Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008166.1 Hibiscus syriacus cultivar Beakdansim tig00110747_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: 2544747
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:222410 original size:20 final size:20
Alignment explanation
Indices: 222385--222699 Score: 258
Period size: 20 Copynumber: 16.7 Consensus size: 20
222375 CACATTCATT
222385 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
222405 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
222425 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
222445 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
222462 T-A--ATCGCAAAGCGAAAA
1 TGACTATCGCAACGCGAATA
*
222479 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
222499 TGA-TAATCGCAACG-G--GA
1 TGACT-ATCGCAACGCGAATA
* *
222516 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
222533 TGACTATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
222553 TGACTATCGCAAAGCGAATA
1 TGACTATCGCAACGCGAATA
* *
222573 TGACTATCACAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
222593 TAACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
222613 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
222630 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
222646 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
222666 TGATTATCGTAACAG-GAATT
1 TGACTATCGCAAC-GCGAATA
222686 TGACTATCGCAACG
1 TGACTATCGCAACG
222700 AGAAATCGCA
Statistics
Matches: 243, Mismatches: 31, Indels: 43
0.77 0.10 0.14
Matches are distributed among these distances:
14 23 0.09
15 2 0.01
16 7 0.03
17 10 0.04
18 4 0.02
19 17 0.07
20 179 0.74
21 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:222492 original size:54 final size:54
Alignment explanation
Indices: 222410--222674 Score: 291
Period size: 54 Copynumber: 4.8 Consensus size: 54
222400 GAATATGACT
* * *
222410 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATA
* *
222464 ATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTG-ATAATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAAT-ATCGCAACGAGATA
* * * ** * *
222518 ATCGCAATGCGAAAATGACTATCGCAATGCAAAAATGACTATCGCAAAGCGAATATGA
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGC-AA-CG-AGAT-A
* ** * *
222576 CTATCACAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
1 --ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATA
*
222632 ATCGCAACGCG-AAATGACTATCGCAACGCGAATTTGATTATCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCG
222675 TAACAGGAAT
Statistics
Matches: 177, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
53 30 0.17
54 95 0.54
55 3 0.02
56 3 0.02
57 5 0.03
58 3 0.02
59 2 0.01
60 36 0.20
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (54 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATA
Found at i:222542 original size:74 final size:74
Alignment explanation
Indices: 222385--222586 Score: 214
Period size: 74 Copynumber: 2.7 Consensus size: 74
222375 CACATTCATT
* * * * *
222385 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAAT
1 TGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGGGAAATCGAAT
* **
222450 ATCGCAACG
66 AGCGCAAAA
* *
222459 GGA-TAATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTGA-TAATCGCAACGGGATAATCG
1 TGACT-ATCGCAAAGCGAAAATGACTATCGCAACGCGAATATGACT-ATCGCAACGGGA-AATCG
222522 CAAT-GCG-AAAA
63 -AATAGCGCAAAA
* * * *
222533 TGACTATCGCAATGCAAAAATGACTATCGCAAAGCGAATATGACTATCACAACG
1 TGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACG
222587 CGAATTTAAC
