Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_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: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:282532 original size:14 final size:14
Alignment explanation
Indices: 282509--282550 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
282499 TTTGAAGTGC
282509 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAA-A
282524 AAAAG-AAGAAAAA
1 AAAAGAAAGAAAAA
**
282537 AAATCAAAGAAAAA
1 AAAAGAAAGAAAAA
282551 GAAGTAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:282535 original size:23 final size:23
Alignment explanation
Indices: 282509--282563 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
282499 TTTGAAGTGC
282509 AAAAGAAAGAAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
* **
282532 AAAAAAAATCAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
*
282555 TAAAGAAAG
1 AAAAGAAAG
282564 TTGCAAAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGAAAAGAAAAAGAAG
Found at i:284550 original size:4 final size:4
Alignment explanation
Indices: 284541--284567 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
284531 GCCAGCATGT
284541 ATTC ATTC ATTC ATTC ATTC ATTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATT
284568 AACTCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTC
Found at i:286339 original size:14 final size:14
Alignment explanation
Indices: 286316--286358 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
286306 TTTGGAGTGC
286316 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAA-A
286331 AAAAG-AAGAAAAA
1 AAAAGAAAGAAAAA
*
286344 AAAATCAAAGAAAAA
1 AAAA-GAAAGAAAAA
286359 TAAGTGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:290258 original size:9 final size:9
Alignment explanation
Indices: 290246--290273 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
290236 TATTCAATCC
290246 TTTCATTTT
1 TTTCATTTT
290255 TTTCATTTT
1 TTTCATTTT
290264 TTTCATTTT
1 TTTCATTTT
290273 T
1 T
290274 AACTATCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCATTTT
Found at i:294530 original size:59 final size:59
Alignment explanation
Indices: 294438--294566 Score: 258
Period size: 59 Copynumber: 2.2 Consensus size: 59
294428 GCAAGGCATA
294438 TTATGGTAGCTTTGGTAGCTAAAAGTACAAGCATATCAGCTCAGAGTATCTCATGAATG
1 TTATGGTAGCTTTGGTAGCTAAAAGTACAAGCATATCAGCTCAGAGTATCTCATGAATG
294497 TTATGGTAGCTTTGGTAGCTAAAAGTACAAGCATATCAGCTCAGAGTATCTCATGAATG
1 TTATGGTAGCTTTGGTAGCTAAAAGTACAAGCATATCAGCTCAGAGTATCTCATGAATG
294556 TTATGGTAGCT
1 TTATGGTAGCT
294567 CATTTAATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (59 bp):
TTATGGTAGCTTTGGTAGCTAAAAGTACAAGCATATCAGCTCAGAGTATCTCATGAATG
Found at i:295464 original size:14 final size:14
Alignment explanation
Indices: 295445--295494 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
295435 ACTATTTGTT
295445 CATCACCATCTTTC
1 CATCACCATCTTTC
*
295459 CATCACAATCTTTC
1 CATCACCATCTTTC
295473 CATCACCATCTTT-
1 CATCACCATCTTTC
295486 CATCACCAT
1 CATCACCAT
295495 TCACGCCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 9 0.26
14 25 0.74
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.34
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:295659 original size:15 final size:15
Alignment explanation
Indices: 295639--295669 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
295629 TCTTTGATAA
295639 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
295654 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
295669 C
1 C
295670 CTTTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:301603 original size:11 final size:11
Alignment explanation
Indices: 301589--301627 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
301579 TCTTTTTTTG
301589 TTTTTTTGCCTT
1 TTTTTTTGCC-T
**
301601 TTTTTTTGTTT
1 TTTTTTTGCCT
301612 TTTTTTTGCCT
1 TTTTTTTGCCT
301623 TTTTT
1 TTTTT
301628 GTTTTTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:301604 original size:12 final size:12
Alignment explanation
Indices: 301589--301627 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
301579 TCTTTTTTTG
301589 TTTTTTTGCCTT
1 TTTTTTTGCCTT
*
301601 TTTTTTTG-TTT
1 TTTTTTTGCCTT
301612 TTTTTTTGCCTT
1 TTTTTTTGCCTT
301624 TTTT
1 TTTT
301628 GTTTTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:301605 original size:31 final size:30
Alignment explanation
Indices: 301570--301635 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
301560 AAATTTTGGC
*
301570 TTTTTTGGTTCTTTTTTTG-TTTTTTTGCCTT
1 TTTTTTGGTTCTTTTTTTGCCTTTTTTG--TT
* *
301601 TTTTTTTGTTTTTTTTTTGCCTTTTTTGTT
1 TTTTTTGGTTCTTTTTTTGCCTTTTTTGTT
301631 TTTTT
1 TTTTT
301636 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 17 0.55
32 7 0.23
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.82
Consensus pattern (30 bp):
TTTTTTGGTTCTTTTTTTGCCTTTTTTGTT
Found at i:301615 original size:23 final size:22
Alignment explanation
Indices: 301581--301635 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
301571 TTTTTGGTTC
*
301581 TTTTTTTGTTTTTTTGCCTTTT
1 TTTTTTTTTTTTTTTGCCTTTT
301603 TTTTTGTTTTTTTTTTGCCTTTT
1 TTTTT-TTTTTTTTTTGCCTTTT
*
301626 TTGTTTTTTT
1 TTTTTTTTTT
301636 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTTTTTTTGCCTTTT
Found at i:309861 original size:24 final size:24
Alignment explanation
Indices: 309834--309892 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
309824 CAAGCTATAG
*
309834 CTCACCTAGTTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
309858 CTCACCTAGCTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
309882 CTCACCTAGCT
1 CTCACCTAGCT
309893 TACCATTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (24 bp):
CTCACCTAGCTAGCTACCAAGACA
Found at i:310208 original size:19 final size:19
Alignment explanation
Indices: 310184--310232 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
310174 GGCCAAGAGC
* *
310184 ATGTATCTTCATTAAAATA
1 ATGTATTTTCATGAAAATA
*
310203 ATGTATTTTCATGAAAATC
1 ATGTATTTTCATGAAAATA
310222 ATGTATTTTCA
1 ATGTATTTTCA
310233 AAGGGATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (19 bp):
ATGTATTTTCATGAAAATA
Found at i:310593 original size:14 final size:14
Alignment explanation
Indices: 310573--310619 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
310563 ACTATTTATT
*
310573 CATCACCATCTTTC
1 CATCACCATCTTCC
*
310587 TATCACCATCTTCC
1 CATCACCATCTTCC
*
310601 CATCACCAACTT-C
1 CATCACCATCTTCC
310614 CATCAC
1 CATCAC
310620 TATTCATGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 7 0.24
14 22 0.76
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.30
Consensus pattern (14 bp):
CATCACCATCTTCC
Found at i:311028 original size:7 final size:6
Alignment explanation
Indices: 311009--311049 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
310999 GTGCTGCAAT
* *
311009 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG CAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
311050 GACTCCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:313220 original size:30 final size:30
Alignment explanation
Indices: 313184--313259 Score: 152
Period size: 30 Copynumber: 2.5 Consensus size: 30
313174 ATAGAGCTTC
313184 AACTTAGCTGGAGGAGCTAGCATGTAACTG
1 AACTTAGCTGGAGGAGCTAGCATGTAACTG
313214 AACTTAGCTGGAGGAGCTAGCATGTAACTG
1 AACTTAGCTGGAGGAGCTAGCATGTAACTG
313244 AACTTAGCTGGAGGAG
1 AACTTAGCTGGAGGAG
313260 AACTTTGGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (30 bp):
AACTTAGCTGGAGGAGCTAGCATGTAACTG
Found at i:313400 original size:24 final size:24
Alignment explanation
Indices: 313373--313431 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
313363 CAAGCTATAG
* *
313373 CTCACCTAGTTAGTTACCAAAACA
1 CTCACCTAGCTAGCTACCAAAACA
*
313397 CTCACCTAGCTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAAACA
313421 CTCACCTAGCT
1 CTCACCTAGCT
313432 TACCATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.36, G:0.10, T:0.22
Consensus pattern (24 bp):
CTCACCTAGCTAGCTACCAAAACA
Found at i:313746 original size:19 final size:19
Alignment explanation
Indices: 313722--313771 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
313712 CGGCCAAGAG
* *
313722 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATGAAAAT
313741 CATGTATTTTCATGAAAAT
1 CATGTATTTTCATGAAAAT
313760 CATGTATTTTCA
1 CATGTATTTTCA
313772 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATGAAAAT
Found at i:314132 original size:14 final size:14
Alignment explanation
Indices: 314112--314158 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
314102 ACTATTTATT
*
314112 CATCACCATCTTTC
1 CATCACCATCTTCC
*
314126 TATCACCATCTTCC
1 CATCACCATCTTCC
*
314140 CATCACTATCTT-C
1 CATCACCATCTTCC
314153 CATCAC
1 CATCAC
314159 TATTCACGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 7 0.24
14 22 0.76
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (14 bp):
CATCACCATCTTCC
Found at i:314555 original size:6 final size:6
Alignment explanation
