Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001913.1 Hibiscus syriacus cultivar Beakdansim tig00003871_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: 71156
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1987 original size:93 final size:93
Alignment explanation
Indices: 1846--2018 Score: 242
Period size: 93 Copynumber: 1.9 Consensus size: 93
1836 TTTTACCTCT
* *
1846 AAAATTAATCTCTTTTTTTAAAAAAAATATTTTGAGAGATGTTCTAAAATTAAT-TCTCTTTTTC
1 AAAATTAATCTCTTTTTTTAAAAAAAATATTTGGAGAGATCTTCTAAAATTAATCTCTCTTTTTC
*
1910 -TTTGAAAGATGTTTTGAGATTTCTTTG
66 TTTTGAAAAATGTTTTGAGATTTCTTTG
*** * *
1937 AAAATTAATCTCTCTTTTCTTTTGAAAAATATTTGGAGAGATCTTCTAAAATTAATCTTTTTTTT
1 AAAATTAATCTCT-TTTT-TTAAAAAAAATATTTGGAGAGATCTTCTAAAATTAATCTCTCTTTT
2002 TCTTTTGAAAAATGTTT
64 TCTTTTGAAAAATGTTT
2019 AAGCGATCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 13 0.19
92 4 0.06
93 32 0.46
94 8 0.11
95 13 0.19
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (93 bp):
AAAATTAATCTCTTTTTTTAAAAAAAATATTTGGAGAGATCTTCTAAAATTAATCTCTCTTTTTC
TTTTGAAAAATGTTTTGAGATTTCTTTG
Found at i:1988 original size:47 final size:46
Alignment explanation
Indices: 1843--2041 Score: 199
Period size: 47 Copynumber: 4.3 Consensus size: 46
1833 GCATTTTACC
*** *
1843 TCTAAAATTAATCTCT-TTTTTTAAAAAAAATATTTTGAGAGATGT
1 TCTAAAATTAATCTCTCTTTTTTTTGAAAAATATTTTGAGAGATCT
* * **
1888 TCTAAAATTAAT-TCTCTTTTTCTTTGAAAGATGTTTTGAGATTTCT
1 TCTAAAATTAATCTCTCTTTTT-TTTGAAAAATATTTTGAGAGATCT
*
1934 T-TGAAAATTAATCTCTCTTTTCTTTTGAAAAATATTTGGAGAGATCT
1 TCT-AAAATTAATCTCTCTTTT-TTTTGAAAAATATTTTGAGAGATCT
* * * * *
1981 TCTAAAATTAATCTTTTTTTTTCTTTTGAAAAAT-GTTTAAGCGATCT
1 TCTAAAATTAATC-TCTCTTTT-TTTTGAAAAATATTTTGAGAGATCT
2028 TCTAAAATTAATCT
1 TCTAAAATTAATCT
2042 TGCATTTTAT
Statistics
Matches: 128, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
44 3 0.02
45 18 0.14
46 27 0.21
47 60 0.47
48 20 0.16
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (46 bp):
TCTAAAATTAATCTCTCTTTTTTTTGAAAAATATTTTGAGAGATCT
Found at i:2202 original size:35 final size:35
Alignment explanation
Indices: 2156--2234 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
2146 ATTTCCTCTA
2156 TTTTCTTGTGCTGTCATAATGTCTTTGGCATTCTG
1 TTTTCTTGTGCTGTCATAATGTCTTTGGCATTCTG
2191 TTTTCTTGTGCTGTCATAATGTCTTTGGCATTCTG
1 TTTTCTTGTGCTGTCATAATGTCTTTGGCATTCTG
2226 TTTTCTTGT
1 TTTTCTTGT
2235 CGTCTGATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.10, C:0.16, G:0.19, T:0.54
Consensus pattern (35 bp):
TTTTCTTGTGCTGTCATAATGTCTTTGGCATTCTG
Found at i:4240 original size:21 final size:21
Alignment explanation
Indices: 4214--4453 Score: 278
Period size: 21 Copynumber: 11.6 Consensus size: 21
4204 GTTTCCAGAT
* *
4214 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
4235 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
4256 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
4277 TCGCAATGTGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
4297 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
4318 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
4339 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
4359 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
4380 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
4401 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
4421 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
4442 TCGCAATGCGAA
1 TCGCAATGCGAA
4454 TATGTAAATC
Statistics
Matches: 185, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
20 49 0.26
21 136 0.74
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:4312 original size:41 final size:42
Alignment explanation
Indices: 4214--4472 Score: 302
Period size: 41 Copynumber: 6.3 Consensus size: 42
4204 GTTTCCAGAT
* * * * *
4214 TCGCAACGCGAACTTCGACTATCGCAATGCAAACT-TGGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTACAA
*
4256 TCGCAATGCGAACTTGGACTATCGCAATGTGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
* * *
4297 TCGCAATGCGAACTTGGACTATCGCAACGCGAACT-TGGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTACAA
* * *
4339 TCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACTA
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--ACAA
4380 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
