Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001277.1 Hibiscus syriacus cultivar Beakdansim tig00002507_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: 391084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:279831 original size:20 final size:20
Alignment explanation
Indices: 279783--279835 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
279773 TAATACAAAA
* *
279783 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
279803 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
279823 TCGCAACGCGATT
1 TCGCAACGCGATT
279836 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:280386 original size:19 final size:19
Alignment explanation
Indices: 280348--280414 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
280338 TTCGAGAATG
*
280348 AAAATCGTAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
280368 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
280387 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
280406 AAAATCGCA
1 AAAATCGCA
280415 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:280432 original size:19 final size:19
Alignment explanation
Indices: 280410--280574 Score: 116
Period size: 19 Copynumber: 9.1 Consensus size: 19
280400 GAAACAAAAA
*
280410 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
280429 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
280448 TCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
280467 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
280481 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
280500 TCGCGTTTCG--GTTC---
1 TCGCGTTGCGATTTTCATT
* **
280514 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
280533 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
280553 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
280573 TC
1 TC
280575 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
14 17 0.15
16 4 0.04
17 5 0.04
19 54 0.48
20 31 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:280504 original size:33 final size:33
Alignment explanation
Indices: 280462--280549 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
280452 GTTACGATTT
280462 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* * *
280495 TCATTTCGCGTTTCGGTTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
280528 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
280550 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 36 0.73
34 13 0.27
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:280551 original size:20 final size:20
Alignment explanation
Indices: 280517--280574 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
280507 TCGGTTCTCT
**
280517 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
280537 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
280557 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
280575 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:282427 original size:91 final size:90
Alignment explanation
Indices: 282264--282448 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
282254 TAGATTGCTT
282264 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTA-TT
282329 GTCTTTTTGTTTTGTCTTTTGGTTGA
65 GTCTTTTTGTTTTGTCTTTTGGTTGA
**
282355 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATACTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGT-T-TA--TTAACACTGTGAAGTTAGT
*
282420 ATT-TTTTTTTGTTTTGTCTTTTGGTTGA
62 ATTGTCTTTTTGTTTTGTCTTTTGGTTGA
282448 A
1 A
282449 AGTTTGAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 37 0.43
92 1 0.01
93 27 0.31
94 2 0.02
95 20 0.23
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (90 bp):
AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTG
TCTTTTTGTTTTGTCTTTTGGTTGA
Found at i:282741 original size:42 final size:41
Alignment explanation
Indices: 282670--282757 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
282660 GACTCGCCTG
* *
282670 TCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTT-AAGAGGCCCCTA
* * * * *
282712 TCATTCCTCGAGAGTCCCCTCCCACCGTTAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTAAGAGGCCCCTA
282753 TCATC
1 TCATC
282758 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.24
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTAAGAGGCCCCTA
Found at i:286102 original size:12 final size:12
Alignment explanation
Indices: 286085--286109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
286075 TCTTCGGGGA
286085 CTTTTTCTTCTT
1 CTTTTTCTTCTT
286097 CTTTTTCTTCTT
1 CTTTTTCTTCTT
286109 C
1 C
286110 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:286320 original size:25 final size:25
Alignment explanation
Indices: 286284--286339 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
286274 CTGAAACATA
*
286284 ATCAAAAATCCGAGTATTGACCAAT
1 ATCAAAAATCCGAGTATTGACCAAG
* *
286309 ATCAAAAGTCCGGGTATTGACCAAG
1 ATCAAAAATCCGAGTATTGACCAAG
286334 ATCAAA
1 ATCAAA
286340 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (25 bp):
ATCAAAAATCCGAGTATTGACCAAG
Found at i:287385 original size:19 final size:19
Alignment explanation
Indices: 287327--287396 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
287317 ATTCATTTGA
*
287327 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGC-GAAATGG
* *
287347 CTATTGCAACGTGAAAATGG
1 CTATCGCAACGCG-AAATGG
*
287367 CTATTGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
287386 CTATCGCAACG
1 CTATCGCAACG
287397 ATAAAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:287463 original size:19 final size:19
Alignment explanation
Indices: 287422--287486 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
287412 GAAATGAAAA
287422 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
287438 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
287455 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
287474 TCGCATTGCGATT
1 TCGCATTGCGATT
287487 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:287517 original size:20 final size:20
Alignment explanation
Indices: 287492--287530 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
287482 CGATTCTCTC
287492 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
287512 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
287531 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:287632 original size:14 final size:14
Alignment explanation
Indices: 287613--287649 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
287603 CATCAATTAA
287613 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
287627 ACAAATCATCTTTT
1 ACAAATCAACATTT
287641 ACAAATCAA
1 ACAAATCAA
287650 TTATACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:289573 original size:19 final size:20
Alignment explanation
Indices: 289518--289585 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
289508 GAAACTTAAA
*
289518 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAGAAATGACT
* *
289538 ATCGTAACGCAGAAATGGCT
1 ATCGCAACGCAGAAATGACT
* **
289558 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCAGAAATGACT
289577 ATCGCAACG
1 ATCGCAACG
289586 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAGAAATGACT
Found at i:289593 original size:14 final size:14