Indices: 314544--314584 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
314534 GTGCTGCAAT
* *
314544 AAAAAG AAAAAG AAAAAAG AAAAAC AAAAAG CAAAAG AAAA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAA
314585 GACTCCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:314560 original size:13 final size:13
Alignment explanation
Indices: 314544--314584 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
314534 GTGCTGCAAT
314544 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
*
314557 AAAAAGAAAAA-C
1 AAAAAGAAAAAGA
*
314569 AAAAAGCAAAAGA
1 AAAAAGAAAAAGA
314582 AAA
1 AAA
314585 GACTCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:317069 original size:19 final size:20
Alignment explanation
Indices: 317045--317089 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
317035 GGCCAAGAGA
*
317045 ATGTATCTACAT-TAAAATC
1 ATGTATCTACATAAAAAATC
* *
317064 ATGTATTTTCATAAAAAATC
1 ATGTATCTACATAAAAAATC
317084 ATGTAT
1 ATGTAT
317090 TTTCAAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGTATCTACATAAAAAATC
Found at i:317884 original size:24 final size:24
Alignment explanation
Indices: 317854--317915 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
317844 TGCTGCAACA
317854 AAAAGCAAAAGAAAGAAGAAAAAC
1 AAAAGCAAAAGAAAGAAGAAAAAC
317878 AAAAGCAAAAGAAAGAAGAAAAAC
1 AAAAGCAAAAGAAAGAAGAAAAAC
317902 AAAAGCAAAAGAAA
1 AAAAGCAAAAGAAA
317916 AGACTCCTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAGCAAAAGAAAGAAGAAAAAC
Found at i:317912 original size:6 final size:6
Alignment explanation
Indices: 317854--317917 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
317844 TGCTGCAACA
* * * *
317854 AAAAGC AAAAGA AAGAAG- AAAAAC AAAAGC AAAAGA AAGAAG- AAAAAC
1 AAAAGC AAAAGC AA-AAGC AAAAGC AAAAGC AAAAGC AA-AAGC AAAAGC
317902 AAAAGC AAAAG- AAAAG
1 AAAAGC AAAAGC AAAAG
317918 ACTCCTACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
5 9 0.19
6 33 0.69
7 6 0.12
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:320426 original size:20 final size:19
Alignment explanation
Indices: 320398--320441 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
320388 ATTTTTTTTC
*
320398 AAAAAAAAAAAAAAGGCAA
1 AAAAAAAAAAAAAAGCCAA
*
320417 AAAAACAAAAAAAGAGCCAA
1 AAAAA-AAAAAAAAAGCCAA
320437 AAAAA
1 AAAAA
320442 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAGCCAA
Found at i:320438 original size:9 final size:10
Alignment explanation
Indices: 320405--320448 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
320395 TTCAAAAAAA
*
320405 AAAAAAAGGC
1 AAAAAAAGCC
*
320415 AAAAAAA-CA
1 AAAAAAAGCC
320424 AAAAAAGAGCC
1 AAAAAA-AGCC
320435 AAAAAAAGCC
1 AAAAAAAGCC
320445 AAAA
1 AAAA
320449 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 6 0.21
10 16 0.55
11 7 0.24
ACGTcount: A:0.75, C:0.14, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:326593 original size:13 final size:14
Alignment explanation
Indices: 326564--326599 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
326554 ACTATTTGTT
326564 CATCACCATCTTTC
1 CATCACCATCTTTC
*
326578 CATCACTATC-TTC
1 CATCACCATCTTTC
326591 CATCACCAT
1 CATCACCAT
326600 TCACTCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:329951 original size:13 final size:14
Alignment explanation
Indices: 329918--329953 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
329908 ACTATTTGTT
329918 CATCACCATCTTTC
1 CATCACCATCTTTC
*
329932 TATCACCATC-TTC
1 CATCACCATCTTTC
329945 CATCACCAT
1 CATCACCAT
329954 TCATGCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:332705 original size:36 final size:35
Alignment explanation
Indices: 332608--332719 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
332598 TTGGTGGTTA
* * * *
332608 TATAGGCGTGAAATTGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
332643 TATAGGCGTGCAATGGTGATGAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
332678 TATAGGCGTAAAAATGGTGATGGAAGATGGTGGTGT
1 TATAGGCGT-GAAATGGTGATGGAAGATGGTGATGT
332714 TATAGG
1 TATAGG
332720 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 38 0.58
36 28 0.42
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:335616 original size:7 final size:6
Alignment explanation
Indices: 335597--335637 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
335587 GTGCTACAAC
* *
335597 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG TAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
335638 GACTCCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:335689 original size:23 final size:23
Alignment explanation
Indices: 335663--335717 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
335653 TTTAGAGTGC
335663 AAAAGAAAGAAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
* *
335686 AAAAAAAATAAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
**
335709 TGAAGAAAG
1 AAAAGAAAG
335718 TTGCAAAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGAAAAGAAAAAGAAG
Found at i:355763 original size:19 final size:21
Alignment explanation
Indices: 355739--355790 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
355729 CGGCCAAGAG
*
355739 CATGTATATTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
355758 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
355779 CATGTATTTTCA
1 CATGTATTTTCA
355791 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:357987 original size:22 final size:22
Alignment explanation
Indices: 357962--358005 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
357952 TGTTGATGGT
357962 CGAATGCCTTGATGATGATTGA
1 CGAATGCCTTGATGATGATTGA
357984 CGAATGCCTTGATGATGATTGA
1 CGAATGCCTTGATGATGATTGA
358006 AGGATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (22 bp):
CGAATGCCTTGATGATGATTGA
Found at i:358485 original size:19 final size:20
Alignment explanation
Indices: 358444--358486 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
358434 TAAACCCCTT
**
358444 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
*
358464 TGAAATTACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
358483 TGAA
1 TGAA
358487 GGTACATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:361508 original size:36 final size:36
Alignment explanation
Indices: 361456--361568 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
361446 GATACTATTT
*
361456 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
361492 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
361528 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
361563 ACATCA
1 TCATCA
361569 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:361511 original size:13 final size:11
Alignment explanation
Indices: 361456--361554 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
361446 GATACTATTT
361456 TCATCACCATAA
1 TCATCACCAT-A
*
361468 TCCATCTCCATTA
1 T-CATCACCA-TA
*
361481 TCA-CGCCTATA
1 TCATCACC-ATA
361492 TCATCACCATA
1 TCATCACCATA
361503 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
361517 TCA-CGCCTATA
1 TCATCACC-ATA
361528 TCATCACCATA
1 TCATCACCATA
361539 TTCCATCACCATA
1 -T-CATCACCATA
361552 TCA
1 TCA
361555 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:361583 original size:33 final size:33
Alignment explanation
Indices: 361468--361607 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
361458 ATCACCATAA
* * *
361468 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
361502 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
361540 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
361573 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
361606 TC
1 TC
361608 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:363987 original size:15 final size:16
Alignment explanation
Indices: 363967--363999 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
363957 GTGATGGACT
363967 ATGGTGATAGAAA-AG
1 ATGGTGATAGAAATAG
*
363982 ATGGTGATGGAAATAG
1 ATGGTGATAGAAATAG
363998 AT
1 AT
364000 AGTATCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (16 bp):
ATGGTGATAGAAATAG
Found at i:366411 original size:30 final size:31
Alignment explanation
Indices: 366375--366434 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
366365 CTTAGCTTTA
**
366375 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
366405 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
366435 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:368884 original size:19 final size:21
Alignment explanation
Indices: 368860--368911 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
368850 TAGCCAAGAG
*
368860 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
368879 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
368900 CATGTATTTTCA
1 CATGTATTTTCA
368912 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:369553 original size:19 final size:20
Alignment explanation
Indices: 369512--369562 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
369502 GACACCCCTT
**
369512 TGAATATACATGATTTTTTA
