Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002067.1 Hibiscus syriacus cultivar Beakdansim tig00004219_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: 110386
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9069 original size:22 final size:23
Alignment explanation
Indices: 9044--9116 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 23
9034 CAATTCATAA
9044 TTTAA-ACCATAATCTATAAATG
1 TTTAATACCATAATCTATAAATG
* * * *
9066 TTTAATGCAATTAAT-TTTAAA-A
1 TTTAATACCA-TAATCTATAAATG
*
9088 TTAAATACCATAATCTATAAATG
1 TTTAATACCATAATCTATAAATG
9111 TTTAAT
1 TTTAAT
9117 GCAATTAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
23 12 0.32
24 4 0.11
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTAATACCATAATCTATAAATG
Found at i:9098 original size:45 final size:45
Alignment explanation
Indices: 9049--9139 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
9039 CATAATTTAA
9049 ACCATAATCTATAAATGTTTAATGCAATTAATTTTAAAATTAAAT
1 ACCATAATCTATAAATGTTTAATGCAATTAATTTTAAAATTAAAT
9094 ACCATAATCTATAAATGTTTAATGCAATTAATTTTAAAATTAAAT
1 ACCATAATCTATAAATGTTTAATGCAATTAATTTTAAAATTAAAT
9139 A
1 A
9140 TTTCTAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (45 bp):
ACCATAATCTATAAATGTTTAATGCAATTAATTTTAAAATTAAAT
Found at i:11075 original size:14 final size:14
Alignment explanation
Indices: 11056--11082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11046 AAATAATCTC
11056 AAAAATAAATAAAT
1 AAAAATAAATAAAT
11070 AAAAATAAATAAA
1 AAAAATAAATAAA
11083 AACAATCTCG
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:13561 original size:13 final size:13
Alignment explanation
Indices: 13543--13569 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13533 CATAGTTGAA
13543 CAGTCTTCATATG
1 CAGTCTTCATATG
13556 CAGTCTTCATATG
1 CAGTCTTCATATG
13569 C
1 C
13570 GCGTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:16563 original size:6 final size:6
Alignment explanation
Indices: 16552--16585 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16542 ATAGTATTCG
16552 CGACCA CGACCA CGACCA CGACCA CGACC- CGACC
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACC
16586 CGAGACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:17116 original size:6 final size:5
Alignment explanation
Indices: 17072--17112 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
17062 CCGTCTCGTC
17072 TCGGG TCGGG TCGGG TCGGG TCGGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TC-GGG TCG-GG TCG-GG TCG
17113 TGGTAATACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 18 0.53
6 16 0.47
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:17280 original size:21 final size:21
Alignment explanation
Indices: 17209--17286 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
17199 TGCGATTTTG
* *
17209 GACTATCGCAACGCAAACTTC
1 GACTATCGCAATGCGAACTTC
*
17230 GACTATCGCAATGCGAA-TATA
1 GACTATCGCAATGCGAACT-TC
* *
17251 TA-AATCGCAATGCGAACTTC
1 GACTATCGCAATGCGAACTTC
*
17271 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
17287 TTTACATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTTC
Found at i:17321 original size:21 final size:21
Alignment explanation
Indices: 17295--17431 Score: 154
Period size: 21 Copynumber: 6.6 Consensus size: 21
17285 GATTTACATA
17295 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
17316 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
17336 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
17357 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
17378 TTTGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCCAAG
* *
17399 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
17420 TTCGCGTTGCGA
1 TTCGCATTGCGA
17432 ATCTGGAAAC
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
20 17 0.17