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
73 2 0.02
74 94 0.89
75 7 0.07
76 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (74 bp):
TGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGGGAAATCGAAT
AGCGCAAAA
Found at i:222685 original size:73 final size:72
Alignment explanation
Indices: 222558--222742 Score: 237
Period size: 73 Copynumber: 2.5 Consensus size: 72
222548 AAAAATGACT
* * *
222558 ATCGCAAAGCGAATATGACTATCACAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAAAGCGAA-ATGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGC
222623 AACGAGATA
65 AACGAGA-A
* *
222632 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGTAACAG-GAATTTGACTATCGC
1 ATCGCAAAGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAAC-GCGAATTTGACTATCGC
222696 AACGAGAA
65 AACGAGAA
* * * * *
222704 ATCGCAAAGTGTATTAGACTATCGCAACGTGAATATGAT
1 ATCGCAAAGCGAAAT-GACTATCGCAACGCGAATTTGAT
222743 GCAGATTGAA
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
72 12 0.12
73 73 0.74
74 13 0.13
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (72 bp):
ATCGCAAAGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCA
ACGAGAA
Found at i:222884 original size:24 final size:25
Alignment explanation
Indices: 222850--222932 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 25
222840 AAACAAGCAC
222850 AAATAAGAATTATTTACACATCAATT
1 AAAT-AGAATTATTTACACATCAATT
222876 AAAT-GAATTATTTACACATCAATT
1 AAATAGAATTATTTACACATCAATT
222900 AAACAAATAAGAATTATTTACACATCAATT
1 ----AAAT-AGAATTATTTACACATCAATT
222930 AAA
1 AAA
222933 CAAATCAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
24 20 0.39
26 7 0.14
28 4 0.08
30 20 0.39
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATAGAATTATTTACACATCAATT
Found at i:222914 original size:30 final size:30
Alignment explanation
Indices: 222848--222937 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
222838 TTAAACAAGC
222848 ACAAATAAGAATTATTTACACATCAATT--
1 ACAAATAAGAATTATTTACACATCAATTAA
222876 --AAAT--GAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
222902 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
222932 ACAAAT
1 ACAAAT
222938 CAACTCTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
24 20 0.36
26 4 0.07
28 4 0.07
30 28 0.50
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.31
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:224378 original size:42 final size:42
Alignment explanation
Indices: 224311--224402 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
224301 GTGAATCGGG
* * *
224311 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
224353 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
224395 CTCTTGAA
1 CTCTTGAA
224403 CGATGACAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:224407 original size:21 final size:21
Alignment explanation
Indices: 224326--224412 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
224316 GAATGTTGGG
* *
224326 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * * **
224347 AGTGGCCTCTTGAATGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
224368 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
224389 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
224410 AGG
1 AGG
224413 TGAGTCGGGT
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:224998 original size:20 final size:20
Alignment explanation
Indices: 224909--224982 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
224899 TCGCAACATG
* *
224909 AATGACTATCGTAACGCGAA
1 AATGACTATCGCAACGCAAA
*
224929 AATGACTATCGTAACGCAAA