4421 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
4462 TCGCAATGCGA
1 TCGCAATGCGA
4473 TAGTCGAAGT
Statistics
Matches: 189, Mismatches: 17, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 119 0.63
42 62 0.33
43 3 0.02
44 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
Found at i:4492 original size:21 final size:21
Alignment explanation
Indices: 4462--4668 Score: 253
Period size: 21 Copynumber: 9.9 Consensus size: 21
4452 AATATGTAAA
* *
4462 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
4483 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
4504 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
4525 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTCCA-AGT
4545 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
4566 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
4587 TCGCATTGCGATAGTCTAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
4608 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
4628 ATCGCATTGCGATTTATTCCAAAT
1 -TCGCATTGCGA--TAGTCCAAGT
4652 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
4669 AATCGCAACG
Statistics
Matches: 163, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.04
20 19 0.12
21 128 0.79
23 6 0.04
24 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:4493 original size:62 final size:62
Alignment explanation
Indices: 4234--4453 Score: 379
Period size: 62 Copynumber: 3.5 Consensus size: 62
4224 AACTTCGACT
* *
4234 ATCGCAATGCAAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
*
4296 ATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* *
4358 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
4420 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA
4454 TATGTAAATC
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
61 1 0.01
62 146 0.99
63 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:4619 original size:83 final size:83
Alignment explanation
Indices: 4462--4619 Score: 280
Period size: 83 Copynumber: 1.9 Consensus size: 83
4452 AATATGTAAA
* *
4462 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTC
4527 GCATTGCGATTTACATAT
66 GCATTGCGATTTACATAT
* *
4545 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCTAAGTTC
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTC
4610 GCATTGCGAT
66 GCATTGCGAT
4620 AGTCGACTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (83 bp):
TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTC
GCATTGCGATTTACATAT
Found at i:4675 original size:63 final size:62
Alignment explanation
Indices: 4468--4675 Score: 197
Period size: 62 Copynumber: 3.3 Consensus size: 62
4458 TAAATCGCAA
* ** * * *
4468 TGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAAATCGCATTGCGATAGTCCAACTTCGCATTGCGATAGTCCAAATTCG-AT
* * * * * *
4531 TGCGAT-TTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAAATCGCATTGCGATAGTCCAACTTCGCATTGCGATAGTCCAAATTCG-AT
* ** * *
4593 TGCGATAGTCTAAGTTCGCATTGCGATAGT-CGACTATCGCATTGCGATTTATTCCAAATTCG-T
1 TGCGATAGTCCAAAATCGCATTGCGATAGTCCAACT-TCGCATTGCGA--TAGTCCAAATTCGAT
4656 TGCGATAGTCCAAAATCGCA
1 TGCGATAGTCCAAAATCGCA
4676 ACGACTGGTG
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
62 59 0.48
63 53 0.43
65 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (62 bp):
TGCGATAGTCCAAAATCGCATTGCGATAGTCCAACTTCGCATTGCGATAGTCCAAATTCGAT
Found at i:4799 original size:16 final size:16
Alignment explanation
Indices: 4778--4808 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4768 CGACCTCGAC
4778 CACGACCCAAGACGAG
1 CACGACCCAAGACGAG
*
4794 CACGACCCGAGACGA
1 CACGACCCAAGACGA
4809 AACGAGACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.39, G:0.26, T:0.00
Consensus pattern (16 bp):
CACGACCCAAGACGAG
Found at i:5309 original size:6 final size:6
Alignment explanation
Indices: 5298--5322 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5288 CTGTCTCGTC
5298 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
5323 ATTACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:5464 original size:42 final size:42
Alignment explanation
Indices: 5415--5637 Score: 313
Period size: 42 Copynumber: 5.3 Consensus size: 42
5405 TGCGATTTTG
* * * *
5415 GACTATCGCAATGAATTTGGAATAAATCTCAATGCGATA-GTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGA-ACTTC
