Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003407.1 Hibiscus syriacus cultivar Beakdansim tig00007179_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: 758105
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 4
Found at i:306392 original size:33 final size:33
Alignment explanation
Indices: 306334--306411 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
306324 GAAATGAAAA
***
306334 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
306367 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
306400 TCGCGTTGCGAT
1 TCGCATTGCGAT
306412 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:306518 original size:14 final size:14
Alignment explanation
Indices: 306499--306535 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
306489 CATCAATTAA
306499 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
306513 ACAAATCATCTTTT
1 ACAAATCAACATTT
306527 ACAAATCAA
1 ACAAATCAA
306536 TTAAACAATC
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:308428 original size:39 final size:37
Alignment explanation
Indices: 308385--308539 Score: 131
Period size: 39 Copynumber: 4.2 Consensus size: 37
308375 TAGTTTACTT
* *
308385 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAA-TGAAAATCGCAACGCGAAATGA-AA
* *** **
308424 TCGCAACGCGGAAATGGCTATCGCAACGCGGAAATGGCTA
1 TCGCAACAC-GAAATGAAAATCGCAACGC-GAAAT-GAAA
**
308464 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAATGAAAATCGCAACGCGAAATGAAA
*
308501 TCGC-A-ACG--A-CAAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAATGAAAATCGCAACGCGAAATGAAA
308533 TCGCAAC
1 TCGCAAC
308540 GACAAAATCG
Statistics
Matches: 97, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
32 26 0.27
33 2 0.02
35 2 0.02
36 1 0.01
37 6 0.06
38 5 0.05
39 35 0.36
40 19 0.20
41 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.21, T:0.14
Consensus pattern (37 bp):
TCGCAACACGAAATGAAAATCGCAACGCGAAATGAAA
Found at i:308439 original size:20 final size:19
Alignment explanation
Indices: 308404--308508 Score: 131
Period size: 20 Copynumber: 5.5 Consensus size: 19
308394 GAAACTTAAA
308404 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
308423 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
308443 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
308463 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
308482 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
308500 ATCGCAACG
1 ATCGCAACG
308509 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
18 10 0.13
19 32 0.41
20 37 0.47
ACGTcount: A:0.37, C:0.24, G:0.25, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:308517 original size:14 final size:14
Alignment explanation
Indices: 308498--308554 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
308488 ACGCGAAATG
308498 AAATCGCAACGACA
1 AAATCGCAACGACA
*
308512 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
308528 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
308544 AAATCGCAACG
1 AAATCGCAACG
308555 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:308520 original size:32 final size:32
Alignment explanation
Indices: 308479--308559 Score: 162
Period size: 32 Copynumber: 2.5 Consensus size: 32
308469 ATGCGAAATG
308479 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
308511 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
308543 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
308560 CACAAATCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.48, C:0.25, G:0.19, T:0.09
Consensus pattern (32 bp):
AAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:308588 original size:19 final size:19
Alignment explanation
Indices: 308566--308647 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
308556 GAAACACAAA
308566 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
308585 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
308601 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
308617 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
308636 TCGCATTGCGAT
1 TCGCATTGCGAT
308648 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.17
16 8 0.15
18 9 0.17
19 28 0.52
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:308666 original size:20 final size:19
Alignment explanation
Indices: 308602--308686 Score: 91
Period size: 20 Copynumber: 4.4 Consensus size: 19
308592 GCGATTTTGT
*
308602 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
308620 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
308639 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
308659 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
308679 TGTTGCGA
1 CGTTGCGA
308687 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 9 0.16
19 22 0.39
20 23 0.40
21 3 0.05
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:309183 original size:18 final size:18
Alignment explanation
Indices: 309157--309201 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
309147 GTCGATCAGA
*
309157 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
309175 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
309193 TGATGGCTC
1 TGATGGCTC
309202 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:310544 original size:20 final size:20
Alignment explanation
Indices: 310519--310556 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
310509 AATAGTTTCT
310519 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
310539 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
310557 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:310845 original size:22 final size:22
Alignment explanation
Indices: 310820--310863 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
310810 GATTTAGATA
310820 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
310842 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
310864 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:311076 original size:20 final size:20
Alignment explanation
Indices: 311051--311144 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
311041 GATTATGTAT
311051 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
311071 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
311091 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
311112 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
311132 TATCGCATTGCGA
1 TATCGCGTTGCGA
311145 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:311116 original size:41 final size:42
Alignment explanation
Indices: 311071--311206 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
311061 CGAAAGTCAG
* * * *
311071 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
311112 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
311154 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
311195 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
311207 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:311145 original size:20 final size:20
Alignment explanation
Indices: 311031--311145 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
311021 CGCTTTGAAA
*
311031 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
311052 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
311072 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
311092 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
311113 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
311133 ATCGCATTGCGAT
1 ATCGCATTGCGAT
311146 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:311178 original size:20 final size:20
Alignment explanation
Indices: 311134--311226 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
311124 ATAGTCAGTA
*
311134 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
311155 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
311175 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
311196 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
311216 TCGCATTGCGA
1 TCGCATTGCGA
311227 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:311207 original size:41 final size:41
Alignment explanation
Indices: 311134--311229 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
311124 ATAGTCAGTA
* *
311134 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
311175 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
311216 TCGCATTGCGAATT
1 TCGCATTGCGAATT
311230 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:311310 original size:21 final size:21
Alignment explanation
Indices: 311257--311304 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
