Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003421.1 Hibiscus syriacus cultivar Beakdansim tig00007204_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: 882701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 5
Found at i:268285 original size:19 final size:18
Alignment explanation
Indices: 268231--268322 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
268221 AAAATCGCAA
268231 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
268250 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
268264 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
268283 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
268297 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
268316 TGCGATT
1 TGCGATT
268323 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:268332 original size:14 final size:14
Alignment explanation
Indices: 268280--268336 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
268270 TTTGGTTTCG
*
268280 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
268294 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
268313 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
268327 CGTTGCGATT
1 CGTTGCGATT
268337 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:268611 original size:93 final size:93
Alignment explanation
Indices: 268452--268767 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
268442 TCAGGGTATT
268452 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
268517 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
268545 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
268610 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
* *
268638 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTTAACCAAAAGACAAAACAAATACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
268703 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
268731 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
268768 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:270484 original size:20 final size:20
Alignment explanation
Indices: 270453--270549 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 20
270443 TTTTGGTTGA
270453 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
270473 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
270493 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
270512 -A-G--AATCGCAACGCA-A-
1 AATGAAAATCGCAACG-AGAG
270527 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
270547 AAT
1 AAT
270550 CGCAACGCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 9 0.15
16 3 0.05
17 2 0.03
18 1 0.02
19 14 0.23
20 20 0.33
21 12 0.20
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:270505 original size:21 final size:21
Alignment explanation
Indices: 270451--270515 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
270441 TCTTTTGGTT
270451 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
270472 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
270492 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
270513 GAA
1 GAA
270516 TCGCAACGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:270519 original size:14 final size:14
Alignment explanation
Indices: 270500--270556 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
270490 GAGAAATGAA
270500 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
270514 AATCGCAACGCAAAATGAA
1 AATCGCAACG----A-GAG
270533 AATCGCAACGAGAG
1 AATCGCAACGAGAG
270547 AATCGCAACG
1 AATCGCAACG
270557 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
18 1 0.03
19 12 0.33
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:270533 original size:33 final size:33
Alignment explanation
Indices: 270452--270573 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
270442 CTTTTGGTTG
*
270452 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACG-CA
270492 GAAATGAAAATCGCAACGAGAGAATCGCAACGCA
1 -AAATGAAAATCGCAACGAGAGAATCGCAACGCA
*
270526 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCA
270559 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
270574 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 47 0.59
34 1 0.01
35 8 0.10
38 1 0.01
40 1 0.01
41 21 0.27
ACGTcount: A:0.48, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCA
Found at i:270578 original size:19 final size:19
Alignment explanation
Indices: 270451--270578 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
270441 TCTTTTGGTT
*
270451 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
270470 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
270492 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
270509 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
270525 AAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
270542 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
270558 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
270577 GA
1 GA
270579 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 3 0.04
17 2 0.02
18 2 0.02
19 26 0.32
20 12 0.15
21 11 0.13
22 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:270609 original size:14 final size:14
Alignment explanation
Indices: 270590--270646 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
270580 TTTGGTTTCG
270590 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
270604 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
270623 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
270637 CGTTGCGATT
1 CGTTGCGATT
270647 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:270622 original size:33 final size:33
Alignment explanation
Indices: 270574--270653 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
270564 AAAATCGCAA
**
270574 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
270607 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
270640 TGCGATTTTCATTT
1 TGCGATTTTCATTT
270654 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:270659 original size:21 final size:21
Alignment explanation
Indices: 270634--270707 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
270624 GTTGCGATTC
270634 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
270655 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
270676 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
270697 TCTCGTTGCGA
1 TCTCGTTGCGA
270708 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:270828 original size:33 final size:33
Alignment explanation
Indices: 270786--270858 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
270776 AATACTAACT
*
270786 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
270819 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
270852 T-AAAATC
1 TGAAAATC
270859 TAAGTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 6 0.16
33 31 0.84
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.12
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:271261 original size:20 final size:20
Alignment explanation
Indices: 271236--271428 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
271226 CTTTAAAAAT
271236 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
271256 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
271276 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
271297 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
271317 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
271337 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
271357 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
271377 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
271397 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
271417 CGCGTTGCGATT
1 CGCGTTGCGATT
271429 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:276739 original size:34 final size:34
Alignment explanation
Indices: 276696--276764 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
276686 GTTTTGAAAA
*
276696 AGAAAGTTCATATTCCAAGGTTTCAGTCTGCATT
1 AGAAAGTTCATAGTCCAAGGTTTCAGTCTGCATT
276730 AGAAAGTTCATAGTCCAAGGTTTCAGTCTGCATT
1 AGAAAGTTCATAGTCCAAGGTTTCAGTCTGCATT
276764 A
1 A
276765 ACACATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (34 bp):
AGAAAGTTCATAGTCCAAGGTTTCAGTCTGCATT
Found at i:277516 original size:134 final size:134
Alignment explanation
Indices: 277366--277642 Score: 527
Period size: 134 Copynumber: 2.1 Consensus size: 134
277356 TGCAAACTTT
277366 ATATAGATGTGTGTGTATAAATGATTTATCTTTTGTTTGGCAACTCTCAGACCTTGTGAAAGTAG
1 ATATAGATGTGTGTGTATAAATGATTTATCTTTTGTTTGGCAACTCTCAGACCTTGTGAAAGTAG
277431 TAGTAACAAGGCACCTAACCATGGACGACATGGTGAAACTCATTGTGTGTTTTGCACGACATTAC
66 TAGTAACAAGGCACCTAACCATGGACGACATGGTGAAACTCATTGTGTGTTTTGCACGACATTAC
*
277496 ATGC
131 AAGC
277500 ATATAGATGTGTGTGTATAAATGATTTATCTTTTGTTTGGCAACTCTCAGACCTTGTGAAAGTAG
1 ATATAGATGTGTGTGTATAAATGATTTATCTTTTGTTTGGCAACTCTCAGACCTTGTGAAAGTAG
*
277565 TAGTAACAAGGCACCTAACCATGGACGACATGGTGAAATTCATTGTGTGTTTTGCACGACATTAC
66 TAGTAACAAGGCACCTAACCATGGACGACATGGTGAAACTCATTGTGTGTTTTGCACGACATTAC
277630 AAGC
131 AAGC
*
277634 AGATAGATG
1 ATATAGATG
277643 GATGCAGTGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 140 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (134 bp):
ATATAGATGTGTGTGTATAAATGATTTATCTTTTGTTTGGCAACTCTCAGACCTTGTGAAAGTAG
TAGTAACAAGGCACCTAACCATGGACGACATGGTGAAACTCATTGTGTGTTTTGCACGACATTAC
AAGC
Found at i:277707 original size:29 final size:29
Alignment explanation
Indices: 277669--277729 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
277659 AAATTCATTT
* *
277669 CCTCCCATCTTATCAATTGGAAAACTTTC
1 CCTCCCATCTTATCAATTAGAAAACTCTC
277698 CCTCCCATCTTATCAATTAGAAAACTCTC
1 CCTCCCATCTTATCAATTAGAAAACTCTC
277727 CCT
1 CCT
277730 TCGTCGTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.34, G:0.05, T:0.33
Consensus pattern (29 bp):
CCTCCCATCTTATCAATTAGAAAACTCTC
Found at i:278146 original size:3 final size:3
Alignment explanation