1 TGAATATACATGATTTTAAA
*
369532 TGAAAATACATG-TTTTAAA
1 TGAATATACATGATTTTAAA
369551 TGAATATACATG
1 TGAATATACATG
369563 CTCTTGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAATATACATGATTTTAAA
Found at i:370004 original size:302 final size:301
Alignment explanation
Indices: 369459--370039 Score: 1144
Period size: 302 Copynumber: 1.9 Consensus size: 301
369449 GGGACACAAT
369459 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
1 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
369524 ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
66 ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
369589 CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
131 CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
369654 TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAC
196 TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAC
369719 ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
261 ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
369760 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
1 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
369825 ATTTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTC
66 A-TTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTC
*
369890 ACCTATAAAGATAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTAT
130 ACCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTAT
369955 ATGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAA
195 ATGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAA
370020 CACAACATGCACATTGATAT
260 CACAACATGCACATTGATAT
370040 TTAAGCATGT
Statistics
Matches: 278, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
301 66 0.24
302 212 0.76
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (301 bp):
AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAC
ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
Found at i:371586 original size:15 final size:15
Alignment explanation
Indices: 371575--371603 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
371565 ACTCAAAAAG
371575 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
371590 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
371604 GTTGAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:376174 original size:16 final size:18
Alignment explanation
Indices: 376142--376176 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
376132 ATATAAAAAC
376142 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
376160 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
376176 A
1 A
376177 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:376233 original size:18 final size:16
Alignment explanation
Indices: 376181--376235 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
376171 TAAATAAATG
*
376181 AGTAAAATATATAAAA
1 AGTAAAATATATAATA
*
376197 AGTAAAAGCATATATATA
1 AGTAAAA-TATATA-ATA
376215 AGTAAAATA-ATAATA
1 AGTAAAATATATAATA
376230 A-TAAAA
1 AGTAAAA
376236 AAAAAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 10 0.29
17 6 0.18
18 9 0.26
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.25
Consensus pattern (16 bp):
AGTAAAATATATAATA
Found at i:376800 original size:36 final size:36
Alignment explanation
Indices: 376754--376854 Score: 179
Period size: 34 Copynumber: 2.9 Consensus size: 36
376744 ATAGTAGAAC
376754 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
376790 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
376824 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
376855 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 33 0.54
36 28 0.46
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:377819 original size:209 final size:208
Alignment explanation
Indices: 377398--378018 Score: 849
Period size: 209 Copynumber: 3.0 Consensus size: 208
377388 GCATTGTTCC
* * ** *
377398 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTA-TTGTTGACA
* * * * * *
377462 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGA
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGA
* ** * *
377527 AGTTAAAATTGAATCTGAA-T-GAA-AT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 AGTTGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTTG
377588 AACTTACGTTGTCTG
194 AACTTACGTTGTCTG
* *
377603 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAG
*
377668 CAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAG
* *
377732 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTGGACAAGCAGCGGTCCCTTCTTTGTGAAGTTG
131 TTGAAATTGGCTCTGA-ATT-GGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTTG
*
377797 AACTTGCGTTGTCTG
194 AACTTACGTTGTCTG
* * *
377812 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAGG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAG
* * * *
377877 CAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTGGAGTCGAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAG
* *
377942 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
131 TTGAAATTGGCTCTG-AATTG-GAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTT
*
378007 GAACTTATGTTG
193 GAACTTACGTTG
378019 CCTCGAGTGC
Statistics
Matches: 367, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
203 65 0.18
204 17 0.05
205 46 0.13
206 1 0.00
207 3 0.01
208 1 0.00
209 115 0.31
210 77 0.21
211 42 0.11
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (208 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTTGAA
CTTACGTTGTCTG
Found at i:377863 original size:105 final size:105
Alignment explanation
Indices: 377398--378012 Score: 816
Period size: 105 Copynumber: 5.9 Consensus size: 105
377388 GCATTGTTCC
* * * ** * * *
377398 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-GTTGTTGACAA
* * * *
377463 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* * **
377505 -AGTCTAATATCCTTCGTTGTGAAGTTAAAATTGAATCTG-AA-TGA-AA--T-TTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
377563 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
377603 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
377668 CAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCATTGTCT-
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
377706 AGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTGGACAA
1 A-AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
* *
377771 GCAGCGGTCCCTTCTTTGTGAAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
377812 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAGG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
377877 CAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
377917 GAGTCGAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * *
377982 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTT
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
378013 ATGTTGCCTC
Statistics
Matches: 454, Mismatches: 43, Indels: 23
0.87 0.08 0.04
Matches are distributed among these distances:
98 1 0.00
99 80 0.18
100 1 0.00
101 3 0.01
102 2 0.00
103 2 0.00
104 101 0.22
105 195 0.43
106 69 0.15
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:377929 original size:314 final size:311
Alignment explanation
Indices: 377399--378057 Score: 896
Period size: 314 Copynumber: 2.1 Consensus size: 311
377389 CATTGTTCCA
* *
377399 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAAC
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTAGTTGTGGACAAC
* *
377464 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
* *
377529 TTAAAATTGAATCTGAATGAAATTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTA
131 TTAAAATTGAATCTGAATGAAATTTGTTGACAAGCAGCGGTCCCTTCATCATGAAGTTGAACTTA
* *
377594 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-T
196 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTT
* *
377658 TGTTGACAAGCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
261 TGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
* * ** *
377708 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAGATTGGGAAGTT-GTTGTGGACAA
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGA-ACCGGGAAATTAGTTGTGGACAA
* * *
377771 GCAGCGGTCCCTTCTTTGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGA
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCG-AGTCCAATATCCTTCGTTGTGA
* ** *
377835 AGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAGGCAGCGGTCCCTTCATCATGAAGT
129 AGTTAAAATTGAATCTG-AA-TGA-AA--T-TTGTTGACAAGCAGCGGTCCCTTCATCATGAAGT
* *
377900 TGAACTTGCGTTGTCTGGAGTCGAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
188 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* *** * *
377965 AAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTTGCCTCG
253 AAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
* *
378024 AGTGCCACGATATCCTCCTTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTCGTGAAGTTGAAAT
378058 CGCAGATGGC
Statistics
Matches: 303, Mismatches: 34, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