311247 ACTGTAGACC
311257 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
311278 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
311299 ATCGCA
1 ATCGCA
311305 TTGCGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:315456 original size:47 final size:46
Alignment explanation
Indices: 315382--315473 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 46
315372 AACAAAAACG
*
315382 ATGACCGGTCAGTGGATCGGTGATGACAGAGGGTGTGATTGAAAATA
1 ATGACCAGTCAGTGGATCGGTGATGACAGAGGGT-TGATTGAAAATA
315429 ATGACCAGTCAGT-GACTCGGT-AGTGACAGAGGGTTGATTGAAAAT
1 ATGACCAGTCAGTGGA-TCGGTGA-TGACAGAGGGTTGATTGAAAAT
315474 GACTGATGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 14 0.33
47 28 0.67
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.24
Consensus pattern (46 bp):
ATGACCAGTCAGTGGATCGGTGATGACAGAGGGTTGATTGAAAATA
Found at i:316314 original size:25 final size:28
Alignment explanation
Indices: 316272--316324 Score: 85
Period size: 25 Copynumber: 2.0 Consensus size: 28
316262 GATAACAAAT
316272 TCTAATAAAATATAATTTTTTATTAAAA
1 TCTAATAAAATATAATTTTTTATTAAAA
316300 TCTAA-AAAA-AT-ATTTTTTATTAAAA
1 TCTAATAAAATATAATTTTTTATTAAAA
316325 CTCGTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 14 0.56
26 2 0.08
27 4 0.16
28 5 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
TCTAATAAAATATAATTTTTTATTAAAA
Found at i:319244 original size:22 final size:23
Alignment explanation
Indices: 319219--319274 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
319209 TAAGAAAAAT
* *
319219 TCTGCTTTTTTGGTATG-TTTTC
1 TCTGCTTTTATGGTACGTTTTTC
319241 TCTGCTTTTATGGTACGTTTTTC
1 TCTGCTTTTATGGTACGTTTTTC
*
319264 TCTGCCTTTAT
1 TCTGCTTTTAT
319275 TGCACATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.07, C:0.18, G:0.16, T:0.59
Consensus pattern (23 bp):
TCTGCTTTTATGGTACGTTTTTC
Found at i:319286 original size:24 final size:23
Alignment explanation
Indices: 319236--319285 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
319226 TTTTGGTATG
* *
319236 TTTTCTCTGCTTTTATGGTACGT
1 TTTTCTCTGCCTTTATGGCACGT
* *
319259 TTTTCTCTGCCTTTATTGCACAT
1 TTTTCTCTGCCTTTATGGCACGT
319282 TTTT
1 TTTT
319286 TTATCTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.20, G:0.12, T:0.58
Consensus pattern (23 bp):
TTTTCTCTGCCTTTATGGCACGT
Found at i:320247 original size:25 final size:24
Alignment explanation
Indices: 320206--320256 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
320196 ATTTTTCATA
* *
320206 ATTATTATATTTTTTATAGTAAGAT
1 ATTATTATATTTATTAT-GTAAAAT
320231 ATTATTAT-TATTATTATGTAAAAT
1 ATTATTATAT-TTATTATGTAAAAT
320255 AT
1 AT
320257 AGTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTATTATATTTATTATGTAAAAT
Found at i:327417 original size:3 final size:3
Alignment explanation
Indices: 327400--327526 Score: 92
Period size: 3 Copynumber: 42.3 Consensus size: 3
327390 TGCTGGGGCG
* * * * * * * *
327400 GCT GCT GCG GCT GTT GTT GTT GCT GTT GTT GCT GCT GCT GCT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * * * * *
327448 GTT GTT GTT GCT GCT GCT GCT GCT GCT GCT GCT GCT GTT GTT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * *
327496 GTT GTT GCT GCT GTT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
327527 TTGTTGTTGC
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.00, C:0.20, G:0.35, T:0.46
Consensus pattern (3 bp):
GCT
Found at i:327420 original size:6 final size:6
Alignment explanation
Indices: 327409--327538 Score: 107
Period size: 6 Copynumber: 21.7 Consensus size: 6
327399 GGCTGCTGCG
* * * * * *
327409 GCTGTT GTTGTT GCTGTT GTTGCT GCTGCT GCTGTT GTTGTT GTTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * * * * * * *
327457 GCTGCT GCTGCT GCTGCT GCTGCT GCTGTT GTTGTT GTTGTT GTTGCT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * *
327505 GCTGTT GCTGCT GCTGCT GCTGTT GTTGTT GCTG
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTG
327539 AGCATGCCTC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 106 1.00
ACGTcount: A:0.00, C:0.18, G:0.34, T:0.48
Consensus pattern (6 bp):
GCTGTT
Found at i:327426 original size:9 final size:9
Alignment explanation
Indices: 327417--327529 Score: 109
Period size: 9 Copynumber: 12.6 Consensus size: 9
327407 CGGCTGTTGT
*
327417 TGTTGCTGT
1 TGTTGCTGC
327426 TGTTGCTGC
1 TGTTGCTGC
* *
327435 TGCTGCTGT
1 TGTTGCTGC
* *
327444 TGTTGTTGT
1 TGTTGCTGC
327453 TGTTGCTGC
1 TGTTGCTGC
*
327462 TGCTGCTGC
1 TGTTGCTGC
*
327471 TGCTGCTGC
1 TGTTGCTGC
* * *
327480 TGCTGTTGT
1 TGTTGCTGC
* *
327489 TGTTGTTGT
1 TGTTGCTGC
327498 TGTTGCTGC
1 TGTTGCTGC
327507 TGTTGCTGC
1 TGTTGCTGC
*
327516 TGCTGCTGC
1 TGTTGCTGC
327525 TGTTG
1 TGTTG
327530 TTGTTGCTGA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 89 1.00
ACGTcount: A:0.00, C:0.19, G:0.34, T:0.48
Consensus pattern (9 bp):
TGTTGCTGC
Found at i:329390 original size:2 final size:2
Alignment explanation
Indices: 329383--329425 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
329373 GAACTTTCTC
329383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329425 A
1 A
329426 GTTTTCTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:330988 original size:6 final size:6
Alignment explanation
Indices: 330977--331273 Score: 585
Period size: 6 Copynumber: 49.5 Consensus size: 6
330967 TTAGCCATTG
330977 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
331025 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
331073 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
*
331121 CATACA CATACA CATACA CATACA CATACA TATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
331169 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
331217 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
331265 CATACA CAT
1 CATACA CAT
331274 GGGGACATGA
Statistics
Matches: 289, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 289 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
CATACA
Found at i:334656 original size:20 final size:21
Alignment explanation
Indices: 334619--334666 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
334609 ACAAGTAATG
*
334619 TATTAATATAAATTATTT-TT
1 TATTAATATAAATAATTTATT
334639 TATTAA-ATAAATAAATTTATT
1 TATTAATATAAAT-AATTTATT
334660 TAATTAA
1 T-ATTAA
334667 GCTGGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 3 0.12
22 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAATATAAATAATTTATT
Found at i:339351 original size:20 final size:20
Alignment explanation
Indices: 339326--339390 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
339316 TGGGACTTTC
339326 AAATTATTAATAGAAATATT
1 AAATTATTAATAGAAATATT
* *
339346 AAATTATATTAA-AGAAAAAATA
1 AAA-T-TATTAATAG-AAATATT
* *
339368 AAAATATTAATAAAAATATT
1 AAATTATTAATAGAAATATT
339388 AAA
1 AAA
339391 CTTTTTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
20 17 0.49
21 4 0.11
22 14 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATTATTAATAGAAATATT
Found at i:339381 original size:12 final size:12
Alignment explanation
Indices: 339364--339389 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
339354 TTAAAGAAAA
339364 AATAAAAATATT
1 AATAAAAATATT
339376 AATAAAAATATT
1 AATAAAAATATT
339388 AA
1 AA
339390 ACTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAAATATT
Found at i:339389 original size:42 final size:41
Alignment explanation
Indices: 339330--339412 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
339320 ACTTTCAAAT
*
339330 TATTAATAGAAATATTAAA-TTATATTAAAGAAAAAATAAAAA
1 TATTAATAAAAATATTAAACTT-TATTAAA-AAAAAATAAAAA
* *
339372 TATTAATAAAAATATTAAACTTTTTTAAAAAAAATTAAAAA
1 TATTAATAAAAATATTAAACTTTATTAAAAAAAAATAAAAA
339413 CATGATCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.30
42 24 0.65
43 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (41 bp):
TATTAATAAAAATATTAAACTTTATTAAAAAAAAATAAAAA
Found at i:341015 original size:21 final size:24
Alignment explanation
Indices: 340991--341035 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
340981 GGCTTTCATT
340991 AATTAATAAA-TT-ATT-TTAATA
1 AATTAATAAACTTAATTATTAATA
341012 AATTAATAAACTTAATTATTAATA
1 AATTAATAAACTTAATTATTAATA
341036 TATAACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 3 0.14
24 6 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTAATAAACTTAATTATTAATA
Found at i:341751 original size:16 final size:17
Alignment explanation
Indices: 341730--341762 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
341720 AATATATATT
*
341730 AAATTAT-AAAATATAA
1 AAATTATCAAAAAATAA
341746 AAATTATCAAAAAATAA
1 AAATTATCAAAAAATAA