21 82 0.82
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:17321 original size:41 final size:41
Alignment explanation
Indices: 17276--17415 Score: 137
Period size: 41 Copynumber: 3.4 Consensus size: 41
17266 ACTTCGACTA
*
17276 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CATATTCGCATTGCGATAGTCCAAGT
* *
17317 TCGCATTGCGATAGTCGACTA-TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTC-A-TATTCGCATTGCGATAGTCCA-AGT
* *
17358 TCGCATTGCGATAGTCCA-AGTTTGCATTGCGATAGTCTAAGT
1 TCGCATTGCGATAGT-CATA-TTCGCATTGCGATAGTCCAAGT
*
17400 TCGCGTTGCGATAGTC
1 TCGCATTGCGATAGTC
17416 GAAGTTCGCG
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
39 1 0.01
41 46 0.56
42 33 0.40
43 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
TCGCATTGCGATAGTCATATTCGCATTGCGATAGTCCAAGT
Found at i:17321 original size:62 final size:62
Alignment explanation
Indices: 17269--17394 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
17259 AATGCGAACT
17269 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
*
17331 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTTGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
17393 TC
1 TC
17395 TAAGTTCGCG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (62 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
Found at i:17342 original size:83 final size:83
Alignment explanation
Indices: 17254--17417 Score: 201
Period size: 83 Copynumber: 2.0 Consensus size: 83
17244 GAATATATAA
*
17254 ATCGCAATGCGAACTTCGAC-TA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAA
1 ATCGCAATGCG-A-TT-GACATATTCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAA
17315 GTTCGCATTGCGATAGTCGACT
62 GTTCGCATTGCGATAGTCGACT
* * * * *
17337 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCTAAGTTC
1 ATCGCAATGCGATTGACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGTTC
*
17402 GCGTTGCGATAGTCGA
66 GCATTGCGATAGTCGA
17418 AGTTCGCGTT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
80 2 0.03
81 4 0.06
82 14 0.20
83 50 0.71
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (83 bp):
ATCGCAATGCGATTGACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGTTC
GCATTGCGATAGTCGACT
Found at i:17409 original size:62 final size:62
Alignment explanation
Indices: 17272--17411 Score: 228
Period size: 62 Copynumber: 2.3 Consensus size: 62
17262 GCGAACTTCG
*
17272 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCA
*
17334 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCTA
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-A
* *
17397 AGT-TCGCGTTGCGAT
1 ACTATCGCATTGCGAT
17412 AGTCGAAGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 71 0.97
63 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (62 bp):
ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCA
Found at i:28973 original size:168 final size:162
Alignment explanation
Indices: 28763--29082 Score: 446
Period size: 168 Copynumber: 1.9 Consensus size: 162
28753 AATTTAAGTT
* **
28763 TTGTATATTTCAAATTAAATTTAATATATTTTTTACATTTATAATTTAATGATTATTGATATAAT
1 TTGTATAATTCAAATTAAATTTAATATATTTTTTACATTTATAATTTAATGATTATAAATATAAT
* * **
28828 CTAAAAATTGATACTTTTTTAATTTAATTAATAATTTCACTTTTTATTAAAAAAATAAAGTATAC
66 CTAAAAATTGATA--TTTTCAATTTAATTAATAATTTCAATTTTTACAAAAAAAAT-AAGTATAC
*
28893 TGATCATTTATATTTTAATTA-ATTTTTTTATTGAA
128 AG-TCATTTATATTTTAATTATATTTTTTTATTGAA
*
28928 TTGTATAATT-AAATTAAATTTAATACTCATATTTTTCACATTTATAATTTGATGATTATAAATA
1 TTGTATAATTCAAATTAAATTTAATA-T-AT-TTTTT-ACATTTATAATTTAATGATTATAAATA
*
28992 TAATCTAAAAATTGATATTTTCAATTTAATTAATAATTTTAATTTTTACAAAAAAAATAAGTATA
62 TAATCTAAAAATTGATATTTTCAATTTAATTAATAATTTCAATTTTTACAAAAAAAATAAGTATA
* *
29057 CAGTTATTTATGTTTTAATTATATTT
127 CAGTCATTTATATTTTAATTATATTT
29083 ATTGGATTGC
Statistics