Indices: 278138--278188 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
278128 GTTTTCGTCC
* * * *
278138 TGT TGT TGT TGT TAT TAT TAT TAT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
278186 TGT
1 TGT
278189 AGGACTTTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.08, C:0.00, G:0.25, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:279160 original size:18 final size:17
Alignment explanation
Indices: 279137--279187 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
279127 TGAATATTTA
279137 TCCCGAATGACCACTATG
1 TCCCGAA-GACCACTATG
279155 TCCCGAAGAACCACTATG
1 TCCCGAAG-ACCACTATG
*
279173 TCCTGAAAGACCACT
1 TCCCG-AAGACCACT
279188 GATAATCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 1 0.03
18 26 0.87
19 3 0.10
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (17 bp):
TCCCGAAGACCACTATG
Found at i:279444 original size:2 final size:2
Alignment explanation
Indices: 279437--279478 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
279427 TAACGTTAAC
279437 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
279479 GCATGTGCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291856 original size:17 final size:17
Alignment explanation
Indices: 291834--291874 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
291824 GGGAGAAGTG
291834 TTAAATGTGTTTTAAAT
1 TTAAATGTGTTTTAAAT
291851 TTAAATGTGTTTTAAAT
1 TTAAATGTGTTTTAAAT
291868 TTAAATG
1 TTAAATG
291875 ATAAATGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (17 bp):
TTAAATGTGTTTTAAAT
Found at i:295534 original size:18 final size:18
Alignment explanation
Indices: 295511--295545 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
295501 ACTGAATATT
*
295511 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
295529 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
295546 GATAATCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:296209 original size:64 final size:64
Alignment explanation
Indices: 296119--296281 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
296109 ATCCCTTGAC
* * *
296119 GGGTGCATCAATGGACTA-TCTATGCATCGGTACA-TAAAT-CTCATTCGATGTTTGTATTTTAA
1 GGGTGCATCAATGCACTACT-TGTGCATCGATACACT-AATGCT-ATTCGATGTTTGTATTTTAA
*
296181 GG
63 AG
* * *
296183 GGGTGCATCAATGCACTACTTGTGCATCGATACACTGATGGTATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCAATGCACTACTTGTGCATCGATACACTAATGCTATTCGATGTTTGTATTTTAAAG
* * * * *
296247 GAGTGCATCGATACACTTCATGTGCATCGATACAC
1 GGGTGCATCAATGCACTACTTGTGCATCGATACAC
296282 CTTGAAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
64 81 0.96
65 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
GGGTGCATCAATGCACTACTTGTGCATCGATACACTAATGCTATTCGATGTTTGTATTTTAAAG
Found at i:299052 original size:130 final size:131
Alignment explanation
Indices: 298816--299147 Score: 452
Period size: 130 Copynumber: 2.5 Consensus size: 131
298806 CGGTTAAAGT
* * * * * * *
298816 AATAAATGATTTCTTTAAGGCATAAGAGGTAATTTATTCTCGATTGGAAATAATCAGATATTACC
1 AATAAATGATTGCTTTAAGGCATGAGAAGTCATTTATTCTCTATTGGAAATAATTAGATATTATC
* * * * * **
298881 GTTTTCTCTCGAGTCAATATTGATTTTTAAGACGGAATAGTGATATCTCTTCATTTTGATTGGAG
66 GTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATATCTTCATTTCAATTGGAG
298946 C
131 C
* * *
298947 AATAAATGATTGCTTTAAAGCATGAGATGTCATTTATTCTCTATTGGAAATCATTA-ATATTATC
1 AATAAATGATTGCTTTAAGGCATGAGAAGTCATTTATTCTCTATTGGAAATAATTAGATATTATC
*
299011 GTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATATCTTCATTTCAATTGGGG
66 GTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATATCTTCATTTCAATTGGAG
*
299076 T
131 C
* *
299077 AATAAATGACTGTTTTAAGGCATGA-AAGATCATTTATTCTCTATTGGAAATAATTAGATATTAT
1 AATAAATGATTGCTTTAAGGCATGAGAAG-TCATTTATTCTCTATTGGAAATAATTAGATATTAT
299141 CGTTTTC
65 CGTTTTC
299148 TCTCTTAAAA
Statistics
Matches: 176, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
129 2 0.01
130 112 0.64
131 62 0.35
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
AATAAATGATTGCTTTAAGGCATGAGAAGTCATTTATTCTCTATTGGAAATAATTAGATATTATC
GTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATATCTTCATTTCAATTGGAG
C
Found at i:308094 original size:57 final size:58
Alignment explanation
Indices: 308004--308114 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 58
307994 AGATAGTAAA
*
308004 AAACAGCAATAACCAATGACAGGTATGCCGACCT-AAAAGGAAATATGAGAGAATAGT
1 AAACAGCAATAACCAATGACAGGTATACCGACCTGAAAAGGAAATATGAGAGAATAGT
* * *
308061 AAACAGC-ATAAACCAATGGCATGTATACTGACCTGAAAAGGAAATATGAGAGAA
1 AAACAGCAAT-AACCAATGACAGGTATACCGACCTGAAAAGGAAATATGAGAGAA
308115 GGCAGGTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 2 0.04
57 27 0.56
58 19 0.40
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.16
Consensus pattern (58 bp):
AAACAGCAATAACCAATGACAGGTATACCGACCTGAAAAGGAAATATGAGAGAATAGT
Found at i:313097 original size:21 final size:21
Alignment explanation
Indices: 313071--313138 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
313061 CATATTCACA
*
313071 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
313092 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
313111 TTGCGACAGTCTAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
313132 TTGCGAT
1 TTGCGAT
313139 TTATTCCAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 14 0.40
21 21 0.60
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:313127 original size:40 final size:42
Alignment explanation
Indices: 313069--313163 Score: 149
Period size: 40 Copynumber: 2.3 Consensus size: 42
313059 TACATATTCA
313069 CATTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
313109 CGTTGCGACAGTCTAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
313151 CATTGCGATAGTC
1 CATTGCGATAGTC
313164 CAAAATCGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 26 0.54
41 2 0.04
42 20 0.42
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:314067 original size:21 final size:21
Alignment explanation
Indices: 314041--314213 Score: 114
Period size: 21 Copynumber: 8.3 Consensus size: 21
314031 GATTTTGGAC
* *
314041 AATCGCAACAAATTTGGAATA
1 AATCGCAACGAACTTGGAATA
* *
314062 AATCGCAAAGCGAACTTCGACT-
1 AATCGC-AA-CGAACTTGGAATA
314084 -ATCGCAACGAACTTGGAATA
1 AATCGCAACGAACTTGGAATA
314104 AATCGCAACGCGAACTTGGAATA
1 AATCGCAA--CGAACTTGGAATA
* * *
314127 AATCACAACGCGAACTTCGACT-
1 AATCGCAA--CGAACTTGGAATA
*
314149 -ATCGCAACGAACTTGGACT-
1 AATCGCAACGAACTTGGAATA
*
314168 -ATCGCAACGCGAACTTGGACT-
1 AATCGCAA--CGAACTTGGAATA
*
314189 -ATCGCAACGAATTTGG-A-A
1 AATCGCAACGAACTTGGAATA
314207 AATCGCA
1 AATCGCA
314214 TTGCGATAGT
Statistics
Matches: 129, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
19 42 0.33
20 2 0.02
21 43 0.33
22 2 0.02
23 40 0.31
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
AATCGCAACGAACTTGGAATA
Found at i:314121 original size:23 final size:21
Alignment explanation
Indices: 314054--314213 Score: 134
Period size: 19 Copynumber: 7.6 Consensus size: 21
314044 CGCAACAAAT
*
314054 TTGGAATAAATCGCAAAGCGAAC
1 TTGGAAT--ATCGCAACGCGAAC
* *
314077 TTCGACTATCGCAA--CGAAC
1 TTGGAATATCGCAACGCGAAC
314096 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAACGCGAAC
*
314119 TTGGAATAAATCACAACGCGAAC
1 TTGGAAT--ATCGCAACGCGAAC
* *
314142 TTCGACTATCGCAA--CGAAC
1 TTGGAATATCGCAACGCGAAC
*
314161 TTGGACTATCGCAACGCGAAC
1 TTGGAATATCGCAACGCGAAC
* *
314182 TTGGACTATCGCAA--CGAAT
1 TTGGAATATCGCAACGCGAAC
*
314201 TTGGAAAATCGCA
1 TTGGAATATCGCA
314214 TTGCGATAGT
Statistics
Matches: 119, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
19 43 0.36
21 39 0.33
23 37 0.31
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
TTGGAATATCGCAACGCGAAC
Found at i:314140 original size:65 final size:63
Alignment explanation
Indices: 314054--314186 Score: 221
Period size: 65 Copynumber: 2.1 Consensus size: 63
314044 CGCAACAAAT
*
314054 TTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGAATAAATCACAAAGCGAACTTCGACTATCGCAACGAACTTGGAAT--ATCGCAACGCGAAC
* *
314119 TTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAAC
1 TTGGAATAAATCACAAAGCGAACTTCGACTATCGCAACGAACTTGGAATATCGCAACGCGAAC
314182 TTGGA
1 TTGGA
314187 CTATCGCAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 19 0.29
65 46 0.71
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (63 bp):
TTGGAATAAATCACAAAGCGAACTTCGACTATCGCAACGAACTTGGAATATCGCAACGCGAAC
Found at i:314212 original size:40 final size:40
Alignment explanation
Indices: 314105--314213 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 40
314095 CTTGGAATAA
*
314105 ATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGG-A-AAATCGCAACGCGAACTTCGACT
** *
314149 ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAAAATCGCAACGCGAACTTCGACT
*
314189 ATCGCAACGAATTTGGAAAATCGCA
1 ATCGCAACGAACTTGGAAAATCGCA
314214 TTGCGATAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 41 0.71
41 1 0.02
42 9 0.16
44 7 0.12
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAACTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:314238 original size:21 final size:21
Alignment explanation
Indices: 314209--314261 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
314199 ATTTGGAAAA
*
314209 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
314230 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
314251 TCGCGTTGCGA
1 TCGCGTTGCGA
314262 ACCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:324079 original size:11 final size:11
Alignment explanation
Indices: 324063--324140 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
324053 GGACTGGGTC
*
324063 AATCGAGCTTG
1 AATCGAGCTTA
*
324074 AATCGAGCTCAA
1 AATCGAGCT-TA
*
324086 AATCGAGCTTG
1 AATCGAGCTTA
*
324097 AATCGAGCTCAA
1 AATCGAGCT-TA
324109 AATCGAGCTTAA
1 AATCGAGCTT-A
* *
324121 AATTGAGCTTC
1 AATCGAGCTTA
324132 AATCGAGCT
1 AATCGAGCT
324141 CGAGTCGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
11 26 0.48
