAATC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.29
24 51 0.71
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Found at i:18671 original size:23 final size:23
Alignment explanation
Indices: 18611--18685 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
18601 CATAATTCAA
*
18611 GTCAAGTATCAGATCAGAATTCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
18635 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
18659 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
18682 GTCA
1 GTCA
18686 GGTATCATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:20305 original size:17 final size:18
Alignment explanation
Indices: 20273--20309 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20263 TAAAACTAAC
20273 ATTTTTATGCACATCAAT
1 ATTTTTATGCACATCAAT
*
20291 ATTTTTAT-CAGATCAAT
1 ATTTTTATGCACATCAAT
20308 AT
1 AT
20310 GTATGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTTTATGCACATCAAT
Found at i:26780 original size:35 final size:33
Alignment explanation
Indices: 26704--26783 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 33
26694 TCTACAACAC
*
26704 AATCATCAATTATATTAAACCCCAAAATCCAAA
1 AATCTTCAATTATATTAAACCCCAAAATCCAAA
* * *
26737 AATTTTCAATTATATTTTAAACCTCAAATTCC-AA
1 AATCTTCAATTATA--TTAAACCCCAAAATCCAAA
26771 AATACTTCAATTA
1 AAT-CTTCAATTA
26784 CATACCCAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 12 0.31
34 5 0.13
35 22 0.56
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (33 bp):
AATCTTCAATTATATTAAACCCCAAAATCCAAA
Found at i:27146 original size:143 final size:144
Alignment explanation
Indices: 26959--27243 Score: 437
Period size: 148 Copynumber: 2.0 Consensus size: 144
26949 TACTCAATTC
* * * *
26959 AGTTTATAAAATAGTTGACTCGAATTTTTTTTGATTTGATTTTATAAAATTTAAATCAAGTC-GA
1 AGTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAGA
* * *
27023 ATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTGA
66 ATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGA
*
27088 TTCTAATTCAGTTT
131 TTATAATTCAGTTT
27102 AGTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
1 AGTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC--A
* *
27167 TTGAATTGAATTTTCAAGTTTTTGTTTAAATTTAATTATCAATATTTATAATACTATAATATTAT
64 --GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTAT
27232 TTGATTATAATT
127 TTGATTATAATT
27244 TAAATAGTTT
Statistics
Matches: 127, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
143 58 0.46
148 69 0.54
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (144 bp):
AGTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAGA
ATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGA
TTATAATTCAGTTT
Found at i:27800 original size:35 final size:35
Alignment explanation
Indices: 27749--27827 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
27739 GGGTTGGGGT
* *
27749 TGTAACTGAAGTATTTTGAAATTTGAGGTTTAGAA
1 TGTAATTGAAGCATTTTGAAATTTGAGGTTTAGAA
* * *
27784 TGTAATTGAAGCATTTTGGATTTTGGGGTTTAGAA
1 TGTAATTGAAGCATTTTGAAATTTGAGGTTTAGAA
27819 TGTAATTGA
1 TGTAATTGA
27828 TGATTGTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (35 bp):
TGTAATTGAAGCATTTTGAAATTTGAGGTTTAGAA
Found at i:34080 original size:104 final size:102