341763 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTATCAAAAAATAA
Found at i:342598 original size:18 final size:18
Alignment explanation
Indices: 342575--342610 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
342565 AATTCGACTT
342575 GAATTTATTTATTTTTAA
1 GAATTTATTTATTTTTAA
342593 GAATTTATTTATTTTTAA
1 GAATTTATTTATTTTTAA
342611 ATAATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
GAATTTATTTATTTTTAA
Found at i:344149 original size:22 final size:22
Alignment explanation
Indices: 344124--344182 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
344114 TTCTAAAACA
* *
344124 AAAATGATTATTAAAATGTTAT
1 AAAATGATCATTAAAATATTAT
* * *
344146 AAAATAATCACTACAATATTAT
1 AAAATGATCATTAAAATATTAT
344168 AAAATGATCATTAAA
1 AAAATGATCATTAAA
344183 TTTAAAAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAATGATCATTAAAATATTAT
Found at i:346620 original size:3 final size:3
Alignment explanation
Indices: 346612--346646 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
346602 TAATTTAATT
346612 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
346647 GTTTATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:346636 original size:16 final size:16
Alignment explanation
Indices: 346615--346646 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
346605 TTTAATTTTA
346615 TTATTATTATTATTAT
1 TTATTATTATTATTAT
346631 TTATTATTATTATTAT
1 TTATTATTATTATTAT
346647 GTTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:346652 original size:22 final size:22
Alignment explanation
Indices: 346612--346658 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
346602 TAATTTAATT
*
346612 TTATTATTATTATTATTATTTA
1 TTATTATTATTATTATTATTAA
346634 TTATTATTATTATGT-TTATTAA
1 TTATTATTATTAT-TATTATTAA
346656 TTA
1 TTA
346659 CATATTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTATTATTATTATTATTAA
Found at i:347280 original size:12 final size:12
Alignment explanation
Indices: 347263--347293 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
347253 AGGGAGAGGA
*
347263 AAAAAAAACCAG
1 AAAAAAAACAAG
347275 AAAAAAAACAAG
1 AAAAAAAACAAG
347287 AAAAAAA
1 AAAAAAA
347294 GAGAACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAG
Found at i:350065 original size:17 final size:18
Alignment explanation
Indices: 350040--350078 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
350030 GGGTGAATGC
350040 TTTACTCTT-GTATGAAT
1 TTTACTCTTCGTATGAAT
* *
350057 TTTATTCTTCGTATGAGT
1 TTTACTCTTCGTATGAAT
350075 TTTA
1 TTTA
350079 GCAAATAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (18 bp):
TTTACTCTTCGTATGAAT
Found at i:352071 original size:26 final size:25
Alignment explanation
Indices: 352042--352119 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
352032 AATTTTTGAC
352042 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
352068 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
352088 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
352114 ATTCTT
1 ATTCTT
352120 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:352080 original size:20 final size:20
Alignment explanation
Indices: 352057--352131 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
352047 ATCTCTTTGA
352057 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
352077 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
352103 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
352122 CACCTTGAAA
1 GACCTTGAAA
352132 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:353957 original size:4 final size:4
Alignment explanation
Indices: 353950--353999 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
353940 ATACATCAAC
*
353950 ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
353995 ACAT A
1 ACAT A
354000 AAATTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:354334 original size:11 final size:11
Alignment explanation
Indices: 354318--354342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
354308 TTCTTTCTAA
354318 AAAATAATAAT
1 AAAATAATAAT
354329 AAAATAATAAT
1 AAAATAATAAT
354340 AAA
1 AAA
354343 TAAAGTGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:354770 original size:34 final size:35
Alignment explanation
Indices: 354676--354773 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 35
354666 TCGTTTCCTC
*
354676 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTCT
** **
354712 AAAAACAAATTTTGTCTCATTTGAGATTATATCT-T
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTCT
*
354747 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
354774 TCATTTTCTC
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
33 3 0.06
34 18 0.36
35 1 0.02
36 28 0.56
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTCT
Found at i:355062 original size:29 final size:28
Alignment explanation
Indices: 355028--355098 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
355018 GTTTCTCTTG
*
355028 AAAAAATCTTAGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
355056 ATAAAAATCTTTGAG-TTGTTTCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
355084 AAAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
355099 CTATTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 13 0.33
28 14 0.36
29 12 0.31
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGA
Found at i:355075 original size:28 final size:27
Alignment explanation
Indices: 355028--355098 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
355018 GTTTCTCTTG
*
355028 AAAAAATCTTAGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAG-TTGTTCCTTTTGA
*
355056 ATAAAAATCTTTGAGTTGTTTCTTTTGA
1 A-AAAAATCTTTGAGTTGTTCCTTTTGA
355084 AAAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
355099 CTATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.35
28 14 0.35
29 12 0.30
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTGTTCCTTTTGA
Found at i:355123 original size:28 final size:27
Alignment explanation
Indices: 355028--355113 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 27
355018 GTTTCTCTTG
* *
355028 AAAAAATCTTAGAGTT-TGTTCCTTTTGA
1 AAAAAATCTTTGAGTTAT-TT-ATTTTGA
* *
355056 ATAAAAATCTTTGAGTTGTTTCTTTTGA
1 A-AAAAATCTTTGAGTTATTTATTTTGA
355084 AAAAAATCTTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGT-TATTTATTTTGA
355112 AA
1 AA
355114 CAAAGTTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 14 0.27
28 21 0.40
29 16 0.31
30 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTATTTATTTTGA
Found at i:355194 original size:50 final size:52
Alignment explanation
Indices: 355109--355209 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 52
355099 CTATTTATTT
*
355109 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAA-ATCTTTGAGTC
1 TGAAACAAAGTGTTG-CTCTCTTGAGACAATTTCGTGAAAAGATCTTTGAGTC
355161 TGAAACAAAGTGTTG-TCTCTTGAGACAATTTCGTGAAAAGATCTTTGAG
1 TGAAACAAAGTGTTGCTCTCTTGAGACAATTTCGTGAAAAGATCTTTGAG
355210 ATTGTTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 24 0.51
51 9 0.19
52 14 0.30
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (52 bp):
TGAAACAAAGTGTTGCTCTCTTGAGACAATTTCGTGAAAAGATCTTTGAGTC
Found at i:355496 original size:120 final size:119
Alignment explanation
Indices: 355348--355572 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
355338 CTTAACAAAA
* * * *
355348 TCATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAA
355411 AACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGAT
64 AA--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
* ** **
355468 TCATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
* * *
355533 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
355573 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (119 bp):
TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
Found at i:355549 original size:64 final size:63
Alignment explanation
Indices: 355470--355594 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
355460 GATGTGATTC
* *
355470 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
355534 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
355595 TACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:355775 original size:15 final size:15
Alignment explanation
Indices: 355757--355785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
355747 GTCGTTTCAC
355757 TTGAAACATTTTCTT
1 TTGAAACATTTTCTT
355772 TTGAAACATTTTCT
1 TTGAAACATTTTCT
355786 CTTAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (15 bp):
TTGAAACATTTTCTT
Found at i:355793 original size:15 final size:15
Alignment explanation