Alignment explanation
Indices: 289574--289613 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
289564 ATGCGAAATG
289574 AAAATCGCAACGAC
1 AAAATCGCAACGAC
289588 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
289602 AAAACCGCAACG
1 AAAATCGCAACG
289614 CGAAACACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:289666 original size:14 final size:14
Alignment explanation
Indices: 289647--289704 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
289637 TTTCATTTCG
289647 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
*
289661 CGTTGCAATTTCATTT
1 CGTTGCGATTT--TTT
*
289677 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
289693 CGTTGCGATTTT
1 CGTTGCGATTTT
289705 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 9 0.24
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:289711 original size:33 final size:33
Alignment explanation
Indices: 289630--289717 Score: 142
Period size: 32 Copynumber: 2.7 Consensus size: 33
289620 ACAAATCGCA
* *
289630 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
289663 TTGC-AATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
289695 TTGCGATTTTCATTTCGCATTGC
1 TTGCGATTTTCATTTCGCATTGC
289718 AATAGCCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 29 0.58
33 21 0.42
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:289742 original size:20 final size:19
Alignment explanation
Indices: 289705--289759 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
289695 TTGCGATTTT
* *
289705 CATTTCGCATTGCAATAGC
1 CATTTCGCGTTGCGATAGC
*
289724 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
289744 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
289760 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:290267 original size:18 final size:18
Alignment explanation
Indices: 290241--290285 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
290231 GTCGATCAGA
*
290241 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
290259 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
290277 TGATGGCTC
1 TGATGGCTC
290286 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:291630 original size:20 final size:20
Alignment explanation
Indices: 291605--291642 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
291595 AATAGTTTCT
291605 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
291625 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
291643 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:291931 original size:22 final size:22
Alignment explanation
Indices: 291904--291947 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
291894 GATGGAGATA
291904 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
291926 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
291948 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:292161 original size:20 final size:20
Alignment explanation
Indices: 292136--292187 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
292126 ATTATGTATT
292136 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
292156 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
292176 ATCTCGTTGCGA
1 ATCGCGTTGCGA
292188 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:294977 original size:3 final size:3
Alignment explanation
Indices: 294969--295003 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
294959 TGAGAAAGCT
294969 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
295004 TGATGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:295008 original size:3 final size:3
Alignment explanation
Indices: 295002--295028 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
294992 AGAAGAAGAA
295002 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
295029 TTCTTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:296452 original size:21 final size:21
Alignment explanation
Indices: 296428--296477 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
296418 CACATAAGTG
*
296428 CCACATATTTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
296449 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCCGAAGGA
296470 CCACATAA
1 CCACATAA
296478 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:302338 original size:11 final size:13
Alignment explanation
Indices: 302314--302371 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
302304 TAAAATAAAT
302314 AAAATATAATTTA
1 AAAATATAATTTA
*
302327 AAAATAT-ATTAA
1 AAAATATAATTTA
*
302339 AAAAT-TAGTTTA
1 AAAATATAATTTA
*
302351 AAAA-ATGAAGTTA
1 AAAATAT-AATTTA
302364 AAAA-ATAA
1 AAAATATAA
302372 CCTTGTAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 1 0.03
12 19 0.51
13 17 0.46
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (13 bp):
AAAATATAATTTA
Found at i:302341 original size:12 final size:13
Alignment explanation
Indices: 302314--302370 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
302304 TAAAATAAAT
* *
302314 AAAATATAATTTA
1 AAAATATAGTTAA
302327 AAAATATA-TTAA
1 AAAATATAGTTAA
302339 AAAAT-TAGTTTAA
1 AAAATATAG-TTAA
302352 AAAATGA-AGTTAA
1 AAAAT-ATAGTTAA
302365 AAAATA
1 AAAATA
302371 ACCTTGTAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 2 0.05
12 9 0.23
13 26 0.67
14 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (13 bp):
AAAATATAGTTAA
Found at i:303807 original size:10 final size:10
Alignment explanation
Indices: 303792--303817 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
303782 TTATGAAGAA
303792 TTGATGAAAT
1 TTGATGAAAT
303802 TTGATGAAAT
1 TTGATGAAAT
303812 TTGATG
1 TTGATG
303818 TTGTGATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (10 bp):
TTGATGAAAT
Found at i:311970 original size:29 final size:31
Alignment explanation
Indices: 311928--311991 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
311918 ACAAGTCTTA
* * *
311928 GAAAATTTTGGGGACC-ATTTG-TAATTTTT
1 GAAAAGTTTGGGGACTAATTTGATAATTTTG
311957 GAAAAGTTTGGGGACTAATTTGATAATTTTG
1 GAAAAGTTTGGGGACTAATTTGATAATTTTG
311988 GAAA
1 GAAA
311992 CATTGTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
30 5 0.17
31 11 0.37
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (31 bp):
GAAAAGTTTGGGGACTAATTTGATAATTTTG
Found at i:313539 original size:2 final size:2
Alignment explanation
Indices: 313532--313563 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
313522 GGATTTTAAC
313532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
313564 TTGAAGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:316754 original size:67 final size:67
Alignment explanation
Indices: 316645--316778 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
316635 CGAAGTGTTT
* * * *
316645 ACACATAAGGTCGTGCTCACCATATGCACTAAGTGTCTTTACACACTATAGCGCTATCCCAAATA
1 ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
316710 TG
66 TG
* * * *
316712 ACACACAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTATCTCGAATA
1 ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
316777 TG
66 TG
316779 CAGTGTACTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (67 bp):
ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
TG
Found at i:318209 original size:19 final size:20
Alignment explanation