Alignment explanation
Indices: 33900--34091 Score: 296
Period size: 104 Copynumber: 1.9 Consensus size: 102
33890 TCTGTTGACG
* *
33900 TTCAATCTAAAGTTTGATCTTGAGTGGATTTTTTGCTGTTTTTACTCTGGTTTGAGCTTAGAGAT
1 TTCAATCTAAAGTTTGATCTTGAGTGGATTTTTTGCTGTTTTTACTCTGGTTTGAGCTTAAAAAT
33965 CGATTCTTTGATTCAGTTTGTGAATGCCCATTTGAACA
66 CGATTCTTTGA-TCAGTTTGTGAATGCCCATTTGAACA
*
34003 TTCAATCTAAAGTTTTGATCTTGAGTGGATTTTTTGCTGTTTTTAGTCTGGTTTGAGCTTAAAAA
1 TTCAATCTAAAG-TTTGATCTTGAGTGGATTTTTTGCTGTTTTTACTCTGGTTTGAGCTTAAAAA
* * *
34068 TTGGTT-TGTTGATCATTTTGTGAA
65 TCGATTCT-TTGATCAGTTTGTGAA
34092 CACCCTACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
103 24 0.30
104 57 0.70
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (102 bp):
TTCAATCTAAAGTTTGATCTTGAGTGGATTTTTTGCTGTTTTTACTCTGGTTTGAGCTTAAAAAT
CGATTCTTTGATCAGTTTGTGAATGCCCATTTGAACA
Found at i:37614 original size:26 final size:26
Alignment explanation
Indices: 37578--37640 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
37568 TTCGACTCAA
37578 ACTCGAAAACTTTCAAAGCCAGCTCG
1 ACTCGAAAACTTTCAAAGCCAGCTCG
37604 ACTCGAAAACTTTCAAAGCCAGCTCG
1 ACTCGAAAACTTTCAAAGCCAGCTCG
*
37630 AGTCGAAAACT
1 ACTCGAAAACT
37641 CGCGAGCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.19
Consensus pattern (26 bp):
ACTCGAAAACTTTCAAAGCCAGCTCG
Found at i:38515 original size:32 final size:31
Alignment explanation
Indices: 38479--38554 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
38469 CGGGGCCGTG
*
38479 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
38511 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
38542 GAGCCTACCTAAG
1 GGGCCTACCTAAG
38555 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:38538 original size:63 final size:63
Alignment explanation
Indices: 38432--38554 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
38422 ACCTAAGGGA
* * ** *
38432 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
38495 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
38555 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:40088 original size:18 final size:18
Alignment explanation
Indices: 40065--40099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40055 TTCCATCCGG
*
40065 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
40083 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
40100 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:42381 original size:23 final size:23
Alignment explanation
Indices: 42351--42454 Score: 172
Period size: 23 Copynumber: 4.5 Consensus size: 23
42341 GACAGAAACT
* **
42351 ATTGAAGCTCTATTCCGAGAGCG
1 ATTGAAGCTCGATTCCGAGCTCG
*
42374 ATTGAAGCTCTATTCCGAGCTCG
1 ATTGAAGCTCGATTCCGAGCTCG
42397 ATTGAAGCTCGATTCCGAGCTCG
1 ATTGAAGCTCGATTCCGAGCTCG
42420 ATTGAAGCTCGATTCCGAGCTCG
1 ATTGAAGCTCGATTCCGAGCTCG
42443 ATTGAAGCTCGA
1 ATTGAAGCTCGA
42455 CATTGCCCAA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (23 bp):
ATTGAAGCTCGATTCCGAGCTCG
Found at i:42407 original size:11 final size:11
Alignment explanation
Indices: 42372--42454 Score: 82
Period size: 11 Copynumber: 7.3 Consensus size: 11
42362 ATTCCGAGAG
42372 CGATTGAAGCT
1 CGATTGAAGCT
*
42383 CTATTCCG-AGCT
1 CGATT--GAAGCT
