Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002861.1 Hibiscus syriacus cultivar Beakdansim tig00005899_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: 62861
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3138 original size:153 final size:156
Alignment explanation
Indices: 2871--3178 Score: 509
Period size: 154 Copynumber: 2.0 Consensus size: 156
2861 ATACCTAAAG
2871 AAATGAGGTAATGACATTCCCGGTAATATACCCAAAAAGAAATCCACTATTGGTAATCTTACATT
1 AAATGAGGTAATGACATTCCCGGTAATATACCC-AAAAGAAATCCACTATTGGTAATCTTACATT
* *
2936 ACTGGGAATAAGATTCTCGAGCTAACCAAACGGGAATGTGGATTCCATTCCCATGGTAATCCC-C
65 ACTCGGAATAAGATTCTCGAGCTAACCAAACGGGAATGTGGATTCCATTCCCATGATAATCCCAC
3000 ATTCCCCCATCCAAACACCCCCTAAGA
130 ATTCCCCCATCCAAACACCCCCTAAGA
*
3027 AAATGGAGGTAATGACATTCCCGGTAATATACCC-CAA-AAATCCACTATTGGTAATCTTACATT
1 AAAT-GAGGTAATGACATTCCCGGTAATATACCCAAAAGAAATCCACTATTGGTAATCTTACATT
* *
3090 AC-CGGAATGAGATT-TCGGGCTAACCAAACGGGGAATGTGGATTCCATTCCCATGATAATCCCA
65 ACTCGGAATAAGATTCTCGAGCTAACCAAAC-GGGAATGTGGATTCCATTCCCATGATAATCCCA
3153 CATTCCCCCATCCAAACACCCCCTAA
129 CATTCCCCCATCCAAACACCCCCTAA
3179 AGTGCTTGTA
Statistics
Matches: 144, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
152 14 0.10
153 41 0.28
154 54 0.38
155 2 0.01
156 4 0.03
157 29 0.20
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (156 bp):
AAATGAGGTAATGACATTCCCGGTAATATACCCAAAAGAAATCCACTATTGGTAATCTTACATTA
CTCGGAATAAGATTCTCGAGCTAACCAAACGGGAATGTGGATTCCATTCCCATGATAATCCCACA
TTCCCCCATCCAAACACCCCCTAAGA
Found at i:3376 original size:20 final size:20
Alignment explanation
Indices: 3311--3376 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
3301 TTCTAAATTT
* *
3311 AATTTTATTTTAAAAATAGTA
1 AATTTAATTTT-AAAATATTA
* * * *
3332 AATTCATTTTTTATATATTA
1 AATTTAATTTTAAAATATTA
3352 AATTTAATTTTAAAATATTA
1 AATTTAATTTTAAAATATTA
3372 AATTT
1 AATTT
3377 TTATTATTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTTAATTTTAAAATATTA
Found at i:3389 original size:24 final size:24
Alignment explanation
Indices: 3358--3415 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
3348 ATTAAATTTA
*
3358 ATTTTAAAATATTAAATT-TTTATT
1 ATTTTAAAATATTAAATTAATTA-T
* *
3382 ATTTT-AAATCTTATATTAATTAT
1 ATTTTAAAATATTAAATTAATTAT
3405 ATTTTAAAATA
1 ATTTTAAAATA
3416 GAATTTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTAAAATATTAAATTAATTAT
Found at i:6369 original size:21 final size:21
Alignment explanation
Indices: 6340--6392 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6330 ATTCTGACTA
6340 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
6361 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
6382 TCGCAATGCGA
1 TCGCATTGCGA
6393 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:6407 original size:20 final size:20
Alignment explanation
Indices: 6382--6455 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
6372 TTTTCCTAAT
6382 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
6402 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
6423 TCGCAATACGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
6443 TCGCAATGCGAAT
1 TCGCAATGCGAAT
6456 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:6428 original size:41 final size:40
Alignment explanation
Indices: 6382--6473 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
6372 TTTTCCTAAT
*
6382 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAA
* * * **
6423 TCGCAATACGATTACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
6463 TCGCAATGCGA
1 TCGCAATGCGA
6474 TTTACATAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
Found at i:6678 original size:22 final size:22
Alignment explanation
Indices: 6652--6717 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
6642 GGCGACATCT
*
6652 GTCCCCATCTCTGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
6674 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
6696 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
6718 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:7092 original size:33 final size:34
Alignment explanation
Indices: 7042--7115 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
7032 ACTATTGCAA
**
7042 TGCGATTCTGTCATTGCGATTTTCA-TTTCGTGT
1 TGCGATTCTGTCATTGCGATAGTCATTTTCGTGT
*
7075 TGCGATTCT-TGCGTTGCGATAGTCATTTTCGTGT
1 TGCGATTCTGT-CATTGCGATAGTCATTTTCGTGT
7109 TGCGATT
1 TGCGATT
7116 TTCATTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.56
34 15 0.42
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (34 bp):
TGCGATTCTGTCATTGCGATAGTCATTTTCGTGT
Found at i:7135 original size:20 final size:19
Alignment explanation
Indices: 7055--7136 Score: 84
Period size: 20 Copynumber: 4.5 Consensus size: 19
7045 GATTCTGTCA
7055 TTGCGATTTTCATTTCGTG
1 TTGCGATTTTCATTTCGTG
*
7074 TTGCGA--TTC--TT-GCG
1 TTGCGATTTTCATTTCGTG
**
7088 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGTG
7108 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGTG
7128 TTGCGATTT
1 TTGCGATTT
7137 AAAGTTTTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 8 0.15
15 2 0.04
16 2 0.04
17 3 0.06
19 8 0.15
20 29 0.56
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGTG
Found at i:9026 original size:20 final size:20
Alignment explanation
Indices: 9001--9154 Score: 105
Period size: 20 Copynumber: 7.3 Consensus size: 20
8991 AGAATAGTTT
9001 ACTATCGCAATGAGAAAATG
1 ACTATCGCAATGAGAAAATG
* *
9021 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGAGAAAATG
* *
9041 ACTATCGCAACGAGAGAATCG
1 ACTATCGCAATGAGAAAAT-G
* * *
9062 -CAATGCGAAATGA-AAATTG
1 ACTAT-CGCAATGAGAAAATG
* *
9081 CAACAACAAAATCGCAATGCGAAAATG
1 -----AC--TATCGCAATGAGAAAATG
*
9108 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGAGAAAATG
**
9128 ACTATCGCAATGAGAATTTG
1 ACTATCGCAATGAGAAAATG
9148 ACTATCG
1 ACTATCG
9155 TAACGAAAGA
Statistics
Matches: 107, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 82 0.77
21 7 0.07
22 2 0.02
25 1 0.01
26 6 0.06
27 8 0.07
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGAGAAAATG
Found at i:9084 original size:33 final size:33
Alignment explanation
Indices: 9024--9104 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
9014 GAAAATGACT
* ** * * *
9024 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
*
9058 ATCGCAATGCGAAATGAAAATTGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
9091 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
9105 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:9229 original size:20 final size:20
Alignment explanation
Indices: 9204--9270 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
9194 GATTCTCTCG
*
9204 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGCA
**
9224 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
9244 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
9264 TTGCGAT
1 TTGCGAT
9271 TTTGTTGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:9315 original size:33 final size:34
Alignment explanation
Indices: 9188--9337 Score: 104
Period size: 34 Copynumber: 4.3 Consensus size: 34
9178 ATGAAAATCT
* * **
9188 CATTACGATTCTCTCGTTGCGATAGTCAAATTCG
1 CATTGCGATTCTCTCATTGCGATAGTCATTTTCG
* *
9222 TATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 CATTGCGAT--TC----TCTCATTGCGATAGTCATTTTCG
* * * ** **
9262 CGTTGCGATTTTGTTGTTGCGATTTTCA-TTTCG
1 CATTGCGATTCTCTCATTGCGATAGTCATTTTCG
*
9295 CATTGCGATTCTCTCATTGCGATAGTCATTTTTG
1 CATTGCGATTCTCTCATTGCGATAGTCATTTTCG
*
9329 CGTTGCGAT
1 CATTGCGAT
9338 AGTCATTTTC
Statistics
Matches: 85, Mismatches: 24, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
33 26 0.31
34 30 0.35
36 2 0.02
38 1 0.01
40 26 0.31
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (34 bp):
CATTGCGATTCTCTCATTGCGATAGTCATTTTCG
Found at i:9335 original size:107 final size:107
Alignment explanation
Indices: 9188--9380 Score: 287
Period size: 107 Copynumber: 1.8 Consensus size: 107
9178 ATGAAAATCT
* *
9188 CATTACGATTCTCTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCATTTTCGCATTGCGATAG
1 CATTACGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
9253 TCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATTTCG
66 TCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATTTCG
* ** * * *
9295 CATTGCGATTCTCTCATTGCGATAGTCATTTTTGCGTTGCGATAGTCATTTTCGCGTTGCGATAG
1 CATTACGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
** *
9360 TCATTTTTTCTTTGCGATTTT
66 TCATTTTCGCGTTGCGATTTT
9381 AAGTTTCAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
107 75 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.45
Consensus pattern (107 bp):
CATTACGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
TCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATTTCG
Found at i:9336 original size:20 final size:20
Alignment explanation
Indices: 9311--9377 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
9301 GATTCTCTCA
9311 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTTGCG
*
9331 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTTGCG
* *
9351 TTGCGATAGTCATTTTTTCT
1 TTGCGATAGTCATTTTTGCG
9371 TTGCGAT
1 TTGCGAT
9378 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
TTGCGATAGTCATTTTTGCG
Found at i:9891 original size:18 final size:19
Alignment explanation
Indices: 9852--9893 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
9842 CTCACCTATC
9852 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
9873 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
9891 ATC
1 ATC
9894 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:9905 original size:42 final size:42
Alignment explanation
Indices: 9846--9929 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
9836 GCCCGACTCA
** * *
9846 CCTATCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCC-CCTCCCACCGTTCAAGAGGCC
*
9888 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
9930 ATTGTCATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.21
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:11336 original size:14 final size:14
Alignment explanation
Indices: 11317--11352 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11307 ATTGTTTAAT
11317 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
11331 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
11345 TGATTTGT
1 TGATTTGT
11353 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11511 original size:33 final size:34