1 AATGACTATCGCAACGCAAA
224949 AATGACTATCGCAACGCAAA
1 AATGACTATCGCAACGCAAA
224969 AATGACTATCGCAA
1 AATGACTATCGCAA
224983 TGCGAATTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCAAA
Found at i:225004 original size:40 final size:40
Alignment explanation
Indices: 224909--225004 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
224899 TCGCAACATG
* *
224909 AATGACTATCGT-AACGCGAAAATGACTATCGTAACGCAAA
1 AATGACTATC-TCAACGCAAAAATGACTATCGCAACGCAAA
* * *
224949 AATGACTATCGCAACGCAAAAATGACTATCGCAATGCGAA
1 AATGACTATCTCAACGCAAAAATGACTATCGCAACGCAAA
**
224989 TTTGACTATCTCAACG
1 AATGACTATCTCAACG
225005 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
AATGACTATCTCAACGCAAAAATGACTATCGCAACGCAAA
Found at i:225073 original size:20 final size:20
Alignment explanation
Indices: 225047--225114 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
225037 GCGATTCTTT
**
225047 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
225067 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
225087 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
225107 CGTTGCGA
1 CGTTGCGA
225115 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:227327 original size:22 final size:22
Alignment explanation
Indices: 227297--227354 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
227287 AGATGGAGAT
227297 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* * *
227319 AGACTGATTTTGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
227341 GGACGGATGTCGCC
1 AGACGGATTTCGCC
227355 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:227551 original size:20 final size:20
Alignment explanation
Indices: 227526--227636 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
227516 GAAAATTGCA
*
227526 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
227546 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
227566 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCG
* * * *
227586 TGGCGAT-TTACATATTCGCG
1 TTGCGATAGT-CAGAATCGCG
* * * *
227606 TTGCGATTGTCATACTCGCA
1 TTGCGATAGTCAGAATCGCG
227626 TTGCGATAGTC
1 TTGCGATAGTC
227637 GGAAAATCGC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 75 0.97
21 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:227583 original size:40 final size:40
Alignment explanation
Indices: 227526--227636 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
227516 GAAAATTGCA
* * *
227526 TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCATTGCGATAGTCAGAATCGCG
* * * *
227566 TTGCGATAGTCATAATCGCATGGCGAT-TTACATATTCGCG
1 TTGCGATAGTCATAATCGCATTGCGATAGT-CAGAATCGCG
* *
227606 TTGCGATTGTCATACTCGCATTGCGATAGTC
1 TTGCGATAGTCATAATCGCATTGCGATAGTC
227637 GGAAAATCGC
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 56 0.97
41 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (40 bp):
TTGCGATAGTCATAATCGCATTGCGATAGTCAGAATCGCG
Found at i:228628 original size:3 final size:3
Alignment explanation
Indices: 228620--228644 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
228610 TCTAATATAA
228620 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
228645 CCATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:230332 original size:26 final size:28
Alignment explanation
Indices: 230303--230366 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
230293 TAATTTGCAC
*
230303 ATTTAGTTTATGTTTTT-TATGTG-GTT
1 ATTTAGTTTATGTTTTTATATATGTGTT
* *
230329 ATTTTATTTTATTTTTTTATATATGTGTT
1 A-TTTAGTTTATGTTTTTATATATGTGTT
230358 ATTT-GTTTA
1 ATTTAGTTTA
230367 AAGTGATACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 18 0.58