307 1 0.00
308 82 0.27
309 46 0.15
310 3 0.01
311 2 0.01
313 1 0.00
314 98 0.32
315 16 0.05
316 30 0.10
317 3 0.01
319 21 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (311 bp):
AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTAGTTGTGGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
TTAAAATTGAATCTGAATGAAATTTGTTGACAAGCAGCGGTCCCTTCATCATGAAGTTGAACTTA
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTT
TGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
Found at i:378509 original size:29 final size:26
Alignment explanation
Indices: 378444--378510 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
378434 GCTTGTCTGG
*
378444 AATCTTGATTCTTGAATCTTCAAATTTT
1 AATC-TGA-TCTTGAATCTTCAAATTTA
378472 AATCCCTGATCTTGAATTCTTCAAATGTTCA
1 AAT--CTGATCTTGAA-TCTTCAAAT-TT-A
378503 AATCTGAT
1 AATCTGAT
378511 GTGCACATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
28 10 0.30
29 17 0.52
30 3 0.09
31 3 0.09
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (26 bp):
AATCTGATCTTGAATCTTCAAATTTA
Found at i:378794 original size:67 final size:67
Alignment explanation
Indices: 378648--378982 Score: 254
Period size: 65 Copynumber: 4.9 Consensus size: 67
378638 GGAAACGATC
* * * *
378648 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAA
378713 TAAAT
63 TAAAT
** * *
378718 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
378783 AT
66 AT
* ** * *
378785 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA--
378847 GTCTCAAGAGT
63 ---T-AA-A-T
* * * * * * * * * *
378858 GACAAA-A-CTT-AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACA
1 -TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATA
*
378920 TAT
65 AAT
* * *
378923 TCAAATA-TTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
378983 CTGTCTCAAG
Statistics
Matches: 213, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
64 4 0.02
65 85 0.40
66 8 0.04
67 24 0.11
68 32 0.15
69 3 0.01
70 7 0.03
71 2 0.01
72 4 0.02
73 40 0.19
74 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:378845 original size:36 final size:35
Alignment explanation
Indices: 378794--379002 Score: 191
Period size: 36 Copynumber: 6.0 Consensus size: 35
378784 TTCAAAGATT
* *
378794 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
378830 TTGTTTCAAGAGAAACTGTCTCAAGAGTGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
378865 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
378903 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
378932 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
378967 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
379003 CTCTTCTAGT
Statistics
Matches: 141, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.12
30 2 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 7 0.05
36 76 0.54
37 29 0.21
38 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:378890 original size:37 final size:36
Alignment explanation
Indices: 378805--378916 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 36
378795 TGTTTCAAGG
* *
378805 GAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGA
1 GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
378841 GAAACTGTCTCAAGAGT-GAC-AAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGA-TAGACGAAAA-TT-GTTCCAAAA
** * *
378878 GAAACTGTCTCAAGGGAGACGAAATTTGTTTC-AAA
1 GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
378913 GAAA
1 GAAA
378917 ACATATTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
35 11 0.17
36 24 0.37
37 27 0.42
38 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
Found at i:378903 original size:138 final size:138
Alignment explanation
Indices: 378742--379004 Score: 402
Period size: 138 Copynumber: 1.9 Consensus size: 138
378732 TTTCAAGAGT
* ** * * *
378742 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
* *
378807 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGTGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
378871 TCCAAAAGA
130 TCCAAAAGA
* * *
378880 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGAGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
*
378945 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
379005 CTTCTAGTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
137 4 0.04
138 108 0.96
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:379024 original size:35 final size:36
Alignment explanation
Indices: 378936--379036 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
378926 AATATTTTGT
* *
378936 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
378972 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
379006 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
379037 TCTTGTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 5 0.09
35 22 0.39
36 28 0.50
37 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:379052 original size:35 final size:35
Alignment explanation
Indices: 378932--379052 Score: 113
Period size: 35 Copynumber: 3.4 Consensus size: 35
378922 TTCAAATATT
378932 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATC
* *
378968 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATC
* * * *
379004 -T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATC
*
379039 TTGTTTTAAGAAAA
1 TTGTTTCAAGAAAA
379053 ACAATCATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
34 3 0.04
35 32 0.47
36 30 0.44
37 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAAAACTGTCTCAAGAGAGACAAATC
Found at i:379509 original size:18 final size:18
Alignment explanation
Indices: 379482--379517 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
379472 TGTTGAATCC
* *
379482 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
379500 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
379518 TTGATGTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:380597 original size:16 final size:15
Alignment explanation
Indices: 380578--380630 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
380568 TTCTTTTTGA
*
380578 TTTTTGTTCTTTATTT
1 TTTTTGTTCTTT-TCT
380594 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
380609 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
380625 TTTTTG
1 TTTTTG
380631 GTTTTTTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.30
16 21 0.64
17 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:380638 original size:16 final size:16
Alignment explanation
Indices: 380592--380638 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
380582 TGTTCTTTAT
* *
380592 TTTTTTTGTTTTCTTC
1 TTTTTTGGTTTTTTTC
* *
380608 TTTTTTGCTTCTTTTC
1 TTTTTTGGTTTTTTTC
380624 TTTTTTGGTTTTTTT
1 TTTTTTGGTTTTTTT
380639 GCCCTTTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTTTTGGTTTTTTTC
Found at i:385050 original size:16 final size:18
Alignment explanation
Indices: 385018--385052 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
385008 GAATAAAAAC
385018 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
385036 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
385052 A
1 A
385053 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:385629 original size:37 final size:35
Alignment explanation
Indices: 385614--385715 Score: 170
Period size: 34 Copynumber: 2.9 Consensus size: 35
385604 ATAGTAGAAC
385614 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG--AAAT
*
385651 TTTATCCTATTTTTAGGAGTTTGAATCCTA-AAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
385685 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
385716 TAGGACAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 33 0.53
37 29 0.47
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
Found at i:386570 original size:18 final size:18
Alignment explanation
Indices: 386547--386585 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
386537 AAATATTTTA
*
386547 TTTGATATATTATATTGT
1 TTTGATATATTATATTAT
* *
386565 TTTGATTTGTTATATTAT
1 TTTGATATATTATATTAT
386583 TTT
1 TTT
386586 TATGCTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (18 bp):
TTTGATATATTATATTAT
Found at i:398784 original size:54 final size:54
Alignment explanation
Indices: 398693--398931 Score: 347
Period size: 54 Copynumber: 4.4 Consensus size: 54
398683 TTGACATAAT
* *
398693 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTTCAACCCATGAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAA
* *
398747 TTCATAATGAGTTTGTGAATTACCATATC-ATCGCTATGTGTGCAACCCACG-AA
1 TTCATAATGAGTTTGTGAATTACCGTATCGA-CACTATGTGTGCAACCCACGAAA
* * * *
398800 GTCATAATGAGTTTGTGAATTACCGTGTTGGCACTATGTGTGCAACCCACGAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAA
* * *
398854 TTCTTAATTAGTTTGTGAATTACCGTATCGACACTATGTGTACAACCCACGAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAA
*
398908 TTCATAACGAGTTTGTGAATTACC
1 TTCATAATGAGTTTGTGAATTACC
398932 CCACGAAATT
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 47 0.29