Indices: 355760--355794 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
355750 GTTTCACTTG
* *
355760 AAACATTTTCTTTTG
1 AAACATTTTCTCTTA
355775 AAACATTTTCTCTTA
1 AAACATTTTCTCTTA
355790 AAACA
1 AAACA
355795 AGATCATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (15 bp):
AAACATTTTCTCTTA
Found at i:356585 original size:43 final size:43
Alignment explanation
Indices: 356532--356897 Score: 263
Period size: 43 Copynumber: 8.5 Consensus size: 43
356522 TGACCAGATC
* * * *
356532 TCCTCTTCATGTAGGAGCCATGTCAACCATAGATGGCCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAGCCG
* * * * *
356575 TCCTCATCATGTAGGAACCGTGTCATCC-T--CTGACCAGATC-
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAG-CCG
* * *
356615 TCCTCATCATGTAGGAGCCATGTCAACCATAGATGGCCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAGCCG
* * **
356658 TCCTCATCACGTAGGAACCGTGTCATCC---CCTGACCAGACC-
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAG-CCG
*
356698 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAGCCG
* * * *
356741 TCCTCATCACGTAGGAACTAAGTTATCACCACTCCTAAAGATGACCAGCCG
1 TCCTCATCACGTAGGAGC--CG-TGTCA--A--CC-ATAGATGACCAGCCG
* * *
356792 TCCTCATCACGTAGGAACCGTGTCATCTC-T---CGACCAGACC-
1 TCCTCATCACGTAGGAGCCGTGTCAAC-CATAGATGACCAG-CCG
* * * *
356832 TCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAACCAGCTG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAGCCG
* *
356875 TCCTCATCATGTAGGAACCGTGT
1 TCCTCATCACGTAGGAGCCGTGT
356898 TATCACCTTT
Statistics
Matches: 256, Mismatches: 42, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
39 1 0.00
40 95 0.37
41 6 0.02
42 5 0.02
43 103 0.40
44 1 0.00
45 2 0.01
46 4 0.02
48 5 0.02
49 1 0.00
50 2 0.01
51 31 0.12
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCAACCATAGATGACCAGCCG
Found at i:356618 original size:83 final size:83
Alignment explanation
Indices: 356480--356758 Score: 452
Period size: 83 Copynumber: 3.4 Consensus size: 83
356470 TTATCCCTAG
** * *
356480 AGATGGCCAGTAGTCCTCAT-ACATAGGAACCGTGTCATCCTCTGACCAGATCTCCTCTTCATGT
1 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGATCTCCTCATCATGT
356544 AGGAGCCATGTCAACCAT
66 AGGAGCCATGTCAACCAT
*
356562 AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCTCTGACCAGATCTCCTCATCATGT
1 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGATCTCCTCATCATGT
356627 AGGAGCCATGTCAACCAT
66 AGGAGCCATGTCAACCAT
* * *
356645 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGT
1 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGATCTCCTCATCATGT
*
356710 AGGAGCCGTGTCAACCAT
66 AGGAGCCATGTCAACCAT
**
356728 AGATAACCAGCCGTCCTCATCACGTAGGAAC
1 AGATGGCCAGCCGTCCTCATCACGTAGGAAC
356759 TAAGTTATCA
Statistics
Matches: 184, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 18 0.10
83 166 0.90
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.22
Consensus pattern (83 bp):
AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGATCTCCTCATCATGT
AGGAGCCATGTCAACCAT
Found at i:356839 original size:134 final size:134
Alignment explanation
Indices: 356645--356892 Score: 426
Period size: 134 Copynumber: 1.9 Consensus size: 134
356635 TGTCAACCAT
*
356645 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGT
1 AGATGACCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGT
356710 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACTAAGTTATCACCACTC
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACTAAGTTATCACCACTC
356775 CTAA
131 CTAA
*
356779 AGATGACCAGCCGTCCTCATCACGTAGGAACCGTGTCAT-CTCTCGACCAGACCTCCTCATCACG
1 AGATGACCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCT-GACCAGACCTCCTCATCACG
* * * *
356843 TAGGAGCCGTGTCACCCTTAGATAACCAGCTGTCCTCATCATGTAGGAAC
65 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAAC
356893 CGTGTTATCA
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
133 3 0.03
134 104 0.97
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (134 bp):
AGATGACCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGT
AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACTAAGTTATCACCACTC
CTAA
Found at i:357121 original size:3 final size:3
Alignment explanation
Indices: 357113--357147 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
357103 TAATTTAATT
357113 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
357148 GTTTATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:357137 original size:16 final size:16
Alignment explanation
Indices: 357116--357147 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
357106 TTTAATTTTA
357116 TTATTATTATTATTAT
1 TTATTATTATTATTAT
357132 TTATTATTATTATTAT
1 TTATTATTATTATTAT
357148 GTTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:357153 original size:22 final size:22
Alignment explanation
Indices: 357113--357159 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
357103 TAATTTAATT
*
357113 TTATTATTATTATTATTATTTA
1 TTATTATTATTATTATTATTAA
357135 TTATTATTATTATGT-TTATTAA
1 TTATTATTATTAT-TATTATTAA
357157 TTA
1 TTA
357160 CATATTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTATTATTATTATTATTAA
Found at i:357781 original size:13 final size:14
Alignment explanation
Indices: 357760--357795 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
357750 GTTCAGGGAG
*
357760 AGAAAAAAAAAACC
1 AGAAAAAAAAAACA
357774 AGAAAAAAAAAACA
1 AGAAAAAAAAAACA
357788 AGAAAAAA
1 AGAAAAAA
357796 GAGAACTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAACA
Found at i:365580 original size:2 final size:2
Alignment explanation
Indices: 365573--365607 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
365563 ATAAAACAAT
365573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
365608 TAAAATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:365792 original size:30 final size:30
Alignment explanation
Indices: 365757--365837 Score: 109
Period size: 25 Copynumber: 2.9 Consensus size: 30
365747 CATTTCTAAC
365757 ATCAATATTCTCTTAATTTTATTTTTTAAT
1 ATCAATATTCTCTTAATTTTATTTTTTAAT
*
365787 GTCAATATTCTC-TAA---T-TTTTTTAAT
1 ATCAATATTCTCTTAATTTTATTTTTTAAT
*
365812 ATCAATATTCTCTTAATTTTACTTTT
1 ATCAATATTCTCTTAATTTTATTTTT
365838 CAACGTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 20 0.47
26 4 0.09
29 4 0.09
30 15 0.35
ACGTcount: A:0.28, C:0.12, G:0.01, T:0.58
Consensus pattern (30 bp):
ATCAATATTCTCTTAATTTTATTTTTTAAT
Found at i:371764 original size:14 final size:14
Alignment explanation
Indices: 371745--371788 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
371735 TGTTTGGTAA
371745 TATGTTCGTTCATT
1 TATGTTCGTTCATT
371759 TATGTTCG----TT
1 TATGTTCGTTCATT
*
371769 TATGTGCGTTCATT
1 TATGTTCGTTCATT
371783 TATGTT
1 TATGTT
371789 TAGCCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 9 0.38
14 15 0.62
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:371993 original size:23 final size:23
Alignment explanation
Indices: 371963--372071 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
371953 TTTTCATTTA
371963 TGTTCGTTTACGTTCATTTATCG
1 TGTTCGTTTACGTTCATTTATCG
*
371986 TGTTCGTTTACGTTCATTTATTTG
1 TGTTCGTTTACGTTCATTTA-TCG
* * * *
372010 TGTTTGTTTACATTCGTTTATTG
1 TGTTCGTTTACGTTCATTTATCG
* *
372033 TGTTCGTTTATGTTCGTTTACATC-
1 TGTTCGTTTACGTTCATTT--ATCG
*
372057 TGTTCGTTTATGTTC
1 TGTTCGTTTACGTTC
372072 GTTCAATTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
23 39 0.52
24 34 0.45
25 2 0.03
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTACGTTCATTTATCG
Found at i:372018 original size:24 final size:23
Alignment explanation
Indices: 371963--372090 Score: 130
Period size: 24 Copynumber: 5.4 Consensus size: 23
371953 TTTTCATTTA
* *
371963 TGTTCGTTTACGTTCATTTATCG
1 TGTTCGTTTACGTTCGTTTATTG
*
371986 TGTTCGTTTACGTTCATTTATTTG
1 TGTTCGTTTACGTTCGTTTA-TTG
* *
372010 TGTTTGTTTACATTCGTTTATTG
1 TGTTCGTTTACGTTCGTTTATTG
* * *
372033 TGTTCGTTTATGTTCGTTTACATC
1 TGTTCGTTTACGTTCGTTTA-TTG
* *
372057 TGTTCGTTTATGTTCGTTCAATTG
1 TGTTCGTTTACGTTCGTT-TATTG
*
372081 TGTTTGTTTA
1 TGTTCGTTTA
372091 TAATTTAAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
23 40 0.45
24 48 0.54
25 1 0.01
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTACGTTCGTTTATTG
Found at i:372073 original size:47 final size:47
Alignment explanation
Indices: 371963--372091 Score: 141
Period size: 47 Copynumber: 2.7 Consensus size: 47
371953 TTTTCATTTA
* * * ** *
371963 TGTTCGTTTACGTTCATTTATCGTGTTCGTTTACGTTCATTTATTTG
1 TGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCATTTACATC
* * *
372010 TGTTTGTTTACATTCGTTTATTGTGTTCGTTTATGTTCGTTTACATC