Indices: 318185--318228 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
318175 AAACAATTCG
*
318185 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
318204 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
318224 ATTTC
1 ATTTC
318229 TAGAATAGTC
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:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:318412 original size:18 final size:19
Alignment explanation
Indices: 318377--318413 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
318367 CACGGAATGT
318377 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
318397 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
318414 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:320037 original size:29 final size:29
Alignment explanation
Indices: 319969--320038 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
319959 AGTCAAAACA
319969 TCTAAAATTTTAAAATTACACTTTAAGTC
1 TCTAAAATTTTAAAATTACACTTTAAGTC
*** * *
319998 -CTTATTTTTTTAAAATTACCCTTTTAGTC
1 TC-TAAAATTTTAAAATTACACTTTAAGTC
*
320027 TCTAAACTTTTA
1 TCTAAAATTTTA
320039 CAAACTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.49
Consensus pattern (29 bp):
TCTAAAATTTTAAAATTACACTTTAAGTC
Found at i:320867 original size:10 final size:10
Alignment explanation
Indices: 320852--320877 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
320842 TTATGAAGAA
320852 TTGATGAAAT
1 TTGATGAAAT
320862 TTGATGAAAT
1 TTGATGAAAT
320872 TTGATG
1 TTGATG
320878 TTGTGATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (10 bp):
TTGATGAAAT
Found at i:329087 original size:29 final size:31
Alignment explanation
Indices: 329045--329108 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
329035 ACAAGTCTTA
* * *
329045 GAAAATTTTGGGGACC-ATTTG-TAATTTTT
1 GAAAAGTTTGGGGACTAATTTGATAATTTTG
329074 GAAAAGTTTGGGGACTAATTTGATAATTTTG
1 GAAAAGTTTGGGGACTAATTTGATAATTTTG
329105 GAAA
1 GAAA
329109 CATTGTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
30 5 0.17
31 11 0.37
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (31 bp):
GAAAAGTTTGGGGACTAATTTGATAATTTTG
Found at i:330663 original size:2 final size:2
Alignment explanation
Indices: 330656--330704 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
330646 ATTTTAACAT
330656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
330698 TA TA TA T
1 TA TA TA T
330705 TTGAAGAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:333900 original size:67 final size:67
Alignment explanation
Indices: 333791--333924 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
333781 CGAAGTGTTT
* * * *
333791 ACACATAAGGTCGTGCTCACCATATGCACTAAGTGTCTTTACACACTATAGCGCTATCCCAAATA
1 ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
333856 TG
66 TG
* * * *
333858 ACACACAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTATCTCGAATA
1 ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
333923 TG
66 TG
333925 CAGTGTACTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (67 bp):
ACACACAAGGTCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
TG
Found at i:335358 original size:19 final size:20
Alignment explanation
Indices: 335334--335377 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
335324 AAACAATTCG
*
335334 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
335353 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
335373 ATTTC
1 ATTTC
335378 TAGAATAGTC
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:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:335561 original size:18 final size:19
Alignment explanation
Indices: 335526--335562 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
335516 CACGGAATGT
335526 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
335546 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
335563 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:337186 original size:29 final size:29
Alignment explanation
Indices: 337118--337187 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
337108 AGTCAAAACA
337118 TCTAAAATTTTAAAATTACACTTTAAGTC
1 TCTAAAATTTTAAAATTACACTTTAAGTC
*** * *
337147 -CTTATTTTTTTAAAATTACCCTTTTAGTC
1 TC-TAAAATTTTAAAATTACACTTTAAGTC
*
337176 TCTAAACTTTTA
1 TCTAAAATTTTA
337188 CAAACTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.49
Consensus pattern (29 bp):
TCTAAAATTTTAAAATTACACTTTAAGTC
Found at i:344405 original size:21 final size:22
Alignment explanation
Indices: 344387--344483 Score: 83
Period size: 23 Copynumber: 4.4 Consensus size: 22
344377 TATCGAAGTG
344387 CCACATA-TTTGTCCTGAAGCA
1 CCACATAGTTTGTCCTGAAGCA
* *
344408 CCACATAGGTTTGTCCTAAAGGA
1 CCACATA-GTTTGTCCTGAAGCA
**
344431 CCAC-TAGTTTTGTCCCAAATG-A
1 CCACATAG-TTTGTCCTGAA-GCA
* *
344453 CCACATAGTTTTGTCCCGAAGGA
1 CCACATAG-TTTGTCCTGAAGCA
344476 CCACATAG
1 CCACATAG
344484 AACACTCGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.12
22 18 0.27
23 40 0.61
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (22 bp):
CCACATAGTTTGTCCTGAAGCA
Found at i:344445 original size:22 final size:23
Alignment explanation
Indices: 344407--344483 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
344397 GTCCTGAAGC
* *
344407 ACCACATAGGTTTGTCCTAAAGG
1 ACCACATAGTTTTGTCCCAAAGG
*
344430 ACCAC-TAGTTTTGTCCCAAATG
1 ACCACATAGTTTTGTCCCAAAGG
*
344452 ACCACATAGTTTTGTCCCGAAGG
1 ACCACATAGTTTTGTCCCAAAGG
344475 ACCACATAG
1 ACCACATAG
344484 AACACTCGAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 19 0.40
23 29 0.60
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (23 bp):
ACCACATAGTTTTGTCCCAAAGG
Found at i:345178 original size:19 final size:19
Alignment explanation
Indices: 345144--345205 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
345134 TATTGTATGT
*
345144 ATACCTTCCTCTTGGTATCG
1 ATACCTACC-CTTGGTATCG
345164 ATACCTACCCTTGGTATCG
1 ATACCTACCCTTGGTATCG
*
345183 ATACCTACCCTTCGTATCG
1 ATACCTACCCTTGGTATCG
345202 ATAC
1 ATAC
345206 GTACACCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 32 0.80
20 8 0.20
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (19 bp):
ATACCTACCCTTGGTATCG
Found at i:345225 original size:39 final size:39
Alignment explanation
Indices: 345144--345225 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
345134 TATTGTATGT
* * **
345144 ATACCTTCCTCTTGGTATCGATACCTACCCTTGGTATCG
1 ATACCTACCTCTTCGTATCGATACCTACCCTCAGTATCG
* *
345183 ATACCTACC-CTTCGTATCGATACGTACACCTCAGTATTG
1 ATACCTACCTCTTCGTATCGATACCTAC-CCTCAGTATCG
345222 ATAC
1 ATAC
345226 TTCTTTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (39 bp):
ATACCTACCTCTTCGTATCGATACCTACCCTCAGTATCG
Found at i:346395 original size:71 final size:71
Alignment explanation
Indices: 346256--346404 Score: 153
Period size: 71 Copynumber: 2.1 Consensus size: 71
346246 TTATAATTTA
* * * * * ** *
346256 ATAATT-ATATATAACATTACAAATTATTTCTTTCATTAAC-TACAATTTAATATTATATAAT-T
1 ATAATTAATAAATAAAATTAAAAATTATTT-TTTCATTAACAAAAAATAAAATA-TATAAAATAT
346318 AT-TAAATT
64 -TGTAAATT
* *
346326 ATAATTAATAAATAAAATTAAGAATTATTTTTTAATTAACAAAAAATAAAATATATAAAATATTG
1 ATAATTAATAAATAAAATTAAAAATTATTTTTTCATTAACAAAAAATAAAATATATAAAATATTG
346391 TAAATT
66 TAAATT
346397 ATAATTAA
1 ATAATTAA
346405 GAACTATTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