Alignment explanation
Indices: 11474--11549 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
11464 GGAAATGACT
*
11474 ATCGCAACGAGAGAATCGCAATGC-GAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATAAAA
* * *
11507 ATCGCAATGAGTGAATCGCAATGCAAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATAAAA
*
11541 ATCACAACG
1 ATCGCAACG
11550 CGAAACTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 22 0.61
34 14 0.39
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCAAAAATAAAA
Found at i:11621 original size:33 final size:34
Alignment explanation
Indices: 11564--11659 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 34
11554 ACTAATTTTG
* *
11564 CGTTGCGATTTTCATTTTCGCATTGTGATTCACT
1 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
*
11598 CGTTGCAATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
* ** * *
11631 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCAATTTTCATTTTCGCATTGCGAT
11660 AGTCAATTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
Found at i:11656 original size:20 final size:20
Alignment explanation
Indices: 11631--11719 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
11621 GCGATTCTCT
11631 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
11651 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
11671 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
11691 TGTTGCGATAGTTATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
11711 CGTTGCGAT
1 CGTTGCGAT
11720 TTTCGCGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:11726 original size:14 final size:14
Alignment explanation
Indices: 11707--11733 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11697 GATAGTTATA
11707 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
11721 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
11734 AGTCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:14192 original size:24 final size:24
Alignment explanation
Indices: 14158--14211 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
14148 CTGAAAAATC
14158 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
14182 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
14206 ATCAAA
1 ATCAAA
14212 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:14225 original size:24 final size:24
Alignment explanation
Indices: 14158--14225 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
14148 CTGAAAAATC
* * *
14158 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
14182 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
14206 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
14226 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:15085 original size:20 final size:20
Alignment explanation
Indices: 15065--15219 Score: 170
Period size: 20 Copynumber: 7.7 Consensus size: 20
15055 CAATAGTCAG
*
15065 ATTCGCGTTGCGATTTACAG-
1 ATTCGCATTGCGATTTAC-GT
*
15085 ATTCCCCATTGCGATTTACAG-
1 ATT-CGCATTGCGATTTAC-GT
* *
15106 ATTCGTATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
15126 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
15146 AATCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
15166 ATTCGCATTACGATTTACCAA
1 ATTCGCATTGCGATTTA-CGT
*
15187 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
15207 ATTCGCATTGCGA
1 ATTCGCATTGCGA
15220 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.69
21 34 0.30
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:15130 original size:61 final size:61
Alignment explanation
Indices: 15065--15219 Score: 163
Period size: 61 Copynumber: 2.5 Consensus size: 61
15055 CAATAGTCAG
* * ** **
15065 ATTCGCGTTGCGATTTACAG-ATTCCCCATTGCGATTTACAG-ATTCGTATTGTGATTTA-CGT
1 ATTCGCGTTGCGATTTAC-GTAAT-CCCATTGCGATTTAC-GTATTCGCATTACGATTTACCAA
* * *
15126 ATTCGCATTGCGATTTACGTAATCGCATTGTGATTTACGTATTCGCATTACGATTTACCAA
1 ATTCGCGTTGCGATTTACGTAATCCCATTGCGATTTACGTATTCGCATTACGATTTACCAA
* *
15187 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCGTTGCGATTTACGTAATCCCATTGCGA
15220 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
59 1 0.01
60 28 0.35
61 50 0.63
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (61 bp):
ATTCGCGTTGCGATTTACGTAATCCCATTGCGATTTACGTATTCGCATTACGATTTACCAA
Found at i:15240 original size:21 final size:21
Alignment explanation
Indices: 15216--15261 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
15206 TATTCGCATT
15216 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
15237 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
15258 GCGA
1 GCGA
15262 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:17823 original size:3 final size:3
Alignment explanation
Indices: 17817--17885 Score: 54
Period size: 3 Copynumber: 23.7 Consensus size: 3
17807 ACATGAGTAG
* * * * *
17817 TAA TAA TAT TAA TAA TTA TTA TAA T-A TAA TAG TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
17864 TAA T-A TAAA TTA TAA T-A TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TA
17886 TTTATAATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
2 6 0.12
3 44 0.85
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:17868 original size:38 final size:38