28 8 0.26
29 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (28 bp):
ATTTAGTTTATGTTTTTATATATGTGTT
Found at i:234478 original size:14 final size:14
Alignment explanation
Indices: 234447--234512 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
234437 AGGATAGGAA
*
234447 AAAGATAAGAAA-C
1 AAAGAAAAGAAAGC
234460 AAAGAAAA-AAGAGC
1 AAAGAAAAGAA-AGC
*
234474 AAAGAGAAA-AAATC
1 AAAGA-AAAGAAAGC
234488 AAAGGAAAAGAAAG-
1 AAA-GAAAAGAAAGC
234502 AAAGAAAAGAA
1 AAAGAAAAGAA
234513 GAACACGCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 2 0.04
13 16 0.36
14 17 0.38
15 10 0.22
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAAGAAAGC
Found at i:237228 original size:36 final size:35
Alignment explanation
Indices: 237188--237266 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
237178 TTAAGATTTT
* *
237188 TTTCTCTAATAAC-AATTTTTTTCTCCCTTGAGACAA
1 TTTCTCTAA-AACTAA-TTTTGTCTCACTTGAGACAA
*
237224 TTTCTCTTGAAACTAATTTTGTCTCACTTGAGACAA
1 TTTCTC-TAAAACTAATTTTGTCTCACTTGAGACAA
237260 TTTCTCT
1 TTTCTCT
237267 TGAAACACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
35 1 0.03
36 33 0.87
37 4 0.11
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.46
Consensus pattern (35 bp):
TTTCTCTAAAACTAATTTTGTCTCACTTGAGACAA
Found at i:237267 original size:36 final size:36
Alignment explanation
Indices: 237204--237272 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
237194 TAATAACAAT
* *
237204 TTTTTTCTCCCTTGAGACAATTTCTCTTGAAACTAA
1 TTTTGTCTCACTTGAGACAATTTCTCTTGAAACTAA
237240 TTTTGTCTCACTTGAGACAATTTCTCTTGAAAC
1 TTTTGTCTCACTTGAGACAATTTCTCTTGAAAC
237273 ACAAATCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTGTCTCACTTGAGACAATTTCTCTTGAAACTAA
Found at i:237491 original size:66 final size:67
Alignment explanation
Indices: 237392--237632 Score: 240
Period size: 66 Copynumber: 3.6 Consensus size: 67
237382 TATTTTCCTA
* * * * *
237392 AAAACAAAATTTCATCTCGCTTGAGACAATTTCTTTTGAAACATAAACCTTTGAGTTTGTTTCTA
1 AAAACAAAGTTTCGTCTCGCTTGAGATAGTTTCTTTTGAAACATAAACCTTTGAGATTGTTTCTA
237457 TC
66 TC
* *
237459 AAAACAAAGTTT-GTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTC
1 AAAACAAAGTTTCGTCTCGCTTGAGATAGTTTCTTTTGAAACATAAACCTTTGAGATTGTTTCTA
237523 TC
66 TC
* * * *
237525 GAAACAAAGTTTCGTCTCTCTTTAGATAGTTT-TTCCTTGAAACATAAA--TTTGA-AATGTTTC
1 AAAACAAAGTTTCGTCTCGCTTGAGATAGTTTCTT--TTGAAACATAAACCTTTGAGATTGTTTC
*
237586 AATC
64 TATC
* * * ** * * * *
237590 GAAATAAAATTTTATCTCGCCTAAGATAGCTTCTATTGAAACA
1 AAAACAAAGTTTCGTCTCGCTTGAGATAGTTTCTTTTGAAACA
237633 AATTTGCTTC
Statistics
Matches: 147, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
64 8 0.05
65 33 0.22
66 66 0.45
67 28 0.19
68 12 0.08
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (67 bp):
AAAACAAAGTTTCGTCTCGCTTGAGATAGTTTCTTTTGAAACATAAACCTTTGAGATTGTTTCTA
TC
Found at i:238011 original size:139 final size:138
Alignment explanation
Indices: 237753--238262 Score: 567
Period size: 139 Copynumber: 3.7 Consensus size: 138
237743 ATCACTGGCA
* * * * *
237753 ACTGACCATATCTCCTCAACGAGTAGGAGTAGCGTCATCCTCAGGCAATCAGACTTCCTCATCAT
1 ACTGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* * *
237818 GTAGGAACTGTGTTGTCTCCAAAGTATCCCTAAAGATAACTAGACGTCCTCATCACGTAGGAACA
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGA-AACTAGACATCCTCATCACGTAGGAACA
*
237883 ATGTCATCG
130 ATGTCATCC
* * * * *
237892 ACTGACCAAATATCCTCAATGCGTAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCATCAC
1 ACTGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* * * *