70 23 0.35
71 42 0.65
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (71 bp):
ATAATTAATAAATAAAATTAAAAATTATTTTTTCATTAACAAAAAATAAAATATATAAAATATTG
TAAATT
Found at i:346497 original size:75 final size:72
Alignment explanation
Indices: 346409--346604 Score: 222
Period size: 75 Copynumber: 2.7 Consensus size: 72
346399 AATTAAGAAC
* * * *
346409 TATTTATTTCATTAATAAAAATTAAAAATATGTAAAAACT-TCTGTAAATTATTGTTAATAAATA
1 TATTTCTTCCATTAA-AAAAATTAAAAATATATAAAAACTAT-TGTAAATTATAGTTAATAAA-A
346473 AAAATAAAAAT
63 AAAA-AAAAAT
* *
346484 TATTTCTTCCATTAACAAAAATAAAAAATATAT-AAAACTATTGTAATTTATAGTTAATAAAAAA
1 TATTTCTTCCATTAA-AAAAATTAAAAATATATAAAAACTATTGTAAATTATAGTTAATAAAAAA
*
346548 TAAAAAAT
65 AAAAAAAT
* * *
346556 AATTTCTTCC-TT-AAAAAATTTAAAATATATAAAAA-TGTTGTAAATTATA
1 TATTTCTTCCATTAAAAAAATTAAAAATATATAAAAACTATTGTAAATTATA
346605 TTCAAATATG
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
69 27 0.25
70 5 0.05
71 2 0.02
72 15 0.14
73 4 0.04
74 24 0.23
75 29 0.27
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (72 bp):
TATTTCTTCCATTAAAAAAATTAAAAATATATAAAAACTATTGTAAATTATAGTTAATAAAAAAA
AAAAAAT
Found at i:346586 original size:71 final size:72
Alignment explanation
Indices: 346425--346604 Score: 208
Period size: 74 Copynumber: 2.5 Consensus size: 72
346415 TTTCATTAAT
* * * *
346425 AAAAATTAAAAATATGTAAAAACTTCTGTAAATTATTGTTAATAAATAAAAATAAAAATTATTTC
1 AAAAATTTAAAATATATAAAAACTT-TGTAAATTATAGTTAATAAATAAAAATAAAAATAATTTC
346490 TTCCATTA
65 TTCCATTA
* * * *
346498 ACAAAA-ATAAAAAATATATAAAACTATTGTAATTTATAGTTAATAAA-AAATA-AAAAATAATT
1 A-AAAATTTAAAATATATA-AAAACT-TTGTAAATTATAGTTAATAAATAAAAATAAAAATAATT
346560 TCTTCC-TTA
63 TCTTCCATTA
346569 AAAAATTTAAAATATATAAAAA-TGTTGTAAATTATA
1 AAAAATTTAAAATATATAAAAACT-TTGTAAATTATA
346605 TTCAAATATG
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
69 12 0.13
70 8 0.09
71 14 0.15
72 15 0.16
73 13 0.14
74 28 0.31
75 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (72 bp):
AAAAATTTAAAATATATAAAAACTTTGTAAATTATAGTTAATAAATAAAAATAAAAATAATTTCT
TCCATTA
Found at i:346597 original size:69 final size:73
Alignment explanation
Indices: 346418--346604 Score: 222
Period size: 69 Copynumber: 2.6 Consensus size: 73
346408 CTATTTATTT
* * *
346418 CATTAATAAAAATTAAAAATATGTAAAAACTTCTGTAAATTATTGTTAATAAATAAAAATAAAAA
1 CATTAACAAAAATTAAAAATATATAAAAA-TT-TGTAAATTATAGTTAATAAATAAAAATAAAAA
*
346483 TTATTTCTTC
64 TAATTTCTTC
* * * *
346493 CATTAACAAAAATAAAAAATATATAAAACTATTGTAATTTATAGTTAATAAA-AAATA-AAAAAT
1 CATTAACAAAAATTAAAAATATATAAAAAT-TTGTAAATTATAGTTAATAAATAAAAATAAAAAT
346556 AATTTCTTC
65 AATTTCTTC
*
346565 C-TT-A-AAAAATTTAAAATATATAAAAATGTTGTAAATTATA
1 CATTAACAAAAATTAAAAATATATAAAAAT-TTGTAAATTATA
346605 TTCAAATATG
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
69 31 0.32
70 1 0.01
71 2 0.02
72 15 0.15
73 4 0.04
74 19 0.19
75 26 0.27
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (73 bp):
CATTAACAAAAATTAAAAATATATAAAAATTTGTAAATTATAGTTAATAAATAAAAATAAAAATA
ATTTCTTC
Found at i:347825 original size:30 final size:30
Alignment explanation
Indices: 347766--347844 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
347756 AAATGATACG
* *
347766 CTCTCAACCCGTAAACAT--TACATCAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
*
347794 CTCTCAACCCGAAAACATCACACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
347824 CTCTCAACCCGTAAACATCAC
1 CTCTCAACCCGTAAACATCAC
347845 CCGATAATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.38
30 28 0.62
ACGTcount: A:0.38, C:0.39, G:0.04, T:0.19
Consensus pattern (30 bp):
CTCTCAACCCGTAAACATCACACAACAATC
Found at i:347931 original size:18 final size:16
Alignment explanation
Indices: 347899--347931 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
347889 CATTGTAAGG
347899 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
347915 TAATATTTTTT-ATATA
1 TAAT-TTTTTTAATATA
347931 T
1 T
347932 GATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:353680 original size:28 final size:28
Alignment explanation
Indices: 353649--353734 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
353639 TTCTAAAAAT
*
353649 ATTAATAATTACAA-AAATT-AATATATAA
1 ATTAATAA-TA-AATAAATTAAATAAATAA
353677 ATTAATAATAAATAAATTAAATAAATAA
1 ATTAATAATAAATAAATTAAATAAATAA
* * *
353705 ATTATTACT-AATAATTTAAATTAAAATAA
1 ATTAATAATAAATAAATTAAA-T-AAATAA
353734 A
1 A
353735 ATTTAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.04
27 17 0.34
28 24 0.48
29 7 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
ATTAATAATAAATAAATTAAATAAATAA
Found at i:353701 original size:13 final size:13
Alignment explanation
Indices: 353663--353708 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
353653 ATAATTACAA
*
353663 AAATT-AATATAT
1 AAATTAAATAAAT
353675 AAATTAATAATAAAT
1 AAATT-A-AATAAAT
353690 AAATTAAATAAAT
1 AAATTAAATAAAT
353703 AAATTA
1 AAATTA
353709 TTACTAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 13 0.43
14 1 0.03
15 11 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATTAAATAAAT
Found at i:354012 original size:21 final size:22
Alignment explanation
Indices: 353988--354029 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
353978 TTAATAGAAT
353988 AGGATAGAGG-GTGTGAACGGG
1 AGGATAGAGGAGTGTGAACGGG
* *
354009 AGGATGGGGGAGTGTGAACGG
1 AGGATAGAGGAGTGTGAACGG
354030 TCCAGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.55, T:0.14
Consensus pattern (22 bp):
AGGATAGAGGAGTGTGAACGGG
Found at i:356596 original size:2 final size:2
Alignment explanation
Indices: 356589--356622 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
356579 TAAAATAGTC
356589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
356623 TTATGGGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359136 original size:54 final size:57
Alignment explanation
Indices: 359041--359159 Score: 149
Period size: 55 Copynumber: 2.2 Consensus size: 57
359031 TTGGATAAAT
* ** *
359041 TTAGCTT-TTTCGAAAAGATTCATTTACAATTATCAATAAACCCCT-AAACTTAGGC
1 TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAATAAACCCCTAAAAATTAGGC
359096 TTAGCTTCTTTC-AAAA-ATTCATTTAAAAACATC-ATGAAACCCCTAAAAATTAGGC
1 TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAAT-AAACCCCTAAAAATTAGGC
*
359151 TTAGTTTCT
1 TTAGCTTCT
359160 AAAAATCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
53 2 0.04
54 22 0.39
55 28 0.50
56 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (57 bp):
TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAATAAACCCCTAAAAATTAGGC
Found at i:359389 original size:42 final size:42
Alignment explanation
Indices: 359308--359456 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 42
359298 GCCCGAAGGT
* * * *
359308 CTTATGGATCGCCCG-AGGTACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATAGCCCGAAGG-ACTTAAGCATCATGCTCGAAAGA
* *
359349 CTTATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATAGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
* * ** *
359391 CTTACT-GATGGCCCAAAGGACTTACTCATCATGCTCAAAAGA
1 CTTA-TAGATAGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
359433 CTTA-ATGATAGCCCGAAGGACTTA
1 CTTATA-GATAGCCCGAAGGACTTA
359457 TGCTGATTCG