42395 CGATTGAAGCT
1 CGATTGAAGCT
42406 CGATTCCG-AGCT
1 CGATT--GAAGCT
42418 CGATTGAAGCT
1 CGATTGAAGCT
42429 CGATTCCG-AGCT
1 CGATT--GAAGCT
42441 CGATTGAAGCT
1 CGATTGAAGCT
42452 CGA
1 CGA
42455 CATTGCCCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
10 3 0.05
11 29 0.48
12 26 0.43
13 3 0.05
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (11 bp):
CGATTGAAGCT
Found at i:42419 original size:12 final size:12
Alignment explanation
Indices: 42379--42445 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
42369 GAGCGATTGA
*
42379 AGCTCTATTCCG
1 AGCTCGATTCCG
42391 AGCTCGATT--G
1 AGCTCGATTCCG
42401 AAGCTCGATTCCG
1 -AGCTCGATTCCG
42414 AGCTCGATT--G
1 AGCTCGATTCCG
42424 AAGCTCGATTCCG
1 -AGCTCGATTCCG
42437 AGCTCGATT
1 AGCTCGATT
42446 GAAGCTCGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
10 2 0.04
11 18 0.38
12 26 0.54
13 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (12 bp):
AGCTCGATTCCG
Found at i:43613 original size:20 final size:21
Alignment explanation
Indices: 43590--43643 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
43580 TTAATTTGGG
43590 AGTTTAGGATTT-AGGGTTAT
1 AGTTTAGGATTTAAGGGTTAT
* * *
43610 AGTTTATGTTTTAAGGTTTAT
1 AGTTTAGGATTTAAGGGTTAT
* *
43631 AGTTGAGGGTTTA
1 AGTTTAGGATTTA
43644 TAGATTAGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (21 bp):
AGTTTAGGATTTAAGGGTTAT
Found at i:43641 original size:14 final size:14
Alignment explanation
Indices: 43624--43671 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
43614 TATGTTTTAA
43624 GGTTTATAG-TTGAG
1 GGTTTATAGATT-AG
43638 GGTTTATAGATTAG
1 GGTTTATAGATTAG
43652 GGTTTA-AGGATTAG
1 GGTTTATA-GATTAG
*
43666 GATTTA
1 GGTTTA
43672 GGGTTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 1 0.03
14 28 0.90
15 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
GGTTTATAGATTAG
Found at i:46701 original size:20 final size:20
Alignment explanation
Indices: 46678--46732 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
46668 AGATTCGCAA
*
46678 TGCGATTTTGAAAAATGTGT
1 TGCGATATTGAAAAATGTGT
46698 TGCGATAGTT--AAAATGTGT
1 TGCGATA-TTGAAAAATGTGT
*
46717 TGCGATAGTGAAAAAT
1 TGCGATATTGAAAAAT
46733 CCAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 11 0.37
21 2 0.07
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
TGCGATATTGAAAAATGTGT
Found at i:46713 original size:19 final size:19
Alignment explanation
Indices: 46689--46730 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
46679 GCGATTTTGA
*
46689 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
46708 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
46727 AAAA
1 AAAA
46731 ATCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:46878 original size:65 final size:64
Alignment explanation
Indices: 46774--46896 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 64
46764 ATTCACGTGG
46774 AGTTTGAAACAATAAAGAATGTGTTGCAATAGTGTAAAAGATTCACAAGTCATTTGTAAGATCTT
1 AGTTTGAAACAATAAAGAATGTGTTGCAATAGTGTAAAAGATTCACAAGT-ATTTGTAAGATCTT
* * * *
46839 AGTTTGAAACAATCAAGAATGTGTTGCGATAGTGTAAAAGATTCCCAAGTGTTTGTAA
1 AGTTTGAAACAATAAAGAATGTGTTGCAATAGTGTAAAAGATTCACAAGTATTTGTAA
46897 TTCTCAATCC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 7 0.13