1 TGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCATTTACATC
* * *
372057 TGTTCGTTTATGTTCGTTCAATTGTGTTTGTTTAT
1 TGTTCGTTTACGTTCGTT-TATTGTGTTCGTTTAT
372092 AATTTAAATG
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 53 0.79
48 14 0.21
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (47 bp):
TGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCATTTACATC
Found at i:372371 original size:16 final size:16
Alignment explanation
Indices: 372337--372377 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
372327 ATTTACTTCA
* *
372337 GAATGATT-AAGTTTT
1 GAATGATTCAAATGTT
372352 GAATGATTCAAATGTT
1 GAATGATTCAAATGTT
372368 GAATGATTCA
1 GAATGATTCA
372378 GAGACTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (16 bp):
GAATGATTCAAATGTT
Found at i:387941 original size:64 final size:63
Alignment explanation
Indices: 387872--388078 Score: 206
Period size: 64 Copynumber: 3.2 Consensus size: 63
387862 TGGACCCTTA
* *
387872 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGAT
* * * *
387935 GATGCATCGATGTA-CAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGT
1 G-TGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATACTCAGAGTGCATCGATGCAT-GG
387998 AT
62 AT
* * ** *
388000 GTGCATCGGTGCATGAAATGCATTCAATG-TTCAATTTATTCCATGA-TGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACT-CA-GAGTGCATCGATGCATGGA-
388063 T
63 T
*
388064 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
388079 CACTCTGAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 23 0.19
64 60 0.50
65 35 0.29
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGAT
Found at i:388465 original size:15 final size:15
Alignment explanation
Indices: 388445--388499 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
388435 CCCCCTTTAA
388445 AACATTTTAACACTT
1 AACATTTTAACACTT
** *
388460 AACATTTCTCCCCCTT
1 AACATTT-TAACACTT
388476 AAAACATTTTAACACTT
1 --AACATTTTAACACTT
388493 AACATTT
1 AACATTT
388500 CTCCCCCCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 14 0.45
16 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.38
Consensus pattern (15 bp):
AACATTTTAACACTT
Found at i:388478 original size:33 final size:34
Alignment explanation
Indices: 388425--388506 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 34
388415 CCCCCTTACT
*
388425 TTAACACTTC-CCCCCTTTAAAACATTTTAACAC
1 TTAACATTTCTCCCCCTTTAAAACATTTTAACAC
388458 TTAACATTTCTCCCCC-TTAAAACATTTTAACAC
1 TTAACATTTCTCCCCCTTTAAAACATTTTAACAC
388491 TTAACATTTCTCCCCC
1 TTAACATTTCTCCCCC
388507 CTTTTTGTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 42 0.89
34 5 0.11
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.35
Consensus pattern (34 bp):
TTAACATTTCTCCCCCTTTAAAACATTTTAACAC
Found at i:389876 original size:13 final size:13
Alignment explanation
Indices: 389844--389878 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
389834 TGGGCATAGT
389844 TTTGAAAA-AATA
1 TTTGAAAATAATA
389856 TTTAGAAAATAATA
1 TTT-GAAAATAATA
389870 TTTGAAAAT
1 TTTGAAAAT
389879 TATAATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 11 0.52
14 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:389945 original size:13 final size:13
Alignment explanation
Indices: 389927--389951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389917 AATCAAAAAC
389927 ATCAAATTTAGAA
1 ATCAAATTTAGAA
389940 ATCAAATTTAGA
1 ATCAAATTTAGA
389952 TTTTTGATTT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:394333 original size:118 final size:118
Alignment explanation
Indices: 394112--394333 Score: 261
Period size: 118 Copynumber: 1.9 Consensus size: 118
394102 CTTTCAAATC
* *
394112 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
394177 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * * *
394230 AAAA-TTTCTTTTTCAA-AGTTTTCAGATTTTAGTTTTGAAAGCTCTAACTCTTTTTTTCAACAT
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTCAGTTTTGAAAGCTCTAAATC-CTTCTTCAACAT
* * * **
394293 TTCATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
394334 TATCATTTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
116 1 0.01
117 39 0.45
118 42 0.49
119 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:395643 original size:20 final size:20
Alignment explanation
Indices: 395606--395643 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
395596 CTTAAACTTC
*
395606 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
395626 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
395644 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:395842 original size:23 final size:23
Alignment explanation
Indices: 395800--395868 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
395790 CACCACAGCT
*
395800 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
395823 CGTCGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
395846 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
395869 TATAATATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:399854 original size:21 final size:20
Alignment explanation
Indices: 399828--399926 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
399818 AATCAGTTTC
399828 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
399849 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
399870 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
399890 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
399911 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
399927 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:399919 original size:20 final size:20
Alignment explanation
Indices: 399894--400086 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
399884 GATTTTCCAG
* ** *
399894 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
399914 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
399934 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
399954 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
399974 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
399994 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
400014 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
400034 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
400055 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
400075 AATCGCAACGCG
1 AATCGCAACGCG
400087 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:400505 original size:33 final size:33
Alignment explanation
Indices: 400466--400536 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
400456 TTCACTTAGA
400466 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
400499 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
400532 TTTCA
1 TTTCA
400537 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:400648 original size:21 final size:20
Alignment explanation
Indices: 400622--400695 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
400612 TGCAGAAGAG
400622 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
400643 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
400663 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
400685 TCGCAACGAGA
1 TCGCAACGAGA
400696 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:400702 original size:14 final size:14
Alignment explanation
Indices: 400683--400738 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
400673 GAAAAATGAA
400683 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
400697 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
400714 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
400729 AATCGCAACG
1 AATCGCAACG
400739 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:400721 original size:32 final size:33
Alignment explanation
Indices: 400676--400754 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
400666 GCAACGAGAA
400676 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
400709 AAATG-AAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
400741 AAACCAAAATCGCA
1 AAATGAAAATCGCA
400755 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:400772 original size:19 final size:19
Alignment explanation
Indices: 400750--400863 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
400740 GAAACCAAAA
*
400750 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
400769 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
400783 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
400802 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
400822 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
400842 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
400862 TC
1 TC