12 28 0.52
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (11 bp):
AATCGAGCTTA
Found at i:324089 original size:23 final size:23
Alignment explanation
Indices: 324063--324118 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
324053 GGACTGGGTC
324063 AATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
324086 AATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
324109 AATCGAGCTT
1 AATCGAGCTT
324119 AAAATTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTCAA
Found at i:324130 original size:35 final size:35
Alignment explanation
Indices: 324063--324129 Score: 57
Period size: 35 Copynumber: 1.9 Consensus size: 35
324053 GGACTGGGTC
* **
324063 AATCGAGCTTGAATCGAGCTCAAAATCGAGCT-TG
1 AATCGAGCTTCAATCGAGCTCAAAATCGAGCTCAA
* *
324097 AATCGAGC-TCAAAATCGAGCTTAAAATTGAGCT
1 AATCGAGCTTC--AATCGAGCTCAAAATCGAGCT
324130 TCAATCGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 1 0.04
34 8 0.29
35 19 0.68
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (35 bp):
AATCGAGCTTCAATCGAGCTCAAAATCGAGCTCAA
Found at i:324403 original size:16 final size:16
Alignment explanation
Indices: 324382--324450 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
324372 GGGTCTCCAA
324382 CATTTATGTTCGTGTT
1 CATTTATGTTCGTGTT
324398 CATTTATGTTCGTGTT
1 CATTTATGTTCGTGTT
* *
324414 CGTTTATGTTCGTATT
1 CATTTATGTTCGTGTT
*
324430 CGTTTATGTTCGT-TT
1 CATTTATGTTCGTGTT
324445 -ATTTAT
1 CATTTAT
324451 TAAATGAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 43 0.86
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (16 bp):
CATTTATGTTCGTGTT
Found at i:343790 original size:20 final size:20
Alignment explanation
Indices: 343765--343809 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
343755 AAAACTGAAA
*
343765 AAAAATCCAGTCTGGGGTTT
1 AAAAATCCAGTATGGGGTTT
*
343785 AAAAATCCGGTATGGGGTTT
1 AAAAATCCAGTATGGGGTTT
343805 AAAAA
1 AAAAA
343810 ATTAGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCAGTATGGGGTTT
Found at i:348378 original size:24 final size:24
Alignment explanation
Indices: 348346--348399 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
348336 TTTTGTGCCT
*
348346 TGCGCCTGAGGCAATAAAGGTTTA
1 TGCGCCTGAGGCAATAAAGATTTA
348370 TGCGCCTGAGGCAATAAAGATTTA
1 TGCGCCTGAGGCAATAAAGATTTA
348394 TGCGCC
1 TGCGCC
348400 CTGAACCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (24 bp):
TGCGCCTGAGGCAATAAAGATTTA
Found at i:350164 original size:42 final size:42
Alignment explanation
Indices: 350100--350185 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
350090 CAGGTTGCTG
350100 GGAGTGCATGGCGACCTGTGTTGGGGTGTTGGGGACGTGCAT
1 GGAGTGCATGGCGACCTGTGTTGGGGTGTTGGGGACGTGCAT
*
350142 GGAGTGCATGGCGACCTTTGTTGGGGTGTTGGGGACGTGCAT
1 GGAGTGCATGGCGACCTGTGTTGGGGTGTTGGGGACGTGCAT
350184 GG
1 GG
350186 CACATGCAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.12, C:0.14, G:0.48, T:0.27
Consensus pattern (42 bp):
GGAGTGCATGGCGACCTGTGTTGGGGTGTTGGGGACGTGCAT
Found at i:351080 original size:14 final size:14
Alignment explanation
Indices: 351061--351088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
351051 GACAACAATT
351061 TTGTAGAAAACAGA
1 TTGTAGAAAACAGA
351075 TTGTAGAAAACAGA
1 TTGTAGAAAACAGA
351089 CAAGTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
TTGTAGAAAACAGA
Found at i:353385 original size:51 final size:51
Alignment explanation
Indices: 353309--353410 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
353299 GTAAGGAAAG
* *
353309 AATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACT
1 AATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTATAACT
353360 AATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTATAACT
1 AATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTATAACT
353411 CTCCCCCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (51 bp):
AATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTATAACT
Found at i:355188 original size:14 final size:15
Alignment explanation
Indices: 355153--355193 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
355143 CCTGATACCA
355153 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
355169 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
355183 TGTAGAAAACA
1 TGTAGAAAACA
355194 AACAAGTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.17
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:356679 original size:18 final size:18
Alignment explanation
Indices: 356656--356697 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
356646 ATGACGTAGG
356656 AAACAAAATATAACTAGA
1 AAACAAAATATAACTAGA
356674 AAACAAAATATAACTAGA
1 AAACAAAATATAACTAGA
356692 AAACAA
1 AAACAA
356698 GTACACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.14
Consensus pattern (18 bp):
AAACAAAATATAACTAGA
Found at i:366583 original size:17 final size:17
Alignment explanation
Indices: 366563--366596 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
366553 TTTGTTTGTA
*
366563 GTTAGGTTTATTTTAAT
1 GTTAGGTTTAGTTTAAT
366580 GTTAGGTTTAGTTTAAT
1 GTTAGGTTTAGTTTAAT
366597 ATATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (17 bp):
GTTAGGTTTAGTTTAAT
Found at i:375434 original size:42 final size:42
Alignment explanation
Indices: 375387--375469 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
375377 TAAGCAATTT
* *
375387 AAGTCCTTAGTGTCATCAGTAAGTCTTTCGAGCATGATGATG
1 AAGTCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATG
* *
375429 AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGAT
1 AAGTCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGAT
375470 TAAATCATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (42 bp):
AAGTCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATG
Found at i:375481 original size:42 final size:42
Alignment explanation
Indices: 375400--375482 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
375390 TCCTTAGTGT
* *
375400 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGC
* *
375442 CATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCGGG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGG
375483 TAATTTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGC
Found at i:375788 original size:42 final size:42
Alignment explanation
Indices: 375729--375933 Score: 164
Period size: 42 Copynumber: 4.7 Consensus size: 42
375719 TCTTTCAGGC
375729 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGAGT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGAGT
* *
375771 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT-AAGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGA-GT
* ** * * * * *
375813 AATTTGTAAGCCTTCACGGAAG-A-GTAGTGAAGCAAACCCATCAGTAAGT
1 CATCAGTAAGTCTT-TC-G-AGCATG-A-TGATG-AAATCCTTC-G--AGT
*
375862 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
1 --CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGAGT
* *
375906 CATCTGTAAGTCTTTCGAGCAAGATGAT
1 CATCAGTAAGTCTTTCGAGCATGATGAT
375934 AAGTCTTCCG
Statistics
Matches: 125, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
41 1 0.01
42 74 0.59
43 2 0.02
44 5 0.04
45 5 0.04
46 7 0.06
47 7 0.06
48 6 0.05
49 5 0.04
50 3 0.02
51 10 0.08
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGAGT
Found at i:375789 original size:20 final size:19
Alignment explanation
Indices: 375716--375792 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
375706 CACAATTTAC
375716 AAGTCTTTC-AGGCCATCAGT
1 AAGTCTTTCGA-G-CATCAGT
*
375736 AAGTCTTTCGAGCATGATGAT
1 AAGTCTTTCGAGCATCA-G-T
* *
375757 GAAATCCTTCGAGTCATCAGT
1 -AAGTCTTTCGAG-CATCAGT
375778 AAGTCTTTCGAGCAT
1 AAGTCTTTCGAGCAT
375793 GATGATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
19 7 0.15
20 21 0.46
21 3 0.07
22 11 0.24
23 4 0.09
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (19 bp):
AAGTCTTTCGAGCATCAGT
Found at i:375868 original size:13 final size:13
Alignment explanation
Indices: 375850--375874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
375840 TGAAGCAAAC
375850 CCATCAGTAAGTG
1 CCATCAGTAAGTG
375863 CCATCAGTAAGT
1 CCATCAGTAAGT
375875 CTTTCGAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:376391 original size:53 final size:53
Alignment explanation
Indices: 376328--376534 Score: 287
Period size: 53 Copynumber: 3.9 Consensus size: 53
376318 AGAATCACAC
* * *
376328 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAG-GAGGAGCAAACCCGTAGA
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAG-GGAGCGAACCCGTAGA
376381 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGGA
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTA-GA
* *
376435 -AGAAGATAT-TTTGAGTTATACTCCTTGAAGCAAGAGGGAGCGAACCCGTA-A
1 CAGAAGAT-TGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGA
* *
376486 GCAGAAGATTGTTCGAGTTTTACTCCTTGAATCAAGAGGGAGCGAACCC
1 -CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCC
376535 ACTGGTTGAA
Statistics
Matches: 140, Mismatches: 8, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
51 1 0.01
52 1 0.01
53 134 0.96
54 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGA
Found at i:377681 original size:17 final size:17
Alignment explanation
Indices: 377661--377695 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
377651 TTGTTTGTAG
*
377661 TTAGGTTTATTTTAATA
1 TTAGGTTTAGTTTAATA
377678 TTAGGTTTAGTTTAATA
1 TTAGGTTTAGTTTAATA
377695 T
1 T
377696 ATATATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (17 bp):
TTAGGTTTAGTTTAATA
Found at i:380980 original size:23 final size:23
Alignment explanation
Indices: 380947--380991 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
380937 ACGGACGGAA
*
380947 GACGGCGGGCGGCGATGATAAAC
1 GACGGCAGGCGGCGATGATAAAC
*
380970 GACGGCAGGCGGCGATGGTAAA
1 GACGGCAGGCGGCGATGATAAA
380992 GATGAGCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.44, T:0.09
Consensus pattern (23 bp):
GACGGCAGGCGGCGATGATAAAC