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 15 0.17
42 72 0.82
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
CTTATAGATAGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:359434 original size:22 final size:22
Alignment explanation
Indices: 359375--359436 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
359365 AGGATTTAAG
*
359375 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCAAAAGACTTACT
* * * *
359397 GAT--GGCCCAAAGGACTTACT
1 CATCATGCTCAAAAGACTTACT
359417 CATCATGCTCAAAAGACTTA
1 CATCATGCTCAAAAGACTTA
359437 ATGATAGCCC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 15 0.52
22 14 0.48
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (22 bp):
CATCATGCTCAAAAGACTTACT
Found at i:359635 original size:85 final size:85
Alignment explanation
Indices: 359519--359687 Score: 268
Period size: 85 Copynumber: 2.0 Consensus size: 85
359509 GTGAGGCATT
* * * *
359519 GCTGATTCGAAGTATTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTAT
1 GCTGATTCGAAGTAGTGTGAATCGAGAAAAGGAAACGTTGAAAACATCTTGCCCAAAGGTCTTAT
*
359584 GGATGGCCCGAAGGACTTAA
66 GGATGGCACGAAGGACTTAA
*
359604 GCTGATTCGAAGT-GTGTGAATCGAGAAAAAGGAAACGTTGAAAACATCTTGCCTAAAGGTCTTA
1 GCTGATTCGAAGTAGTGTGAATCGAG-AAAAGGAAACGTTGAAAACATCTTGCCCAAAGGTCTTA
359668 TGGATGGCACGAAGGACTTA
65 TGGATGGCACGAAGGACTTA
359688 TCATCTTGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 11 0.14
85 66 0.86
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (85 bp):
GCTGATTCGAAGTAGTGTGAATCGAGAAAAGGAAACGTTGAAAACATCTTGCCCAAAGGTCTTAT
GGATGGCACGAAGGACTTAA
Found at i:360010 original size:52 final size:53
Alignment explanation
Indices: 359814--360062 Score: 234
Period size: 52 Copynumber: 4.6 Consensus size: 53
359804 TTCTTAGTTG
* * * *
359814 TCAAGAAACCCCTAAAAATTACGCTTACCTTCCTTTTAAAAACTCTTTTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATTAGGCTTA-GTTTC-TTT-AAAACTCATTTG-AAA--A-CA
* * *
359874 TCAAGAAACCCCTAAAAATCAGGCTTAGTTTC-TAAAAACTCATTT-AAAAAA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACA
* * * *
359925 TCAAGAAATCCTTAAAAATTAGGCTTAATTTCTTTAAAATTCATTTGAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACA
* * * * * *
359978 TTAAGAAACCCCT-AAAATTAGGTTTAGCTTCTTTCAAATTCATTTAAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACA
* * *
360030 TCGAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
360063 AAAAATCTTT
Statistics
Matches: 159, Mismatches: 27, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
51 29 0.18
52 57 0.36
53 31 0.19
54 3 0.02
56 10 0.06
57 1 0.01
59 3 0.02
60 25 0.16
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (53 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACA
Found at i:360118 original size:39 final size:39
Alignment explanation
Indices: 360064--360146 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
360054 TTAGTTTCTA
* * * * *
360064 AAAATCTTTTGTTTCGAGCGAAACTATCTTAAGTGAGAT
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
* *
360103 AAAATCTTCTATTTCGAGTGAAACTGTCTAAAGGGAGAC
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
360142 AAAAT
1 AAAAT
360147 TTGTTTCAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (39 bp):
AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
Found at i:360219 original size:35 final size:36
Alignment explanation
Indices: 360122--360269 Score: 217
Period size: 36 Copynumber: 4.1 Consensus size: 36
360112 TATTTCGAGT
*
360122 GAAACTGTCTAAAGGGAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
* * *
360158 AAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
* * *
360194 GAAATTG-CTAAAGAGAGACACAATTTGTTTGAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
*
360229 GAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
360265 GAAAC
1 GAAAC
360270 GTTCTCAAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
35 31 0.32
36 67 0.68
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.24
Consensus pattern (36 bp):
GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
Found at i:360220 original size:71 final size:71
Alignment explanation
Indices: 360130--360268 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
360120 GTGAAACTGT
* * * *
360130 CTAAAGGGAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGG
1 CTAAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGG
360195 AAATTG
66 AAATTG
* * *
360201 CTAAAGAGAGACACAATTTGTTTGAAGGGAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGG
1 CTAAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGG
360266 AAA
66 AAA
360269 CGTTCTCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (71 bp):
CTAAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGG
AAATTG
Found at i:360333 original size:65 final size:65
Alignment explanation
Indices: 360229--360398 Score: 243
Period size: 65 Copynumber: 2.6 Consensus size: 65
360219 TGTTTGAAGG
* * * *
360229 GAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACGT-TCTCAAAGTTTATTTTTCAAG
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTAT-TCAAAGTTTATATTTCAAG
360293 A
65 A
* * *
360294 GAAACTATCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
* *
360359 GAAACTGTTTCAAGGGAGACAAAAGTAGTTTCAAGGGAAA
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAA
360399 ATATCTTAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 92 0.99
66 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.27
Consensus pattern (65 bp):
GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
Found at i:360391 original size:101 final size:102
Alignment explanation
Indices: 360286--360484 Score: 253
Period size: 101 Copynumber: 2.0 Consensus size: 102
360276 AAAGTTTATT
* * * * *
360286 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTT-AAAGGGAAA-CGTATTCAAAG-TTT
1 TTTCAAGAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAA-AGAAATAG-ATTCAAAGATTT
* *
360348 AT-ATTTCAAGAGAAACTGTTTCAAGGGAGACAAAAGTAG
64 -TGATTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTAG
* *
360387 TTTCAAGGGAAAATATCTTAAGAGAGACAAAATTTATTTCAAAAGAAATAGATTCAAAGATTTTG
1 TTTCAAGAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAAAGAAATAGATTCAAAGATTTTG
*
360452 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
66 ATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
360485 CTTTGTTTCG
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
101 47 0.56
102 37 0.44
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.27
Consensus pattern (102 bp):
TTTCAAGAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAAAGAAATAGATTCAAAGATTTTG
ATTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTAG
Found at i:360789 original size:73 final size:72
Alignment explanation
Indices: 360657--360799 Score: 182
Period size: 73 Copynumber: 2.0 Consensus size: 72
360647 AGAGAAATTC
* *
360657 TCTCAATCGAGACAAAATTTGGTTCAAGTAAATCAACATTGAAATTTGATCTCCGAAGGAAAATA
1 TCTCAATCGAGACAAAATTTGGTTCAAGAAAAACAACATTGAAATTTGATCTCCGAAGGAAAATA
360722 TCTCATG
66 TCTCATG
* * * *
360729 TCTCAAGT-GAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTG-TGTTCCGAAGGAAA
1 TCTCAA-TCGAGACAAAATTTG-GTTCAAGAAAAACAACATTGAAATTTGAT-CTCCGAAGGAAA
*
360792 ATGTCTCA
63 ATATCTCA