54 115 0.71
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (54 bp):
TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAA
Found at i:398891 original size:107 final size:108
Alignment explanation
Indices: 398694--398931 Score: 345
Period size: 107 Copynumber: 2.2 Consensus size: 108
398684 TGACATAATT
* *
398694 TCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTTCAACCCATGAAATTCATAATGAGT
1 TCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGT
* *
398759 TTGTGAATTACCATATCATCGCTATGTGTGCAACCCACG-AAG
66 TTGTGAATTACCATATCATCACTATGTGTACAACCCACGAAAG
* * * * *
398801 TCATAATGAGTTTGTGAATTACCGTGTTGGCACTATGTGTGCAACCCACGAAATTCTTAATTAGT
1 TCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGT
* *
398866 TTGTGAATTACCGTATCGA-CACTATGTGTACAACCCACGAAAT
66 TTGTGAATTACCATATC-ATCACTATGTGTACAACCCACGAAAG
*
398909 TCATAACGAGTTTGTGAATTACC
1 TCATAATGAGTTTGTGAATTACC
398932 CCACGAAATT
Statistics
Matches: 117, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
107 92 0.79
108 25 0.21
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (108 bp):
TCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGT
TTGTGAATTACCATATCATCACTATGTGTACAACCCACGAAAG
Found at i:398940 original size:32 final size:32
Alignment explanation
Indices: 398899--398961 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
398889 ATGTGTACAA
* *
398899 CCCACGAAATTCATAACGAGTTTGTGAATTAC
1 CCCACGAAATTAATAACGAGTTTATGAATTAC
*
398931 CCCACGAAATTAATAATGAGTTTATGAATTA
1 CCCACGAAATTAATAACGAGTTTATGAATTA
398962 TCGTATCGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (32 bp):
CCCACGAAATTAATAACGAGTTTATGAATTAC
Found at i:399022 original size:53 final size:52
Alignment explanation
Indices: 398965--399076 Score: 136
Period size: 53 Copynumber: 2.1 Consensus size: 52
398955 TGAATTATCG
398965 TATCGGCACCTA-CGTAAAACCCACGGAATTCATAATGAATTTGTAAATTTCCA
1 TATCGGCA-CTAGCGTAAAACCCACGGAATT-ATAATGAATTTGTAAATTTCCA
* ** * * *
399018 TATCGGCACTATGTGTGCAACCCATGGAATTATAATGAGTTTGTGAATTTCCA
1 TATCGGCACTA-GCGTAAAACCCACGGAATTATAATGAATTTGTAAATTTCCA
399071 TATCGG
1 TATCGG
399077 TACTTAGGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
52 3 0.06
53 34 0.67
54 14 0.27
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (52 bp):
TATCGGCACTAGCGTAAAACCCACGGAATTATAATGAATTTGTAAATTTCCA
Found at i:401507 original size:18 final size:18
Alignment explanation
Indices: 401480--401519 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
401470 ATCCTTACAA
*
401480 CATTTACCACGATAACAC
1 CATTTACCACGACAACAC
* *
401498 CATTTGCCACGACAACGC
1 CATTTACCACGACAACAC
401516 CATT
1 CATT
401520 CATACTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.23
Consensus pattern (18 bp):
CATTTACCACGACAACAC
Found at i:401784 original size:18 final size:19
Alignment explanation
Indices: 401761--401798 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
401751 CGGGGTTAGT
401761 AAAAAAATAAAA-AAAAAA
1 AAAAAAATAAAAGAAAAAA
401779 AAAAAAATAAAAGAAAAAA
1 AAAAAAATAAAAGAAAAAA
401798 A
1 A
401799 GTTTAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (19 bp):
AAAAAAATAAAAGAAAAAA
Found at i:409884 original size:15 final size:15
Alignment explanation
Indices: 409873--409901 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
409863 ACTCAAAAAG
409873 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
409888 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
409902 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:417088 original size:16 final size:17
Alignment explanation
Indices: 417067--417109 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
417057 TTTGACTTTT
417067 TAGTCAAAGTCAAC-CC
1 TAGTCAAAGTCAACTCC
417083 TAGTCAAAGT--ACTCC
1 TAGTCAAAGTCAACTCC
*
417098 TGGTCAAAGTCA
1 TAGTCAAAGTCA
417110 GCGATCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (17 bp):
TAGTCAAAGTCAACTCC
Found at i:417189 original size:20 final size:20
Alignment explanation
Indices: 417166--417211 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
417156 CATGTTTGGT
*
417166 TTGACTTAGATTA-GTTCAAG
1 TTGACTT-GACTATGTTCAAG
*
417186 TTGACTTGACTATGTTCGAG
1 TTGACTTGACTATGTTCAAG
417206 TTGACT
1 TTGACT
417212 CAGTCCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGACTTGACTATGTTCAAG
Found at i:417221 original size:20 final size:20
Alignment explanation
Indices: 417198--417253 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
417188 GACTTGACTA
417198 TGTTCGAGTTGACTCAGTCC
1 TGTTCGAGTTGACTCAGTCC
* *
417218 TGTTCGAGTTAACTCAGTCG
1 TGTTCGAGTTGACTCAGTCC
417238 TGTTCGAGTTGACTCA
1 TGTTCGAGTTGACTCA
417254 AATCGGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
TGTTCGAGTTGACTCAGTCC
Found at i:423656 original size:21 final size:22
Alignment explanation
Indices: 423619--423662 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
423609 TACCTATTGC
423619 AATCAACACAAAACAACACAAA
1 AATCAACACAAAACAACACAAA
* *
423641 AATCAAC-CAAATCAACATAAA
1 AATCAACACAAAACAACACAAA
423662 A
1 A
423663 TTGAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.66, C:0.25, G:0.00, T:0.09
Consensus pattern (22 bp):
AATCAACACAAAACAACACAAA
Found at i:434150 original size:12 final size:12
Alignment explanation
Indices: 434127--434173 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
434117 ATGTTTTTTT
434127 ATTTACTATATTC
1 ATTTA-TATATTC
* *
434140 CTTTATATATTT
1 ATTTATATATTC
434152 ATTTATATATT-
1 ATTTATATATTC
434163 ATTATATATAT
1 ATT-TATATAT
434174 ATATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 3 0.10
12 23 0.77
13 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTATATATTC
Found at i:434158 original size:10 final size:10
Alignment explanation
Indices: 434143--434204 Score: 83
Period size: 10 Copynumber: 6.4 Consensus size: 10
434133 TATATTCCTT
*
434143 TATATATTTA
1 TATATATATA
*
434153 TTTATATAT-
1 TATATATATA
434162 TAT-TATATA
1 TATATATATA
434171 TATATATATA
1 TATATATATA
434181 TATATATATA
1 TATATATATA
*
434191 TATATATATG
1 TATATATATA
434201 TATA
1 TATA
434205 GATGTATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
8 5 0.11
9 5 0.11
10 36 0.78
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TATATATATA
Found at i:434172 original size:4 final size:4
Alignment explanation
Indices: 434143--434204 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
434133 TATATTCCTT
* *
434143 TATA TATT TATT TATA TAT- TAT- TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
434189 TATA TATA TATG TATA
1 TATA TATA TATA TATA
434205 GATGTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 6 0.11
4 47 0.89
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (4 bp):
TATA
Found at i:434332 original size:31 final size:31
Alignment explanation
Indices: 434307--434365 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
434297 TATTTTTGTT
434307 TTTA-TTTATTTATATATATTATATTTTTAC
1 TTTATTTTATTTATATATATTATATTTTTAC
* * *
434337 TTTATTTTATTTTTTTATATTATTTTTTT
1 TTTATTTTATTTATATATATTATATTTTT
434366 CTTAATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTATTTTATTTATATATATTATATTTTTAC
Found at i:434498 original size:17 final size:17
Alignment explanation
Indices: 434466--434510 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
434456 TATGTACACA
*
434466 TTATTTTATT-CC-TTT
1 TTATTTTTTTACCTTTT
434481 TTATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
434499 TTATTTTTTTAC
1 TTATTTTTTTAC
434511 TTCATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.23
16 3 0.12
17 8 0.31
18 9 0.35
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:434571 original size:24 final size:23
Alignment explanation
Indices: 434539--434588 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
434529 TATCTGTGTC
434539 TTTGTTTTTTTAATATTTTATTCAT
1 TTTGTTTTTTTAAT-TTTT-TTCAT
*
434564 TTTG-TTTTTTAATTTTTTTTAT
1 TTTGTTTTTTTAATTTTTTTCAT
434586 TTT
1 TTT
434589 TTACGTGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 4 0.17
24 9 0.38
25 4 0.17
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTGTTTTTTTAATTTTTTTCAT
Found at i:436970 original size:17 final size:17
Alignment explanation
Indices: 436926--436997 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
436916 ATTCATGTAT
436926 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
436943 GTTAGTACATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
436961 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
436978 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
436995 CTA
1 CTA
436998 ATTGTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:443087 original size:32 final size:32
Alignment explanation
Indices: 443012--443121 Score: 96
Period size: 32 Copynumber: 3.4 Consensus size: 32
443002 TGGCTAGTAG
* * * * **
443012 TGCATTCAGATAATGCACAATAAAGTCAATAT
1 TGCATTCAGATAATGTACAGTAGAGTCAGTGC
*
443044 TGCAGTT-AGATAATGTATAGTAGAGTCAGTGC
1 TGCA-TTCAGATAATGTACAGTAGAGTCAGTGC
* * * *