*
5457 GACTATCGCAACGAATTTGGAATAAATCGCAAAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGC--AACGCGAACTTC
* *
5501 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
5543 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* ** *
5585 GAATATCGCAACGAACATGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
5627 GACTATCGCAA
1 GACTATCGCAA
5638 TGCGAATATG
Statistics
Matches: 164, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
42 127 0.77
43 1 0.01
44 36 0.22
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:5487 original size:21 final size:21
Alignment explanation
Indices: 5461--5628 Score: 141
Period size: 21 Copynumber: 7.8 Consensus size: 21
5451 ATAGTCGACT
*
5461 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
5482 ATCGCAAAACGCGAACTTTGACT--
1 ATCGC--AA--CGAACTTGGAATAA
5505 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
5526 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
5547 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
5568 ATCGCAACGCGAACTTCGAAT--
1 ATCGCAA--CGAACTTGGAATAA
*
5589 ATCGCAACGAACATGGAATAA
1 ATCGCAACGAACTTGGAATAA
5610 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
5629 CTATCGCAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
19 30 0.25
21 42 0.36
23 37 0.31
25 9 0.08
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:5560 original size:86 final size:84
Alignment explanation
Indices: 5415--5637 Score: 331
Period size: 86 Copynumber: 2.6 Consensus size: 84
5405 TGCGATTTTG
* * * * * *
5415 GACTATCGCAATGAATTTGGAATAAATCTCAATGCGATA-GTCGACTATCGCAACGAATTTGGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGA-ACTTGGACTATCGCAACGAATTTGGAA
*
5479 TAAATCGCAAAACGCGAACTTT
65 TAAATCGC--AACGCGAACTTC
5501 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
5566 AAATCGCAACGCGAACTTC
66 AAATCGCAACGCGAACTTC
* *
5585 GAATATCGCAACGAACATGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
5638 TGCGAATATG
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 62 0.49
85 1 0.01
86 64 0.50
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (84 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
AAATCGCAACGCGAACTTC
Found at i:5634 original size:21 final size:21
Alignment explanation
Indices: 5489--5643 Score: 142
Period size: 21 Copynumber: 7.4 Consensus size: 21
5479 TAAATCGCAA
* *
5489 AACGCGAACTTTGACTATCGC
1 AACGCGAACTTGGAATATCGC
5510 AA--CGAACTTGGAATAAATCGC
1 AACGCGAACTTGGAAT--ATCGC
*
5531 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGAATATCGC
*
5552 AA--CGAATTTGGAATAAATCGC
1 AACGCGAACTTGGAAT--ATCGC
*
5573 AACGCGAACTTCGAATATCGC
1 AACGCGAACTTGGAATATCGC
*
5594 AA--CGAACATGGAATAAATCGC
1 AACGCGAACTTGGAAT--ATCGC
*
5615 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGAATATCGC
*
5636 AATGCGAA
1 AACGCGAA
5644 TATGTAAATC
Statistics
Matches: 110, Mismatches: 12, Indels: 24
0.75 0.08 0.16
Matches are distributed among these distances:
19 30 0.27
21 49 0.45
23 31 0.28
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (21 bp):
AACGCGAACTTGGAATATCGC
Found at i:7735 original size:16 final size:16
Alignment explanation
Indices: 7714--7744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7704 TAGTAATTTG
*
7714 CCCTAAAATTTATTCA
1 CCCTAAAAGTTATTCA
7730 CCCTAAAAGTTATTC
1 CCCTAAAAGTTATTC
7745 GCCCGACGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (16 bp):
CCCTAAAAGTTATTCA
Found at i:10326 original size:13 final size:13
Alignment explanation
Indices: 10302--10326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10292 CCTGACCCAT
10302 TGACCCGACCCGC
1 TGACCCGACCCGC
10315 TGACCCGACCCG
1 TGACCCGACCCG
10327 ATCCATTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.52, G:0.24, T:0.08
Consensus pattern (13 bp):
TGACCCGACCCGC
Found at i:10336 original size:18 final size:17
Alignment explanation
Indices: 10284--10337 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
10274 GGTCACAACC
*
10284 TGACCCGACCTGACCCAT
1 TGACCCGACCCGA-CCAT
10302 TGACCCGACCCG--C--
1 TGACCCGACCCGACCAT
10315 TGACCCGACCCGATCCAT
1 TGACCCGACCCGA-CCAT
10333 TGACC
1 TGACC
10338 GTTGACTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 12 0.40
15 1 0.03
16 1 0.03
18 16 0.53