237957 GTAGGAACCGTGTTGTCTCCAAATTATCCCCAAAGACGACTAGACTTACC-CATCACGTAGGAGC
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGA-AACTAGACAT-CCTCATCACGTAGGAAC
*
238021 AATGTCTTCC
129 AATGTCATCC
** * * * * *
238031 ACCAACCAGATCTCCTCAACGCGTAGGAGCCA-CGTCATCCTTAGATAACCATACTTTCTCATCA
1 ACTGACCAGATCTCCTCAACGCGTAGGAG-CAGCGTCATCCTCAGACAATCAGACTTCCTCATCA
* * *
238095 CGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGATAGCTAGACATCCTCACCATGTAGGAAC
65 CGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGA-AACTAGACATCCTCATCACGTAGGAAC
*
238160 AATGTCGTCC
129 AATGTCATCC
* * * * * * * * *
238170 ACCT-AACAGATCTCCTCAATGCGAATGAGTAGTGTCAACCTCAGACAATTAGACTTTCTCATCA
1 A-CTGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCA
* * *
238234 TGTAGGAACTGTGTTGTCACCAAATTATC
65 CGTAGGAACCGTGTTGTCTCCAAATTATC
238263 TCCAGATTGA
Statistics
Matches: 311, Mismatches: 55, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
138 3 0.01
139 303 0.97
140 5 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (138 bp):
ACTGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGAAACTAGACATCCTCATCACGTAGGAACAA
TGTCATCC
Found at i:238259 original size:278 final size:278
Alignment explanation
Indices: 237757--238262 Score: 719
Period size: 278 Copynumber: 1.8 Consensus size: 278
237747 CTGGCAACTG
* * * * *
237757 ACCATATCTCCTCAACGAGTAGGAGTAGCGTCATCCTCAGGCAATCAGACTTCCTCATCATGTAG
1 ACCAGATCTCCTCAACGAGTAGGAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAG
* * *
237822 GAACTGTGTTGTCTCCAAAGTATCCCTAAAGATAACTAGACGTCCTCATCACGTAGGAACAATGT
66 GAACCGTGTTGTCTCCAAAGTATCCCTAAAGATAACTAGACATCCTCACCACGTAGGAACAATGT
* * * *
237887 CATCGACTGACCAAATATCCTCAATGCGTAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTC
131 CATCCACTGAACAAATATCCTCAATGCGAAGGAGCAGTGTCAACCTCAGACAATTAGACTTCCTC
*
237952 ATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCCAAAGACGACTAGACTTACCCATCACGTAG
196 ATCACGTAGGAACCGTGTTGTCACCAAATTATCCCCAAAGACGACTAGACTTACCCATCACGTAG
238017 GAGCAATGTCTTCCACCA
261 GAGCAATGTCTTCCACCA
* * * * *
238035 ACCAGATCTCCTCAACGCGTAGGAGCCA-CGTCATCCTTAGATAACCATACTTTCTCATCACGTA
1 ACCAGATCTCCTCAACGAGTAGGAG-CAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTA
* * *
238099 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGATAGCTAGACATCCTCACCATGTAGGAACAATG
65 GGAACCGTGTTGTCTCCAAAGTATCCCTAAAGATAACTAGACATCCTCACCACGTAGGAACAATG
* * * * * *
238164 TCGTCCACCT-AACAGATCTCCTCAATGCGAATGAGTAGTGTCAACCTCAGACAATTAGACTTTC
130 TCATCCA-CTGAACAAATATCCTCAATGCGAAGGAGCAGTGTCAACCTCAGACAATTAGACTTCC
* *
238228 TCATCATGTAGGAACTGTGTTGTCACCAAATTATC
194 TCATCACGTAGGAACCGTGTTGTCACCAAATTATC
238263 TCCAGATTGA
Statistics
Matches: 197, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
278 194 0.98
279 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (278 bp):
ACCAGATCTCCTCAACGAGTAGGAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCACGTAG
GAACCGTGTTGTCTCCAAAGTATCCCTAAAGATAACTAGACATCCTCACCACGTAGGAACAATGT
CATCCACTGAACAAATATCCTCAATGCGAAGGAGCAGTGTCAACCTCAGACAATTAGACTTCCTC
ATCACGTAGGAACCGTGTTGTCACCAAATTATCCCCAAAGACGACTAGACTTACCCATCACGTAG
GAGCAATGTCTTCCACCA
Found at i:242884 original size:40 final size:40
Alignment explanation
Indices: 242835--243037 Score: 343
Period size: 40 Copynumber: 5.1 Consensus size: 40
242825 CCCCGTAGTG
* *
242835 TTACACATAAGGCCGTGCGCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
242875 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
*
242915 TTACACATAAGGTCGTGCCAACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