Found at i:383142 original size:60 final size:58
Alignment explanation
Indices: 383077--383221 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 58
383067 GTTTTGGGAC
* *
383077 CAATTTAGAATGAAGGTCATAGTTTGAGG-ATGAAATTGAAATAATCAAAAGTTT-GATGAT
1 CAATTTAAAATGAAGGTCATA-TTTGAGGAATGAAATTGAAAT--TCAAAAATTTAGA-GAT
* * * *
383137 TAATTTAAAATGATA-ATCATAATTT-AGGAATGAAGTTGAAATTTAAAAATTTAGAGAT
1 CAATTTAAAATGA-AGGTCAT-ATTTGAGGAATGAAATTGAAATTCAAAAATTTAGAGAT
*
383195 CAATTTAAAATGAGGGTCATATTTGAG
1 CAATTTAAAATGAAGGTCATATTTGAG
383222 AACATTGATA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
57 4 0.06
58 29 0.41
59 5 0.07
60 30 0.43
61 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (58 bp):
CAATTTAAAATGAAGGTCATATTTGAGGAATGAAATTGAAATTCAAAAATTTAGAGAT
Found at i:386113 original size:37 final size:34
Alignment explanation
Indices: 386064--386133 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 34
386054 TCTTTTTAAT
386064 TTTTACTGTAATTAAAGGATAATTATTCAAAAAAATA
1 TTTTACTGTAATTAAAGGAT-A-TATT-AAAAAAATA
* *
386101 TTTTACTTTAATTAAAGGGTATATTAAAAAAAT
1 TTTTACTGTAATTAAAGGATATATTAAAAAAAT
386134 TATTCGGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 8 0.26
35 4 0.13
36 1 0.03
37 18 0.58
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (34 bp):
TTTTACTGTAATTAAAGGATATATTAAAAAAATA
Found at i:388146 original size:76 final size:76
Alignment explanation
Indices: 388054--388204 Score: 239
Period size: 76 Copynumber: 2.0 Consensus size: 76
388044 GGTGTAGGAA
* * *
388054 ATAGAATGATGTAATTGAACAACTTGGAGGGTTAAATTGATGCGAAAATACGATAGGGACGAAAA
1 ATAGAATGATATAATTGAACAACTTGGAGGGTTAAATTAATACGAAAATACGATAGGGACGAAAA
*
388119 TGATAAATTGT
66 TAATAAATTGT
* * *
388130 ATAGAATGATATAATTGAACAACTTGGAGGGTTAAATTAATATGAAAATATGATAGGGGCGAAAA
1 ATAGAATGATATAATTGAACAACTTGGAGGGTTAAATTAATACGAAAATACGATAGGGACGAAAA
388195 TAATAAATTG
66 TAATAAATTG
388205 GATCTACTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.27
Consensus pattern (76 bp):
ATAGAATGATATAATTGAACAACTTGGAGGGTTAAATTAATACGAAAATACGATAGGGACGAAAA
TAATAAATTGT
Found at i:390968 original size:198 final size:198
Alignment explanation
Indices: 390419--391020 Score: 1051
Period size: 199 Copynumber: 3.0 Consensus size: 198
390409 TTTTTTGTAG
* * *
390419 TCTTCTTTAATGTTTTAGCTACTCAAGTTTCCAGTTTTTTTTTCACCCTGTTCCATGTAAAGACT
1 TCTTTTTTAAGGTTTTAGCTACTCAAGTTTCCAGTTTTTTTTT-ACCCTGCTCCATGTAAAGACT
390484 CTAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTACATCTTTTT
65 CTAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTACATCTTTTT
390549 GGGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGGGATC
130 GGGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGGGATC
390614 TTTT
195 TTTT
*
390618 TCTTTTTTAAGGTTTTAGCTACTCAAGTTTCCAGTTTTGTTTTTACCCTGCTCCATGTAAATACT
1 TCTTTTTTAAGGTTTTAGCTACTCAAGTTTCCAGTTTT-TTTTTACCCTGCTCCATGTAAAGACT
* *
390683 CTAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGAATATCTTTTT
65 CTAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTACATCTTTTT
*
390748 GGGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGAGATC
130 GGGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGGGATC
390813 TTTT
195 TTTT
* *
390817 TCTTTTTTAAGGTTTTACCTACTCAAGTTTCAAGTTTTTTTTTACCCTGCTCCATGTAAAGACTC
1 TCTTTTTTAAGGTTTTAGCTACTCAAGTTTCCAGTTTTTTTTTACCCTGCTCCATGTAAAGACTC
* *
390882 TAGCTTTGTAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTGCATCTTTTTG
66 TAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTACATCTTTTTG
* * * *
390947 GGTTCTTGCAACTTGGCTAAAATTTACTATCTGGGTTTTCCTCATTCTTCAATTTCATGGGATAT
131 GGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGGGATCT
391012 TTT
196 TTT
391015 TCTTTT
1 TCTTTT
391021 GAATCTGAGA
Statistics
Matches: 383, Mismatches: 19, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
198 156 0.41
199 222 0.58
200 5 0.01
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (198 bp):
TCTTTTTTAAGGTTTTAGCTACTCAAGTTTCCAGTTTTTTTTTACCCTGCTCCATGTAAAGACTC
TAGCTTTATAGTTCTGAACATGTTTTTGCTTAATTATTCATGATCATGAAAAGTACATCTTTTTG
GGTTCTTGCAACTTAGCTAAAATTTATTATCTGGGTTTTTCTCATTCTTCAATTTCATGGGATCT
TTT
Found at i:394955 original size:36 final size:36
Alignment explanation
Indices: 394903--394973 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
394893 AATTAGAGTA
394903 ACTTTCTTCTCAATTCAATTTATTTAAAGTCCAGTG
1 ACTTTCTTCTCAATTCAATTTATTTAAAGTCCAGTG
*
394939 ACTTTCTTCTCGATTCAATTTATTTAAAGTCCAGT
1 ACTTTCTTCTCAATTCAATTTATTTAAAGTCCAGT
394974 CATAGCTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (36 bp):
ACTTTCTTCTCAATTCAATTTATTTAAAGTCCAGTG
Found at i:405873 original size:24 final size:24
Alignment explanation
Indices: 405810--405862 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
405800 TGTAACGACA
*
405810 ATTACGGTCTGAATACCTAAAATG
1 ATTACAGTCTGAATACCTAAAATG
405834 ATTACAGTCTGAATACCTAAAATG
1 ATTACAGTCTGAATACCTAAAATG
405858 ATTAC
1 ATTAC
405863 GTTAGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (24 bp):
ATTACAGTCTGAATACCTAAAATG
Found at i:409488 original size:22 final size:22
Alignment explanation
Indices: 409463--409507 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
409453 TTTAAATATT
*
409463 ATATAAAATAGATATATCTATA
1 ATATAAAATAGATATAGCTATA
409485 ATATAAAATAGATATAGCTATA
1 ATATAAAATAGATATAGCTATA
409507 A
1 A
409508 AATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (22 bp):
ATATAAAATAGATATAGCTATA
Found at i:410714 original size:3 final size:3
Alignment explanation
Indices: 410706--410750 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
410696 ATTTATCATA
410706 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
410751 GGGCAGCGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:418508 original size:22 final size:22
Alignment explanation
Indices: 418480--418522 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
418470 AAACCATTCA
*
418480 GGGGGGGAATCGGTACCCTCTT
1 GGGGGGGAATCAGTACCCTCTT
*
418502 GGGGGGGAATCAGTTCCCTCT
1 GGGGGGGAATCAGTACCCTCT
418523 GGACAAACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGGGGGAATCAGTACCCTCTT
Found at i:426308 original size:39 final size:39
Alignment explanation
Indices: 426243--426336 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 39
426233 CATAAGGACA
* *
426243 TGCGGTAAGGACTTTCCCTGAGCACAAA-GCTGAGGAGCT
1 TGCGGTAAGGACTTACCCTGAGCACAAAGGC-GAGGAGCC
* *
426282 TGCGGTAAGGACTTACCTTGATCACAAAGGCGAGGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGGCGAGGAGCC
* *
426321 TGCAGTAAAGACTTAC
1 TGCGGTAAGGACTTAC
426337 AAGTCATAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (39 bp):
TGCGGTAAGGACTTACCCTGAGCACAAAGGCGAGGAGCC
Found at i:428297 original size:47 final size:46
Alignment explanation
Indices: 428228--428320 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 46
428218 GAGAAGTTTG
*
428228 TTGATTCATATGCCTAGAATGTGAAGTATAATCAAGACTATTAGTTA
1 TTGATTCATATGCCTAAAATGTGAAGTATAATCAAGACT-TTAGTTA
* *
428275 TTGATTCATATGCCTAAAATGTGAAGTGTAATCAATACTTTAGTTA
1 TTGATTCATATGCCTAAAATGTGAAGTATAATCAAGACTTTAGTTA
428321 AATTGTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 7 0.16
47 36 0.84
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (46 bp):
TTGATTCATATGCCTAAAATGTGAAGTATAATCAAGACTTTAGTTA
Found at i:429504 original size:44 final size:45
Alignment explanation
Indices: 429435--429551 Score: 119
Period size: 46 Copynumber: 2.6 Consensus size: 45
429425 ATTTTTCTCA
** * * *
429435 CAAACGCTGCAAAAAATCATACTATATAGTGG-TTTTTTTAATCC
1 CAAACGCCACAAAAGATCATGCTATATAATGGCTTTTTTTAATCC
* * *
429479 CAAACGCCACAAAAGGTCATGCTATACAATGGCCTTTTTTTTATCC
1 CAAACGCCACAAAAGATCATGCTATATAATGG-CTTTTTTTAATCC
* * *
429525 CAAATGCCTCAAAAGATCATGTTATAT
1 CAAACGCCACAAAAGATCATGCTATAT
429552 TGTGTCGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 25 0.43
46 33 0.57
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (45 bp):
CAAACGCCACAAAAGATCATGCTATATAATGGCTTTTTTTAATCC
Found at i:429721 original size:20 final size:20
Alignment explanation
Indices: 429696--429737 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
429686 ATATTCAAAA
429696 TCATTTCATTTT-CTTAATTT
1 TCATTTC-TTTTACTTAATTT
*
429716 TCATTTCTTTTACTTTATTT
1 TCATTTCTTTTACTTAATTT
429736 TC
1 TC
429738 TTTTTCCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (20 bp):
TCATTTCTTTTACTTAATTT
Found at i:433226 original size:2 final size:2
Alignment explanation
Indices: 433219--433249 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
433209 GTAATTACAA
433219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
433250 AATGTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:434359 original size:7 final size:7
Alignment explanation
Indices: 434347--434435 Score: 97
Period size: 7 Copynumber: 12.7 Consensus size: 7
434337 GTTAGATTAT
434347 ACCCTAA
1 ACCCTAA
434354 ACCCTAA
1 ACCCTAA
434361 ACCCTAA
1 ACCCTAA
434368 ACCCTAA
1 ACCCTAA
434375 ACCCTAA
1 ACCCTAA
* *
434382 GCCTTAA
1 ACCCTAA
* *
434389 GCGCTAA
1 ACCCTAA
434396 ACCCTAA
1 ACCCTAA
*
434403 ATCCTAA
1 ACCCTAA
* *
434410 GCCTTAA
1 ACCCTAA
**
434417 ATACTAA
1 ACCCTAA
434424 ACCCTAA
1 ACCCTAA
434431 ACCCT
1 ACCCT
434436 TAATCCGATT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.39, C:0.37, G:0.04, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:434395 original size:28 final size:28
Alignment explanation
Indices: 434347--434435 Score: 115
Period size: 28 Copynumber: 3.2 Consensus size: 28
434337 GTTAGATTAT
* * *
434347 ACCCTAAACCCTAAACCCTAAACCCTAA
1 ACCCTAAGCCTTAAACACTAAACCCTAA
* *
434375 ACCCTAAGCCTTAAGCGCTAAACCCTAA
1 ACCCTAAGCCTTAAACACTAAACCCTAA
* *
434403 ATCCTAAGCCTTAAATACTAAACCCTAA
1 ACCCTAAGCCTTAAACACTAAACCCTAA
434431 ACCCT
1 ACCCT
434436 TAATCCGATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.39, C:0.37, G:0.04, T:0.19
Consensus pattern (28 bp):
ACCCTAAGCCTTAAACACTAAACCCTAA