ACGTcount: A:0.20, C:0.46, G:0.19, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCAT
Found at i:12828 original size:24 final size:24
Alignment explanation
Indices: 12801--12916 Score: 119
Period size: 24 Copynumber: 4.8 Consensus size: 24
12791 TTCGATTTGA
12801 TTTCTGATCTGATACTTGACATGG
1 TTTCTGATCTGATACTTGACATGG
12825 TTTCTGATCTGATA-TCTGACATGG
1 TTTCTGATCTGATACT-TGACATGG
* * * * *
12849 ATTCTTATATGATACTTTACTTGG
1 TTTCTGATCTGATACTTGACATGG
* * *
12873 ATTCTAATCTGATACTTGACTTGG
1 TTTCTGATCTGATACTTGACATGG
*
12897 ATTT-TGATATGATACTTGAC
1 -TTTCTGATCTGATACTTGAC
12917 GTGAATTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.01
24 74 0.95
25 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (24 bp):
TTTCTGATCTGATACTTGACATGG
Found at i:12862 original size:48 final size:48
Alignment explanation
Indices: 12799--12916 Score: 141
Period size: 48 Copynumber: 2.4 Consensus size: 48
12789 TTTTCGATTT
* * *
12799 GATTTCTGATCTGATACTTGACATGGTTTCTGATCTGATA-TCTGACATG
1 GATTT-TGATATGATACTTGACATGGATTCTAATCTGATACT-TGACATG
* * *
12848 GATTCTT-ATATGATACTTTACTTGGATTCTAATCTGATACTTGACTTG
1 GATT-TTGATATGATACTTGACATGGATTCTAATCTGATACTTGACATG
12896 GATTTTGATATGATACTTGAC
1 GATTTTGATATGATACTTGAC
12917 GTGAATTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
47 2 0.03
48 50 0.85
49 6 0.10
50 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (48 bp):
GATTTTGATATGATACTTGACATGGATTCTAATCTGATACTTGACATG
Found at i:12928 original size:24 final size:24
Alignment explanation
Indices: 12805--12933 Score: 98
Period size: 24 Copynumber: 5.4 Consensus size: 24
12795 ATTTGATTTC
* * * *
12805 TGATCTGATACTTGACATGGTTTC
1 TGATATGATACTTGACTTGGATTA
* * *
12829 TGATCTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACTTGGATTA
* * *
12853 TTATATGATACTTTACTTGGATTC
1 TGATATGATACTTGACTTGGATTA
* * *
12877 TAATCTGATACTTGACTTGGATTT
1 TGATATGATACTTGACTTGGATTA
* *
12901 TGATATGATACTTGACGTGAATTA
1 TGATATGATACTTGACTTGGATTA
*
12925 TGATTTGAT
1 TGATATGAT
12934 TTTTGATATA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
23 1 0.01
24 86 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACTTGGATTA
Found at i:15006 original size:18 final size:18
Alignment explanation
Indices: 14983--15021 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
14973 ATCGGTCAGA
14983 ACCCGACCCGACCAGTTG
1 ACCCGACCCGACCAGTTG
*
15001 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCAGTTG
15019 ACC
1 ACC
15022 GTTGACCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCAGTTG
Found at i:17461 original size:24 final size:25
Alignment explanation
Indices: 17441--17558 Score: 147
Period size: 24 Copynumber: 4.9 Consensus size: 25
17431 TTTTTGATTT
*
17441 GATTTCTGATCTGATACTTGACATG
1 GATTTCTGATCTGATACTTGACTTG
* *
17466 GA-TTCTGATCTGATA-TCTAACATG
1 GATTTCTGATCTGATACT-TGACTTG
*
17490 GA-TTCTGATCTGATACTTGACTAG
1 GATTTCTGATCTGATACTTGACTTG
17514 GATTT-TGATCTGATACTTGACTTG
1 GATTTCTGATCTGATACTTGACTTG
*
17538 GATTT-TGATATGATACTTGAC
1 GATTTCTGATCTGATACTTGAC
17559 GTGAATTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
23 1 0.01
24 78 0.93
25 5 0.06
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (25 bp):
GATTTCTGATCTGATACTTGACTTG
Found at i:22602 original size:51 final size:51
Alignment explanation
Indices: 22539--22653 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
22529 AGGATTATAT
* * * **
22539 TTATTATTTTATTAGGAATTAAGATATAGTTC-AAACATTATTTTTTGTTTA
1 TTATTATTTTATTAGGAATTAAGACATA-ATCAAAACATTATATTTAATTTA
*
22590 TTATTATTTTATTAGGAATTAAGACATAATCAAAATATTATATTTAATTTA
1 TTATTATTTTATTAGGAATTAAGACATAATCAAAACATTATATTTAATTTA
22641 TTATTATTTTATT
1 TTATTATTTTATT
22654 CAATAGTTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.04
51 55 0.96
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (51 bp):
TTATTATTTTATTAGGAATTAAGACATAATCAAAACATTATATTTAATTTA
Found at i:31959 original size:14 final size:14
Alignment explanation
Indices: 31940--32013 Score: 59
Period size: 14 Copynumber: 5.4 Consensus size: 14
31930 TTTGTCCTGG
31940 TTATAAATATTATA
1 TTATAAATATTATA
*
31954 TTATAATTATTA-A
1 TTATAAATATTATA
*
31967 -TAT-TATATTATTA
1 TTATAAATATTA-TA
*
31980 TTAT-ATTATTATTA
1 TTATAAATATTA-TA
31994 TTATAACA-ATTATA
1 TTATAA-ATATTATA
32008 TTATAA
1 TTATAA