Alignment explanation
Indices: 17817--17893 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
17807 ACATGAGTAG
*
17817 TAATAATATTAATAAT-T--ATTATAATATAATAGTTA
1 TAATAATAATAATAATATAAATTATAATATAATAGTTA
*
17852 TAATAATAATAATAATATAAATTATAATATAATATTTA
1 TAATAATAATAATAATATAAATTATAATATAATAGTTA
17890 TAAT
1 TAAT
17894 CTAGACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 15 0.41
36 1 0.03
38 21 0.57
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
TAATAATAATAATAATATAAATTATAATATAATAGTTA
Found at i:17878 original size:12 final size:13
Alignment explanation
Indices: 17828--17893 Score: 75
Period size: 14 Copynumber: 5.0 Consensus size: 13
17818 AATAATATTA
17828 ATAATTATTATAAT
1 ATAA-TATTATAAT
17842 ATAATAGTTATAAT
1 ATAATA-TTATAAT
17856 AATAATA--ATAAT
1 -ATAATATTATAAT
17868 ATAA-ATTATAAT
1 ATAATATTATAAT
17880 ATAATATTTATAAT
1 ATAATA-TTATAAT
17894 CTAGACAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.02
11 4 0.09
12 14 0.30
13 3 0.07
14 18 0.39
15 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
ATAATATTATAAT
Found at i:17883 original size:26 final size:26
Alignment explanation
Indices: 17826--17885 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
17816 GTAATAATAT
* *
17826 TAATAATTATTATAATATAATAGTTA
1 TAATAATAATAATAATATAATAGTTA
17852 TAATAATAATAATAATATAA-A-TTA
1 TAATAATAATAATAATATAATAGTTA
17876 TAAT-ATAATA
1 TAATAATAATA
17886 TTTATAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 6 0.19
24 7 0.22
25 1 0.03
26 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TAATAATAATAATAATATAATAGTTA
Found at i:18130 original size:54 final size:54
Alignment explanation
Indices: 18058--18981 Score: 970
Period size: 54 Copynumber: 17.1 Consensus size: 54
18048 AGACTTGAAA
* * *
18058 AATCTTCTGTC-AACGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCAAAT
1 AATCTTCTGCCTAA-GGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * *
18112 AATCTTTTGCCTAAGGGTTCG-TTCTTTCTTTTTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAAGGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18166 AATTTTCTG-TTAATGGGTTCGCTGT-CTCTTTCTTTAGGAAGTAGGAACTCGAAT
1 AATCTTCTGCCTAA-GGGTTCGCT-TCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18220 AATCTTTTGCC-AACGAGTTCGCTCCCTCTTTTTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* *
18274 AATCTTCTGCC-AACGGGTTCAC-TCTCTTTTTCTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
* **
18328 AATCTTCTGCC-AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTAAAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18382 AATCTTCTTCATACGGGTTTGC-TCCTTCTTTCTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAAGGGTTCGCTTCC-TCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18436 AATCTTCTGTCTACA-GGTTC-TTTCTCTCTTTCTTTAGGTAATAGGAACTCGAAC
1 AATCTTCTGCCTA-AGGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * * *
18490 AATCTTCTACCT-ACGGTTCGCTCCCTCTTTCTTTAGGGAGCAGGAACTCAAAC
1 AATCTTCTGCCTAAGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18543 AATCTTCTG-CTAACGGGTTCAC-TCCATCTTTCTTGAGGGTGTAGGAACTCAAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTCC-TCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18597 AATCTTCTGCCTACGGGTTTGC-TCTTTATTTCTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAAGGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
*
18651 AATCTTCTACC-AACGGGTTCGC-TCTCTCTTTCTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * * * *
18705 ATTCTTCTGCTTACGGGTTTG-TTCCCTTTTTCTTTAGGGAATAGGAACTCGAAC
1 AATCTTCTGCCTAAGGGTTCGCTT-CCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * *
18759 AATCTTCTACCTACGGGTTCGC-TCACTCTTTCTTTAGGGAGTAGGAACTCAAAC
1 AATCTTCTGCCTAAGGGTTCGCTTC-CTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * *
18813 AATCTTCTGCCCATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAAGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * * * * *
18867 AATCTTCTGCCCACGAGTTCGCTCCCTATTTCTTTAGGGAGTAGGAACGCAAAC
1 AATCTTCTGCCTAAGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * *
18921 AATCTTCTGCC-AACGGGTTTGCTCCCTCTTTATTTAGGGAGTAGGAACTCGAAC
1 AATCTTCTGCCTAA-GGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
18975 AATCTTC
1 AATCTTC
18982 ATTTGCTTCA
Statistics
Matches: 734, Mismatches: 107, Indels: 58
0.82 0.12 0.06
Matches are distributed among these distances:
52 3 0.00
53 53 0.07
54 665 0.91
55 12 0.02
56 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (54 bp):
AATCTTCTGCCTAAGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
Found at i:18209 original size:108 final size:109
Alignment explanation
Indices: 18058--18981 Score: 1139
Period size: 108 Copynumber: 8.6 Consensus size: 109
18048 AGACTTGAAA
* * * * *
18058 AATCTTCTGTCAACGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCAAATAATCTTTTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
* ** * *
18123 TAA-GGGTTCGTTCTTTCTTTTTTTAGGGAGTAGGAACTCGAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* ** * ** * * *
18166 AATTTTCTGTTAATGGGTTCGCTGTCTCTTTCTTTAGGAAGTAGGAACTCGAATAATCTTTTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
* * *