443076 TGCATTCAGATAATGTACATTATAGTTAGTGT
1 TGCATTCAGATAATGTACAGTAGAGTCAGTGC
*
443108 TGCATTCAAATAAT
1 TGCATTCAGATAAT
443122 ACACAACAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.03
32 59 0.94
33 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
TGCATTCAGATAATGTACAGTAGAGTCAGTGC
Found at i:443169 original size:96 final size:96
Alignment explanation
Indices: 442987--443191 Score: 211
Period size: 96 Copynumber: 2.1 Consensus size: 96
442977 TATTGTATTT
* * * * *
442987 AGATAATGTACAATATGGCTAGTAGTGCATTCAGATAATGCACAATAAAGTCAATATTGCAGTTA
1 AGATAATGTACATTATAGCTAGTAGTGCATTCAAATAATACACAACAAAGTCAATATTGCAGTTA
* * * *
443052 GATAATGTATAGTAGAGTCAGT-GCTGCATTC
66 GATAATGCACAGGAGAGTCAGTATC-GCATTC
* * * *
443083 AGATAATGTACATTATAGTTAGT-GTTGCATTCAAATAATACACAACAGAGTTAGTATTGCA-TC
1 AGATAATGTACATTATAGCTAGTAG-TGCATTCAAATAATACACAACAAAGTCAATATTGCAGT-
*
443146 TAGATAATGCACAGGAGCA-TCAGTATCGCATTT
64 TAGATAATGCACAGGAG-AGTCAGTATCGCATTC
*
443179 AGATAATGCACAT
1 AGATAATGTACAT
443192 CAAATATAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
95 2 0.02
96 86 0.96
97 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AGATAATGTACATTATAGCTAGTAGTGCATTCAAATAATACACAACAAAGTCAATATTGCAGTTA
GATAATGCACAGGAGAGTCAGTATCGCATTC
Found at i:444120 original size:9 final size:9
Alignment explanation
Indices: 444106--444148 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
444096 GTGTCTCCAA
444106 TATACAATT
1 TATACAATT
444115 TATAC-ATT
1 TATACAATT
*
444123 GATACAATT
1 TATACAATT
444132 TATACAA-T
1 TATACAATT
*
444140 GATACAATT
1 TATACAATT
444149 CCATAAATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (9 bp):
TATACAATT
Found at i:444129 original size:17 final size:17
Alignment explanation
Indices: 444103--444148 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
444093 TCAGTGTCTC
444103 CAAT-ATACAATTTATA
1 CAATGATACAATTTATA
*
444119 CATTGATACAATTTATA
1 CAATGATACAATTTATA
444136 CAATGATACAATT
1 CAATGATACAATT
444149 CCATAAATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (17 bp):
CAATGATACAATTTATA
Found at i:444749 original size:45 final size:45
Alignment explanation
Indices: 444697--444786 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
444687 CAATTATTGT
444697 CCATAAATCATCTTTGTAATCATCGTTTAATACATCTTCCAAAGG
1 CCATAAATCATCTTTGTAATCATCGTTTAATACATCTTCCAAAGG
444742 CCATAAATCATCTTTGTAATCATCGTTTAATACATCTTCCAAAGG
1 CCATAAATCATCTTTGTAATCATCGTTTAATACATCTTCCAAAGG
444787 TCTTTATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (45 bp):
CCATAAATCATCTTTGTAATCATCGTTTAATACATCTTCCAAAGG
Found at i:453716 original size:13 final size:13
Alignment explanation
Indices: 453698--453722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453688 ATTTGTCTCA
453698 TATTTTTATATTT
1 TATTTTTATATTT
453711 TATTTTTATATT
1 TATTTTTATATT
453723 AAATAATTTG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTATATTT
Found at i:453764 original size:41 final size:41
Alignment explanation
Indices: 453701--453796 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 41
453691 TGTCTCATAT
*
453701 TTTTATATTTTATTTTTATATTA-AATAATTTGAA-TTTATAAA
1 TTTTATA-TTTATTTATATATTATAA-AATTTGAATTTTA-AAA
* * *
453743 TTTTATATTTATTTATGTATTATAAACTTTTAATTTTAAAA
1 TTTTATATTTATTTATATATTATAAAATTTGAATTTTAAAA
453784 TTTTATATTTATT
1 TTTTATATTTATT
453797 CTAGGTAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 35 0.73
42 13 0.27
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (41 bp):
TTTTATATTTATTTATATATTATAAAATTTGAATTTTAAAA
Found at i:454319 original size:15 final size:15
Alignment explanation
Indices: 454296--454329 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
454286 TTATTTGTCT
454296 ATGGAATAT-TTT-A
1 ATGGAATATATTTCA
454309 ATGGAATATATTTCA
1 ATGGAATATATTTCA
454324 ATGGAA
1 ATGGAA
454330 AATGGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 3 0.16
15 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (15 bp):
ATGGAATATATTTCA
Found at i:455809 original size:118 final size:118
Alignment explanation
Indices: 455601--455840 Score: 480
Period size: 118 Copynumber: 2.0 Consensus size: 118
455591 ATGGAATCGA
455601 ATAGCTATTTTGGAAAGTTTGAAGTTATGATGGTTTAGTTTTATATCGATTTAGTACAGATTATG
1 ATAGCTATTTTGGAAAGTTTGAAGTTATGATGGTTTAGTTTTATATCGATTTAGTACAGATTATG
455666 CCTTACGGAATTTATTTTATCATAATTAGATTGTGTTAGTAGAATACTAACAT
66 CCTTACGGAATTTATTTTATCATAATTAGATTGTGTTAGTAGAATACTAACAT
455719 ATAGCTATTTTGGAAAGTTTGAAGTTATGATGGTTTAGTTTTATATCGATTTAGTACAGATTATG
1 ATAGCTATTTTGGAAAGTTTGAAGTTATGATGGTTTAGTTTTATATCGATTTAGTACAGATTATG
455784 CCTTACGGAATTTATTTTATCATAATTAGATTGTGTTAGTAGAATACTAACAT
66 CCTTACGGAATTTATTTTATCATAATTAGATTGTGTTAGTAGAATACTAACAT
455837 ATAG
1 ATAG
455841 TTTGAAAATG
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 122 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (118 bp):
ATAGCTATTTTGGAAAGTTTGAAGTTATGATGGTTTAGTTTTATATCGATTTAGTACAGATTATG
CCTTACGGAATTTATTTTATCATAATTAGATTGTGTTAGTAGAATACTAACAT
Found at i:458718 original size:20 final size:19
Alignment explanation
Indices: 458689--458733 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
458679 ACCATGCTAT
* *
458689 AAATTAATGTTAGAATGTTG
1 AAATTGATGTCAGAATG-TG
*
458709 AAATTGATGTCATAATGTG
1 AAATTGATGTCAGAATGTG
458728 AAATTG
1 AAATTG
458734 GGTCATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (19 bp):
AAATTGATGTCAGAATGTG
Found at i:464020 original size:27 final size:26
Alignment explanation
Indices: 463983--464046 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
463973 AAAGAAAAAT
463983 GAAA-AAAAAAA-AAATAAAAAGAACA
1 GAAAGAAAAAAATAAA-AAAAAGAACA
*
464008 GAAAGAAAGAAAATGAAAAAAAGAACA
1 GAAAGAAA-AAAATAAAAAAAAGAACA
*
464035 AAAATGAAAAAA
1 GAAA-GAAAAAA
464047 TGAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 20 0.61
28 6 0.18
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (26 bp):
GAAAGAAAAAAATAAAAAAAAGAACA
Found at i:464053 original size:27 final size:27
Alignment explanation
Indices: 463998--464053 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
463988 AAAAAAAAAT
*
463998 AAAAAGAACAGAAAGAAAGAAAATGAA
1 AAAAAGAACAAAAAGAAAGAAAATGAA
464025 AAAAAGAACAAAAATG-AA-AAAATGAA
1 AAAAAGAACAAAAA-GAAAGAAAATGAA
464051 AAA
1 AAA
464054 GAAAAAAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.41
27 15 0.56
28 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (27 bp):
AAAAAGAACAAAAAGAAAGAAAATGAA
Found at i:464060 original size:8 final size:8
Alignment explanation
Indices: 463984--464068 Score: 61
Period size: 9 Copynumber: 10.4 Consensus size: 8
463974 AAGAAAAATG
463984 AAAAA-AA
1 AAAAAGAA
*
463991 AAAAA-AT
1 AAAAAGAA
463998 AAAAAGAA
1 AAAAAGAA
*
464006 CAGAAAGAA
1 -AAAAAGAA
464015 AGAAAATGAA
1 A-AAAA-GAA
464025 AAAAAGAA
1 AAAAAGAA
464033 CAAAAATGAA
1 -AAAAA-GAA
*
464043 AAAATG--
1 AAAAAGAA
464049 AAAAAGAA
1 AAAAAGAA
464057 AAAAAGCAA
1 AAAAAG-AA
464066 AAA
1 AAA
464069 GGGCGACTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
6 5 0.08
7 11 0.17
8 12 0.19
9 28 0.44
10 7 0.11
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.05
Consensus pattern (8 bp):
AAAAAGAA
Found at i:464068 original size:24 final size:24
Alignment explanation
Indices: 463984--464068 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 24
463974 AAGAAAAATG
*
463984 AAAAAAAAAAAAAT-AAAAAGAAC
1 AAAAAGAAAAAAATGAAAAAGAAC
*
464007 AGAAAGAAAGAAAATGAAAAAAAGAAC
1 AAAAAGAAA-AAAATG--AAAAAGAAC
464034 AAAAATG-AAAAAATGAAAAAGAA-
1 AAAAA-GAAAAAAATGAAAAAGAAC
*
464057 AAAAAGCAAAAA
1 AAAAAGAAAAAA
464069 GGGCGACTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.02
23 17 0.32
24 13 0.25
26 6 0.11
27 15 0.28
28 1 0.02
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.05
Consensus pattern (24 bp):
AAAAAGAAAAAAATGAAAAAGAAC
Found at i:464934 original size:24 final size:24
Alignment explanation
Indices: 464903--464951 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
464893 TGCCACATAG
*
464903 ATTTGTCCTGAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
*
464927 ATTTGTCCCGAAGGACCTCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
464951 A
1 A
464952 CCTTTGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCGAAGGACCGCGTAGA
Found at i:466467 original size:21 final size:20
Alignment explanation
Indices: 466433--466471 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
466423 AGTTTGGGTA
*
466433 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGATT-AAGAAAGC
*
466454 TTATATAGGATTAAGAAA
1 TTATATAAGATTAAGAAA
466472 ACAAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (20 bp):
TTATATAAGATTAAGAAAGC
Found at i:467636 original size:23 final size:23
Alignment explanation
Indices: 467578--467638 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
467568 TCGGGATAAT
467578 TATGTGGCACTTCAGTGCAAACC
1 TATGTGGCACTTCAGTGCAAACC
** *
467601 TATAAGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCAGTGCAAACC
467624 TATGTGGTC-CTTCAG