Found at i:434518 original size:7 final size:7
Alignment explanation
Indices: 434506--434601 Score: 104
Period size: 7 Copynumber: 13.7 Consensus size: 7
434496 GTTAGATTAC
434506 ACCCTAA
1 ACCCTAA
434513 ACCCTAA
1 ACCCTAA
434520 ACCCTAA
1 ACCCTAA
*
434527 ACTCTAA
1 ACCCTAA
434534 ACCCTAA
1 ACCCTAA
*
434541 A-TCTCAA
1 ACCCT-AA
434548 ACCCTAA
1 ACCCTAA
434555 ACCCTAA
1 ACCCTAA
**
434562 ACTATAA
1 ACCCTAA
434569 ACCCTAA
1 ACCCTAA
**
434576 GTCCTAA
1 ACCCTAA
*
434583 GCCCTAA
1 ACCCTAA
*
434590 ATCCTAA
1 ACCCTAA
434597 ACCCT
1 ACCCT
434602 TAATCTGATT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
6 2 0.03
7 69 0.95
8 2 0.03
ACGTcount: A:0.41, C:0.38, G:0.02, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:434557 original size:35 final size:35
Alignment explanation
Indices: 434508--434598 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
434498 TAGATTACAC
*
434508 CCTAAACCCTAAACCCTAAACTCTAAACCCTAAAT
1 CCTAAACCCTAAACCCTAAACTATAAACCCTAAAT
*
434543 -CTCAAACCCTAAACCCTAAACTATAAACCCTAAGT
1 CCT-AAACCCTAAACCCTAAACTATAAACCCTAAAT
* *
434578 CCTAAGCCCTAAATCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
434599 CCTTAATCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 2 0.04
35 46 0.92
36 2 0.04
ACGTcount: A:0.42, C:0.36, G:0.02, T:0.20
Consensus pattern (35 bp):
CCTAAACCCTAAACCCTAAACTATAAACCCTAAAT
Found at i:434588 original size:159 final size:159
Alignment explanation
Indices: 434298--434590 Score: 419
Period size: 159 Copynumber: 1.8 Consensus size: 159
434288 CATTTTATAT
* *
434298 TACTAAAAGAAAAATAAAAGTCCATTTAATTAAGAACATGTTAGATTATACCCTAAACCCTAAAC
1 TACTAAAAGAAAAATAAAAGTCCATTTAATCAAGAACATGTTAGATTACACCCTAAACCCTAAAC
* * * * * * *
434363 CCTAAACCCTAAACCCTAAGCCTTAAGCGCTAAACCCTAAATCCTAAGCCTTAAATACTAAACCC
66 CCTAAACCCTAAACCCTAAACCTCAAACCCTAAACCCTAAATCATAAACCCTAAATACTAAACCC
434428 TAAACCCTTAATCCGATTATGTGTTAGGG
131 TAAACCCTTAATCCGATTATGTGTTAGGG
*
434457 TACTAAAAGAAAAATAAAAG-CTCATTTAATCAAGCACATGTTAGATTACACCCTAAACCCTAAA
1 TACTAAAAGAAAAATAAAAGTC-CATTTAATCAAGAACATGTTAGATTACACCCTAAACCCTAAA
* * * * *
434521 CCCTAAACTCTAAACCCTAAATCTCAAACCCTAAACCCTAAA-CTATAAACCCTAAGTCCTAAGC
65 CCCTAAACCCTAAACCCTAAACCTCAAACCCTAAACCCTAAATC-ATAAACCCTAAATACTAAAC
434585 CCTAAA
129 CCTAAA
434591 TCCTAAACCC
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
158 2 0.02
159 115 0.98
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.24
Consensus pattern (159 bp):
TACTAAAAGAAAAATAAAAGTCCATTTAATCAAGAACATGTTAGATTACACCCTAAACCCTAAAC
CCTAAACCCTAAACCCTAAACCTCAAACCCTAAACCCTAAATCATAAACCCTAAATACTAAACCC
TAAACCCTTAATCCGATTATGTGTTAGGG
Found at i:436732 original size:323 final size:319
Alignment explanation
Indices: 436095--436739 Score: 915
Period size: 323 Copynumber: 2.0 Consensus size: 319
436085 GGCAACCGAC
* * * * *
436095 AAACTTAGCTTATCGGTAGGTATCGATAACTTGCACAGAAGTATCGATACATAACAATATAACAT
1 AAACTTAGCTTATCGATAGGCATCGATAACTTACACACAAGTATAGATACATAACAATATAACAT
* * *
436160 GTTGAAGTTTGATAAAACCAGTTTCAATTTGACAATGAGAAACTGTATATGTTGAAATTTGTATC
66 GTTGAAGTTTGAAAAAACCAGTTTCAATTTGACAATGAGAAACCGAATATGTTGAAA-TTGTATC
* *
436225 GATACTTTTCTAAGTATATGCACCAAATTATCATTACTTCAGAAATTTAAAAGAATTACAATAAT
130 -ATACTTTTCTAAGTATATGCACCAAAGTATCAGTACTTCAGAAATTTAAAAGAATTACAATAAT
*
436290 AGCACCTAGAAAGTATCGATACCTTAGAAACATGTATCGATACATGACAATATAATAAGTTAAAA
194 AGCACCTAGAAAGTATCGATACCTTAGAAAAATGTATCGATACATGACAATATAATAAGTTAAAA
436355 TTTGACAAAACCAATTTCAATATGACAAAACCGGTAAAGTACTACCGAATATGTTGAAGGT
259 TTTGACAAAACCAATTTCAATATGACAAAACCGGTAAAGTACTACCGAATATGTTGAAGGT
*
436416 AAACTTAGCTTATCGATAGGCATCGAT-ACTTACACACATGTATTAG-TACATAACAATATAACA
1 AAACTTAGCTTATCGATAGGCATCGATAACTTACACACAAGTA-TAGATACATAACAATATAACA
*
436479 TGTTGAAGTTTGAAAAAACCAGTTTCAGTTTGACAAAATCGGTAGAGATACCGAA-ATTGTTGAA
65 TGTTGAAGTTTGAAAAAACCAGTTTCAATTTGAC--AAT--G-AGA-A-ACCGAATA-TGTTGAA
* * * * * *
436543 A-TGTAT-ATACTTTTCTAAGTATATGCACCAAAGTATCGGTATTTTAGGAATTTAAAATAATTG
122 ATTGTATCATACTTTTCTAAGTATATGCACCAAAGTATCAGTACTTCAGAAATTTAAAAGAATTA
* * *
436606 CAATAATAGCGCCTTGAAAGTATCGATACCTTAGAAAAATGTATCGATACATGACAATATAATAG
187 CAATAATAGCACCTAGAAAGTATCGATACCTTAGAAAAATGTATCGATACATGACAATATAATAA
* * *
436671 GTTAAAATTTGACAAAATCGATTTCAATATGACAAAACCGGTAAAGTGA-TACCGGATATGTTGA
252 GTTAAAATTTGACAAAACCAATTTCAATATGACAAAACCGGTAAAGT-ACTACCGAATATGTTGA
436735 AGGT
316 AGGT
436739 A
1 A
436740 TCGATACTTT
Statistics
Matches: 289, Mismatches: 25, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
320 61 0.21
321 27 0.09
322 3 0.01
323 174 0.60
324 2 0.01
325 8 0.03
326 2 0.01
327 12 0.04
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (319 bp):
AAACTTAGCTTATCGATAGGCATCGATAACTTACACACAAGTATAGATACATAACAATATAACAT
GTTGAAGTTTGAAAAAACCAGTTTCAATTTGACAATGAGAAACCGAATATGTTGAAATTGTATCA
TACTTTTCTAAGTATATGCACCAAAGTATCAGTACTTCAGAAATTTAAAAGAATTACAATAATAG
CACCTAGAAAGTATCGATACCTTAGAAAAATGTATCGATACATGACAATATAATAAGTTAAAATT
TGACAAAACCAATTTCAATATGACAAAACCGGTAAAGTACTACCGAATATGTTGAAGGT
Found at i:439112 original size:24 final size:24
Alignment explanation
Indices: 439085--439146 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
439075 TTTATGCAGT
439085 TTTCAATTTCAATTTGAGATTGAA
1 TTTCAATTTCAATTTGAGATTGAA
* * *
439109 TTTCAATTTTAAATTGAGTTTGAA
1 TTTCAATTTCAATTTGAGATTGAA
*
439133 TTTTAATTTCAATT
1 TTTCAATTTCAATT
439147 GGCTCCGCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATTTCAATTTGAGATTGAA
Found at i:439124 original size:18 final size:18
Alignment explanation
Indices: 439089--439138 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
439079 TGCAGTTTTC
* *
439089 AATTTCAATTTGAGATTG
1 AATTTCAATTTTAAATTG
439107 AATTTCAATTTTAAATTG
1 AATTTCAATTTTAAATTG
* *
439125 AGTTTGAATTTTAA
1 AATTTCAATTTTAA
439139 TTTCAATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (18 bp):
AATTTCAATTTTAAATTG
Found at i:441396 original size:19 final size:20
Alignment explanation
Indices: 441372--441411 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
441362 ACAGGTAACG
*
441372 AATTTGACAAAA-CAATTAA
1 AATTTGAAAAAATCAATTAA
441391 AATTTGAAAAAATCAATTAA
1 AATTTGAAAAAATCAATTAA
441411 A
1 A
441412 TATAACAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (20 bp):
AATTTGAAAAAATCAATTAA
Found at i:441944 original size:246 final size:246
Alignment explanation
Indices: 441413--442124 Score: 1013
Period size: 246 Copynumber: 2.9 Consensus size: 246
441403 TCAATTAAAT
* * * * * *
441413 ATAACAGGTTGAAAATTG-AAAAACTCGATTTCAATAA-TAGTGCCTATAAAGTATTGACACGTC
1 ATAACAAGTTGAAAATTGAAAAAAATCGATTTCAATAATTA-CGCCTATAAAGTATCGATACCTC
* *
441476 AGACACATGTATCGATACATGACAATATAACAGGTTGAAAATTGACAAAATCAGTTTCAATATGA
65 AGACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAACCAGTTTCAATATGA
* * * *
441541 CAAAACCGGTAAAGCGCTACCGGTTTATACAAAAACGAAACGTCTTGAAAGTATAT-ATACCTTA
130 CAAAACCGGTAAA-AGCTACTGGTTTACACAAAAATGAAACGTC-TGAAAGTAT-TGATACCTTA
* * * *
441605 CATAAAAGTATTAATACTTAGGTAAGGGTAATGGTATCGATTAAATATAAATAAC
192 CACAAAAGTATTGACACTTAGGTAAGGATAATGGTATCGATTAAATATAAATAAC
* * *
441660 ATAACAAGTTGAAAATT-AACAAAACCGATTTCAATAATTACGCCTATAAAATATCGATACCTCA
1 ATAACAAGTTGAAAATTGAAAAAAATCGATTTCAATAATTACGCCTATAAAGTATCGATACCTCA
*
441724 GACACATGTATCGATACATAACAATATAATAGGTTGAAAATTGACAAAACCAGTTTCAATATGAC
66 GACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAACCAGTTTCAATATGAC
** * * * *
441789 AAAATAGATAAAATGATATTGGTTTACA-AAAAATGAAACGTCTGAAAAGTATTGATAGCTTACA
131 AAAACCGGTAAAA-GCTACTGGTTTACACAAAAATGAAACGTCTG-AAAGTATTGATACCTTACA
* *
441853 CAAAAGTATCGACACTTTGGTAAGGATAATGGTATCGATTAAATATAAATAAC
194 CAAAAGTATTGACACTTAGGTAAGGATAATGGTATCGATTAAATATAAATAAC
* *
441906 ATAACAAGTTGAAAATTGAAAAAAATGGA-TTCAATAATTGCGCCTATAAAGTATCGATACCTCA
1 ATAACAAGTTGAAAATTGAAAAAAATCGATTTCAATAATTACGCCTATAAAGTATCGATACCTCA
*
441970 GACACATGTATCGATACATAACAATATAACAAGTTGAAAATTGACAAAACCAGTTTCAATATGAC
66 GACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAACCAGTTTCAATATGAC
*
442035 AAAACCGGTAAAGAGCTACTGGTTTACACAAAAATGAAACGTCTCGAAAGTATCGATACCTTACA
131 AAAACCGGTAAA-AGCTACTGGTTTACACAAAAATGAAACGTCT-GAAAGTATTGATACCTTACA
*
442100 CAAAAGTATTGACACTTCGGTAAGG
194 CAAAAGTATTGACACTTAGGTAAGG
442125 GTATTCAATA
Statistics
Matches: 412, Mismatches: 44, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
245 3 0.01
246 210 0.51
247 196 0.48
248 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (246 bp):
ATAACAAGTTGAAAATTGAAAAAAATCGATTTCAATAATTACGCCTATAAAGTATCGATACCTCA
GACACATGTATCGATACATAACAATATAACAGGTTGAAAATTGACAAAACCAGTTTCAATATGAC
AAAACCGGTAAAAGCTACTGGTTTACACAAAAATGAAACGTCTGAAAGTATTGATACCTTACACA
AAAGTATTGACACTTAGGTAAGGATAATGGTATCGATTAAATATAAATAAC
Found at i:444111 original size:22 final size:22
Alignment explanation
Indices: 444083--444148 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
444073 GGTTTCATAT
444083 GTCCTTCGGGACATATTCACAG
1 GTCCTTCGGGACATATTCACAG
* * * *
444105 GTTCTTCGGGACACATGCATAG
1 GTCCTTCGGGACATATTCACAG
444127 GTCCTTCGGGACATATTTCACA
1 GTCCTTCGGGACATA-TTCACA
444149 TGCCACTCAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACATATTCACAG
Found at i:447161 original size:2 final size:2
Alignment explanation
Indices: 447154--447376 Score: 446
Period size: 2 Copynumber: 111.5 Consensus size: 2
447144 AAATGTATCG
447154 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
447196 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
447238 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
447280 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
447322 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
447364 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
447377 TATTCCATAT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 221 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:447848 original size:272 final size:269
Alignment explanation
Indices: 447354--447852 Score: 775