65 47 0.87
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (64 bp):
AGTTTGAAACAATAAAGAATGTGTTGCAATAGTGTAAAAGATTCACAAGTATTTGTAAGATCTT
Found at i:47060 original size:17 final size:17
Alignment explanation
Indices: 47047--47085 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
47037 GGGTCGGGGT
47047 GGGGTCGTGGTCGGGCC
1 GGGGTCGTGGTCGGGCC
*
47064 GGGGTCGTGGCCGTGGCC
1 GGGGTCGTGGTCG-GGCC
47082 GGGG
1 GGGG
47086 CCGGGGCCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.00, C:0.23, G:0.62, T:0.15
Consensus pattern (17 bp):
GGGGTCGTGGTCGGGCC
Found at i:47080 original size:6 final size:6
Alignment explanation
Indices: 47059--47150 Score: 121
Period size: 6 Copynumber: 15.3 Consensus size: 6
47049 GGTCGTGGTC
* * * * *
47059 GGGCCG GGGTCG TGGCCG TGGCCG GGGCCG GGGCCG GGGTCG TGGCCG
1 GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG
* *
47107 GGGCCG GGGCCG GGGCCG GGGTCG TGGCCG GGGCCG GGGCCG GG
1 GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GGGCCG GG
47151 TAGGGGTCGG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.00, C:0.29, G:0.63, T:0.08
Consensus pattern (6 bp):
GGGCCG
Found at i:47094 original size:30 final size:30
Alignment explanation
Indices: 47059--47150 Score: 175
Period size: 30 Copynumber: 3.1 Consensus size: 30
47049 GGTCGTGGTC
*
47059 GGGCCGGGGTCGTGGCCGTGGCCGGGGCCG
1 GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
47089 GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
1 GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
47119 GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
1 GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
47149 GG
1 GG
47151 TAGGGGTCGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.00, C:0.29, G:0.63, T:0.08
Consensus pattern (30 bp):
GGGCCGGGGTCGTGGCCGGGGCCGGGGCCG
Found at i:47326 original size:2 final size:2
Alignment explanation
Indices: 47319--47343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47309 TTTACACTTA
47319 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 A
47344 AAGAATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52853 original size:173 final size:180
Alignment explanation
Indices: 52574--52930 Score: 638
Period size: 176 Copynumber: 2.0 Consensus size: 180
52564 AAACGAAAAA
52574 ACACAATTATAATAAGATCAATATCTTATTTCATTAGATAAAACTTTAATTTTTTGTTACCTTTT
1 ACACAATTATAATAAGATCAATATCTTATTTCATTAGATAAAACTTTAATTTTTTGTTACC-TTT
52639 TATATATTTTCTATTAATAATTTAATTTTTATTTTTAAAATTTTATAAATTC-TATTCTAATGTA
65 TATATATTTTCTATTAATAATTTAATTTTTATTTTTAAAATTTTATAAATTCATATTCTAATGTA
52703 T-CATTCCTATTGTAATAGGAC-TA-ATTT-ATTTCAAGTAATTTCAATGG
130 TACATTCCTATTGTAATAGGACATACATTTCATTTCAAGTAATTTCAATGG
52750 ACACAATTATAATAAGATCAATATCTTATTTCATTAGATAAAACTTTAATTTTTTGTTACC-TTT
1 ACACAATTATAATAAGATCAATATCTTATTTCATTAGATAAAACTTTAATTTTTTGTTACCTTTT
52814 -TATATTTTCTATTAATAATTTAATTTTTATTTTTAAAATTTTATAAATTCATATTCTAATGTAT
66 ATATATTTTCTATTAATAATTTAATTTTTATTTTTAAAATTTTATAAATTCATATTCTAATGTAT
52878 ACATTCCTATTGTAATAGGACTAATACATTTCATTTCAAGTAATTTCAATGG
131 ACATTCCTATTGTAATAGGAC--ATACATTTCATTTCAAGTAATTTCAATGG
52930 A
1 A
52931 AACACCCATA
Statistics