360800 AGTGAGACGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
72 20 0.33
73 41 0.67
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (72 bp):
TCTCAATCGAGACAAAATTTGGTTCAAGAAAAACAACATTGAAATTTGATCTCCGAAGGAAAATA
TCTCATG
Found at i:360834 original size:37 final size:37
Alignment explanation
Indices: 360789--360903 Score: 133
Period size: 37 Copynumber: 3.1 Consensus size: 37
360779 GTTCCGAAGG
360789 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
* *
360826 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTATGA-A
1 AAAATGTCTCAAGTGAGACGAAATTTG-TTTTAAGAGA
* * * **
360863 AACAATGTCTCTAGCGAGACGACATTTTGTTTCGAGAGA
1 AA-AATGTCTCAAGTGAGACGA-AATTTGTTTTAAGAGA
360902 AA
1 AA
360904 TAACACCCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 29 0.45
38 28 0.43
39 8 0.12
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (37 bp):
AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
Found at i:362292 original size:13 final size:13
Alignment explanation
Indices: 362274--362300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
362264 AGCTTTATTG
362274 TATACATATATAT
1 TATACATATATAT
362287 TATACATATATAT
1 TATACATATATAT
362300 T
1 T
362301 TTTGTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACATATATAT
Found at i:363259 original size:20 final size:21
Alignment explanation
Indices: 363225--363272 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
363215 TGCTCATGCA
363225 AATGCAAAGATGCAAAATGGG
1 AATGCAAAGATGCAAAATGGG
**
363246 AATGCAAA-ATGCAAAATGTA
1 AATGCAAAGATGCAAAATGGG
363266 AATGCAA
1 AATGCAA
363273 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (21 bp):
AATGCAAAGATGCAAAATGGG
Found at i:369568 original size:24 final size:25
Alignment explanation
Indices: 369536--369588 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
369526 CATTTAGACT
*
369536 AACTAAACAGATACATGATTGATTC
1 AACTAAACAGATACATGATTCATTC
*
369561 AACT-AACAGATACATGATTCCTTC
1 AACTAAACAGATACATGATTCATTC
369585 AACT
1 AACT
369589 GTTCGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (25 bp):
AACTAAACAGATACATGATTCATTC
Found at i:372018 original size:2 final size:2
Alignment explanation
Indices: 372011--372063 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
372001 GATCGGAGTT
*
372011 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
372053 TA TA TA TA TA T
1 TA TA TA TA TA T
372064 GTGTTCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:372120 original size:14 final size:14
Alignment explanation
Indices: 372101--372127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
372091 ATATTATATA
372101 GTTTTTTGAAAACG
1 GTTTTTTGAAAACG
372115 GTTTTTTGAAAAC
1 GTTTTTTGAAAAC
372128 ATATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (14 bp):
GTTTTTTGAAAACG
Found at i:372263 original size:72 final size:72
Alignment explanation
Indices: 372178--372340 Score: 240
Period size: 72 Copynumber: 2.3 Consensus size: 72
372168 AAAAATATAT
* * * *
372178 TATATAA-TTTTGAAAATATTTTGTAAAATATATATTATATAG-TTTTGAAAACGTTTTGAAAAT
1 TATATAATTTTTGAAAACATTTTG-AAAATATATATAATATAGTTTTTGAAAACATTTTGAAAAC
372241 ATATACAA
65 ATATACAA
*
372249 TATATAATTTTTGAAAACATTTTGAAAATATATATAATATAGTTTTTGTAAACATTTTGAAAACA
1 TATATAATTTTTGAAAACATTTTGAAAATATATATAATATAGTTTTTGAAAACATTTTGAAAACA
*
372314 TATATAA
66 TATACAA
*
372321 TATATAGTTTTTGAAAACAT
1 TATATAATTTTTGAAAACAT
372341 ATATATTATA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 24 0.29
72 59 0.71
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (72 bp):
TATATAATTTTTGAAAACATTTTGAAAATATATATAATATAGTTTTTGAAAACATTTTGAAAACA
TATACAA
Found at i:372295 original size:35 final size:35
Alignment explanation
Indices: 372163--372340 Score: 200
Period size: 35 Copynumber: 5.0 Consensus size: 35
372153 AAAAAATCGG
* * * *
372163 TTTTCAAAA-ATATATTATATA-ATTTTGAAAATA
1 TTTTGAAAATATATATAATATAGTTTTTGAAAACA
* *
372196 TTTTGTAAAATATATATTATATAG-TTTTGAAAACG
1 TTTTG-AAAATATATATAATATAGTTTTTGAAAACA
* *
372231 TTTTGAAAATATATACAATATATAATTTTTGAAAACA
1 TTTTGAAAATATATA-TA-ATATAGTTTTTGAAAACA
*
372268 TTTTGAAAATATATATAATATAGTTTTTGTAAACA
1 TTTTGAAAATATATATAATATAGTTTTTGAAAACA
*
372303 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATAT-A-ATATAGTTTTTGAAAACA
372340 T
1 T
372341 ATATATTATA
Statistics
Matches: 125, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.03
34 14 0.11
35 57 0.46
36 7 0.06
37 43 0.34
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATATATATAATATAGTTTTTGAAAACA
Found at i:372333 original size:26 final size:26
Alignment explanation
Indices: 372303--372404 Score: 159
Period size: 26 Copynumber: 3.9 Consensus size: 26
372293 TTTGTAAACA
*
372303 TTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATATATATTATATAGT
372329 TTTTGAAAACATATATATTATATAGT
1 TTTTGAAAACATATATATTATATAGT
*
372355 TTTTGAAATCATATATATTATATAGT
1 TTTTGAAAACATATATATTATATAGT
* *
372381 TTTTGAAAATATTTATATGTATAT
1 TTTTGAAAACATATATAT-TATAT
372405 TATATATTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 65 0.93
27 5 0.07
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (26 bp):
TTTTGAAAACATATATATTATATAGT
Found at i:372416 original size:18 final size:17
Alignment explanation
Indices: 372389--372464 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 17
372379 GTTTTTGAAA
372389 ATAT-TTATATGTATATT
1 ATATATTATAT-TATATT
* *
372406 ATATATTATATTGTA-C
1 ATATATTATATTATATT
**
372422 ATATATTATATTATGGT
1 ATATATTATATTATATT
372439 ATTATATTATA-TATATT
1 A-TATATTATATTATATT
*
372456 ATTTATTAT
1 ATATATTAT
372465 GGTTTATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
16 20 0.42
17 13 0.27
18 15 0.31
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
ATATATTATATTATATT
Found at i:372431 original size:34 final size:32
Alignment explanation
Indices: 372368--372450 Score: 80
Period size: 34 Copynumber: 2.5 Consensus size: 32
372358 TGAAATCATA
372368 TATATTATATAGTT-T-TTGAAAATATTTATAT
1 TATATTATATA-TTATATTGAAAATATTTATAT
* *
372399 GTATATTATATATTATATTGTACATATATTATAT
1 -TATATTATATATTATATTGAAAATAT-TTATAT
**
372433 TATGGTATTATATTATAT
1 TATATTA-TATATTATAT
372451 ATATTATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 2 0.05
32 12 0.28
33 13 0.30
34 16 0.37
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.54
Consensus pattern (32 bp):
TATATTATATATTATATTGAAAATATTTATAT
Found at i:372441 original size:29 final size:29
Alignment explanation
Indices: 372394--372471 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
372384 TGAAAATATT
* *
372394 TATATGTATATTAT-ATATTATATTGTACA
1 TATAT-TATATTATGGTATTATATTATACA
*
372423 TATATTATATTATGGTATTATATTATATA
1 TATATTATATTATGGTATTATATTATACA
372452 TATTATT-TATTATGGT-TTAT
1 TA-TATTATATTATGGTATTAT
372472 TATTTATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 12 0.27
29 28 0.64
30 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (29 bp):
TATATTATATTATGGTATTATATTATACA
Found at i:372475 original size:29 final size:26
Alignment explanation
Indices: 372389--372482 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 26
372379 GTTTTTGAAA
* *
372389 ATATTTATAT-GTATATTAT-ATATT
1 ATATTTATATATTATATTATGGTATT
372413 ATATTGTACATATATTATATTATGGTATT