32014 TAATTATTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
11 5 0.10
12 3 0.06
13 2 0.04
14 34 0.69
15 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATAAATATTATA
Found at i:31968 original size:20 final size:20
Alignment explanation
Indices: 31940--32029 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
31930 TTTGTCCTGG
*
31940 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
*
31960 TTATTAATATTATATTATTA
1 TTATTAATATTATATTATAA
*
31980 TTA-TATTATTATTATTATAA
1 TTATTAATATTA-TATTATAA
**
32000 CAATT-ATATTATA--ATAA
1 TTATTAATATTATATTATAA
*
32017 TTATTAGTATTAT
1 TTATTAATATTAT
32030 TAATATCAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.12
18 6 0.11
19 9 0.16
20 34 0.60
21 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:31975 original size:11 final size:11
Alignment explanation
Indices: 31945--31994 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
31935 CCTGGTTATA
31945 AATATTATATT
1 AATATTATATT
*
31956 -ATAAT-TATT
1 AATATTATATT
31965 AATATTATATT
1 AATATTATATT
*
31976 ATTATTATATT
1 AATATTATATT
*
31987 ATTATTAT
1 AATATTAT
31995 TATAACAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 4 0.12
10 8 0.24
11 22 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTATATT
Found at i:31978 original size:3 final size:3
Alignment explanation
Indices: 31947--32031 Score: 70
Period size: 3 Copynumber: 29.7 Consensus size: 3
31937 TGGTTATAAA
* *
31947 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
31992 TAT TAT AAC AAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32032 ATATCAGGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 8 0.12
3 58 0.88
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:31981 original size:17 final size:17
Alignment explanation
Indices: 31947--32031 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
31937 TGGTTATAAA
31947 TATT-ATATTATA--AT
1 TATTAATATTATATTAT
31961 TATTAATATTATATTAT
1 TATTAATATTATATTAT
31978 TATT-ATATTATTATTAT
1 TATTAATATTA-TATTAT
*
31995 TA-TAACAATTATATTA-
1 TATTAA-TATTATATTAT
*
32011 TAATAATTATTAGTATTAT
1 TATTAA-TATTA-TATTAT
32030 TA
1 TA
32032 ATATCAGGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 4 0.07
15 8 0.14
16 9 0.15
17 27 0.46
18 9 0.15
19 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TATTAATATTATATTAT
Found at i:32018 original size:14 final size:14
Alignment explanation
Indices: 31948--32020 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
31938 GGTTATAAAT
*
31948 ATTATATTATAATT
1 ATTATATTATAATA
*
31962 ATTA-A-TATTAT-
1 ATTATATTATAATA
*
31973 ATTATTATTAT-ATT
1 ATTA-TATTATAATA
*
31987 ATTATTATTATAACA
1 ATTA-TATTATAATA
32002 ATTATATTATAATA
1 ATTATATTATAATA
32016 ATTAT
1 ATTAT
32021 TAGTATTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.08
12 5 0.10
13 4 0.08
14 32 0.64
15 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATATTATAATA
Found at i:43903 original size:18 final size:17
Alignment explanation
Indices: 43882--43921 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
43872 AAAAAGATTT
43882 AAAAAAAGAAAAAAAATG
1 AAAAAAAGAAAAAAAA-G
* *
43900 AAAAAAGGAAGAAAAAG
1 AAAAAAAGAAAAAAAAG
43917 AAAAA
1 AAAAA
43922 GGGAGGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:45243 original size:55 final size:55
Alignment explanation
Indices: 45125--45507 Score: 534
Period size: 55 Copynumber: 6.9 Consensus size: 55
45115 ACGAACCCGT
* * *
45125 TTGTTGAAGATGGTTCGAGTCTTATACTCTCTGCAAGAAATAGAGAGGAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGA
* *
45181 TTTTTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * * *
45236 GTGTTGAAGATTGGTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * *
45291 GTGTTGAAGATTGTTCGAGTTTTATACTCTCTGAAGAAATAGGGAGCATACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * * *
45346 TTTTTGAAGATTATTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* *
45401 ATGTTGAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * * *
45456 TTTTTGAAGATTGTTCGAGT-TCTATACTCCCTGAAAGAAAAAGAGAGCAGAC
1 TTGTTGAAGATTGTTCGAGTCT-TATACTCTCTG-AAGAAATAGGGAGCAGAC
45508 CCGTAGGAAG
Statistics
Matches: 290, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.00
55 243 0.84
56 46 0.16
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (55 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