Matches: 138, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
164 31 0.22
165 23 0.17
166 38 0.28
167 5 0.04
168 41 0.30
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (162 bp):
TTGTATAATTCAAATTAAATTTAATATATTTTTTACATTTATAATTTAATGATTATAAATATAAT
CTAAAAATTGATATTTTCAATTTAATTAATAATTTCAATTTTTACAAAAAAAATAAGTATACAGT
CATTTATATTTTAATTATATTTTTTTATTGAA
Found at i:31860 original size:18 final size:18
Alignment explanation
Indices: 31833--31871 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31823 AGTGAAACAG
* *
31833 GAGCAGGAGAAGAAGGTT
1 GAGCACGAGAAGAAAGTT
31851 GAGCACGAGAAGAAAGTT
1 GAGCACGAGAAGAAAGTT
31869 GAG
1 GAG
31872 TAGTGGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.41, T:0.10
Consensus pattern (18 bp):
GAGCACGAGAAGAAAGTT
Found at i:32332 original size:24 final size:24
Alignment explanation
Indices: 32305--32358 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
32295 CGTTCATTTA
32305 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * * *
32329 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
32353 CGTTCG
1 CGTTCG
32359 ATTATGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.48
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:32337 original size:14 final size:14
Alignment explanation
Indices: 32315--32347 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
32305 CGTTCGTGAA
*
32315 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
32329 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
32343 CGTTT
1 CGTTT
32348 ATGTTCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:32363 original size:24 final size:24
Alignment explanation
Indices: 32316--32390 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
32306 GTTCGTGAAC
* * *
32316 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
32340 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
32364 GTTTGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
32388 GTT
1 GTT
32391 TAACACAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 44 0.98
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:33133 original size:10 final size:10
Alignment explanation
Indices: 33114--33188 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
33104 GGGTCTCCAA
33114 CGTTTATGTT
1 CGTTTATGTT
*
33124 CGTTTGTGTT
1 CGTTTATGTT
33134 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
33145 ATGTTCGTGTT
1 -CGTTTATGTT
33156 CGTTTATGTT
1 CGTTTATGTT
33166 CG----TGTT
1 CGTTTATGTT
33172 CGTTTATGTT
1 CGTTTATGTT
33182 CGTTTAT
1 CGTTTAT
33189 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.67
11 7 0.14
12 3 0.06
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:33149 original size:16 final size:16
Alignment explanation
Indices: 33120--33184 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
33110 CCAACGTTTA
*
33120 TGTTCGTTTGTGTTCG
1 TGTTCGTTTATGTTCG
*
33136 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
33152 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
33168 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
33184 T
1 T
33185 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:33275 original size:16 final size:16
Alignment explanation
Indices: 33254--33286 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33244 AAAAAAAATT
33254 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
33270 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
33286 T
1 T
33287 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:34493 original size:17 final size:17
Alignment explanation
Indices: 34466--34504 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
34456 AATTTACAAT
34466 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
34482 TAATTATAAATAATATC
1 TAATTATAAATAATATC
34499 TAATTA
1 TAATTA