* * *
242955 TTACACATAAGGGCGTGCCCACCATATACACTGAAGTGTT
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
*
242995 TTACACATAAAGTCGTGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
243035 TTA
1 TTA
243038 TAAACCTGCA
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 152 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
Found at i:249823 original size:13 final size:14
Alignment explanation
Indices: 249804--249842 Score: 71
Period size: 13 Copynumber: 2.9 Consensus size: 14
249794 AATTCAAAAA
249804 AAAATAAATCAACT
1 AAAATAAATCAACT
249818 -AAATAAATCAACT
1 AAAATAAATCAACT
249831 AAAATAAATCAA
1 AAAATAAATCAA
249843 ATACTCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAATCAACT
Found at i:250116 original size:5 final size:5
Alignment explanation
Indices: 250106--250130 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
250096 TTCGTTTTAG
250106 CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT
250131 TCCTCAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:252204 original size:29 final size:28
Alignment explanation
Indices: 252161--252217 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
252151 CCTAGTGCCA
*
252161 TCGTGTGGCCGTAGACTCGAACTCATTTC
1 TCGTGTGGCCGTAGACTCAAACT-ATTTC
*
252190 TCGTGTGGCCTTAGACTCAAACTATTTC
1 TCGTGTGGCCGTAGACTCAAACTATTTC
252218 CTTGTATGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (28 bp):
TCGTGTGGCCGTAGACTCAAACTATTTC
Found at i:253800 original size:15 final size:16
Alignment explanation
Indices: 253768--253798 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
253758 ATAAATTAGG
253768 TAATTTTAATAAAAAA
1 TAATTTTAATAAAAAA
*
253784 TAATTTTACTAAAAA
1 TAATTTTAATAAAAA
253799 TATTAGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTTTAATAAAAAA
Found at i:264030 original size:43 final size:43
Alignment explanation
Indices: 263978--264085 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
263968 TGGGGATTAA
* *
263978 GCCCCCCGTAAAGGATCCCAAATAAAAACAGGATGGAGATATT
1 GCCCTCCGTAGAGGATCCCAAATAAAAACAGGATGGAGATATT
* * *
264021 GCCCTCCGTAGAGGATCCTAAATAGAAACATGATGGAGATATT
1 GCCCTCCGTAGAGGATCCCAAATAAAAACAGGATGGAGATATT
* *
264064 ACCCTCTGTAGAGGATCCCAAA
1 GCCCTCCGTAGAGGATCCCAAA
264086 CAAATGATAG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (43 bp):
GCCCTCCGTAGAGGATCCCAAATAAAAACAGGATGGAGATATT
Found at i:271082 original size:12 final size:12
Alignment explanation
Indices: 271065--271095 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
271055 AAGTTTAACA
271065 TTTCTCCCTGAT
1 TTTCTCCCTGAT
271077 TTTCTCCCTGAT
1 TTTCTCCCTGAT
271089 TTTCTCC
1 TTTCTCC
271096 ACATCCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.06, T:0.52
Consensus pattern (12 bp):
TTTCTCCCTGAT
Found at i:272282 original size:17 final size:17
Alignment explanation
Indices: 272255--272288 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
272245 GATGAGTAGC
272255 AAATGGAAATGTTATGAA
1 AAATGGAAATGTT-TGAA
272273 AAAT-GAAATGTTTGAA
1 AAATGGAAATGTTTGAA
272289 GTATAACCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (17 bp):
AAATGGAAATGTTTGAA
Found at i:275256 original size:7 final size:7
Alignment explanation
Indices: 275244--275805 Score: 199
Period size: 8 Copynumber: 77.6 Consensus size: 7
275234 TAGTTATATA
275244 TATAAAG
1 TATAAAG
275251 TATAAAG
1 TATAAAG
*
275258 TGT---G
1 TATAAAG
*
275262 TATATA-
1 TATAAAG
*
275268 TATAAAC
1 TATAAAG
*
275275 TATAAAC
1 TATAAAG
275282 TATAAAG
1 TATAAAG
275289 TATATAA-
1 TATA-AAG
275296 TATAAAG
1 TATAAAG
275303 TATTAAA-
1 TA-TAAAG
*