Found at i:45399 original size:165 final size:166
Alignment explanation
Indices: 45126--45507 Score: 595
Period size: 165 Copynumber: 2.3 Consensus size: 166
45116 CGAACCCGTT
* * * *
45126 TGTTGAAGATGGTTCGAGTCTTATACTCTCTGCAAGAAATAGAGAGGAGACACGATTTTTGAAGA
1 TGTTGAAGATTGTTCGAGTTTTATACTCTCTGAAAGAAATAGAGAGCAGACACGATTTTTGAAGA
* *
45191 TTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAGTGTTGAAGATTGGTCAAGT
66 TTATTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAGATTGGTCAAGT
45256 CTTATACTCTCTGAAGAAATAGGGAGCAGACAAGAG
131 CTTATACTCTCTGAAGAAATAGGGAGCAGACAAGAG
* *
45292 TGTTGAAGATTGTTCGAGTTTTATACTCTCTG-AAGAAATAGGGAGCATACACGATTTTTGAAGA
1 TGTTGAAGATTGTTCGAGTTTTATACTCTCTGAAAGAAATAGAGAGCAGACACGATTTTTGAAGA
* * **
45356 TTATTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGAATGTTGAAGATTGTTTGAGT
66 TTATTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAGATTGGTCAAGT
* *
45421 CTTATACTCTCTGAAGAAATAGGGAGCAGACACGAT
131 CTTATACTCTCTGAAGAAATAGGGAGCAGACAAGAG
* * * *
45457 TTTTGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAAAGAGAGCAGAC
1 TGTTGAAGATTGTTCGAGTTTTATACTCTCTGAAAGAAATAGAGAGCAGAC
45508 CCGTAGGAAG
Statistics
Matches: 196, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
165 151 0.77
166 45 0.23
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (166 bp):
TGTTGAAGATTGTTCGAGTTTTATACTCTCTGAAAGAAATAGAGAGCAGACACGATTTTTGAAGA
TTATTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAGATTGGTCAAGT
CTTATACTCTCTGAAGAAATAGGGAGCAGACAAGAG
Found at i:45763 original size:14 final size:14
Alignment explanation
Indices: 45744--45824 Score: 80
Period size: 14 Copynumber: 5.9 Consensus size: 14
45734 TTTGTCCTGG
*
45744 TTATAAATATTATA
1 TTATAATTATTATA
45758 TTATAATTATTACTA
1 TTATAATTATTA-TA
45773 TTAT-ATTA-T-TA
1 TTATAATTATTATA
45784 TTAT-ATTATTATTA
1 TTATAATTATTA-TA
**
45798 TTATAACAATTATA
1 TTATAATTATTATA
*
45812 TTATAATAATTAT
1 TTATAATTATTAT
45825 TAGTATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 10 0.17
12 1 0.02
13 1 0.02
14 35 0.60
15 11 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:45779 original size:11 final size:11
Alignment explanation
Indices: 45751--45814 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
45741 TGGTTATAAA
45751 TATTATATTA-
1 TATTATATTAC
*
45761 TAAT-TATTAC
1 TATTATATTAC
*
45771 TATTATATTAT
1 TATTATATTAC
*
45782 TATTATATTAT
1 TATTATATTAC
*
45793 TATTATTATAAC
1 TATTA-TATTAC
*
45805 AATTATATTA
1 TATTATATTA
45815 TAATAATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
9 5 0.11
10 6 0.14
11 25 0.57
12 8 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATATTAC
Found at i:45782 original size:3 final size:3
Alignment explanation
Indices: 45751--45835 Score: 70
Period size: 3 Copynumber: 29.7 Consensus size: 3
45741 TGGTTATAAA
* *
45751 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
45796 TAT TAT AAC AAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
45836 ATATCATGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 8 0.12
3 58 0.88
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:45785 original size:17 final size:16
Alignment explanation
Indices: 45751--45835 Score: 75
Period size: 17 Copynumber: 5.1 Consensus size: 16
45741 TGGTTATAAA
45751 TATTATATTATA--AT
1 TATTATATTATATTAT
45765 TATTACTATTATATTAT
1 TATTA-TATTATATTAT
45782 TATTATATTATTATTAT
1 TATTATATTA-TATTAT
* *
45799 TATAACAATTATATTAT
1 TATTA-TATTATATTAT
* *
45816 AATAATTATTAGTATTAT
1 TATTA-TATTA-TATTAT
45834 TA
1 TA
45836 ATATCATGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
14 5 0.08
15 7 0.12
16 5 0.08
17 31 0.53
18 11 0.19
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTATATTATATTAT
Found at i:45832 original size:23 final size:23
Alignment explanation
Indices: 45776--45833 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
45766 ATTACTATTA
* * *
45776 TATTATTATTATATTATTATTAT
1 TATTACTATTATATTATAATAAT
* *
45799 TATAACAATTATATTATAATAAT
1 TATTACTATTATATTATAATAAT
*
45822 TATTAGTATTAT
1 TATTACTATTAT
45834 TAATATCATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTACTATTATATTATAATAAT
Found at i:49633 original size:22 final size:23
Alignment explanation
Indices: 49591--49634 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