400864 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 28 0.36
20 21 0.27
21 13 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:400841 original size:40 final size:41
Alignment explanation
Indices: 400780--400863 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
400770 CGCGTTGCGA
***
400780 TTCTCTCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
*
400820 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
400861 TTC
1 TTC
400864 AACCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 19 0.49
41 20 0.51
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.48
Consensus pattern (41 bp):
TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
Found at i:400845 original size:20 final size:20
Alignment explanation
Indices: 400779--400861 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
400769 TCGCGTTGCG
400779 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
400799 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
400818 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
400839 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
400859 ATT
1 ATT
400862 TCAACCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.30
20 24 0.45
21 13 0.25
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:402706 original size:93 final size:93
Alignment explanation
Indices: 402547--402862 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
402537 TAGATTGCTT
*
402547 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
402612 TTTGTCTTTGTTTCGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
402640 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
402705 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
402733 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAGTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
402798 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
402826 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
402863 AATACCATGA
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 219 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:403000 original size:19 final size:19
Alignment explanation
Indices: 402960--403039 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
402950 TAGTTTACTT
* *
402960 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
402980 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
402999 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
**
403013 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
403032 TCGCAACG
1 TCGCAACG
403040 ACAAAATCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
14 8 0.16
16 5 0.10
17 4 0.08
19 21 0.42
20 12 0.24
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:403020 original size:33 final size:33
Alignment explanation
Indices: 402976--403069 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
402966 CACGAAACTT
**
402976 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
403009 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
403042 AAAATCGCAATGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
403070 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:403046 original size:14 final size:14
Alignment explanation
Indices: 402995--403051 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
402985 ACGCGAAATG
402995 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
403009 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
403028 AAAATCGCAACGAC
1 AAAATCGCAACGAC
403042 AAAATCGCAA
1 AAAATCGCAA
403052 TGCGAAACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.28, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:403065 original size:19 final size:19
Alignment explanation
Indices: 403011--403075 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
403001 GCAACGACAG
*
403011 AATCGCAACGCGAAACCAA
1 AATCGCAATGCGAAACCAA
403030 AATCGCAA--CG--A-CAA
1 AATCGCAATGCGAAACCAA
403044 AATCGCAATGCGAAACCAA
1 AATCGCAATGCGAAACCAA
*
403063 AATCGCATTGCGA
1 AATCGCAATGCGA
403076 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.57
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAATGCGAAACCAA
Found at i:403087 original size:19 final size:19
Alignment explanation
Indices: 403065--403237 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
403055 GAAACCAAAA
*
403065 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
403084 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
403098 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
403117 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
403133 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
403150 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
403169 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
403188 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
403207 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
403227 TCGTGTTGCGA
1 TCGCGTTGCGA
403238 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 80 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:403195 original size:38 final size:38
Alignment explanation
Indices: 403065--403237 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
403055 GAAACCAAAA
*
403065 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * *
403100 T--CGTTGTGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
403133 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
403169 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
403207 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
403238 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 50 0.44
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:405167 original size:14 final size:14
Alignment explanation
Indices: 405148--405183 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
405138 ATTGTTTAAT
405148 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
405162 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
405176 TGATTTGT
1 TGATTTGT
405184 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:405306 original size:19 final size:19
Alignment explanation
Indices: 405290--405387 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
405280 AAAAATGACT
405290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
405309 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
405328 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
405342 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
405361 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
405381 ATCGCAA
1 ATCGCAA
405388 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.55
20 16 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:405397 original size:53 final size:52
Alignment explanation
Indices: 405294--405406 Score: 208
Period size: 53 Copynumber: 2.2 Consensus size: 52
405284 ATGACTATCG
405294 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCA
*
405346 CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCA
405399 CAATGCGA
1 CAATGCGA
405407 TTTCATTTCG
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 25 0.42
53 34 0.58
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (52 bp):
CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:405522 original size:105 final size:106
Alignment explanation
Indices: 405402--405637 Score: 424
Period size: 105 Copynumber: 2.2 Consensus size: 106
405392 AGAATCGCAA
405402 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
405466 TTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-GT
405506 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
405571 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
*
405612 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
405638 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
104 5 0.04
105 80 0.63
106 41 0.32
107 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (106 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
Found at i:405630 original size:86 final size:84
Alignment explanation
Indices: 405472--405651 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
405462 TCATTTCGCA
405472 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCG-ATTGCGATTTTCAT
405537 TTCCGCATTGCGATTCTCTCG
64 TTCCGCATTGCGATTCTCTCG
* *
405558 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA-T-G-TTGGGATTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTCGATTGCGATTT
405620 TCATTT-CGCATTGCGATTCTCTCG
60 TCATTTCCGCATTGCGATTCTCTCG
405644 TTGCGATT
1 TTGCGATT
405652 GTAATTTCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 51 0.59