Period size: 272 Copynumber: 1.8 Consensus size: 269
447344 ACACACACAC
447354 ACACACACACACACACACACACATATTCCATATTATAATTCTGAAACTATTACTTTAAAGTAATA
1 ACACACACACACACACACACACATATTCCATATTATAATTCTGAAACTATTACTTTAAAGTAATA
* *
447419 GGTTAATTTTCAATGAAAACGGTTAAAGTCAATCAGTATCATGATAATATGCGTAAACAATGTAC
66 GATTAATTTGCAATGAAAACGGTTAAAGTCAATCAGTATCATGATAATATGCGTAAACAATGTAC
* *
447484 ACGATAATATGTTGATAAAGATTGATAACAAATCAAGTAATTAACCGGTTATGTTATGGTCAGAT
131 ACGATAATATGTTGATAAAGATTAATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGAT
* *
447549 TTCTAAGGCTCCATCAGTTTTAACTTTGGTTAATTCCACATAAAGGCTCAAACAATCTGCACGTA
196 TTCTAAGGCTCCATCAGCTTAAACTTT-GTTAATTCCACATAAAGGCTCAAACAATCTGCACGTA
447614 AAATGTATCA
260 AAATGTATCA
* * * *
447624 ACACACACACACACACATATATATTTTCCATACTTATAATT-TCGAAACCTATTACTTTAAAGTA
1 ACACACACACACACACACACACATATTCCATA-TTATAATTCT-GAAA-CTATTACTTTAAAGTA
* * ** *
447688 GTATATTAATTTGCAATGAAAACGGTTAAAGTCAATTGGTATCATGATGATATGCGTAAACAATG
63 ATAGATTAATTTGCAATGAAAACGGTTAAAGTCAATCAGTATCATGATAATATGCGTAAACAATG
* * * *
447753 TACATGGTAATATGTTGATAAAGCTTAATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCG
128 TACACGATAATATGTTGATAAAGATTAATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCA
*
447818 GATTTCTAAGGCTTCATCAGCTTAAACTTTGTTAA
193 GATTTCTAAGGCTCCATCAGCTTAAACTTTGTTAA
447853 CATTTTAGGC
Statistics
Matches: 206, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
270 29 0.14
271 17 0.08
272 160 0.78
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (269 bp):
ACACACACACACACACACACACATATTCCATATTATAATTCTGAAACTATTACTTTAAAGTAATA
GATTAATTTGCAATGAAAACGGTTAAAGTCAATCAGTATCATGATAATATGCGTAAACAATGTAC
ACGATAATATGTTGATAAAGATTAATAACAAATCAAGTAATTAACCGGTTATGTTATCGTCAGAT
TTCTAAGGCTCCATCAGCTTAAACTTTGTTAATTCCACATAAAGGCTCAAACAATCTGCACGTAA
AATGTATCA
Found at i:448916 original size:47 final size:45
Alignment explanation
Indices: 448811--448917 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
448801 GTGCACTAAC
* *
448811 AGTGCATGGATGCATAAAATGCATTCGATGTTTCAAAATAGCATG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCATG
* * * *
448856 AGTGCATTGATGCATCAAATGCATTTGATGTTTTTCATAAAT-CCCTG
1 AGTGCATCGATGCATAAAATGCATTCGATG--TTTCA-AAATACCATG
*
448903 AGTGCATCAATGCAT
1 AGTGCATCGATGCAT
448918 GGTATGTGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 27 0.52
47 21 0.40
48 4 0.08
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (45 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCATG
Found at i:455609 original size:22 final size:21
Alignment explanation
Indices: 455567--455606 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
455557 GAGCTTATTT
*
455567 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
455588 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
455607 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:457620 original size:47 final size:47
Alignment explanation
Indices: 457520--457644 Score: 175
Period size: 47 Copynumber: 2.7 Consensus size: 47
457510 GGTGCACTAA
* *
457520 GAGTGCATGGATGCATAAAATGCATTCGATG--TTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCT
*
457565 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA-ACCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCA-AAATACCCT
* *
457612 GAGTGCATCGATGCATGAAATACATTCGATGTT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTT
457645 CAATTTATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
45 29 0.40
47 40 0.56
48 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (47 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCT
Found at i:458307 original size:226 final size:226
Alignment explanation
Indices: 457903--458310 Score: 597
Period size: 226 Copynumber: 1.8 Consensus size: 226
457893 GTTTTCAACA
* *
457903 TAGGTGTTACCTAATACGTTGATAATACTAATAACAAACTAAGTAATTAACCTATTTTGTTATCT
1 TAGGCGTTACCTAATACGTTGATAATACTAATAACAAACTAAGTAATTAACCTATTTTGTTATCG
* * *
457968 TCGGATTTCTAAAGGGCCATTAGCTTTAAAAAGATGCTGCATATTATGTTACATAAGAACTACCT
66 TCGGATTTCTAAAGGCCCATCAGCTTTAAAAAGATGCTACATATTATGTTACATAAGAACTACCT
* * * *
458033 AATATGTTATTATGCTTGATAATGTTTTCAGTAATTGACCGTTTATGTTATCTTCAGATTCCTAA
131 AATATGTTATTATGCTTGATAATGTTTCCACTAATTAACCGGTTATGTTATCTTCAGATTCCTAA
458098 GGCTCCATTAGCTTAAACTTTGGTAATATTT
196 GGCTCCATTAGCTTAAACTTTGGTAATATTT
* * * *
458129 TAGGCGTTACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCG
1 TAGGCGTTACCTAATACGTTGATAATACTAATAACAAACTAAGTAATTAACCTATTTTGTTATCG
* * * * **
458194 TCGTATTTCT-AAGGCCTCATCATCTTT-AAAA-ATGCGTTACCTATTATGTTACATTAGCGCTA
66 TCGGATTTCTAAAGGCC-CATCAGCTTTAAAAAGATGC--TACATATTATGTTACATAAGAACTA
458256 CCTAATATGTTATTATGCTTGATAATGTTTCCACTAATTAACCGGTTATGTTATC
128 CCTAATATGTTATTATGCTTGATAATGTTTCCACTAATTAACCGGTTATGTTATC
458311 GTCAATATTT
Statistics
Matches: 160, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
224 4 0.03
225 9 0.06
226 147 0.92
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (226 bp):
TAGGCGTTACCTAATACGTTGATAATACTAATAACAAACTAAGTAATTAACCTATTTTGTTATCG
TCGGATTTCTAAAGGCCCATCAGCTTTAAAAAGATGCTACATATTATGTTACATAAGAACTACCT
AATATGTTATTATGCTTGATAATGTTTCCACTAATTAACCGGTTATGTTATCTTCAGATTCCTAA
GGCTCCATTAGCTTAAACTTTGGTAATATTT
Found at i:459563 original size:55 final size:55
Alignment explanation
Indices: 459386--459714 Score: 383
Period size: 55 Copynumber: 5.9 Consensus size: 55
459376 CTATACGGAA
* * ** * * * **
459386 ATTCATCAACTTATGATAAATTCCGTGGGT-TGCACATGTAGTGCTTGTATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAGTG
* * * *
459440 ATTCATCAACTCATGATGAACTCCGATCCGTGGATTTACACACAAAGTGCATGTACAGTG
1 ATTCATCAACTCATGATGAA-T----TCCGTGAATATGCACACGAAGTGCATGTACAGTG
* * * * *
459500 ATTCATCAACTCATGATGAATTCTGTGAATATGTACATGAAGTGTATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAGTG
*
459555 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTAC-GTTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAG-TG
459610 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAGTG
* * * *
459665 ATTCATCAACTTATAATGAATTCCATGAATATGCACACGAAGTGCCTGTA
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTA
459715 GTACACATAG
Statistics
Matches: 238, Mismatches: 29, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
54 19 0.08
55 172 0.72
56 1 0.00
59 9 0.04
60 37 0.16
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCATGTACAGTG
Found at i:459670 original size:165 final size:166
Alignment explanation
Indices: 459386--459708 Score: 425
Period size: 165 Copynumber: 1.9 Consensus size: 166
459376 CTATACGGAA
* ** * * * *
459386 ATTCATCAACTTATGATAAATTCCGTGGGTTGCACATGTAGTGCTTGTATGGTGATTCATCAACT
1 ATTCATCAACTCATGATAAATTCCGTGAATTGCACACGAAGTGCCTGTACGGTGATTCATCAACT
* * *
459451 CATGATGAACTCCGATCCGTGGATTTACACACAAAGTGCATGTACAGTGATTCATCAACTCATGA
66 CATGATGAACT-C--TCCGTGAATATACACACAAAGTGCATGTACAGTGATTCATCAACTCATAA
** * *
459516 TGAATTCTGTGAATATGTACATGAAGTGTATGTACGGTG
128 TGAATTCCATGAATATGCACACGAAGTGTATGTACGGTG
* *
459555 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGTTGATTCATCAAC
1 ATTCATCAACTCATGATAAATTCCGTGAAT-TGCACACGAAGTGCCTGTACGGTGATTCATCAAC
* * *
459620 TCATGATGAA-T-TCCGTGAATATGCACACGAAGTGCATGTACAGTGATTCATCAACTTATAATG
65 TCATGATGAACTCTCCGTGAATATACACACAAAGTGCATGTACAGTGATTCATCAACTCATAATG
459683 AATTCCATGAATATGCACACGAAGTG
130 AATTCCATGAATATGCACACGAAGTG
459709 CCTGTAGTAC
Statistics
Matches: 134, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
165 68 0.51
169 27 0.20
170 39 0.29
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (166 bp):
ATTCATCAACTCATGATAAATTCCGTGAATTGCACACGAAGTGCCTGTACGGTGATTCATCAACT
CATGATGAACTCTCCGTGAATATACACACAAAGTGCATGTACAGTGATTCATCAACTCATAATGA
ATTCCATGAATATGCACACGAAGTGTATGTACGGTG
Found at i:461738 original size:16 final size:16
Alignment explanation
Indices: 461717--461757 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
461707 TGTATTTATA
461717 TGTGATGAGGGTGACT
1 TGTGATGAGGGTGACT
461733 TGTGATGAGGGTGACT
1 TGTGATGAGGGTGACT
461749 TGTGATGAG
1 TGTGATGAG
461758 TCAAACTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.20, C:0.05, G:0.44, T:0.32
Consensus pattern (16 bp):
TGTGATGAGGGTGACT
Found at i:472362 original size:41 final size:41
Alignment explanation
Indices: 472308--472407 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 41
472298 CCTTGATCCA
*
472308 CGCTATATGCCACGTA-GAGGTATAGCGCGGAT-AGGGGCCG
1 CGCTATACGCCACGTAGGA-GTATAGCGCGGATCAGGGGCCG
* *
472348 CGTTTATACTCCACGTAGGAGTATAGCGCGGATCAGGGGCCG
1 CG-CTATACGCCACGTAGGAGTATAGCGCGGATCAGGGGCCG
472390 CGCTATACGCCACGTAGG
1 CGCTATACGCCACGTAGG
472408 GGTGAATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.04
41 38 0.73
42 12 0.23
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (41 bp):
CGCTATACGCCACGTAGGAGTATAGCGCGGATCAGGGGCCG
Found at i:472704 original size:16 final size:14
Alignment explanation
Indices: 472659--472706 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
472649 TATAAGGTAA
*
472659 TTTTATTATAATAT
1 TTTTATTATATTAT
472673 TTTTAATTATACTTAT
1 TTTT-ATTATA-TTAT
472689 TGTTTATTATCATTAT
1 T-TTTATTAT-ATTAT
472705 TT
1 TT
472707 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 14 0.48
17 4 0.14
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTTATTATATTAT
Found at i:475977 original size:35 final size:34
Alignment explanation
Indices: 475892--475978 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
475882 ATTTGGTATT
*
475892 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
475926 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
475964 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
475979 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:478293 original size:17 final size:18
Alignment explanation
Indices: 478250--478290 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
478240 GAATTATATT
478250 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