1 ATATT-T--ATATATTATATTATGGTATT
372442 ATATTATATATATTATTTATTATGGT-TT
1 ATATT-TATATATTA--TATTATGGTATT
372470 ATTATTTAT-TATT
1 A-TATTTATATATT
372483 TTCTTTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
24 5 0.08
25 1 0.02
27 16 0.27
28 14 0.24
29 23 0.39
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (26 bp):
ATATTTATATATTATATTATGGTATT
Found at i:372581 original size:18 final size:18
Alignment explanation
Indices: 372558--372596 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
372548 AGTCCAACCG
372558 AGCCTGCAAGCCTGACCC
1 AGCCTGCAAGCCTGACCC
372576 AGCCTGCAAGCCTGACCC
1 AGCCTGCAAGCCTGACCC
372594 AGC
1 AGC
372597 AAACAGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.44, G:0.23, T:0.10
Consensus pattern (18 bp):
AGCCTGCAAGCCTGACCC
Found at i:373700 original size:13 final size:13
Alignment explanation
Indices: 373682--373715 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
373672 ATTTAATTGT
373682 TTTTATTTTTTCA
1 TTTTATTTTTTCA
373695 TTTTA-TTTTTCA
1 TTTTATTTTTTCA
373707 TTTTATTTT
1 TTTTATTTT
373716 ATTTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTTCA
Found at i:373716 original size:17 final size:17
Alignment explanation
Indices: 373689--373744 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 17
373679 TGTTTTTATT
373689 TTTTCATTTTATTTTTCA
1 TTTT-ATTTTATTTTTCA
373707 TTTTATTTTATTTTTCA
1 TTTTATTTTATTTTTCA
* *
373724 TTTCTTTTTTATTTTTAA
1 TTT-TATTTTATTTTTCA
373742 TTT
1 TTT
373745 AGCTAACATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTTTCA
Found at i:373739 original size:29 final size:30
Alignment explanation
Indices: 373682--373739 Score: 57
Period size: 30 Copynumber: 1.9 Consensus size: 30
373672 ATTTAATTGT
*
373682 TTTTATTTTTTCATTTTATTTT-TCATTTT-A
1 TTTTA-TTTTTCATTTTATTTTAT-TTTTTCA
*
373712 TTTTATTTTTCATTTCTTTTTTATTTTT
1 TTTTATTTTTCATTT-TATTTTATTTTT
373740 AATTTAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
29 10 0.42
30 13 0.54
31 1 0.04
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTATTTTTCATTTTATTTTATTTTTTCA
Found at i:373740 original size:29 final size:30
Alignment explanation
Indices: 373682--373738 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
373672 ATTTAATTGT
373682 TTTTATTTTTTCATTTTATTTTTCATTTTA
1 TTTTATTTTTTCATTTTATTTTTCATTTTA
373712 TTTTA-TTTTTCATTTCT-TTTTT-ATTTT
1 TTTTATTTTTTCATTT-TATTTTTCATTTT
373739 TAATTTAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 5 0.19
29 15 0.58
30 6 0.23
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTATTTTTTCATTTTATTTTTCATTTTA
Found at i:373745 original size:29 final size:30
Alignment explanation
Indices: 373683--373745 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
373673 TTTAATTGTT
*
373683 TTTATTTTTTCATTTTATTTTTCATTTTAT
1 TTTATTTTTTCATTTTATTTTTCATTTTAA
373713 TTTA-TTTTTCATTTCT-TTTTT-ATTTTTAA
1 TTTATTTTTTCATTT-TATTTTTCA-TTTTAA
373742 TTTA
1 TTTA
373746 GCTAACATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTATTTTTTCATTTTATTTTTCATTTTAA
Found at i:380175 original size:85 final size:85
Alignment explanation
Indices: 379914--380239 Score: 472
Period size: 85 Copynumber: 3.8 Consensus size: 85
379904 TCCCAACCTA
* * * ** *
379914 TTACAGTATAGTTCAAGGCGAGAATGGCTATCTGTCAACAGCAACCTTCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
379979 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
* * *
379999 TTACAACATAGCTCAAGGCGAGAAGGGTTATGTGTCAACAAAAAACCTTCGAGTTCGATTACATT
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACATT
* *
380064 TAGTTCAAGGGCATATCAAAT
65 CAGCTCAAGGGCATATCAAAT
* * *
380085 TTACAGCATAGCTCAAGGTGAAAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
380150 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
** * * *
380170 TTACAGCATAATTCAAGGCGAGAAGAGTTATCTGTCAACAAAAACCTTCGAGTTCGATTTCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
380235 AGCTC
66 AGCTC
380240 GATGACAGCG
Statistics
Matches: 213, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 138 0.65
86 75 0.35
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (85 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGGCATATCAAAT
Found at i:380851 original size:13 final size:13
Alignment explanation
Indices: 380833--380858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
380823 TATAGTATAA
380833 TTTTTGAAAATAT
1 TTTTTGAAAATAT
380846 TTTTTGAAAATAT
1 TTTTTGAAAATAT
380859 ATATTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTTGAAAATAT
Found at i:381017 original size:34 final size:34
Alignment explanation
Indices: 380926--381096 Score: 202
Period size: 34 Copynumber: 4.9 Consensus size: 34
380916 AAAAAAGCGG
* * * *
380926 TTTTCGAATATATATATTATATAATTTTAAAAACA
1 TTTT-GAAAATATATATAATATAGTTTTGAAAACA
* *
380961 TTTTGGAAAATATATATTATATAGTTTTGAAAACG
1 TTTT-GAAAATATATATAATATAGTTTTGAAAACA
*
380996 TTTTGAAAATACATATAATATATAGTTTTGGAAAACA
1 TTTTGAAAATATATAT-A-ATATAGTTTT-GAAAACA
381033 TTTTGAAAATATATAT-ATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATAG-TTTTGAAAACA
*
381067 TTTTGAAAACATATAT-ATATAGTTTTGAAA
1 TTTTGAAAATATATATAATATAGTTTTGAAA
381097 TATTATATTT
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
33 8 0.07
34 45 0.37
35 38 0.31
36 10 0.08
37 21 0.17
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (34 bp):
TTTTGAAAATATATATAATATAGTTTTGAAAACA
Found at i:381045 original size:71 final size:71
Alignment explanation
Indices: 380932--381096 Score: 232
Period size: 71 Copynumber: 2.4 Consensus size: 71
380922 GCGGTTTTCG
* * *
380932 AATATATATATTATATAATTTT-AAAAACATTTTGGAAAATATATATTATATAG-TTTTGAAAAC
1 AATACATATAATATATAGTTTTGAAAAACATTTTGGAAAATATATA-TATATAGTTTTTGAAAAC
*
380995 GTTTTGAA
65 ATTTTG-A
*
381003 AATACATATAATATATAGTTTTGGAAAACATTTT-GAAAATATATATATATAGTTTTTGAAAACA
1 AATACATATAATATATAGTTTTGAAAAACATTTTGGAAAATATATATATATAGTTTTTGAAAACA
381067 TTTTGA
66 TTTTGA
381073 AA-ACATAT-ATATATAGTTTTGAAA
1 AATACATATAATATATAGTTTTGAAA
381097 TATTATATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
68 15 0.17
69 6 0.07
70 10 0.12
71 45 0.52
72 10 0.12
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (71 bp):
AATACATATAATATATAGTTTTGAAAAACATTTTGGAAAATATATATATATAGTTTTTGAAAACA
TTTTGA
Found at i:381119 original size:2 final size:2
Alignment explanation
Indices: 381112--381179 Score: 104
Period size: 2 Copynumber: 34.5 Consensus size: 2
381102 TATTTACATG
*
381112 TA TA TA TA T- TA TA TA TA T- TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
381152 TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA T
381180 GGTATTATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 57 0.93
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381130 original size:30 final size:29
Alignment explanation
Indices: 381096--381207 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 29
381086 TAGTTTTGAA
*
381096 ATATTATATTTACATGTATATATATTATAT
1 ATATTATA-TTATATGTATATATATTATAT
381126 ATA-T-TA-TATATGTATATATA-TATAT
1 ATATTATATTATATGTATATATATTATAT
* *
381151 ATA-TATATATATATATATATATATGATAT
1 ATATTATAT-TATATGTATATATATTATAT
*
381180 GGTATTATATTATATGTAT-TATTATTAT
1 -ATATTATATTATATGTATATA-TATTAT
381208 GGTTTATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