87 14 0.16
88 3 0.03
89 3 0.03
90 3 0.03
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGATTGCGATTTTCATTT
CCGCATTGCGATTCTCTCG
Found at i:405635 original size:33 final size:34
Alignment explanation
Indices: 405402--405651 Score: 196
Period size: 33 Copynumber: 7.2 Consensus size: 34
405392 AGAATCGCAA
405402 TGCGA-TTTCATTTCGCATTGCGATTTTCAT--T
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
* * * *
405433 TCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTCA--TCG--T
*
405473 TGCGATTTTCATTTCGCATTGCGATTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
405506 TGCGATTTTCATTTCGCATTGCGATTTTCAT--T
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
* * * *
405538 TCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTCA--TCG--T
405578 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCATCGT
* *
405612 TGGGATTTTCATTTCGCATTGCGATTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
405645 TGCGATT
1 TGCGATT
405652 GTAATTTCCG
Statistics
Matches: 175, Mismatches: 21, Indels: 44
0.73 0.09 0.18
Matches are distributed among these distances:
31 3 0.02
32 12 0.07
33 58 0.33
34 45 0.26
35 3 0.02
36 3 0.02
37 1 0.01
38 14 0.08
39 22 0.13
40 14 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (34 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
Found at i:405666 original size:53 final size:53
Alignment explanation
Indices: 405402--405637 Score: 424
Period size: 53 Copynumber: 4.5 Consensus size: 53
405392 AGAATCGCAA
405402 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
405454 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
405506 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
405559 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
405612 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
405638 CTCTCGTTGC
Statistics
Matches: 179, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
52 57 0.32
53 121 0.68
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:407947 original size:12 final size:12
Alignment explanation
Indices: 407930--407954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407920 TCTTCGGGGA
407930 CTTTTTCTTCTT
1 CTTTTTCTTCTT
407942 CTTTTTCTTCTT
1 CTTTTTCTTCTT
407954 C
1 C
407955 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:408163 original size:24 final size:24
Alignment explanation
Indices: 408129--408175 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
408119 CTGAAACATC
408129 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
408153 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
408176 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:408899 original size:20 final size:20
Alignment explanation
Indices: 408876--409096 Score: 237
Period size: 20 Copynumber: 11.1 Consensus size: 20
408866 GTGTTGTGAA
* *
408876 TTACAGATTCTCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
**
408896 TTACGGATTATCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
* *
408916 TTACAGATTCTCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
**
408936 TTACGGATTATCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
*
408956 TTACGGATACGCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
* *
408976 TTACGGATACGCATTGCGAT
1 TTACGGATTCGCGTTGCGAT
* *
408996 TTACGGATACGCGTTGCTAT
1 TTACGGATTCGCGTTGCGAT
* * *
409016 TTACGGATACACGTTGCGGT
1 TTACGGATTCGCGTTGCGAT
*
409036 TTACGGATACGCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
*
409056 TTATGTG-TTCGCGTTGCGAT
1 TTACG-GATTCGCGTTGCGAT
* **
409076 TTTCATATTCGCGTTGCGAT
1 TTACGGATTCGCGTTGCGAT
409096 T
1 T
409097 CTTGAAAATC
Statistics
Matches: 176, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 175 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
TTACGGATTCGCGTTGCGAT
Found at i:409149 original size:21 final size:20
Alignment explanation
Indices: 409064--409161 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
409054 ATTTATGTGT
* *
409064 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
409084 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
409105 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
409126 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
409147 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
409162 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:409157 original size:42 final size:43
Alignment explanation
Indices: 409064--409162 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
409054 ATTTATGTGT
* *
409064 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
409105 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
409147 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
409163 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:410069 original size:14 final size:14
Alignment explanation
Indices: 410050--410084 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
410040 TTATGACTGT
410050 ATGTATGTATATGC
1 ATGTATGTATATGC
410064 ATGTATGTATATGC
1 ATGTATGTATATGC
410078 ATGTATG
1 ATGTATG
410085 CATTCATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (14 bp):
ATGTATGTATATGC
Found at i:424303 original size:21 final size:19
Alignment explanation
Indices: 424268--424316 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
424258 GTAATACTTT
424268 TAATTTTTTAATATATATTCA
1 TAATTTTTTAATATA-ATT-A
**
424289 TAATTTTTTTTTATAATTA
1 TAATTTTTTAATATAATTA
424308 TATATTTTT
1 TA-ATTTTT
424317 AGAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 9 0.36
21 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTTTTTAATATAATTA
Found at i:424586 original size:15 final size:18
Alignment explanation
Indices: 424568--424607 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
424558 ATTAAAATAA
424568 ATATAAAAT-TTTA-AT-
1 ATATAAAATATTTATATG
424583 ATATAAAATATTTATATG
1 ATATAAAATATTTATATG
424601 ATATAAA
1 ATATAAA
424608 TTAAATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 2 0.09
18 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATAAAATATTTATATG
Found at i:424671 original size:12 final size:12
Alignment explanation
Indices: 424654--424758 Score: 78
Period size: 12 Copynumber: 8.7 Consensus size: 12
424644 ATTTATTTAA
424654 AAAATTAATATT
1 AAAATTAATATT
424666 AAAATTAATATCT
1 AAAATTAATAT-T
*
424679 ATAATATAATATT
1 AAAAT-TAATATT
424692 AAAATATTAATATT
1 -AAA-ATTAATATT
*
424706 -TAATT-AT-TT
1 AAAATTAATATT
424715 AAAAAATTAATATT
1 --AAAATTAATATT
*
424729 AAAATTAA-AAT
1 AAAATTAATATT
424740 -AAATATAATA-T
1 AAAAT-TAATATT
424751 AAAATTAA
1 AAAATTAA
424759 ATAAAACCTC
Statistics
Matches: 76, Mismatches: 5, Indels: 25
0.72 0.05 0.24
Matches are distributed among these distances:
9 2 0.03
10 6 0.08
11 12 0.16
12 29 0.38
13 8 0.11
14 17 0.22
15 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:424703 original size:63 final size:64
Alignment explanation
Indices: 424605--424759 Score: 235
Period size: 63 Copynumber: 2.5 Consensus size: 64
424595 TATATGATAT
*
424605 AAATTAAATATCTAT-A-ATAATATTAAAAAATTAATATTTATTTATTTAAAAAATTAATATTA
1 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTATTTAAAAAATTAATATTA
*
424667 AAATT-AATATCTATAATATAATATTAAAATATTAATATTTAATTATTTAAAAAATTAATATTA
1 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTATTTAAAAAATTAATATTA
** *
424730 AAATTAAAATAAATATAATATAAAATTAAA
1 AAATT-AAATATCTATAATATAATATTAAA
424760 TAAAACCTCT
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
61 9 0.11
62 6 0.07
63 49 0.58
65 20 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (64 bp):
AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTATTTAAAAAATTAATATTA
Found at i:424709 original size:26 final size:25
Alignment explanation
Indices: 424656--424736 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 25
424646 TTATTTAAAA
424656 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-TAT
424681 AATATAATATTAAAATATTAATATT-T
1 AAT-TAATATTAAAA-ATTAATATTAT
*
424707 AATT-AT-TTAAAAAATTAATATTAA
1 AATTAATATT-AAAAATTAATATTAT
424731 AATTAA
1 AATTAA
424737 AATAAATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
23 11 0.22
24 10 0.20
25 5 0.10
26 11 0.22
27 4 0.08
28 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTAATATTAAAAATTAATATTAT
Found at i:424740 original size:14 final size:14
Alignment explanation
Indices: 424622--424733 Score: 70
Period size: 14 Copynumber: 8.9 Consensus size: 14
424612 ATATCTATAA
*
424622 TAATATTAAAAAAT
1 TAATATTAAAATAT
424636 TAATATT----TAT
1 TAATATTAAAATAT
* *
424646 TTAT-TTAAAAAAT
1 TAATATTAAAATAT
424659 TAATATT-AAA-AT