1 TATGTGG-CACTTCAG
467639 GTCAATTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGCAAACC
Found at i:474350 original size:21 final size:21
Alignment explanation
Indices: 474324--474373 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
474314 AGTCGAGGGT
474324 TTATGTGGTCATTT-GAGACAA
1 TTATGTGGTC-TTTCGAGACAA
*
474345 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCTTTCGAGACAA
474366 TTATGTGG
1 TTATGTGG
474374 CACTTCAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (21 bp):
TTATGTGGTCTTTCGAGACAA
Found at i:474397 original size:23 final size:23
Alignment explanation
Indices: 474367--474419 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
474357 TCGGGACAAT
474367 TATGTGGCACTTCAGTGCAAACC
1 TATGTGGCACTTCAGTGCAAACC
** *
474390 TATGTGGCACTTTGGTGTAAACC
1 TATGTGGCACTTCAGTGCAAACC
474413 TATGTGG
1 TATGTGG
474420 TCCTTCGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGCAAACC
Found at i:474446 original size:21 final size:21
Alignment explanation
Indices: 474343--474447 Score: 56
Period size: 23 Copynumber: 4.8 Consensus size: 21
474333 CATTTGAGAC
* *
474343 AATTATGTGGTC-TTTCGGGAC
1 AATTATGTGG-CACTTCGGGAT
*
474364 AATTATGTGGCACTTCAGTGCA-
1 AATTATGTGGCACTTC-G-GGAT
* *
474386 AACCTATGTGGCACTTTGGTG-T
1 AA-TTATGTGGCACTTCGG-GAT
*
474408 AAACCTATGTGGTC-CTTCGGGAT
1 -AA-TTATGTGG-CACTTCGGGAT
474431 AATTATGTGGCACTTCG
1 AATTATGTGGCACTTCG
474448 ATACAAATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
20 2 0.03
21 26 0.39
22 7 0.10
23 31 0.46
24 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
AATTATGTGGCACTTCGGGAT
Found at i:480845 original size:24 final size:24
Alignment explanation
Indices: 480799--480847 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
480789 TGCCACAAAG
* **
480799 ATTTGTCTCGAATGACCGTGTAGA
1 ATTTGTCCCGAATGACCACGTAGA
480823 ATTTGTCCCGAATGACCACGTAGA
1 ATTTGTCCCGAATGACCACGTAGA
480847 A
1 A
480848 CCCTCAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (24 bp):
ATTTGTCCCGAATGACCACGTAGA
Found at i:482142 original size:65 final size:64
Alignment explanation
Indices: 482065--482190 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 64
482055 TGCACTAAGG
* * *
482065 GTGCATCGATGCATAAATTGCTTTCAATGTTTCAAACA-AGCCTG-GAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCAATGTTT-AAAAATAG-CTGAG-GTGCATCGATGCATGGT
482128 AT
63 AT
* *
482130 GTGCATTGATGCATAAAATGCATTCGATGTTTAAAAATAGCTGAGGTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCAATGTTTAAAAATAGCTGAGGTGCATCGATGCATGG
482191 CTTATACATC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 23 0.43
65 31 0.57
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCAATGTTTAAAAATAGCTGAGGTGCATCGATGCATGGTAT
Found at i:484685 original size:23 final size:23
Alignment explanation
Indices: 484655--484737 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
484645 TGCATAGACT
484655 AGTGCATCGATGCACATTCAAGG
1 AGTGCATCGATGCACATTCAAGG
*
484678 AGTGCATCGATGCATC-TTC-ATG
1 AGTGCATCGATGCA-CATTCAAGG
*
484700 A-TGTATCGATGCACATTCAAAGG
1 AGTGCATCGATGCACATTC-AAGG
484723 -GATGCATCGATGCAC
1 AG-TGCATCGATGCAC
484738 TATTTAGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 14 0.28
22 3 0.06
23 19 0.38
24 13 0.26
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
AGTGCATCGATGCACATTCAAGG
Found at i:484749 original size:44 final size:42
Alignment explanation
Indices: 484640--484756 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
484630 CGACGAATGT
** *
484640 ATCGATGCATAGACTAGTGCATCGATGCACATTCAAGGAGTGC
1 ATCGATGCATA-TTTAGTGTATCGATGCACATTCAAGGAGTGC
* *
484683 ATCGATGCATCTTCATGATGTATCGATGCACATTCAAAGG-GATGC
1 ATCGATGCATATTTA-G-TGTATCGATGCACATTC-AAGGAG-TGC
484728 ATCGATGCACTATTTAGTGTATCGATGCA
1 ATCGATGCA-TATTTAGTGTATCGATGCA
484757 ATATGCACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 11 0.18
44 29 0.47
45 17 0.27
46 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (42 bp):
ATCGATGCATATTTAGTGTATCGATGCACATTCAAGGAGTGC
Found at i:492228 original size:135 final size:135
Alignment explanation
Indices: 492011--492275 Score: 345
Period size: 135 Copynumber: 2.0 Consensus size: 135
492001 ATGAATAGGG
* * * *
492011 GAATGAATCAACATTTCCAGATCTGATTTTCCCTGAAGAAATAGTGGAACATATCCTCTCTCTTT
1 GAATGAATCAACATTTACAGATCTGATTTTCCCTCAAGAAATAGTGGAACAGATCCTCTATCTTT
* ** *
492076 CCAGATTTGATCTTCCCTGAGTAGTATTCAAACAAGTCTACCTCAATTCAATCTTCCCTGAAGAA
66 CCAGATTTGATCTTCCCTGAGGAACAATCAAACAAGTCTACCTCAATTCAATCTTCCCTGAAGAA
492141 CAATT
131 CAATT
* * * * *
492146 GAATGAATCAATATTTACATATTTGATTTTCCCTCAA-AAAGTTGTGGAACAGATTCC-CTATTT
1 GAATGAATCAACATTTACAGATCTGATTTTCCCTCAAGAAA-TAGTGGAACAGA-TCCTCTATCT
** * *
492209 TTCCAGATTTGATCTTCCCTGAGGAACAATGGAACAAGTCTTCCTCGATTCAATCTTCCCTGAAG
64 TTCCAGATTTGATCTTCCCTGAGGAACAATCAAACAAGTCTACCTCAATTCAATCTTCCCTGAAG
492274 AA
129 AA
492276 AAGTGGAACA
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
134 3 0.03
135 105 0.95
136 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (135 bp):
GAATGAATCAACATTTACAGATCTGATTTTCCCTCAAGAAATAGTGGAACAGATCCTCTATCTTT
CCAGATTTGATCTTCCCTGAGGAACAATCAAACAAGTCTACCTCAATTCAATCTTCCCTGAAGAA
CAATT
Found at i:492266 original size:41 final size:41
Alignment explanation
Indices: 492220--492324 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
492210 TCCAGATTTG
* *
492220 ATCTTCCCTGAGGAACAA-TGGAACAAGTCTTCCTCGATTCA
1 ATCTTCCCTGAAGAA-AAGTGGAACAAGTCTACCTCGATTCA
492261 ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCA
1 ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCA
* * *
492302 ATCTTCCTTGAATAACAGTGGAA
1 ATCTTCCCTGAAGAAAAGTGGAA
492325 TGAATCAACA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.03
41 56 0.97
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (41 bp):
ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCA
Found at i:492328 original size:176 final size:176
Alignment explanation
Indices: 492106--492456 Score: 490
Period size: 176 Copynumber: 2.0 Consensus size: 176
492096 GTAGTATTCA
* * *
492106 AACAAGTCTACCTCAATTCAATCTTCCCTGAAGAACAATTGAATGAATCAATATTTACATATTTG
1 AACAAGTCTACCTCAATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTACAAATTTG
** * * *
492171 ATTTTCCCTCAAAAAGTTGTGGAACAGATTCCCT-ATTTTTCCAGATTTGATCTTCCCTGA-GGA
66 ATTTTCCCTCAAAAAGCAGTGGAACAG-GTCCCTCATTTTTCCAAATTTGATCTTCCCT-ATAGA
** *
492234 ACAATGGAACAAGTCTTCCTCGATTCAATCTTCCCTGAAGAAAAGTGG
129 ACAATGGAACAAGTCTGACTCGATTCAATCTTCCCTAAAGAAAAGTGG
* * * * *
492282 AACAAGTCTACCTCGATTCAATCTTCCTTGAATAACAGTGGAATGAATCAACATTTCCAAATTTG
1 AACAAGTCTACCTCAATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTACAAATTTG
*
492347 ATTTTCCCTCAAAAAGCAGTGGAACAGGTCCCTCCTTTTTCCAAATTTGATCTTCCCTATAGAAC
66 ATTTTCCCTCAAAAAGCAGTGGAACAGGTCCCTCATTTTTCCAAATTTGATCTTCCCTATAGAAC
* * *
492412 AGTGGAACAAGTCTGACTCGATTCAATCTTTCCTAAAGAACAGTG
131 AATGGAACAAGTCTGACTCGATTCAATCTTCCCTAAAGAAAAGTG
492457 AATGAATCAA
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
175 6 0.04
176 147 0.96
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (176 bp):
AACAAGTCTACCTCAATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTACAAATTTG
ATTTTCCCTCAAAAAGCAGTGGAACAGGTCCCTCATTTTTCCAAATTTGATCTTCCCTATAGAAC
AATGGAACAAGTCTGACTCGATTCAATCTTCCCTAAAGAAAAGTGG
Found at i:492400 original size:135 final size:134
Alignment explanation
Indices: 492261--492607 Score: 398
Period size: 134 Copynumber: 2.6 Consensus size: 134
492251 CCTCGATTCA
*
492261 ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCAATCTTCCTTGAATAACAGTGGAAT
1 ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCAATCTTCC-TGAAGAACAGTGGAAT
* * *
492326 GAATCAACATTTCCAAATTTGATTTTCCCTCAAAAAGCAGTGGAACAGGTCCCTC-CTTTTTCCA
65 GAATCAACATTTCCAAATCTGATTTTCCCTCAAAAAGCAGAGGAACAGATCCCTCTCTTTTT-CA
492390 AATTTG
129 AATTTG
* *
492396 ATCTTCCCT-ATAGAACAGTGGAACAAGTCTGA-CTCGATTCAATCTTTCCTAAAGAACAGT-GA
1 ATCTTCCCTGA-AGAAAAGTGGAACAAGTCT-ACCTCGATTCAATC-TTCCTGAAGAACAGTGGA
* * * * * * **
492458 ATGAATCAACATTTCTAGATCTGATTTTTCCTCAATAAGTAGAGGAATAGATCTTTCTCTTTTTC
63 ATGAATCAACATTTCCAAATCTGATTTTCCCTCAAAAAGCAGAGGAACAGATCCCTCTCTTTTTC
**
492523 GTATTTG
128 AAATTTG
* * **
492530 ATCCTCCTTG-AGTAGTAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAACAGTGGAA
1 ATCTTCCCTGAAG-AAAAGTGGAACAAGTCTACCTCGATTCAATCTT-CCTGAAGAACAGTGGAA
* *
492594 TAAATCAACGTTTC
64 TGAATCAACATTTC
492608 TCGATCTTCT
Statistics
Matches: 180, Mismatches: 23, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
133 5 0.03
134 101 0.56
135 69 0.38
136 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (134 bp):
ATCTTCCCTGAAGAAAAGTGGAACAAGTCTACCTCGATTCAATCTTCCTGAAGAACAGTGGAATG
AATCAACATTTCCAAATCTGATTTTCCCTCAAAAAGCAGAGGAACAGATCCCTCTCTTTTTCAAA
TTTG
Found at i:492791 original size:3 final size:3
Alignment explanation
Indices: 492785--492834 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
492775 ATTATTATTA
492785 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