478267 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
478285 ATTAAA
1 AGTAAA
478291 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:478345 original size:10 final size:10
Alignment explanation
Indices: 478326--478366 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
478316 ATATACCAGA
*
478326 GAGAGTATTT
1 GAGAGAATTT
478336 GAGAGAATTT
1 GAGAGAATTT
478346 GAGAGAATTT
1 GAGAGAATTT
478356 GAGAGAATTT
1 GAGAGAATTT
478366 G
1 G
478367 GTGTGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:484541 original size:80 final size:81
Alignment explanation
Indices: 484303--484704 Score: 490
Period size: 81 Copynumber: 5.0 Consensus size: 81
484293 TATAATTCCT
* * * * * * *
484303 TTATTATTTTACCCAAAGGTATTTAGCCT-TTCACCTAACTTGC-TAATTTGACACATTTCTGTC
1 TTATTCTTTTACTCAACGGTATTTA-ACTGTTCATCTAACTGGCATAA-TTGACACATTTCTGCC
*
484366 AAATGCACAGCTAGTCCA
64 AAATGCACAGCTAGGCCA
* * ** * *
484384 TTATTCTTTTACTCAACCGTGTTTAACCATTCATCTAATTGGCATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
484449 ATGCACAACTAGGCCA
66 ATGCACAGCTAGGCCA
* * *
484465 TTCATT-TTTTAGTCAACGGTATTTAGCTGTTCATCTAACT-GCATAATTGACACATTTCTACCA
1 TT-ATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
*
484528 AATGCACAGCTAGGTCA
65 AATGCACAGCTAGGCCA
* * *
484545 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCATATTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
484610 ATGCACAACTAGGCCA
66 ATGCACAGCTAGGCCA
* * * *
484626 TTATTCTTTTACTCAAC-GTATTTAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGTCGA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
484690 ATGCACAGTTAGGCC
66 ATGCACAGCTAGGCC
484705 TCAAAGGCAC
Statistics
Matches: 274, Mismatches: 42, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
79 3 0.01
80 123 0.45
81 142 0.52
82 6 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
ATGCACAGCTAGGCCA
Found at i:484615 original size:161 final size:162
Alignment explanation
Indices: 484303--484702 Score: 551
Period size: 161 Copynumber: 2.5 Consensus size: 162
484293 TATAATTCCT
* * * *
484303 TTATTATTTTACCCAAAGGTATTTAGCCT-TTCACCTAACTTGC-TAATTTGACACATTTCTGTC
1 TTATTCTTTTACTCAACGGTATTTAG-CTGTTCATCTAAC-TGCATAA-TTGACACATTTCTGTC
* *
484366 AAATGCACAGCTA-GTCCATTATTCTTTTACTCAACCGTGTTTAACCATTCATCTAATTGGCATA
63 AAATGCACAGCTAGGTCCATTATTCTTTTACTCAACCGTATTTAACCATTCATCTAACTGGCATA
*
484430 ATTGACACCTTTCTGCCAAATGCACAACTAGGCCA
128 ATTGACACATTTCTGCCAAATGCACAACTAGGCCA
* **
484465 TTCATT-TTTTAGTCAACGGTATTTAGCTGTTCATCTAACTGCATAATTGACACATTTCTACCAA
1 TT-ATTCTTTTACTCAACGGTATTTAGCTGTTCATCTAACTGCATAATTGACACATTTCTGTCAA
* *
484529 ATGCACAGCTAGGT-CATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAT
65 ATGCACAGCTAGGTCCATTATTCTTTTACTCAACCGTATTTAACCATTCATCTAACTGGCATAAT
* *
484593 TGGCATATTTCTGCCAAATGCACAACTAGGCCA
130 TGACACATTTCTGCCAAATGCACAACTAGGCCA
* * *
484626 TTATTCTTTTACTCAAC-GTATTTAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGTCGA
1 TTATTCTTTTACTCAACGGTATTTAGCTGTTCATCTAACT-GCATAATTGACACATTTCTGTCAA
*
484690 ATGCACAGTTAGG
65 ATGCACAGCTAGG
484703 CCTCAAAGGC
Statistics
Matches: 212, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
160 24 0.11
161 152 0.72
162 33 0.16
163 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (162 bp):
TTATTCTTTTACTCAACGGTATTTAGCTGTTCATCTAACTGCATAATTGACACATTTCTGTCAAA
TGCACAGCTAGGTCCATTATTCTTTTACTCAACCGTATTTAACCATTCATCTAACTGGCATAATT
GACACATTTCTGCCAAATGCACAACTAGGCCA
Found at i:484739 original size:68 final size:68
Alignment explanation
Indices: 484654--485030 Score: 575
Period size: 68 Copynumber: 5.6 Consensus size: 68
484644 TATTTAACTG
* *
484654 TTCATCTAACT-AGCATAATTGACACCTTTCTGTCGAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGA-CATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
484718 GCCT
65 GCCT
* *
484722 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
484787 CCT
66 CCT
* * * *
484790 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTATGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
484855 CCT
66 CCT
* * *
484858 TTCAT-TAACTG-CATAAATGACACTTTTCTGTCAAATGCACAGTTATGCCTCAAAGGCACTTAT
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
484921 CCT
66 CCT
484924 TTCATCTAACTGGA-ATAAATGACACC-TTCATGTCAAATGCACAGTTAGGCCTCAAAGGCACTT
1 TTCATCTAACT-GACATAAATGACACCTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTT
484987 AGCCT
64 AGCCT
* *
484992 TTCATCTAGCTGGCATAAATGACACCTTTCTGTCAAATG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATG
485031 TACAATTTAG
Statistics
Matches: 284, Mismatches: 18, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
66 57 0.20
67 15 0.05
68 208 0.73
69 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:484936 original size:134 final size:134
Alignment explanation
Indices: 484654--485030 Score: 587
Period size: 134 Copynumber: 2.8 Consensus size: 134
484644 TATTTAACTG
* * *
484654 TTCATCTAACTAGCATAATTGACACCTTTCTGTCGAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACA-CTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
484719 CCTTTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACT
65 CCTTTCATCTAACTG-CATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACT
484784 TAGCCT
129 TAGCCT
* *
484790 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTATGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACAC-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* *
484855 CCTTTCAT-TAACTGCATAAATGACACTTTTCTGTCAAATGCACAGTTATG-CCTCAAAGGCACT
65 CCTTTCATCTAACTGCATAAATGACACCTTTCTGTCAAATGAACAGTTA-GCCCTCAAAGGCACT
*
484918 TATCCT
129 TAGCCT
* *
484924 TTCATCTAACTGGAATAAATGACACCTTCATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
484989 CCTTTCATCTAGCTGGCATAAATGACACCTTTCTGTCAAATG
65 CCTTTCATCTAACT-GCATAAATGACACCTTTCTGTCAAATG
485031 TACAATTTAG
Statistics
Matches: 222, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
133 3 0.01
134 115 0.52
135 12 0.05
136 92 0.41
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (134 bp):
TTCATCTAACTGGCATAAATGACACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CTTTCATCTAACTGCATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACTTA
GCCT
Found at i:485026 original size:202 final size:204
Alignment explanation
Indices: 484654--485037 Score: 632
Period size: 202 Copynumber: 1.9 Consensus size: 204
484644 TATTTAACTG
* *
484654 TTCATCTAACTAGCATAATTGACACCTTTCTGTCGAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
484719 CCTTTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACT
66 CCTTTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACT
484784 TAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTATGCCTCAAAGGC
131 TAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTATGCCTCAAAGGC
484849 ACTTAGCCT
196 ACTTAGCCT
* * *
484858 TTCAT-TAACT-GCATAAATGACACTTTTCTGTCAAATGCACAGTTATGCCTCAAAGGCACTTAT
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* *
484921 CCTTTCATCTAACTGGA-ATAAATGACACC-TTCATGTCAAATGCACAGTTAGGCCTCAAAGGCA
66 CCTTTCATCTAACT-GACATAAATGACACCTTTC-TGTCAAATGAACAGTTAGCCCTCAAAGGCA
* * *
484984 CTTAGCCTTTCATCTAGCTGGCATAAATGACACCTTTCTGTCAAATGTACAATT
129 CTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATT
485038 TAGCTTATTA
Statistics
Matches: 168, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
201 3 0.02
202 153 0.91
203 7 0.04
204 5 0.03
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (204 bp):
TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGAACAGTTAGCCCTCAAAGGCACT
TAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTATGCCTCAAAGGC
ACTTAGCCT
Found at i:495323 original size:18 final size:18
Alignment explanation
Indices: 495275--495331 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
495265 AACGGTCAAT
* *
495275 GGGT-GGGTCAACAGATC
1 GGGTCGGGTCAACGGGTC
*
495292 GGGTCGGGTCAACGGGTT
1 GGGTCGGGTCAACGGGTC
495310 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
495328 GGGT
1 GGGT
495332 TGTGACCAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 4 0.11
18 31 0.89
ACGTcount: A:0.14, C:0.18, G:0.49, T:0.19
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:497073 original size:17 final size:16
Alignment explanation
Indices: 497004--497074 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
496994 TAGAATATAA
497004 AAAATATTTAAAAAATT
1 AAAATA-TTAAAAAATT
**
497021 -AAATA-TAAAAATACC
1 AAAATATTAAAAA-ATT
497036 AAAA-A-T-AAAAATT
1 AAAATATTAAAAAATT
*
497049 AAATTATTAAAAAATT
1 AAAATATTAAAAAATT
497065 AAAAATATTA
1 -AAAATATTA
497075 TTAGTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 4 0.10
14 11 0.26
15 4 0.10
16 15 0.36
17 8 0.19
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAAAAATT
Found at i:499652 original size:18 final size:17
Alignment explanation
Indices: 499598--499646 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
499588 TTGGACTCCT
* *
499598 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
499616 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
499634 AGTGCATTCGATG
1 AGTGCA-TCGATG
499647 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:499687 original size:45 final size:45
Alignment explanation
Indices: 499616--499721 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
499606 GGTGCACTAA
* * *
499616 GAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAA-ATAGCC
1 GAGTGCATCGATGCATCAAATACATTCGATGTTTGAAAATAT-GCC
*
499661 TG-GTGCATCGATGCATCAAATACATTCGATGTTTGAAAATATTCC
1 -GAGTGCATCGATGCATCAAATACATTCGATGTTTGAAAATATGCC
499706 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
499722 GGAGAGTGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
44 1 0.02
45 50 0.93
46 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATCAAATACATTCGATGTTTGAAAATATGCC
Found at i:502454 original size:24 final size:23
Alignment explanation
Indices: 502382--502462 Score: 87