1 TAATATTAAAATAT
*
424671 TAATATCTATAATA-
1 TAATAT-TAAAATAT
424685 TAATATTAAAATAT
1 TAATATTAAAATAT
*
424699 TAATATT--TA-AT
1 TAATATTAAAATAT
*
424710 T-AT-TTAAAAAAT
1 TAATATTAAAATAT
424722 TAATATTAAAAT
1 TAATATTAAAAT
424734 TAAAATAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
9 4 0.05
10 7 0.09
11 4 0.05
12 12 0.16
13 17 0.23
14 30 0.40
15 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATTAAAATAT
Found at i:424753 original size:22 final size:21
Alignment explanation
Indices: 424650--424763 Score: 87
Period size: 21 Copynumber: 5.4 Consensus size: 21
424640 ATTTATTTAT
424650 TTAAA-AAATTAATATTAAAA
1 TTAAATAAATTAATATTAAAA
** *
424670 TT-AATATCTATAATA-TAATA
1 TTAAATAAAT-TAATATTAAAA
* *
424690 TTAAA-ATATTAATATTTAATTAT
1 TTAAATAAATTAATA-TTAA--AA
424713 TTAAA-AAATTAATATTAAAA
1 TTAAATAAATTAATATTAAAA
424733 TTAAAATAAATATAATA-TAAAA
1 TT-AAATAAAT-TAATATTAAAA
424755 TTAAATAAA
1 TTAAATAAA
424764 ACCTCTTTGA
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
19 7 0.09
20 16 0.21
21 20 0.26
22 15 0.20
23 18 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAATAAATTAATATTAAAA
Found at i:427087 original size:84 final size:84
Alignment explanation
Indices: 426946--427111 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
426936 TCTGTGACAA
* *
426946 AACTGAGAACTGAAGTTGAGCCATGGGATTGACTCGATGAGGTGGATATCCTCATCCGAGTAGGA
1 AACTGAGAACTGAAGTTGAGCCATGGAATTGACTCGAAGAGGTGGATATCCTCATCCGAGTAGGA
427011 CTGACTACCCTTGGAGTTG
66 CTGACTACCCTTGGAGTTG
* * *
427030 AACTGAGAACTGAAGTTGAGCTATGGAATTGACTCGAAGAGGTGGATGTTCTCATCCGAGTAGGA
1 AACTGAGAACTGAAGTTGAGCCATGGAATTGACTCGAAGAGGTGGATATCCTCATCCGAGTAGGA
*
427095 CTGCCTACCCTTGGAGT
66 CTGACTACCCTTGGAGT
427112 CGGACTGACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (84 bp):
AACTGAGAACTGAAGTTGAGCCATGGAATTGACTCGAAGAGGTGGATATCCTCATCCGAGTAGGA
CTGACTACCCTTGGAGTTG
Found at i:427116 original size:21 final size:21
Alignment explanation
Indices: 427087--427134 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
427077 GTTCTCATCC
*
427087 GAGTAGGACTGCCTACC-CTTG
1 GAGTAGGACTGAC-ACCTCTTG
*
427108 GAGTCGGACTGACACCTCTTG
1 GAGTAGGACTGACACCTCTTG
427129 GAGTAG
1 GAGTAG
427135 AACCAAGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (21 bp):
GAGTAGGACTGACACCTCTTG
Found at i:427312 original size:84 final size:84
Alignment explanation
Indices: 427179--427363 Score: 259
Period size: 84 Copynumber: 2.2 Consensus size: 84
427169 ATGGGTTCTT
* * * *
427179 CTTGATGAGGTGGATGTCCTCGTCCGAGTTGGACTAAGTACTCTTGGAGTTGAACTGACAACTGA
1 CTTGATGAGGTGGATGTCCTCCTCCGAATTGGACTAACTACTCTCGGAGTTGAACTGACAACTGA
427244 AGTTGA-ACTAT-GAGATTGA
66 AGTTGAGAC-ATGGA-ATTGA
*
427263 CTTGATGAGGTGGATGTCCTCACT-CGAATTGGACTAACTACTCTCGGAGTTGAACTGAGAACTG
1 CTTGATGAGGTGGATGTCCTC-CTCCGAATTGGACTAACTACTCTCGGAGTTGAACTGACAACTG
427327 AAGTTGAGACATGGAATTGA
65 AAGTTGAGACATGGAATTGA
**
427347 CAAGATGAGGTGGATGT
1 CTTGATGAGGTGGATGT
427364 TGAGCTATGG
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
84 86 0.95
85 5 0.05
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (84 bp):
CTTGATGAGGTGGATGTCCTCCTCCGAATTGGACTAACTACTCTCGGAGTTGAACTGACAACTGA
AGTTGAGACATGGAATTGA
Found at i:427387 original size:33 final size:33
Alignment explanation
Indices: 427350--427455 Score: 176
Period size: 33 Copynumber: 3.2 Consensus size: 33
427340 GAATTGACAA
* * * *
427350 GATGAGGTGGATGTTGAGCTATGGGACTGGCTG
1 GATGAGGCGGATGTTGAGCAATGGGATTGACTG
427383 GATGAGGCGGATGTTGAGCAATGGGATTGACTG
1 GATGAGGCGGATGTTGAGCAATGGGATTGACTG
427416 GATGAGGCGGATGTTGAGCAATGGGATTGACTG
1 GATGAGGCGGATGTTGAGCAATGGGATTGACTG
427449 GATGAGG
1 GATGAGG
427456 TGGTTGTCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.23, C:0.08, G:0.44, T:0.25
Consensus pattern (33 bp):
GATGAGGCGGATGTTGAGCAATGGGATTGACTG
Found at i:427633 original size:117 final size:117
Alignment explanation
Indices: 427512--427747 Score: 300
Period size: 117 Copynumber: 2.0 Consensus size: 117
427502 AAGAACTGAA
** * *
427512 GTTGAGCTATGGGATTGACTT-TCTGAGGTGGATG-CCTTCATTCGAGTGGGACTGACTA-CTAT
1 GTTGAGCTATGGGATTGA-TTGGATGAGGTGGATGTCC-TAATCCGAGTGGGACTGACTATC-AT
* *
427574 TGGAGTTGAACTGAGAATTGAAGTTAAGCTATGAAATTGA-TTGGATGAGGTGGAT
63 TGGAGTTGAACTGAGAACTGAAGTTAAGCTATGAAATAGACTT-GATGAGGTGGAT
* *
427629 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTAATCCGAGTTGGACTGACTATCCTTGG
1 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTAATCCGAGTGGGACTGACTATCATTGG
* * * *
427694 AGTTGAACTGAGAACTGATGTTGAGCTATGAGATAGACTTGATGTGGTGGAT
66 AGTTGAACTGAGAACTGAAGTTAAGCTATGAAATAGACTTGATGAGGTGGAT
427746 GT
1 GT
427748 CCCTATCGTA
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
116 2 0.02
117 96 0.93
118 5 0.05
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.32
Consensus pattern (117 bp):
GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTAATCCGAGTGGGACTGACTATCATTGG
AGTTGAACTGAGAACTGAAGTTAAGCTATGAAATAGACTTGATGAGGTGGAT
Found at i:427646 original size:33 final size:33
Alignment explanation
Indices: 427600--427663 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
427590 ATTGAAGTTA
427600 AGCTATGAAATTGATTGGATGAGGTGGATGTTG
1 AGCTATGAAATTGATTGGATGAGGTGGATGTTG
**
427633 AGCTATGGGATTGATTGGATGAGGTGGATGT
1 AGCTATGAAATTGATTGGATGAGGTGGATGT
427664 CCTAATCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (33 bp):
AGCTATGAAATTGATTGGATGAGGTGGATGTTG
Found at i:427767 original size:84 final size:84
Alignment explanation
Indices: 427624--427872 Score: 328
Period size: 84 Copynumber: 3.0 Consensus size: 84
427614 TTGGATGAGG
*
427624 TGGATGTTGAGCTATGGGATTGA-TTGGATGAGGTGGATGTCCTAATCCGAGTTGGACTGACTAT
1 TGGATGTTGAGCTATGAGATTGACTT-GATGAGGTGGATGTCCTAATCCGAGTTGGACTGACTA-
*
427688 CCTTGGAGTTGAACTGAGAAC
64 CCTTGGAGTTGGACTGAGAAC
* *
427709 T-GATGTTGAGCTATGAGATAGACTTGATGTGGTGGATGTCCCT-AT-CGTAGTTGGACTGACTA
1 TGGATGTTGAGCTATGAGATTGACTTGATGAGGTGGATGT-CCTAATCCG-AGTTGGACTGACTA
*
427771 CTCTTGGAGTTGGACTGAGAGC
64 C-CTTGGAGTTGGACTGAGAAC
* * * *
427793 TGGA-GTTGAGCTATGAGATTGACTCGATGAGGTGGATATCCTCATCCGAGCTGGACTGACTACC
1 TGGATGTTGAGCTATGAGATTGACTTGATGAGGTGGATGTCCTAATCCGAGTTGGACTGACTA-C
427857 CTTGGAGTTGGACTGA
65 CTTGGAGTTGGACTGA
427873 CTCCCCTTGC
Statistics
Matches: 146, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
83 6 0.04
84 129 0.88
85 11 0.08
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.30
Consensus pattern (84 bp):
TGGATGTTGAGCTATGAGATTGACTTGATGAGGTGGATGTCCTAATCCGAGTTGGACTGACTACC
TTGGAGTTGGACTGAGAAC
Found at i:427767 original size:201 final size:201
Alignment explanation
Indices: 427408--427829 Score: 560
Period size: 201 Copynumber: 2.1 Consensus size: 201
427398 GAGCAATGGG
* * * *
427408 ATTGACTGGATGAGGCGGATGTTGAGCAATGGGATTGACTGGATGAGGTGGTTGTCCTCATCTGA
1 ATTGACTGGATGAGGTGGATGTTGAGCAATGGGATTGACTGGATGAGGTGGATGTCCTAATCCGA
* * * **
427473 GGTGGACTAACTAGCCTTGTAGTTGAACTAAGAACTGAAGTTGAGCTATGGGATTGACTTTCTGA
66 GGTGGACTAACTAGCCTTGGAGTTGAACTAAGAACTGAAGTTGAGCTATGAGATAGACTTGATGA
* *
427538 GGTGGATGCCTTCATTCGAGTGGGACTGACTACTATTGGAGTTGAACTGAGAATTGAAGTTAAGC
131 GGTGGATGCCCTCATTCGAGTGGGACTGACTACTATTGGAGTTGAACTGAGAACTGAAGTTAAGC
427603 TATGAA
196 TATGAA
* * *
427609 ATTGATTGGATGAGGTGGATGTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTAATCCGA
1 ATTGACTGGATGAGGTGGATGTTGAGCAATGGGATTGACTGGATGAGGTGGATGTCCTAATCCGA
* * * * * *
427674 GTTGGACTGACTATCCTTGGAGTTGAACTGAGAACTGATGTTGAGCTATGAGATAGACTTGATGT
66 GGTGGACTAACTAGCCTTGGAGTTGAACTAAGAACTGAAGTTGAGCTATGAGATAGACTTGATGA
* * * * * *
427739 GGTGGATGTCCCT-A-TCGTAGTTGGACTGACTACTCTTGGAGTTGGACTGAGAGCTGGAGTTGA
131 GGTGGATG-CCCTCATTCG-AGTGGGACTGACTACTATTGGAGTTGAACTGAGAACTGAAGTTAA
*
427802 GCTATGAG
194 GCTATGAA
*
427810 ATTGACTCGATGAGGTGGAT
1 ATTGACTGGATGAGGTGGAT
427830 ATCCTCATCC
Statistics
Matches: 190, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
200 3 0.02
201 184 0.97
202 3 0.02
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (201 bp):
ATTGACTGGATGAGGTGGATGTTGAGCAATGGGATTGACTGGATGAGGTGGATGTCCTAATCCGA
GGTGGACTAACTAGCCTTGGAGTTGAACTAAGAACTGAAGTTGAGCTATGAGATAGACTTGATGA
GGTGGATGCCCTCATTCGAGTGGGACTGACTACTATTGGAGTTGAACTGAGAACTGAAGTTAAGC
TATGAA
Found at i:427870 original size:21 final size:21
Alignment explanation
Indices: 427844--427889 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
427834 TCATCCGAGC
*
427844 TGGACTGACTACCCTTGGAGT
1 TGGACTGACTACCCTTGCAGT
*
427865 TGGACTGACTCCCCTTGCAGT
1 TGGACTGACTACCCTTGCAGT
427886 TGGA
1 TGGA
427890 GTTGGACCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TGGACTGACTACCCTTGCAGT
Done.