492833 TT
1 TT
492835 ATTATTATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:492839 original size:3 final size:3
Alignment explanation
Indices: 492833--492877 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
492823 GTTGTTGTTG
* *
492833 TTA TTA TTA TGA GTA TTTA TTA TTA TTAA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA TTA TTA T
492878 AAATAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:492865 original size:13 final size:13
Alignment explanation
Indices: 492835--492877 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
492825 TGTTGTTGTT
* *
492835 ATTATTATGAGTA
1 ATTATTATTATTA
*
492848 TTTATTATTATTA
1 ATTATTATTATTA
492861 ATTATTATTATT-
1 ATTATTATTATTA
492873 ATTAT
1 ATTAT
492878 AAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:494442 original size:29 final size:26
Alignment explanation
Indices: 494371--494440 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 26
494361 AGAATCTATT
494371 TTTTATTTATTTTAATTTATCCATGCAA
1 TTTTATTTATTTTAATTTATCCATG--A
494399 TTTTAGTTTATTTTAATTTAGTCCCCATG-
1 TTTTA-TTTATTTTAATTTA-T--CCATGA
494428 TTTTATTTATTTT
1 TTTTATTTATTTT
494441 TATTCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 13 0.34
29 19 0.50
30 1 0.03
32 5 0.13
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTATTTATTTTAATTTATCCATGA
Found at i:495090 original size:129 final size:131
Alignment explanation
Indices: 494889--495204 Score: 368
Period size: 131 Copynumber: 2.4 Consensus size: 131
494879 GAATGACTGC
* * ** * * * * * * *
494889 TTTAAGGCATGAGATGTCAATTATTCTATATTGGAAATAATAACATATTACCGTTTTCTCTCGAG
1 TTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTCCACTCAAA
* * * *
494954 TCAATATT-GATTTTAAAACAG-AATAGTGACATCTC-TCATTTCGATTGGAGTAATAAATGATT
66 TCAATATTCAATTTTAAAA-AGAAATAGTGACATCTCTTCATTTCAATTGGAGTAATAAATAACT
495016 AA
130 AA
* **
495018 TTTAAGGCATGAGAGGTCATTTATTCTCGATCGGAAATCGTTAGATATTATCGTTTCCACTCAAA
1 TTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTCCACTCAAA
* * * * *
495083 TCAATATTCAATTTTAAGATGAAATAGTGATATCTCTTCGTTTCAATTGGGGTAATAAATAACTA
66 TCAATATTCAATTTTAAAAAGAAATAGTGACATCTCTTCATTTCAATTGGAGTAATAAATAACTA
*
495148 T
131 A
* *
495149 TTTAAGGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATAATATCGTTT
1 TTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
495205 TCTCTCTTAA
Statistics
Matches: 155, Mismatches: 29, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
129 60 0.39
130 21 0.14
131 74 0.48
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (131 bp):
TTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTCCACTCAAA
TCAATATTCAATTTTAAAAAGAAATAGTGACATCTCTTCATTTCAATTGGAGTAATAAATAACTA
A
Found at i:496556 original size:15 final size:15
Alignment explanation
Indices: 496536--496578 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
496526 AGAGTTGCTT
496536 TGGTTGTGAGAATGA
1 TGGTTGTGAGAATGA
496551 TGGTTGTGAGAATGA
1 TGGTTGTGAGAATGA
496566 TGGTTGTGAGAAT
1 TGGTTGTGAGAAT
496579 AAGTTAAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.40, T:0.35
Consensus pattern (15 bp):
TGGTTGTGAGAATGA
Found at i:497644 original size:36 final size:36
Alignment explanation
Indices: 497597--497667 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
497587 GGATTAATTA
* *
497597 TTTTCGTCTTTCATGAACGTTGAATTACAATTTGTC
1 TTTTCATCTTTCATGAACCTTGAATTACAATTTGTC
497633 TTTTCATCTTTCATGAACCTTGAATTACAATTTGT
1 TTTTCATCTTTCATGAACCTTGAATTACAATTTGT
497668 AATTGTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (36 bp):
TTTTCATCTTTCATGAACCTTGAATTACAATTTGTC
Found at i:497929 original size:9 final size:9
Alignment explanation
Indices: 497917--498080 Score: 58
Period size: 9 Copynumber: 17.7 Consensus size: 9
497907 TTTATATTAT
497917 TATATACTA
1 TATATACTA
497926 TATATAAACTA
1 TATAT--ACTA
*
497937 TATA-A-TT
1 TATATACTA
*
497944 TATAT-TTA
1 TATATACTA
497952 TA-ATA-T-
1 TATATACTA
497958 TATATACTA
1 TATATACTA
497967 TATATAAACTA
1 TATAT--ACTA
*
497978 TATATATTA
1 TATATACTA
*
497987 TGTATAAACTA
1 --TATATACTA
*
497998 TATAGTTTATTAA
1 TATA---TACT-A
*
498011 TATAAACTA
1 TATATACTA
498020 TATATAAGCTA
1 TATAT-A-CTA
498031 TATAGTA-TA
1 TATA-TACTA
498040 TATATA-TA
1 TATATACTA
*
498048 TATATAATA
1 TATATACTA
498057 TATTATA-TA
1 TA-TATACTA
*
498066 TATAAACTA
1 TATATACTA
*
498075 TGTATA
1 TATATA
498081 TAAACTATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
6 2 0.02
7 11 0.09
8 18 0.15
9 42 0.35
10 7 0.06
11 32 0.27
12 3 0.03
13 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (9 bp):
TATATACTA
Found at i:497952 original size:41 final size:41
Alignment explanation
Indices: 497890--497981 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
497880 AGAAAAATCG
* * *
497890 AAACAATATAGTTTATATTTATATTATTATATACTATATAT
1 AAACTATATAATTTATATTTATAATATTATATACTATATAT
497931 AAACTATATAATTTATATTTATAATATTATATACTATATAT
1 AAACTATATAATTTATATTTATAATATTATATACTATATAT
497972 AAACTATATA
1 AAACTATATA
497982 TATTATGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (41 bp):
AAACTATATAATTTATATTTATAATATTATATACTATATAT
Found at i:498143 original size:13 final size:13
Alignment explanation
Indices: 497902--498478 Score: 101
Period size: 13 Copynumber: 44.5 Consensus size: 13
497892 ACAATATAGT
*
497902 TTATATTTATATTA
1 TTATATATATA-TA
497916 TTATATACTATATA
1 TTATATA-TATATA
*
497930 -TAAACTATATA-A
1 TTATA-TATATATA
*
497942 TTTATATTTATAATA
1 -TTATATATAT-ATA
497957 TTATATACTATATA
1 TTATATA-TATATA
*
497971 -TAAACTATATATA
1 TTATA-TATATATA
*
497984 TTATGTATA-A-A
1 TTATATATATATA
*
497995 CTATATAGT-T-TA
1 TTATATA-TATATA
*
498007 TTA-ATATAAACTA
1 TTATATATATA-TA
498020 -TATATAAGCTATATA
1 TTATAT-A--TATATA
*
498035 GTATATATATATA
1 TTATATATATATA
498048 -TATATA-ATATA
1 TTATATATATATA
*
498059 TTATATATATAAA
1 TTATATATATATA
* * *
498072 CTATGTATATAAA
1 TTATATATATATA
* *
498085 CTATATACAT-T-
1 TTATATATATATA
*
498096 TTATTTATAT-TA
1 TTATATATATATA
498108 TTATATACTATATA
1 TTATATA-TATATA
*
498122 -TAAACTATATATA
1 TTATA-TATATATA
*
498135 TTATGTATAAACTATA
1 TTA--TATATA-TATA
*
498151 TTTTAT-TA-ATA
1 TTATATATATATA
*
498162 -TAAAT-TATATA
1 TTATATATATATA
* * *
498173 TTTTATATGTAAA
1 TTATATATATATA
*
498186 TTATATA-AGA-A
1 TTATATATATATA
498197 TTATAT-T-TA-A
1 TTATATATATATA
* *
498207 --ATATATACATC
1 TTATATATATATA
* *
498218 TTTTATTTATATA
1 TTATATATATATA
*
498231 TTATGTATACTATA
1 TTATATATA-TATA
*
498245 -AAT-TATATATA
1 TTATATATATATA
* *
498256 CTATGTATA-A-A
1 TTATATATATATA
498267 TTATATAGTTTATATA
1 TTATATA---TATATA
* *
498283 GTTA-AAATATAAA
1 -TTATATATATATA
* *
498296 GTATCTA-AGTATA
1 TTATATATA-TATA
* *
498309 TAATATAAAGTATA
1 TTATATATA-TATA
* *
498323 -TATACATATAAA
1 TTATATATATATA
* *
498335 ATATA-AGTATGTA
1 TTATATA-TATATA
*
498348 TATATACATATATA
1 T-TATATATATATA
* *
498362 TATATATATAAATT
1 T-TATATATATATA
* *
498376 TTAGTACAAAGTATA
1 TTA-TATATA-TATA
*
498391 TAAGTATATA-ATA
1 TTA-TATATATATA
* * *
498404 TAAAATATATAAGAA
1 TTATATATAT-A-TA
* *
498419 TTAAATATAAAGTA
1 TTATATATATA-TA
*
498433 -TATATATACATA
1 TTATATATATATA
*
498445 TAATATATATATA
1 TTATATATATATA
498458 TATATATATATATA
1 T-TATATATATATA
*
498472 TAATATA
1 TTATATA
498479 AAGTATATAA
Statistics
Matches: 412, Mismatches: 89, Indels: 125
0.66 0.14 0.20
Matches are distributed among these distances:
8 4 0.01
9 1 0.00
10 9 0.02
11 45 0.11
12 51 0.12
13 157 0.38
14 90 0.22
15 34 0.08
16 18 0.04
17 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (13 bp):
TTATATATATATA
Found at i:498173 original size:11 final size:11
Alignment explanation
Indices: 497935--498213 Score: 81
Period size: 11 Copynumber: 26.4 Consensus size: 11
497925 ATATATAAAC
*
497935 TATATAATTTA
1 TATATAAATTA
*
497946 TATTTATAA-TA
1 TATATA-AATTA
* *
497957 T-TATATACTA
1 TATATAAATTA
*
497967 TATATAAACTA
1 TATATAAATTA
497978 TATAT--ATTA
1 TATATAAATTA
* *
497987 TGTATAAACTA
1 TATATAAATTA
**
497998 TATAGTTTATTA
1 TATA-TAAATTA
*
498010 -ATATAAACTA
1 TATATAAATTA
**
498020 TATATAAGCTA
1 TATATAAATTA
*
498031 TATAGTATATATA
1 TATA-TAAAT-TA
* *
498044 TATATATATAA
1 TATATAAATTA
*
498055 TATAT-TA-TA
1 TATATAAATTA
*
498064 TATATAAACTATG
1 TATATAAA-T-TA
*
498077 TATATAAA--C
1 TATATAAATTA
* *
498086 TATATACATTT
1 TATATAAATTA
* *
498097 TATTTATATTA
1 TATATAAATTA
* *
498108 T-TATATACTA
1 TATATAAATTA
*
498118 TATATAAACTA
1 TATATAAATTA
498129 TATAT--ATTA
1 TATATAAATTA
* *
498138 TGTATAAACTA
1 TATATAAATTA
**
498149 TAT-TTTATTA
1 TATATAAATTA
498159 -ATATAAATTA
1 TATATAAATTA
*
498169 TATAT--TTTA
1 TATATAAATTA
*
498178 TATGTAAATTA
1 TATATAAATTA
498189 TATA-AGAATTA
1 TATATA-AATTA
*
498200 TATTTAAA-TA
1 TATATAAATTA
498210 TATA
1 TATA
498214 CATCTTTTAT
Statistics
Matches: 197, Mismatches: 47, Indels: 49
0.67 0.16 0.17
Matches are distributed among these distances:
9 37 0.19
10 36 0.18
11 96 0.49
12 13 0.07
13 15 0.08
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (11 bp):
TATATAAATTA
Done.