34505 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:41582 original size:13 final size:13
Alignment explanation
Indices: 41566--41596 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41556 AATATGGGAT
41566 ATAAATAAAAAAA
1 ATAAATAAAAAAA
*
41579 ATAAATGAAAAAA
1 ATAAATAAAAAAA
41592 ATAAA
1 ATAAA
41597 AAATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (13 bp):
ATAAATAAAAAAA
Found at i:43658 original size:2 final size:2
Alignment explanation
Indices: 43651--43679 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43641 TACTTTTAAG
43651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43680 ACATTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48833 original size:20 final size:20
Alignment explanation
Indices: 48810--48847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48800 CAAAAGACCT
*
48810 CATACATGTTCCAAAGAATA
1 CATACATGTCCCAAAGAATA
*
48830 CATATATGTCCCAAAGAA
1 CATACATGTCCCAAAGAA
48848 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (20 bp):
CATACATGTCCCAAAGAATA
Found at i:49404 original size:19 final size:19
Alignment explanation
Indices: 49382--49434 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
49372 ATTCTTCTCA
49382 TAATCAAATATATCATGCT
1 TAATCAAATATATCATGCT
* *
49401 TAATAACATATATATCATGTT
1 TAAT--CAAATATATCATGCT
49422 TAAT-AACATATAT
1 TAATCAA-ATATAT
49435 ATCATATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.04
19 10 0.36
21 17 0.61
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (19 bp):
TAATCAAATATATCATGCT
Found at i:49413 original size:21 final size:21
Alignment explanation
Indices: 49389--49439 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
49379 TCATAATCAA
49389 ATATATCATGCTTAATAACAT
1 ATATATCATGCTTAATAACAT
*
49410 ATATATCATGTTTAATAACAT
1 ATATATCATGCTTAATAACAT
49431 ATATATCAT
1 ATATATCAT
49440 ATAAGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (21 bp):
ATATATCATGCTTAATAACAT
Found at i:49578 original size:19 final size:19
Alignment explanation
Indices: 49554--49602 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
49544 GAAACGTTTT
49554 TATGAATAGTACTATATGG
1 TATGAATAGTACTATATGG
*
49573 TATGAATAGTATTATATGG
1 TATGAATAGTACTATATGG
*
49592 TATGAACAGTA
1 TATGAATAGTA
49603 ATGAACAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (19 bp):
TATGAATAGTACTATATGG
Found at i:50640 original size:41 final size:40
Alignment explanation
Indices: 50580--50997 Score: 221
Period size: 41 Copynumber: 10.2 Consensus size: 40
50570 TAACATTAAC
*
50580 GGCG-TTTTACAATAAACGCCGCTAAAACTCATACTTTAGT
1 GGCGTTTTTA-AACAAACGCCGCTAAAACTCATACTTTAGT
** *
50620 GGCGTTTATTCGACAAACGCCGCTAAAGA-TAAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAA-ACTCA-TACTTTAGT
**
50662 GGCGTTTTTAAACAAACGCCGC-AATAGGGTACATA-TATT-GT
1 GGCGTTTTTAAACAAACGCCGCTAA-A-ACT-CATACT-TTAGT
* * * *
50703 GGCATTTTTAGATAAACGCCGCTAAAAC-CTAGTACTTTAGA
1 GGCGTTTTTAAACAAACGCCGCTAAAACTC-A-TACTTTAGT
** ** *
50744 GGCGCTTTATGCAA-AAATACCGCTAAAACTCGTACTTTAGT
1 GGCG-TTT-TTAAACAAACGCCGCTAAAACTCATACTTTAGT
* * * *
50785 GGCGTTTGTAAACAAACGCCGCCATAGAA-TCGTTCTTTAGT
1 GGCGTTTTTAAACAAACGCCG-C-TAAAACTCATACTTTAGT
** * *
50826 GGCGTTTTTAAACAAACGCCGC-AATAGGGTACATA-TATCGT
1 GGCGTTTTTAAACAAACGCCGCTAA-A-ACT-CATACTTTAGT
* * * *
50867 TGCGTTTTTAAATAAACGCAGCTAAAACCTAATA-TTCTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAA-CTCATACTT-TAGT
* * *
50908 GGCATTTTATTCAA-AAATGCCGCTAAATACTCATACTTTAGT
1 GGC-GTTT-TTAAACAAACGCCGCTAAA-ACTCATACTTTAGT
* * * * * *
50950 GACGATTTTAGACAAATGCCGCTAAAACCTAATACTTTATT
1 GGCGTTTTTAAACAAACGCCGCTAAAA-CTCATACTTTAGT
50991 GGCGTTT
1 GGCGTTT
50998 AACCATTAAC
Statistics
Matches: 287, Mismatches: 59, Indels: 63
0.70 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
39 4 0.01