18231 -AACGAGTTCGCTCCCTCTTTTTTTAGGGAGTAGGAACTCGAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* * *
18274 AATCTTCTGCCAACGGGTTCACTCTCTTTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
*
18339 -AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTAAAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* * * *
18382 AATCTTCT-TCATACGGGTTTGCTCCTTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGT
1 AATCTTCTGCCA-ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGC
* ** * * * *
18446 CT-ACAGGTTCTTTCTCTCTTTCTTTAGGTAATAGGAACTCGAAC
65 CTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* * * *
18490 AATCTTCTACCTAC-GGTTCGCTCCCTCTTTCTTTAGGGAGCAGGAACTCAAACAATCTTCTG-C
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
* * * *
18553 TAACGGGTTCACTCCATCTTTCTTGAGGGTGTAGGAACTCAAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* * ** * *
18597 AATCTTCTGCCTACGGGTTTGCTCTTTATTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTACC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
* *
18662 -AACGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* ** * * * * *
18705 ATTCTTCTGCTTACGGGTTTGTTCCCTTTTTCTTTAGGGAATAGGAACTCGAACAATCTTCTACC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
*
18770 T-ACGGGTTCGCTCACTCTTTCTTTAGGGAGTAGGAACTCAAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* *
18813 AATCTTCTGCCCATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
* * * *
18878 -CACGAGTTCGCTCCCTATTTCTTTAGGGAGTAGGAACGCAAAC
66 TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
* *
18921 AATCTTCTGCCAACGGGTTTGCTCCCTCTTTATTTAGGGAGTAGGAACTCGAACAATCTTC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
18982 ATTTGCTTCA
Statistics
Matches: 711, Mismatches: 96, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
106 2 0.00
107 93 0.13
108 614 0.86
109 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (109 bp):
AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAAC
Found at i:18250 original size:162 final size:162
Alignment explanation
Indices: 18058--18981 Score: 1165
Period size: 162 Copynumber: 5.7 Consensus size: 162
18048 AGACTTGAAA
* * * *
18058 AATCTTCTGTCAACGGGTTCGCTTCCTCTTTCTTTAGGGAGTAGGAACTCAAATAATCTTTTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
* * * * ** *
18123 TAAGGGTTCGTTCTTTCTTTTTTTAGGGAGTAGGAACTCGAACAATTTTCTGTTAATGGGTTCGC
66 TAAGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCGC
** * *
18188 TGTCTCTTTCTTTAGGAAGTAGGAACTCGAAT
131 TCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18220 AATCTTTTGCCAACGAGTTCGCTCCCTCTTTTTTTAGGGAGTAGGAACTCGAACAATCTTCTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
* *
18285 -AACGGGTTCACTCTCTTTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCG
66 TAA-GGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCG
**
18349 CTCCCTCTTTCTTTAGGGAGTAGGAACTAAAAC
130 CTCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * * *
18382 AATCTTCT-TCATACGGGTTTGCTCCTTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGT
1 AATCTTCTGCCA-ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGC
** * * * *
18446 CTACA-GGTTCTTTCTCTCTTTCTTTAGGTAATAGGAACTCGAACAATCTTCTACCTAC-GGTTC
65 CTA-AGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTC
* *
18509 GCTCCCTCTTTCTTTAGGGAGCAGGAACTCAAAC
129 GCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * * *
18543 AATCTTCTGCTAACGGGTTCACTCCATCTTTCTTGAGGGTGTAGGAACTCAAACAATCTTCTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
* * * * *
18608 TACGGGTTTGCTCTTTATTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTACCAACGGGTTCGC
66 TAAGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCGC
*
18673 TCTCTCTTTCTTTAGGGAGTAGGAACTCGAAC
131 TCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* ** * * * * * *
18705 ATTCTTCTGCTTACGGGTTTGTTCCCTTTTTCTTTAGGGAATAGGAACTCGAACAATCTTCTACC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
* * * * *
18770 TACGGGTTCGCTCACTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCCCATGGGTTCGC
66 TAAGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCGC
18835 TCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
131 TCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
* * * *
18867 AATCTTCTGCCCACGAGTTCGCTCCCTATTTCTTTAGGGAGTAGGAACGCAAACAATCTTCTGCC
1 AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
* * *
18932 -AACGGGTTTGCTCCCTCTTTATTTAGGGAGTAGGAACTCGAACAATCTTC
66 TAA-GGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
18982 ATTTGCTTCA
Statistics
Matches: 657, Mismatches: 97, Indels: 16
0.85 0.13 0.02
Matches are distributed among these distances:
161 143 0.22
162 512 0.78
163 1 0.00
164 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (162 bp):
AATCTTCTGCCAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTGCC
TAAGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCAACGGGTTCGC
TCCCTCTTTCTTTAGGGAGTAGGAACTCGAAC
Found at i:19058 original size:37 final size:37
Alignment explanation
Indices: 18982--19064 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
18972 AACAATCTTC
* * * *
18982 ATTTGCTTCATTACTTTTTTGTGAAGACTTCTAGATG
1 ATTTGCTTCACTACTCTTTCGTGAAGACTTCAAGATG
* *