49581 GAAAGATAAG
*
49591 TACAACAAAAGTGACGTGAAAAC
1 TACAACAAAAGTGAAGTGAAAAC
49614 TACAA-AAAAGTGGAAG-GAAAA
1 TACAACAAAAGT-GAAGTGAAAA
49635 TAATATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (23 bp):
TACAACAAAAGTGAAGTGAAAAC
Found at i:53064 original size:55 final size:54
Alignment explanation
Indices: 52994--53495 Score: 598
Period size: 55 Copynumber: 9.1 Consensus size: 54
52984 GGATAAATGA
* * * * *
52994 AACTTGAAAAATCTTCAAATGACGGGTCCACTCCCTATTCCTTCAGGGAGTATA-
1 AACTCGAACAATCTTCAAA-AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* ** * *
53048 AGACTCGAACAATCTTCAATAAACGTGTATGCTCCCTATTCTTTCAGGGAGTATA-
1 A-ACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
** * * *
53103 AGACTCGAACAATCTTCATAAAACAAGTTCGCTCCCTATTCTTTCAGGGAGTATAG
1 A-ACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* *
53159 AACTCGAACAATCTTCATAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
1 AACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
*
53214 AACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
1 AACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * *
53269 AACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGGGAGTACAG
1 AACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * *
53324 AACTCGAAAAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
1 AACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * *
53379 AACTTGAATAATCTTCAACAAACGGGTCCGCTCCCTATT-CTATTAGAGAGTATAG
1 AACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAG
*
53434 AACTCGAACAATCTTCAACAAATGGGTCCGCTCCCTATT-CTATCAGAGAGTATAG
1 AACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAG
*
53489 GACTCGA
1 AACTCGA
53496 TCTTCATAAA
Statistics
Matches: 400, Mismatches: 40, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
54 5 0.01
55 391 0.98
56 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (54 bp):
AACTCGAACAATCTTCAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
Found at i:53276 original size:165 final size:165
Alignment explanation
Indices: 52994--53495 Score: 681
Period size: 165 Copynumber: 3.0 Consensus size: 165
52984 GGATAAATGA
* * * * *
52994 AACTTGAAAAATCTTCA-AATGACGGGTCCACTCCCTATTCCTTCAGGGAGTATA-AGACTCGAA
1 AACTCGAAAAATCTTCATAA-AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAA
* * ** * *
53057 CAATCTTCAATAAACGTGTATGCTCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTCA
64 CAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCA
** *
53121 TA-AAACAAGTTCGCTCCCTATTCTTTCAGGGAGTATAG
128 -ACAAACGGGTCCGCTCCCTATTCTTTCAGGGAGTATAG
* *
53159 AACTCGAACAATCTTCATAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACA
1 AACTCGAAAAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACA
*
53224 ATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACA
66 ATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACA
* *
53289 AACGGGTCCGCTCCCTATTCATTCAGGGAGTACAG
131 AACGGGTCCGCTCCCTATTCTTTCAGGGAGTATAG
* * *
53324 AACTCGAAAAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAATA
1 AACTCGAAAAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACA
*
53389 ATCTTCAACAAACGGGTCCGCTCCCTATT-CTATTAGAGAGTATAGAACTCGAACAATCTTCAAC
66 ATCTTCAACAAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAAC
* * *
53453 AAATGGGTCCGCTCCCTATTCTATCAGAGAGTATAG
130 AAACGGGTCCGCTCCCTATTCTTTCAGGGAGTATAG
*
53489 GACTCGA
1 AACTCGA
53496 TCTTCATAAA
Statistics
Matches: 300, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
164 3 0.01
165 293 0.98
166 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (165 bp):
AACTCGAAAAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACA
ATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACA
AACGGGTCCGCTCCCTATTCTTTCAGGGAGTATAG
Found at i:53561 original size:37 final size:38
Alignment explanation
Indices: 53506--53577 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
53496 TCTTCATAAA
53506 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
**
53544 ATGA-TTTGCTTCACTACTCTTTTGTGAAGGCTTA
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTA
53578 AGATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (38 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
Found at i:54870 original size:7 final size:7