Matches: 174, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
173 50 0.29
174 16 0.09
175 20 0.11
176 61 0.35
178 2 0.01
179 4 0.02
180 21 0.12
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (180 bp):
ACACAATTATAATAAGATCAATATCTTATTTCATTAGATAAAACTTTAATTTTTTGTTACCTTTT
ATATATTTTCTATTAATAATTTAATTTTTATTTTTAAAATTTTATAAATTCATATTCTAATGTAT
ACATTCCTATTGTAATAGGACATACATTTCATTTCAAGTAATTTCAATGG
Found at i:52883 original size:20 final size:20
Alignment explanation
Indices: 52855--52893 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52845 TTTAAAATTT
52855 TATAAATTCATATTCTAATG
1 TATAAATTCATATTCTAATG
* * *
52875 TATACATTCCTATTGTAAT
1 TATAAATTCATATTCTAAT
52894 AGGACTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (20 bp):
TATAAATTCATATTCTAATG
Found at i:54693 original size:24 final size:23
Alignment explanation
Indices: 54636--54741 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 23
54626 CGGAGATATT
* *
54636 AGAAATCAAAACAGAATTCAGATC
1 AGAAATCAGAACAGAATT-AAATC
* * *
54660 AGACACCAGAATAGAATCTAAATC
1 AGAAATCAGAACAGAAT-TAAATC
* * *
54684 AGAAATCAGAACATAATTTAGATA
1 AGAAATCAGAACAGAA-TTAAATC
*
54708 AGAAATCAAAACAGAATTCAAATC
1 AGAAATCAGAACAGAATT-AAATC
*
54732 ATAAATCAGA
1 AGAAATCAGA
54742 TAAAACATTC
Statistics
Matches: 62, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
23 2 0.03
24 58 0.94
25 2 0.03
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (23 bp):
AGAAATCAGAACAGAATTAAATC
Found at i:54724 original size:48 final size:48
Alignment explanation
Indices: 54636--54741 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
54626 CGGAGATATT
* * * * *
54636 AGAAATCAAAACAGAATTCAGATCAGACACCAGAATAGAA-TCTAAATC
1 AGAAATCAGAACAGAATTCAGATAAGAAACCAAAACAGAATTC-AAATC
* * *
54684 AGAAATCAGAACATAATTTAGATAAGAAATCAAAACAGAATTCAAATC
1 AGAAATCAGAACAGAATTCAGATAAGAAACCAAAACAGAATTCAAATC
*
54732 ATAAATCAGA
1 AGAAATCAGA
54742 TAAAACATTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGATAAGAAACCAAAACAGAATTCAAATC
Found at i:54735 original size:36 final size:35
Alignment explanation
Indices: 54636--54744 Score: 89
Period size: 36 Copynumber: 3.0 Consensus size: 35
54626 CGGAGATATT
* * *
54636 AGAAATCAAAACAGAATTCAGATCAGACACCAGA-A
1 AGAAATCAAAACAGAATTCAAATCATA-ATCAGATA
* * *
54671 TAG-AATCTAAATCAGAAATCAGAA-CATAATTTAGATA
1 -AGAAATC-AAAACAGAATTCA-AATCATAA-TCAGATA
54708 AGAAATCAAAACAGAATTCAAATCATAAATCAGATA
1 AGAAATCAAAACAGAATTCAAATCAT-AATCAGATA
54744 A
1 A
54745 AACATTCATG
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
35 7 0.12
36 42 0.74
37 8 0.14
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (35 bp):
AGAAATCAAAACAGAATTCAAATCATAATCAGATA
Found at i:57218 original size:18 final size:18
Alignment explanation
Indices: 57195--57229 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57185 CAAAGTCAAC
*
57195 GGTCAACTGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
57213 GGTCAACGGGTTGGGTC
1 GGTCAACGGGTCGGGTC
57230 AAACTGCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.20, G:0.46, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:59295 original size:24 final size:24
Alignment explanation
Indices: 59264--59355 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