19019 ATTTGCTTCACTACTCTTTCGTGAAGCCTT-AAGTTTG
1 ATTTGCTTCACTACTCTTTCGTGAAGACTTCAAG-ATG
19056 ATTTGCTTC
1 ATTTGCTTC
19065 GTTGGTCGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 2 0.05
37 37 0.95
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTTCGTGAAGACTTCAAGATG
Found at i:20259 original size:6 final size:6
Alignment explanation
Indices: 20250--20320 Score: 106
Period size: 6 Copynumber: 11.2 Consensus size: 6
20240 TTATTTTCTC
20250 TCTTTT TCTTTT TCTTTTT TCTTTT TCTTTT TCTTTTT TCTTTT TCTTTT
1 TCTTTT TCTTTT TC-TTTT TCTTTT TCTTTT TC-TTTT TCTTTT TCTTTT
20300 TCTTTTT TCTTTTT TCTTTT T
1 TC-TTTT TC-TTTT TCTTTT T
20321 TCATTTTTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
6 37 0.60
7 25 0.40
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TCTTTT
Found at i:20268 original size:7 final size:7
Alignment explanation
Indices: 20237--20367 Score: 139
Period size: 7 Copynumber: 19.0 Consensus size: 7
20227 TTAGACCTAC
*
20237 TTTTTAT
1 TTTTTCT
*
20244 TTTCTCT
1 TTTTTCT
20251 CTTTTTC-
1 -TTTTTCT
20258 TTTTTCT
1 TTTTTCT
20265 TTTTTC-
1 TTTTTCT
20271 TTTTTC-
1 TTTTTCT
20277 TTTTTCT
1 TTTTTCT
20284 TTTTTC-
1 TTTTTCT
20290 TTTTTC-
1 TTTTTCT
20296 TTTTTCT
1 TTTTTCT
20303 TTTTTCT
1 TTTTTCT
20310 TTTTTCT
1 TTTTTCT
20317 TTTTTCAT
1 TTTTTC-T
*
20325 TTTTTCC
1 TTTTTCT
20332 TTTTT-T
1 TTTTTCT
* *
20338 TCTCTCTT
1 TTTTTC-T
20346 TTTTTCT
1 TTTTTCT
20353 TTTTTCAT
1 TTTTTC-T
20361 TTTTTCT
1 TTTTTCT
20368 CAAGCAAAAT
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
6 33 0.31
7 50 0.47
8 24 0.22
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:20274 original size:19 final size:19
Alignment explanation
Indices: 20236--20356 Score: 145
Period size: 19 Copynumber: 6.0 Consensus size: 19
20226 TTTAGACCTA
*
20236 CTTTTTATTTTCTCTCTTTTT
1 CTTTTTCTTTT-T-TCTTTTT
20257 CTTTTTCTTTTTTCTTTTT
1 CTTTTTCTTTTTTCTTTTT
20276 CTTTTTCTTTTTTCTTTTT
1 CTTTTTCTTTTTTCTTTTT
20295 CTTTTTCTTTTTTCTTTTTT
1 CTTTTTCTTTTTTC-TTTTT
20315 CTTTTTTCATTTTTTCCTTTTT
1 C-TTTTTC-TTTTTT-CTTTTT
*
20337 -TTCTCTCTTTTTTTCTTTTT
1 CTT-TTTC-TTTTTTCTTTTT
20357 TCATTTTTTC
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
19 40 0.43
20 15 0.16
21 25 0.27
22 11 0.12
23 1 0.01
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (19 bp):
CTTTTTCTTTTTTCTTTTT
Found at i:20338 original size:1 final size:1
Alignment explanation
Indices: 20252--20321 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
20242 ATTTTCTCTC
* * * * * * * * * *
20252 TTTTTCTTTTTCTTTTTTCTTTTTCTTTTTCTTTTTTCTTTTTCTTTTTCTTTTTTCTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20317 TTTTT
1 TTTTT
20322 CATTTTTTCC
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:25651 original size:24 final size:24
Alignment explanation
Indices: 25611--25671 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
25601 CATATGCTAG
25611 CTACCCAATCATGCTTTAGTAGATC
1 CTACCCAA-CATGCTTTAGTAGATC
25636 CTACCCAACATGCTTTAGTAGATC
1 CTACCCAACATGCTTTAGTAGATC
25660 CTACCCAACATG
1 CTACCCAACATG
25672 GTACCTACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.78
25 8 0.22
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.28
Consensus pattern (24 bp):
CTACCCAACATGCTTTAGTAGATC
Found at i:28901 original size:3 final size:3
Alignment explanation
Indices: 28895--28980 Score: 81
Period size: 3 Copynumber: 29.7 Consensus size: 3
28885 ACATGAGTAT
* * * * *
28895 TAA TAA TAC TAA TAA TTA TTA TAA T-A TAA TAG TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
28942 TAA T-A TAA TAA TAA TAA TAA T-A TAAA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA
28981 TTTACTACTC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
2 8 0.12
3 58 0.85
4 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:28925 original size:23 final size:21
Alignment explanation
Indices: 28897--28975 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 21
28887 ATGAGTATTA
28897 ATAATACTAATAATTATTATAAT
1 ATAATA-TAATAATTA-TATAAT
*
28920 ATAATAGTTATAA-TA-ATAAT
1 ATAATA-TAATAATTATATAAT
*
28940 AATAATATAATAATAATAATAAT
1 -ATAATATAATAATTAT-ATAAT
28963 ATAAATTATAATA
1 AT-AA-TATAATA
28976 TAATATTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
20 10 0.22
21 7 0.15
22 4 0.09
23 18 0.39
24 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATATAATAATTATATAAT
Found at i:28933 original size:26 final size:26
Alignment explanation
Indices: 28895--28980 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 26
28885 ACATGAGTAT
*
28895 TAATAATACTAATAATTATTATAATA
1 TAATAATAATAATAATTATTATAATA
* * * *
28921 TAATAGTTATAATAATAATAATAATA
1 TAATAATAATAATAATTATTATAATA
28947 TAATAATAATAATAATATAAATTATAATA
1 TAATAATAATAATAAT-T--ATTATAATA
28976 TAATA
1 TAATA
28981 TTTACTACTC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 35 0.73
29 13 0.27
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (26 bp):
TAATAATAATAATAATTATTATAATA
Found at i:28981 original size:17 final size:18
Alignment explanation
Indices: 28896--28981 Score: 83
Period size: 17 Copynumber: 4.9 Consensus size: 18
28886 CATGAGTATT
*
28896 AATAATACTAATAAT-TA
1 AATAATAATAATAATATA
* *
28913 TTATAAT-ATAATAGT-TA