Period size: 24 Copynumber: 3.6 Consensus size: 23
502372 GCATGGTCTT
* *
502382 ATGCATCGATGCATATTCAAGGC
1 ATGCATCGATGCACATTCAAGGG
* *
502405 ATGCATCGGTG--CA-TCATGCGG
1 ATGCATCGATGCACATTCAAG-GG
502426 ATGCATCGATGCACATTCAAAGGG
1 ATGCATCGATGCACATTC-AAGGG
502450 ATGCATCGATGCA
1 ATGCATCGATGCA
502463 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
23 12 0.26
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (23 bp):
ATGCATCGATGCACATTCAAGGG
Found at i:502475 original size:44 final size:42
Alignment explanation
Indices: 502360--502482 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 42
502350 AAAACCCGAC
* * *
502360 GGATGCATCGGTGCATGGTCTTATGCATCGATGCATATTCAAG
1 GGATGCATCGGTGCATTGT-TAATGCATCGATGCACATTCAAG
* ***
502403 GCATGCATCGGTGCATCATGCGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGGTGCAT--TGTTAATGCATCGATGCACATTC-AAG
* *
502448 GGATGCATCGATGCATTGTTAAGTGCATCGTTGCA
1 GGATGCATCGGTGCATTGTTAA-TGCATCGATGCA
502483 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
43 18 0.28
44 28 0.44
45 18 0.28
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGGTGCATTGTTAATGCATCGATGCACATTCAAG
Found at i:508316 original size:18 final size:17
Alignment explanation
Indices: 508262--508310 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
508252 TTGGACTCCT
* *
508262 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
508280 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
508298 AGTGCATTCGATG
1 AGTGCA-TCGATG
508311 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:508462 original size:64 final size:61
Alignment explanation
Indices: 508279--508470 Score: 215
Period size: 64 Copynumber: 3.0 Consensus size: 61
508269 CGGTGCACTA
*
508279 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT---CTGGTGCATCGATGCATGG
*** * *
508343 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCTGAGTACATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-A-TCTG-GTGCATCGATGCATGG
* *
508407 AGAGTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAAATCATAGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AAATC-T-GGTGCATCGATGCATGG
508471 TTTGATGCAT
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
63 9 0.08
64 94 0.87
65 4 0.04
66 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (61 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATCTGGTGCATCGATGCATGG
Found at i:509092 original size:26 final size:26
Alignment explanation
Indices: 509017--509092 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
509007 GGTCTATACA
509017 GTCCTTCGGGACATATACAATATACAGAG
1 GTCCTTCGGGACA-A-A-AATATACAGAG
* *
509046 GTCCTT-TGGACAAACAGTATACAGAG
1 GTCCTTCGGGACAAA-AATATACAGAG
*
509072 GTCCTTCGGGACAAATATATA
1 GTCCTTCGGGACAAAAATATA
509093 GGTTTTTCGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 22 0.54
27 8 0.20
28 5 0.12
29 6 0.15
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (26 bp):
GTCCTTCGGGACAAAAATATACAGAG
Found at i:509095 original size:22 final size:22
Alignment explanation
Indices: 509064--509131 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
509054 GACAAACAGT
* *
509064 ATACAGAGGTCCTTCGGGACAA
1 ATACATAGGTCATTCGGGACAA
* **
509086 ATATATAGGTTTTTCGGGACAA
1 ATACATAGGTCATTCGGGACAA
509108 ATACATAGGTCATTCGGGACAA
1 ATACATAGGTCATTCGGGACAA
509130 AT
1 AT
509132 TTCACATGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (22 bp):
ATACATAGGTCATTCGGGACAA
Found at i:509828 original size:21 final size:21
Alignment explanation
Indices: 509803--509843 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
509793 GTAGCAGTAT
509803 TGTAGCAGTGCATCAGTACAC
1 TGTAGCAGTGCATCAGTACAC
*
509824 TGTAGCAGTGCATCGGTACA
1 TGTAGCAGTGCATCAGTACA
509844 TAATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (21 bp):
TGTAGCAGTGCATCAGTACAC
Found at i:517997 original size:2 final size:2
Alignment explanation
Indices: 517990--518039 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
517980 GCTTGATTTG
517990 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
518032 TA TA TA TA
1 TA TA TA TA
518040 AATGGTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:519768 original size:22 final size:22
Alignment explanation
Indices: 519743--519802 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
519733 GGTCTACACA
*
519743 GTCCTTCGGGACATATACAAAG
1 GTCCTTCGGGACAAATACAAAG
*
519765 GTCCTTCGGGACAAATACATAG
1 GTCCTTCGGGACAAATACAAAG
519787 GTCCTTCGGGACAAAT
1 GTCCTTCGGGACAAAT
519803 TTCACATGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (22 bp):
GTCCTTCGGGACAAATACAAAG
Found at i:521899 original size:32 final size:32
Alignment explanation
Indices: 521863--521926 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
521853 GAAGTTATGC
*
521863 TTATGAGGGTTCCATACATGTGAAAATGTCGT
1 TTATGAGGGTACCATACATGTGAAAATGTCGT
521895 TTATGAGGGTACCATACATGTGAAAATGTCGT
1 TTATGAGGGTACCATACATGTGAAAATGTCGT
521927 CATATGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (32 bp):
TTATGAGGGTACCATACATGTGAAAATGTCGT
Found at i:522159 original size:2 final size:2
Alignment explanation
Indices: 522152--522183 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
522142 CATTTACAAT
522152 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
522184 CACACACATA
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):
TA
Found at i:525688 original size:24 final size:25
Alignment explanation
Indices: 525660--525706 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
525650 AAATGTTATA
525660 AAAATTAA-TTTTTATTTATAATTC
1 AAAATTAATTTTTTATTTATAATTC
525684 AAAATTAATTTTTTATTTATAAT
1 AAAATTAATTTTTTATTTATAAT
525707 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAATTAATTTTTTATTTATAATTC
Found at i:527272 original size:24 final size:24
Alignment explanation
Indices: 527240--527285 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
527230 TTTTGAGTGC
527240 AATATATATACCAGAAAAACATTA
1 AATATATATACCAGAAAAACATTA
527264 AATATATATACCAGAAAAACAT
1 AATATATATACCAGAAAAACAT
527286 GGTTGACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (24 bp):
AATATATATACCAGAAAAACATTA
Found at i:528638 original size:21 final size:22
Alignment explanation
Indices: 528612--528652 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
528602 GAGAATAGTG
*
528612 AATTTTCGTT-TTCATTTTATT
1 AATTTTAGTTATTCATTTTATT
*
528633 AATTTTAGTTATTTATTTTA
1 AATTTTAGTTATTCATTTTA
528653 AAAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
AATTTTAGTTATTCATTTTATT
Found at i:530224 original size:19 final size:20
Alignment explanation
Indices: 530194--530231 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
530184 TTACTGAAAA
530194 AATTACCTATCAAAATCAAG
1 AATTACCTATCAAAATCAAG
530214 AATTA-CTATCAAAATCAA
1 AATTACCTATCAAAATCAA
530232 ATGTGTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (20 bp):
AATTACCTATCAAAATCAAG
Found at i:541344 original size:114 final size:114
Alignment explanation
Indices: 541201--541428 Score: 393
Period size: 114 Copynumber: 2.0 Consensus size: 114
541191 GAGTAGATCG
* *
541201 ATAAAATCCTTTCTCAATATACACGCTACAAACTTTATCTTGTTGATTTGAAGAAAAATCTCAAA
1 ATAAAATCCTTTCTCAATATACACGCTACAAACTTCATCTTGTTGATTTAAAGAAAAATCTCAAA
*
541266 TAGAATTATGTATTTCATGATCATGCTTAATAGTGAATGCATCAATGAT
66 TAGAATTATGTATTTCATGATCATGCTCAATAGTGAATGCATCAATGAT
* * *
541315 ATAAAATCCTTTCTCAATATACGCTCTACAAACTTCATCTTGTTGATTTAAATAAAAATCTCAAA
1 ATAAAATCCTTTCTCAATATACACGCTACAAACTTCATCTTGTTGATTTAAAGAAAAATCTCAAA
*
541380 TAGAATTATGTATTTCATGATCATGCTCAATAGTGAATGCATTAATGAT
66 TAGAATTATGTATTTCATGATCATGCTCAATAGTGAATGCATCAATGAT
541429 TTCTTTTTCA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (114 bp):
ATAAAATCCTTTCTCAATATACACGCTACAAACTTCATCTTGTTGATTTAAAGAAAAATCTCAAA
TAGAATTATGTATTTCATGATCATGCTCAATAGTGAATGCATCAATGAT
Found at i:543797 original size:17 final size:17
Alignment explanation
Indices: 543775--543825 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
543765 AGGAATTCAT
543775 AGGGTATCGATACCTGG
1 AGGGTATCGATACCTGG
543792 AGGGTAGTATCGATACCTGG
1 A-GG--GTATCGATACCTGG
*
543812 AGGGTACCGATACC
1 AGGGTATCGATACC
543826 ATAAGGTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 2 0.07
20 15 0.50
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (17 bp):
AGGGTATCGATACCTGG
Found at i:543803 original size:20 final size:20
Alignment explanation
Indices: 543778--543817 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
543768 AATTCATAGG
543778 GTATCGATACCTGGAGGGTA
1 GTATCGATACCTGGAGGGTA
543798 GTATCGATACCTGGAGGGTA
1 GTATCGATACCTGGAGGGTA
543818 CCGATACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (20 bp):
GTATCGATACCTGGAGGGTA
Found at i:544654 original size:21 final size:21
Alignment explanation
Indices: 544628--544667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
544618 TTCTACGTGG
* *
544628 TCCTTTGGGAGATATATGTAA
1 TCCTTTGGAACATATATGTAA
544649 TCCTTTGGAACATATATGT
1 TCCTTTGGAACATATATGT
544668 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTAA
Found at i:544781 original size:21 final size:21
Alignment explanation
Indices: 544747--544786 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
544737 ATATGTGTTA
*
544747 TATGTGGTCATTCGGGACATC
1 TATGTGGTCATTCGAGACATC
544768 TATGTGGT-ATTTCGAGACA
1 TATGTGGTCA-TTCGAGACA
544787 AATCATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (21 bp):
TATGTGGTCATTCGAGACATC
Found at i:546923 original size:3 final size:3
Alignment explanation
Indices: 546915--546994 Score: 103
Period size: 3 Copynumber: 27.3 Consensus size: 3
546905 GTATTTATTT
* * *
546915 ATA ATA ATA AT- ATA ATA ATA ATTA ATA AT- ATC TTT A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
546958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
546995 ACAATTAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 5 0.07
3 61 0.88
4 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Done.