40 28 0.10
41 167 0.58
42 75 0.26
43 11 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (40 bp):
GGCGTTTTTAAACAAACGCCGCTAAAACTCATACTTTAGT
Found at i:50835 original size:123 final size:123
Alignment explanation
Indices: 50584--50814 Score: 290
Period size: 123 Copynumber: 1.9 Consensus size: 123
50574 ATTAACGGCG
* * * *
50584 TTTTACAATAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGA
1 TTTTA-AATAAACGCCGCTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACACCGCTAAAGA
* **
50649 TAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCAATAGGGTACATATATTGTGGCAT
65 TAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATACATATATTGTGGCAT
* *
50708 TTTTAGATAAACGCCGCTAAAAC-CTAGTACTTTAGAGGCGCTTTATGC-AAAAATACCGCTAAA
1 TTTTAAATAAACGCCGCTAAAACTC-A-TACTTTAGAGGCG-TTTATGCGAAAAACACCGCTAAA
* *
50771 -ACT-CGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAAT
63 GA-TAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAAT
50815 CGTTCTTTAG
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
122 1 0.01
123 55 0.60
124 30 0.33
125 6 0.07
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (123 bp):
TTTTAAATAAACGCCGCTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACACCGCTAAAGAT
AAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATACATATATTGTGGCAT
Found at i:50835 original size:164 final size:165
Alignment explanation
Indices: 50598--50950 Score: 487
Period size: 164 Copynumber: 2.1 Consensus size: 165
50588 ACAATAAACG
* ** *
50598 CCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTTTAGTG
1 CCGCTAAAACTCATACTTTAGTGGCGTTTAGTAAACAAACGCCGCCAAAGATAAGTACTTTAGTG
* * *
50663 GCGTTTTTAAACAAACGCCGCAATAGGGTACATATATTGTGGCATTTTTAGATAAACGCCGCTAA
66 GCGTTTTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCAGCTAA
* *
50728 AACCTAGTACTT-TAGAGGCGCTTTATGCAAAAATA
131 AACCTAATA-TTCTAGAGGCACTTTATGCAAAAATA
* * * *
50763 CCGCTAAAACTCGTACTTTAGTGGCGTTT-GTAAACAAACGCCGCCATAGA-ATCGTTCTTTAGT
1 CCGCTAAAACTCATACTTTAGTGGCGTTTAGTAAACAAACGCCGCCAAAGATA-AGTACTTTAGT
* *
50826 GGCGTTTTTAAACAAACGCCGCAATAGGGTACATATATCGTTGCGTTTTTAAATAAACGCAGCTA
65 GGCGTTTTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCAGCTA
* * * *
50891 AAACCTAATATTCTAGTGGCATTTTATTCAAAAATG
130 AAACCTAATATTCTAGAGGCACTTTATGCAAAAATA
50927 CCGCTAAATACTCATACTTTAGTG
1 CCGCTAAA-ACTCATACTTTAGTG
50951 ACGATTTTAG
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
163 3 0.02
164 120 0.73
165 42 0.25
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (165 bp):
CCGCTAAAACTCATACTTTAGTGGCGTTTAGTAAACAAACGCCGCCAAAGATAAGTACTTTAGTG
GCGTTTTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCAGCTAA
AACCTAATATTCTAGAGGCACTTTATGCAAAAATA
Found at i:50843 original size:123 final size:123
Alignment explanation
Indices: 50580--50847 Score: 289
Period size: 123 Copynumber: 2.2 Consensus size: 123
50570 TAACATTAAC
* * * *
50580 GGCG-TTTTACAATAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCT
1 GGCGTTTTTA-AATAAACGCCGCTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACACCGCT
* **
50644 AAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCAATAGGGTACATATATTGT
65 AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATACATATATTGT
* * *
50703 GGCATTTTTAGATAAACGCCGCTAAAAC-CTAGTACTTTAGAGGCGCTTTATGC-AAAAATACCG
1 GGCGTTTTTAAATAAACGCCGCTAAAACTC-A-TACTTTAGAGGCG-TTTATGCGAAAAACACCG
* * * *
50766 CTAAA-ACT-CGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAAT-CGT-TCTTTAGT
63 CTAAAGA-TAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATACATAT-ATT-GT
*
50826 GGCGTTTTTAAACAAACGCCGC
1 GGCGTTTTTAAATAAACGCCGC
50848 AATAGGGTAC
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
121 1 0.01
122 5 0.04
123 79 0.65
124 30 0.25
125 6 0.05
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (123 bp):
GGCGTTTTTAAATAAACGCCGCTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACACCGCTA
AAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATACATATATTGT
Found at i:57059 original size:21 final size:21
Alignment explanation
Indices: 57033--57077 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
57023 TAAACTTTAA
57033 TTTATTATTATGGATTTCAAG
1 TTTATTATTATGGATTTCAAG
*
57054 TTTATTGTTATGGATTTCAAG
1 TTTATTATTATGGATTTCAAG
57075 TTT
1 TTT
57078 GTGTCTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTATTATTATGGATTTCAAG
Found at i:57265 original size:43 final size:43
Alignment explanation
Indices: 57214--57505 Score: 467
Period size: 43 Copynumber: 6.8 Consensus size: 43
57204 GTTTGTATAG
**
57214 AAAAACGCCGCTATAAATCTCAACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
* *
57257 AAAAACGCCGCTATAAATCTTGACCTTTAGCGACGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
*
57300 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
*
57343 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
* *
57386 AAAAACGCTGCTATAAATCTTGACCTTTTGCGGTGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
* *
57429 AAAAACGCCGCTATAGATCTTGACCTTTTGTGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
* * *
57472 AAAAATGCCGCTATATATCTTGACCTTTTACGGC
1 AAAAACGCCGCTATAAATCTTGACCTTTTGCGGC
57506 ATTTTTTGTT
Statistics
Matches: 231, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 231 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
Found at i:73356 original size:2 final size:2
Alignment explanation
Indices: 73349--73382 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
73339 GACCCACGTG
73349 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
73383 GCATGCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78112 original size:20 final size:20
Alignment explanation
Indices: 78087--78216 Score: 224
Period size: 20 Copynumber: 6.5 Consensus size: 20
78077 TCGATCTAAA
78087 AAAAAATCGAAAATCGATTT
1 AAAAAATCGAAAATCGATTT
78107 AAAAAATCGAAAATCGATTT
1 AAAAAATCGAAAATCGATTT
**
78127 AAAAACCCGAAAATCGATTT
1 AAAAAATCGAAAATCGATTT
*
78147 AAAAAACCGAAAATCGATTT
1 AAAAAATCGAAAATCGATTT
78167 AAAAAATCGAAAATCGATTT
1 AAAAAATCGAAAATCGATTT
*
78187 AAAAAATCGAAAATCAATTT
1 AAAAAATCGAAAATCGATTT
78207 AAAAAATCGA
1 AAAAAATCGA
78217 TAACCGAAAA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.22
Consensus pattern (20 bp):
AAAAAATCGAAAATCGATTT
Found at i:83934 original size:14 final size:15
Alignment explanation
Indices: 83899--83937 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
83889 CATAAGTTGC
*
83899 AAATTTAGTTCCTAT
1 AAATTTAGTCCCTAT
83914 AAATTTAGTCCCTAT
1 AAATTTAGTCCCTAT
83929 -AATTTAGTC
1 AAATTTAGTC
83938 ATATTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (15 bp):
AAATTTAGTCCCTAT
Found at i:105952 original size:15 final size:15
Alignment explanation
Indices: 105897--105952 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
105887 CGGAAAAAAT
105897 ATAAAATTTA-AAAC
1 ATAAAATTTATAAAC
*
105911 TTAAAAATTTATAATAC
1 AT-AAAATTTATAA-AC
105928 AT--AA--TATAAAC
1 ATAAAATTTATAAAC
105939 ATAAAATTTATAAA
1 ATAAAATTTATAAA
105953 TTCAACTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
11 4 0.12
12 5 0.15
13 2 0.06
14 3 0.09
15 14 0.42
16 2 0.06
17 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATTTATAAAC
Found at i:106041 original size:19 final size:19
Alignment explanation
Indices: 106017--106063 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
106007 AACTAAATTT
106017 GAAATAATTGAGATTAAAA
1 GAAATAATTGAGATTAAAA
106036 GAAATAATTGAGATTAAAA
1 GAAATAATTGAGATTAAAA
106055 GAAATAATT
1 GAAATAATT
106064 TAATAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (19 bp):
GAAATAATTGAGATTAAAA
Done.