25 9 0.13
26 15 0.22
28 15 0.22
29 7 0.10
30 18 0.26
31 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (29 bp):
ATATTATATTATATGTATATATATTATAT
Found at i:381195 original size:15 final size:14
Alignment explanation
Indices: 381097--381207 Score: 79
Period size: 15 Copynumber: 7.8 Consensus size: 14
381087 AGTTTTGAAA
*
381097 TATTATATTTACATG
1 TATTATA-TTATATG
*
381112 TATATATATTATATA
1 TAT-TATATTATATG
381127 TA-T-TA-TATATG
1 TATTATATTATATG
*
381138 TA-TATA-TATATA
1 TATTATATTATATG
*
381150 TATATATATATATATA
1 TAT-TATAT-TATATG
*
381166 TATATATATGATATGG
1 TAT-TATATTATAT-G
381182 TATTATATTATATG
1 TATTATATTATATG
381196 TATTATTATTAT
1 TATTA-TATTAT
381208 GGTTTATTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
11 8 0.10
12 11 0.14
13 1 0.01
14 10 0.12
15 29 0.36
16 22 0.27
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (14 bp):
TATTATATTATATG
Found at i:381204 original size:12 final size:13
Alignment explanation
Indices: 381112--381204 Score: 91
Period size: 14 Copynumber: 6.9 Consensus size: 13
381102 TATTTACATG
381112 TATATATATTATA
1 TATATATATTATA
*
381125 TATAT-TATATATG
1 TATATATAT-TATA
381138 TATATATATATATA
1 TATATATAT-TATA
381152 TATATATATATATA
1 TATATATAT-TATA
*
381166 TATATATATGATA
1 TATATATATTATA
*
381179 TGGTATTATATTATA
1 T-ATA-TATATTATA
*
381194 TGTAT-TATTAT
1 TATATATATTAT
381205 TATGGTTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
12 9 0.13
13 18 0.25
14 35 0.49
15 9 0.13
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATATATTATA
Found at i:381247 original size:11 final size:11
Alignment explanation
Indices: 381210--381250 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
381200 ATTATTATGG
381210 TTTATTTTCTTT
1 TTTATTTTC-TT
* *
381222 TTTCTTTTTTT
1 TTTATTTTCTT
381233 TTTATTTTCTT
1 TTTATTTTCTT
381244 TTTATTT
1 TTTATTT
381251 GGTCCAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTATTTTCTT
Found at i:388024 original size:31 final size:31
Alignment explanation
Indices: 387983--388056 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
387973 CAAAATACAT
387983 AAGATATGGTCACTTACGTTTTTATTTAAAC
1 AAGATATGGTCACTTACGTTTTTATTTAAAC
* * **
388014 AAGATCTGGTCACTTTCGTTTTTATTTAATT
1 AAGATATGGTCACTTACGTTTTTATTTAAAC
*
388045 AAGATGTGGTCA
1 AAGATATGGTCA
388057 TAACTGCCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (31 bp):
AAGATATGGTCACTTACGTTTTTATTTAAAC
Found at i:388411 original size:16 final size:17
Alignment explanation
Indices: 388390--388423 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
388380 ACTCGATTTA
388390 TTATATT-TTTTTTATT
1 TTATATTATTTTTTATT
388406 TTATATTAATTTTTTATT
1 TTATATT-ATTTTTTATT
388424 CATAATCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATATTATTTTTTATT
Found at i:388535 original size:39 final size:39
Alignment explanation
Indices: 388434--388539 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
388424 CATAATCCTC
* * *
388434 AAATTATTGCACACTAACATTCTAAAATCTTAATTTATT
1 AAATTATTTCACATTAACATTCTAAATTCTTAATTTATT
* * *
388473 AAA-T-TTTGACACTATAACGTTCTAAATTCTTAATTTTTT
1 AAATTATTTCACA-T-TAACATTCTAAATTCTTAATTTATT
388512 AAATTATTTCACATTAACATTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
388540 ATTTTTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
37 5 0.09
38 1 0.02
39 41 0.75
40 2 0.04
41 6 0.11
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCTTAATTTATT
Found at i:388841 original size:25 final size:26
Alignment explanation
Indices: 388806--388871 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 26
388796 ATATATATTA
388806 AATTAAAATATTTTTA-TATT-ACTT
1 AATTAAAATATTTTTACTATTAACTT
*
388830 TATT-AAATATATTTTACTATTAACTT
1 AATTAAAATAT-TTTTACTATTAACTT
388856 AATTTAAAAATATTTT
1 AA-TT-AAAATATTTT
388872 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.18
24 8 0.24
25 4 0.12
26 5 0.15
27 2 0.06
28 3 0.09
29 6 0.18
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTAAAATATTTTTACTATTAACTT
Found at i:388869 original size:27 final size:24
Alignment explanation
Indices: 388806--388873 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 24
388796 ATATATATTA
388806 AATT-AAAATATTTTTATATTACTT
1 AATTAAAAATA-TTTTATATTACTT
* *
388830 TATTAAATATATTTTACTATTAACTT
1 AATTAAAAATATTTTA-TATT-ACTT
388856 AATTTAAAAATATTTTAT
1 AA-TTAAAAATATTTTAT
388874 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 8 0.22
25 9 0.25
26 6 0.17
27 13 0.36
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAAAAATATTTTATATTACTT
Found at i:390345 original size:18 final size:17
Alignment explanation
Indices: 390324--390387 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
390314 TATATATAAG
*
390324 TTTTGAAAATAGTATAGT
1 TTTTGAAAACA-TATAGT
390342 TTTTGAAAACATATAGT
1 TTTTGAAAACATATAGT
390359 TTTTGAAAAC--AT-GT
1 TTTTGAAAACATATAGT
*
390373 TTTTGAAAATATATA
1 TTTTGAAAACATATA
390388 TATAGTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.27
15 2 0.05
16 2 0.05
17 16 0.39
18 10 0.24
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTGAAAACATATAGT
Found at i:390421 original size:34 final size:35
Alignment explanation
Indices: 390352--390434 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 35
390342 TTTTGAAAAC
* * * *
390352 ATATAGTTTTTGAAAACATGTTTTTGAAAATATAT
1 ATATAGTTTTTGAAAAAACGGTTTTGAAAACATAT
390387 ATATAGTTTTT-AAAAAACGGTTTTGAAAACATAT
1 ATATAGTTTTTGAAAAAACGGTTTTGAAAACATAT
390421 ATATAGTTTTTGAA
1 ATATAGTTTTTGAA
390435 TATAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 30 0.70
35 13 0.30
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (35 bp):
ATATAGTTTTTGAAAAAACGGTTTTGAAAACATAT
Found at i:390444 original size:2 final size:2
Alignment explanation
Indices: 390434--390472 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
390424 TAGTTTTTGA
390434 AT AT A- AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
390473 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:390454 original size:17 final size:17
Alignment explanation
Indices: 390434--390474 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
390424 TAGTTTTTGA
390434 ATATAATATATATATAT
1 ATATAATATATATATAT
*
390451 ATATTATATATATATAT
1 ATATAATATATATATAT
390468 ATATAAT
1 ATATAAT
390475 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:390558 original size:20 final size:20
Alignment explanation
Indices: 390516--390558 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
390506 ATATATGACG
*
390516 TTTGAAAATATTATATTATT
1 TTTGAAAATATTATATTAGT
390536 TTTGAAATATATTATA-TAGT
1 TTTGAAA-ATATTATATTAGT
390556 TTT
1 TTT
390559 AATACCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTGAAAATATTATATTAGT
Found at i:390584 original size:12 final size:12
Alignment explanation
Indices: 390567--390616 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
390557 TTAATACCAT
390567 ATTTTATTTTTC
1 ATTTTATTTTTC
*
390579 ATTTTATCTTTC
1 ATTTTATTTTTC
*
390591 -TTTTATTATT-
1 ATTTTATTTTTC
390601 ATTTT-TTATTTC
1 ATTTTATT-TTTC
390613 ATTT
1 ATTT
390617 AATTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 2 0.06
11 14 0.45
12 15 0.48
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTATTTTTC
Done.