1 -AATAATAATAATAATATA
28930 TAATAATAATAATAATAT-
1 -AATAATAATAATAATATA
28948 AATAATAATAATAATATA
1 AATAATAATAATAATATA
*
28966 AATTATAAT-ATAATAT
1 AATAATAATAATAATAT
28982 TTACTACTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
17 38 0.64
18 20 0.34
19 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
AATAATAATAATAATATA
Found at i:34604 original size:21 final size:21
Alignment explanation
Indices: 34578--34618 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34568 AGATTATCTT
*
34578 TTTGAAATTCAATTTCTTTTG
1 TTTGAAATTCAATTTATTTTG
34599 TTTGAAATTCAATTTATTTT
1 TTTGAAATTCAATTTATTTT
34619 TTTCACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTGAAATTCAATTTATTTTG
Found at i:35970 original size:113 final size:113
Alignment explanation
Indices: 35768--36101 Score: 474
Period size: 113 Copynumber: 3.0 Consensus size: 113
35758 GCAAAAATTC
* * *
35768 GAATCCATCACTCAATGGATCAACATTTTC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTCGATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
35832 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTT
* * * *
35880 GAATTCATCACTTGATGGATCAACATTGCCAGGTAGGGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTCGATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
35945 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT-AAACCTTTTGCTT
* * * * *
35994 GAATTCATCACTCGATGGATCAACTTTTCCATAGAAAAGTTCATAATAAGAAGAACTTATCTGAA
1 GAATTCATCACTCGATGGATCAACATTTCCA-GGAAGAGTTCATAATGAGAAGAACTCATCTGAA
*
36059 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTT
36102 GTTTGATTCT
Statistics
Matches: 195, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
112 25 0.13
113 71 0.36
114 71 0.36
115 28 0.14
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
GAATTCATCACTCGATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTT
Found at i:36064 original size:114 final size:113
Alignment explanation
Indices: 35768--36222 Score: 483
Period size: 114 Copynumber: 4.0 Consensus size: 113
35758 GCAAAAATTC
* *
35768 GAATCCATCACTCAATGGATCAACATTTT-C-GGAAGAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCACTCGATGGATCAAC-TTTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
35831 GAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * * *
35880 GAATTCATCACTTGATGGATCAACATTGCCAGGTAGGGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTCGATGGATCAACTTTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
35945 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGTTT
* * * *
35994 GAATTCATCACTCGATGGATCAACTTTTCCATAGAAAAGTTCATAATAAGAAGAACTTATCTGAA
1 GAATTCATCACTCGATGGATCAACTTTTCCA-GGAAGAGTTCATAATGAGAAGAACTCATCTGAA
36059 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
** * * * * * *
36106 G-ATTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTA-GAAGTGTTAATAATAATAAGA
1 GAATTC-ATCAC-----TCGATGGATCAAC-T-----TTTCCAGGAAGAGTTCATAATGAGAAGA
* * *
36169 ACTCATCTGAAGAAGGAA-AATAAGTTCATAATGAGAATAACTTGTTCAATCTTT
54 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
36223 CCTATTCATC
Statistics
Matches: 290, Mismatches: 35, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
111 6 0.02
112 35 0.12
113 68 0.23
114 72 0.25
115 28 0.10
117 10 0.03
118 1 0.00
121 58 0.20
122 7 0.02
123 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
GAATTCATCACTCGATGGATCAACTTTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
Found at i:36578 original size:9 final size:9
Alignment explanation
Indices: 36564--36644 Score: 74
Period size: 9 Copynumber: 9.0 Consensus size: 9
36554 CGTTTATTTT
36564 TTATAATTA
1 TTATAATTA
*
36573 TTATAATTG
1 TTATAATTA
36582 TTATAATTA
1 TTATAATTA
*
36591 TTATAATAA
1 TTATAATTA
*
36600 TTATTATTA
1 TTATAATTA
**
36609 -TATTTTTA
1 TTATAATTA
*
36617 TTATCATTA
1 TTATAATTA
*
36626 TTAATAAATA
1 TT-ATAATTA
*
36636 TTATTATTA
1 TTATAATTA
36645 CAAAACAGGC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
8 7 0.12
9 44 0.76
10 7 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
TTATAATTA
Found at i:36593 original size:3 final size:3
Alignment explanation
Indices: 36564--36644 Score: 56
Period size: 3 Copynumber: 27.0 Consensus size: 3
36554 CGTTTATTTT
* * * * * *
36564 TTA TAA TTA TTA TAA TTG TTA TAA TTA TTA TAA TAA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
36611 TTT TTA TTA TCA TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
36645 CAAAACAGGC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:36602 original size:30 final size:32
Alignment explanation
Indices: 36566--36643 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
36556 TTTATTTTTT
*
36566 ATAATTATTATA-ATTGTTATAATTATTA-TA
1 ATAATTATTATATATTGTTATAATCATTATTA
* *
36596 ATAATTATTATTATATTTTTATTATCATTATTA
1 ATAATTATTA-TATATTGTTATAATCATTATTA
*
36629 ATAAATATTAT-TATT
1 ATAATTATTATATATT
36644 ACAAAACAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 10 0.24
31 6 0.15
32 14 0.34
33 11 0.27
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
ATAATTATTATATATTGTTATAATCATTATTA
Found at i:36631 original size:33 final size:32
Alignment explanation
Indices: 36566--36642 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