Alignment explanation
Indices: 54858--54954 Score: 69
Period size: 7 Copynumber: 13.7 Consensus size: 7
54848 TTTTCTCTAT
54858 TTTTTCA
1 TTTTTCA
54865 TTTTTCA
1 TTTTTCA
54872 -TTTTCA
1 TTTTTCA
54878 -TTTTC-
1 TTTTTCA
*
54883 TCTTTTCT
1 T-TTTTCA
*
54891 TTTTTCTTC
1 TTTTTC--A
54900 TTTTTC-
1 TTTTTCA
**
54906 TTTCACCA
1 TTT-TTCA
54914 TTTTTCA
1 TTTTTCA
54921 TTTTTTCA
1 -TTTTTCA
54929 TTTTT-A
1 TTTTTCA
54935 TTTTTCA
1 TTTTTCA
54942 TTTTTTCA
1 -TTTTTCA
54950 TTTTT
1 TTTTT
54955 TTATTTCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
6 20 0.27
7 31 0.41
8 18 0.24
9 6 0.08
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:54932 original size:29 final size:29
Alignment explanation
Indices: 54856--54966 Score: 74
Period size: 29 Copynumber: 3.9 Consensus size: 29
54846 ATTTTTCTCT
*
54856 ATTTTTTCA-TTTTTCA-TTTTCATTTTCTC
1 ATTTTTTCATTTTTTCATTTTTC-TTTAC-C
54885 -TTTTCTT--TTTTCTTC-TTTTTCTTTCACC
1 ATTTT-TTCATTTT-TTCATTTTTCTTT-ACC
* **
54913 A-TTTTTCATTTTTTCATTTTTATTTTTC
1 ATTTTTTCATTTTTTCATTTTTCTTTACC
*
54941 ATTTTTTCATTTTTTTATTTCTTCTT
1 ATTTTTTCATTTTTTCATTT-TTCTT
54967 CAAGCGAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
27 2 0.03
28 19 0.29
29 40 0.62
30 4 0.06
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (29 bp):
ATTTTTTCATTTTTTCATTTTTCTTTACC
Found at i:54961 original size:21 final size:21
Alignment explanation
Indices: 54842--54954 Score: 90
Period size: 21 Copynumber: 5.2 Consensus size: 21
54832 TTGAACCCCC
54842 TTTTATTTTTCTCTATTTTTTCAT
1 TTTTA-TTTT-TC-ATTTTTTCAT
*
54866 TTTTCA-TTTTCATTTTCTC-T
1 TTTT-ATTTTTCATTTTTTCAT
*
54886 TTTCT-TTTTTCTTCTTTTTC-T
1 TTT-TATTTTTCAT-TTTTTCAT
**
54907 TTCACCATTTTTCATTTTTTCAT
1 TT--TTATTTTTCATTTTTTCAT
54930 TTTTATTTTTCATTTTTTCAT
1 TTTTATTTTTCATTTTTTCAT
54951 TTTT
1 TTTT
54955 TTATTTCTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
20 10 0.14
21 37 0.51
22 8 0.11
23 13 0.18
24 4 0.05
25 1 0.01
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTATTTTTCATTTTTTCAT
Found at i:62105 original size:17 final size:17
Alignment explanation
Indices: 62083--62117 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62073 ACCAGCCAAT
*
62083 CTGGCCTTTCTCAATTC
1 CTGGCCCTTCTCAATTC
*
62100 CTGGCCCTTCTTAATTC
1 CTGGCCCTTCTCAATTC
62117 C
1 C
62118 CTTTAGCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.37, G:0.11, T:0.40
Consensus pattern (17 bp):
CTGGCCCTTCTCAATTC
Found at i:66646 original size:10 final size:10
Alignment explanation
Indices: 66625--66681 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
66615 ATTTTTTTTC
66625 AAAAAAAC--
1 AAAAAAACAA
66633 AAAAAAACAA
1 AAAAAAACAA
*
66643 AAAAAAGGCAA
1 AAAAAA-ACAA
**
66654 AAAAAGGCAAA
1 AAAAAAAC-AA
66665 AAAAAAACAA
1 AAAAAAACAA
66675 AAAAAAA
1 AAAAAAA
66682 GCCAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 8 0.20
10 17 0.41
11 16 0.39
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:66647 original size:11 final size:11
Alignment explanation
Indices: 66633--66681 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
66623 TCAAAAAAAC
66633 AAAAAAACAAA
1 AAAAAAACAAA
**
66644 AAAAAGGC-AA
1 AAAAAAACAAA
**
66654 AAAAAGGCAAA
1 AAAAAAACAAA
66665 AAAAAAACAAA
1 AAAAAAACAAA
66676 AAAAAA
1 AAAAAA
66682 GCCAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 10 0.30
11 23 0.70
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:66674 original size:32 final size:32
Alignment explanation
Indices: 66633--66697 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
66623 TCAAAAAAAC
* *
66633 AAAAAAACAAAAAAAAGGCAAAAAAAGGCAAA
1 AAAAAAACAAAAAAAAAGCAAAAAAAGCCAAA
*
66665 AAAAAAACAAAAAAAAAGCCAAAAAAGCCAAA
1 AAAAAAACAAAAAAAAAGCAAAAAAAGCCAAA
66697 A
1 A
66698 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.78, C:0.12, G:0.09, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAAAAAAAGCAAAAAAAGCCAAA
Found at i:66688 original size:11 final size:11
Alignment explanation
Indices: 66640--66690 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
66630 AACAAAAAAA
*
66640 CAAAAAAAAGG
1 CAAAAAAAAGC
*
66651 CAAAAAAAGGC
1 CAAAAAAAAGC
* *
66662 AAAAAAAAAAC
1 CAAAAAAAAGC
*
66673 AAAAAAAAAGC
1 CAAAAAAAAGC
66684 CAAAAAA
1 CAAAAAA
66691 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Done.