59254 TGGAGATATT
59264 AGAAATCAAAACAGAATTCAGATC
1 AGAAATCAAAACAGAATTCAGATC
* ** *
59288 AGACATCATCACAGAATCCAGATC
1 AGAAATCAAAACAGAATTCAGATC
* * *
59312 AGAAATTAGAACAAAATTCAGATC
1 AGAAATCAAAACAGAATTCAGATC
*
59336 AGAAATCAAAACATAATTCA
1 AGAAATCAAAACAGAATTCA
59356 AATCGTAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
AGAAATCAAAACAGAATTCAGATC
Found at i:59365 original size:24 final size:24
Alignment explanation
Indices: 59264--59367 Score: 84
Period size: 24 Copynumber: 4.3 Consensus size: 24
59254 TGGAGATATT
* *
59264 AGAAATCAAAACAGAATTCAGATC
1 AGAAATCAAAACAAAATTCAAATC
* ** * * *
59288 AGACATCATCACAGAATCCAGATC
1 AGAAATCAAAACAAAATTCAAATC
* * *
59312 AGAAATTAGAACAAAATTCAGATC
1 AGAAATCAAAACAAAATTCAAATC
*
59336 AGAAATCAAAACATAATTCAAATC
1 AGAAATCAAAACAAAATTCAAATC
59360 -GTAAATCA
1 AG-AAATCA
59368 GATAAAACAT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
23 1 0.02
24 64 0.98
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
AGAAATCAAAACAAAATTCAAATC
Found at i:61818 original size:21 final size:22
Alignment explanation
Indices: 61794--61846 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
61784 GCCTGTAAAA
*
61794 AATATAA-AATGT-TTAATTAAT
1 AATATAATAATATATTAA-TAAT
61815 AATAATAATAATATAATTAATAAT
1 AAT-ATAATAATAT-ATTAATAAT
61839 AATATAAT
1 AATATAAT
61847 TTTTAACCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 9 0.33
24 7 0.26
25 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATATAATAATATATTAATAAT
Found at i:61852 original size:18 final size:15
Alignment explanation
Indices: 61813--61847 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
61803 TGTTTAATTA
61813 ATAA-TAATAATAAT
1 ATAATTAATAATAAT
61827 ATAATTAATAATAAT
1 ATAATTAATAATAAT
61842 ATAATT
1 ATAATT
61848 TTTAACCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTAATAATAAT
Found at i:62331 original size:128 final size:133
Alignment explanation
Indices: 62037--62337 Score: 316
Period size: 134 Copynumber: 2.3 Consensus size: 133
62027 GTGACAAAAC
* * *
62037 TCCTAAATAATGAGGAGATCTAGTTA-AGTGATGATACTG-CTCATACGTGATGAAGTGTTCTTG
1 TCCTACATAATGAGGAGATCTAGTTAGA-TGATGACAC-GACTCATACGTGATGAAGAGTTCTTG
* * * * *
62100 GCCATTTTAGGAATGGTGATAACTCTGTTCCTATGCGATGAGGGCAACTGGTTATCAAGGATTGA
64 GCCATTCTA-GAATGGTGATAACTCGGTTCCTACGCGATGAGGACAACTGGCTATCAAGGATTGA
62165 CACGAT
128 CACGAT
* ** *
62171 TCCTACATAATGAGGAAATCTAGTCGGGTGATGACACGACTCATACGTGATGAAGAGTT-TTGGC
1 TCCTACATAATGAGGAGATCTAGTTAGATGATGACACGACTCATACGTGATGAAGAGTTCTTGGC
* * * * *
62235 CA-TCTA-AA-GGTGATAACAT-GGTTCCTACGTGATGAGGACGATTGGCTATC-TGGGTTGACA
66 CATTCTAGAATGGTGATAAC-TCGGTTCCTACGCGATGAGGACAACTGGCTATCAAGGATTGACA
62295 CAGA-
130 C-GAT
*
62299 TCCTACATAGTGAGGAGATC-AGGTTAGATGATGACACGA
1 TCCTACATAATGAGGAGATCTA-GTTAGATGATGACACGA
62338 TTTCTATGTG
Statistics
Matches: 140, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
127 1 0.01
128 41 0.29
129 35 0.25
130 3 0.02
132 3 0.02
133 8 0.06
134 49 0.35
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (133 bp):
TCCTACATAATGAGGAGATCTAGTTAGATGATGACACGACTCATACGTGATGAAGAGTTCTTGGC
CATTCTAGAATGGTGATAACTCGGTTCCTACGCGATGAGGACAACTGGCTATCAAGGATTGACAC
GAT