36556 TTTATTTTTT
*
36566 ATAATTATTA-TA-ATTGTTATAATTATTATA
1 ATAATTATTATTATATTGTTATAATCATTATA
* *
36596 ATAATTATTATTATATTTTTATTATCATTATTA
1 ATAATTATTATTATATTGTTATAATCATTA-TA
*
36629 ATAAATATTATTAT
1 ATAATTATTATTAT
36643 TACAAAACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 10 0.25
31 2 0.05
32 13 0.32
33 15 0.38
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
ATAATTATTATTATATTGTTATAATCATTATA
Found at i:38057 original size:30 final size:29
Alignment explanation
Indices: 37996--38073 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
37986 ATGTCACTAA
*
37996 TTTTATTTTCATTTATTTTTAATTACAAG
1 TTTTATTTTCATTTATTTTTAAATACAAG
* *
38025 TTTTA-TTTCTTTTATATTTTAAATATATAG
1 TTTTATTTTCATTTAT-TTTTAAATACA-AG
*
38055 TTTTAAATTT-ATTTATTTT
1 TTTT-ATTTTCATTTATTTT
38074 AGTCACTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 9 0.22
29 14 0.34
30 9 0.22
31 6 0.15
32 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTATTTTCATTTATTTTTAAATACAAG
Found at i:41226 original size:24 final size:24
Alignment explanation
Indices: 41199--41252 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
41189 GGTTGGTTCT
* *
41199 TCTTCATCGGCTGGCTGGTGAACC
1 TCTTCATCGGCGGGCTGGTGAACA
* *
41223 TCTTCATTGGCGGGCTGGTGAGCA
1 TCTTCATCGGCGGGCTGGTGAACA
41247 TCTTCA
1 TCTTCA
41253 GATGCTTTGA
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:0.13, C:0.26, G:0.30, T:0.31
Consensus pattern (24 bp):
TCTTCATCGGCGGGCTGGTGAACA
Found at i:42453 original size:27 final size:26
Alignment explanation
Indices: 42404--42457 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
42394 GGAAGAAGAA
42404 GAAGAGATAAAACAAAGTGAAAAAGT
1 GAAGAGATAAAACAAAGTGAAAAAGT
*
42430 GAAGAAGATAAGAACAAAGTAAAAAAGT
1 GAAG-AGATAA-AACAAAGTGAAAAAGT
42458 AGGGGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 6 0.24
28 15 0.60
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (26 bp):
GAAGAGATAAAACAAAGTGAAAAAGT
Found at i:49135 original size:19 final size:19
Alignment explanation
Indices: 49111--49162 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
49101 AATGCATTTT
49111 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
49130 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
49149 ATGCATCGATGCAC
1 ATGCATCGATGCAC
49163 TCAGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:49208 original size:65 final size:64
Alignment explanation
Indices: 49129--49272 Score: 184
Period size: 65 Copynumber: 2.2 Consensus size: 64
49119 ATGCACATAC
* * *
49129 CATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATGAAAACATCGAATGCAT
1 CATGCATCGATGCACA-AGCCATGCATCGATACACTCAGGCTTGTT-TG-AAACATCGAATGCAC
49192 TT
63 TT
* * *
49194 GATGCATTGATGCACAAGCCATGCATCGATACACTCGGGCTTGTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTTGTTTGAAACATCGAATGCACTT
*
49258 CATGCATCGGTGCAC
1 CATGCATCGATGCAC
49273 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 29 0.43
65 35 0.51
66 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTTGTTTGAAACATCGAATGCACTT
Found at i:51244 original size:21 final size:21
Alignment explanation
Indices: 51220--51259 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51210 AAGAAATTGT
51220 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
51241 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
51260 AAACAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:55464 original size:12 final size:12
Alignment explanation
Indices: 55447--55476 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55437 TTCTATGATG
55447 AACATTATATCA
1 AACATTATATCA
55459 AACATTATATCA
1 AACATTATATCA
*
55471 AGCATT
1 AACATT
55477 GATTGTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (12 bp):
AACATTATATCA
Found at i:57175 original size:2 final size:2
Alignment explanation
Indices: 57168--57233 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
57158 TTAAATCTTA
57168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57210 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
57234 GTTTGGTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57930 original size:64 final size:63
Alignment explanation
Indices: 57842--58000 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
57832 GAATAAATTG
* *
57842 AACATCGAATGCATTATATACATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTTGTT-TG
57905 AA
63 -A
*
57907 AACATCGAATG-ATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
*
57970 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
58001 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
63 14 0.16
64 54 0.64
65 17 0.20
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
Found at i:62417 original size:22 final size:22
Alignment explanation
Indices: 62389--62444 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
62379 GGACTATTAT
62389 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
62411 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
62433 GTCCCGAAGGAC
1 GTCCCGAAGGAC
62445 TAATATACCC
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:0.27, C:0.32, G:0.29, T:0.12
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Done.