Found at i:63510 original size:32 final size:33
Alignment explanation
Indices: 63442--63525 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
63432 CATTAGGATG
* * *
63442 TTGAATC-CCCAAAGATGCCCCAATAATCGATG
1 TTGAATCTTCCAAAGATGCCCCAACAATCGATA
* * *
63474 TTGAAT-TTCCAAAGATGCCCCAGCATTTGATA
1 TTGAATCTTCCAAAGATGCCCCAACAATCGATA
63506 TTGAATCTT-CAAAGATGCCC
1 TTGAATCTTCCAAAGATGCCC
63526 TCATTGTTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
32 42 0.95
33 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (33 bp):
TTGAATCTTCCAAAGATGCCCCAACAATCGATA
Found at i:64641 original size:16 final size:16
Alignment explanation
Indices: 64617--64651 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
64607 CTTGATTCAA
*
64617 TTTCTTTTTTTTTTTT
1 TTTCATTTTTTTTTTT
64633 TTTCATTTTTTTTTTT
1 TTTCATTTTTTTTTTT
64649 TTT
1 TTT
64652 GTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCATTTTTTTTTTT
Found at i:64643 original size:17 final size:16
Alignment explanation
Indices: 64617--64708 Score: 85
Period size: 17 Copynumber: 5.3 Consensus size: 16
64607 CTTGATTCAA
64617 TTTCTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTT
64633 TTTCATTTTTTTTTTTT
1 TTTC-TTTTTTTTTTTT
64650 TTGTCTTTTTTTTGTATTT
1 TT-TCTTTTTTTT-T-TTT
*
64669 TTCTCTTATTTTTTGTATT
1 TT-TCTT-TTTTTT-TTTT
* * *
64688 TTTCTCTTCTTCTTTT
1 TTTCTTTTTTTTTTTT
64704 TTTCT
1 TTTCT
64709 AATGAATGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
16 12 0.18
17 26 0.40
18 6 0.09
19 13 0.20
20 8 0.12
ACGTcount: A:0.04, C:0.11, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:64669 original size:20 final size:17
Alignment explanation
Indices: 64617--64706 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 17
64607 CTTGATTCAA
64617 TTTC-TTTTTTTTTTTT
1 TTTCTTTTTTTTTTTTT
64633 TTTCATTTTTTTTTTTTT
1 TTTC-TTTTTTTTTTTTT
*
64651 TGTCTTTTTTTTGTATTTT
1 TTTCTTTTTTTT-T-TTTT
* * *
64670 TCTCTTATTTTTTGTATT
1 TTTCTT-TTTTTTTTTTT
* *
64688 TTTCTCTTCTTCTTTTTT
1 TTTCT-TTTTTTTTTTTT
64706 T
1 T
64707 CTAATGAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 31 0.53
19 10 0.17
20 6 0.10
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTTTTTTTTT
Found at i:64670 original size:12 final size:11
Alignment explanation
Indices: 64621--64670 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
64611 ATTCAATTTC
64621 TTTTTTTTTT-
1 TTTTTTTTTTG
*
64631 TTTTTCATTTT-
1 TTTTT-TTTTTG
64642 TTTTTTTTTTG
1 TTTTTTTTTTG
*
64653 TCTTTTTTTTG
1 TTTTTTTTTTG
*
64664 TATTTTT
1 TTTTTTT
64671 CTCTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:64703 original size:22 final size:21
Alignment explanation
Indices: 64618--64704 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 21
64608 TTGATTCAAT
*
64618 TTCTTTTTTT-T-TTTTTTTC
1 TTCTTTTTTTGTATTTTTCTC
* *
64637 AT-TTTTTTT-T-TTTTTGTC
1 TTCTTTTTTTGTATTTTTCTC
64655 -T-TTTTTTTGTATTTTTCTC
1 TTCTTTTTTTGTATTTTTCTC
*
64674 TT-ATTTTTTGTATTTTTCTC
1 TTCTTTTTTTGTATTTTTCTC
64694 TTCTTCTTTTT
1 TTCTT-TTTTT
64705 TTCTAATGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.14
18 16 0.28
19 8 0.14
20 20 0.34
21 1 0.02
22 5 0.09
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (21 bp):
TTCTTTTTTTGTATTTTTCTC
Done.