275310 TAAAAAG
1 TATAAAG
275317 TATTAAAG
1 TA-TAAAG
275325 TATATAA-
1 TATA-AAG
* *
275332 TACAAAA
1 TATAAAG
275339 TATTAAAG
1 TA-TAAAG
275347 TATTAAAG
1 TA-TAAAG
* *
275355 TATATAC
1 TATAAAG
275362 TATAAAG
1 TATAAAG
*
275369 TATAAAAC
1 TAT-AAAG
275377 TATATAA-
1 TATA-AAG
275384 TAT-AAG
1 TATAAAG
275390 TATTAAAG
1 TA-TAAAG
*
275398 TGTAAAAG
1 TAT-AAAG
275406 TATAAAAG
1 TAT-AAAG
275414 TATTAAAG
1 TA-TAAAG
*
275422 TATAAAAC
1 TAT-AAAG
*
275430 TATAGA-
1 TATAAAG
275436 TAT-AAG
1 TATAAAG
*
275442 TATTAAAA
1 TA-TAAAG
275450 TATTAAAG
1 TA-TAAAG
*
275458 TATATAG
1 TATAAAG
275465 TATAAAG
1 TATAAAG
*
275472 TATAAAAC
1 TAT-AAAG
275480 TATATAA-
1 TATA-AAG
275487 TAT-AAG
1 TATAAAG
275493 TATTAAAG
1 TA-TAAAG
*
275501 TGTATAAG
1 TATA-AAG
275509 TATTAAAG
1 TA-TAAAG
*
275517 TATAAAAC
1 TAT-AAAG
275525 TATAGAA-
1 TATA-AAG
275532 TAT-AAG
1 TATAAAG
275538 TATTAAAG
1 TA-TAAAG
275546 TATATAAG
1 TATA-AAG
275554 TATTAAAG
1 TA-TAAAG
275562 TATTAAAG
1 TA-TAAAG
*
275570 TATAAAA
1 TATAAAG
*
275577 T-TATAG
1 TATAAAG
*
275583 AATAGAAG
1 TATA-AAG
275591 TATGAAAG
1 TAT-AAAG
275599 TATAAAGG
1 TATAAA-G
*
275607 TATACATATA
1 TATA-A-A-G
*
275617 TATAAAC
1 TATAAAG
*
275624 TATAATG
1 TATAAAG
*
275631 TATAAGTG
1 TATAA-AG
*
275639 TATAAAC
1 TATAAAG
275646 TAT-AAG
1 TATAAAG
*
275652 TCTATAAG
1 TATA-AAG
275660 TATATAA-
1 TATA-AAG
275667 TATAAAG
1 TATAAAG
275674 TAT-AA-
1 TATAAAG
275679 TA-AAAG
1 TATAAAG
*
275685 TTTATATA-
1 --TATAAAG
*
275693 TATATA-
1 TATAAAG
*
275699 TATATA-
1 TATAAAG
*
275705 TATATA-
1 TATAAAG
275711 TATAAAAG
1 TAT-AAAG
275719 TA-ATAAG
1 TATA-AAG
275726 TAATAAAG
1 T-ATAAAG
275734 TATAAAGTG
1 TATAAA--G
*
275743 TATATAAT
1 TATA-AAG
275751 TATTAAA-
1 TA-TAAAG
*
275758 TATAAAA
1 TATAAAG
275765 TATATAAG
1 TATA-AAG
275773 TATATAAG
1 TATA-AAG
275781 TATTAAA-
1 TA-TAAAG
275788 TATAAAG
1 TATAAAG
*
275795 TTTAAAG
1 TATAAAG
275802 TATA
1 TATA
275806 TATAACTATA
Statistics
Matches: 441, Mismatches: 49, Indels: 130
0.71 0.08 0.21
Matches are distributed among these distances:
4 3 0.01
5 11 0.02
6 64 0.15
7 150 0.34
8 186 0.42
9 20 0.05
10 7 0.02
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (7 bp):
TATAAAG
Found at i:275316 original size:14 final size:14
Alignment explanation
Indices: 275285--275323 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
275275 TATAAACTAT
*
275285 AAAGTA-TATAATAT
1 AAAGTATTA-AATAA
275299 AAAGTATTAAATAA
1 AAAGTATTAAATAA
275313 AAAGTATTAAA
1 AAAGTATTAAA
275324 GTATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (14 bp):
AAAGTATTAAATAA
Found at i:275380 original size:22 final size:22
Alignment explanation
Indices: 275266--275392 Score: 84
Period size: 22 Copynumber: 5.8 Consensus size: 22
275256 AGTGTGTATA
* *
275266 TATATAAACTATAAACTAT-AAAG
1 TATAT-AA-TATAAAGTATAAAAC
*
275289 TATATAATATAAAGTATTAAA-
1 TATATAATATAAAGTATAAAAC
* *
275310 TA-AAAAGTATTAAAGTATATAA-
1 TATATAA-TA-TAAAGTATAAAAC
* * * *
275332 TACAAAATATTAAAGTATTAAAG
1 TATATAATA-TAAAGTATAAAAC
*
275355 TATATACTATAAAGTATAAAAC
1 TATATAATATAAAGTATAAAAC
275377 TATATAATAT-AAGTAT
1 TATATAATATAAAGTAT
275393 TAAAGTGTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.03
21 19 0.22
22 50 0.57
23 15 0.17
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (22 bp):
TATATAATATAAAGTATAAAAC
Found at i:275457 original size:103 final size:103
Alignment explanation
Indices: 275261--275610 Score: 373
Period size: 103 Copynumber: 3.5 Consensus size: 103
275251 TATAAAGTGT
* * *
275261 GTATATA-TATAAACTAT-AAACTATA-AAGTATATAATA-TAAAGTATTAAA-TA-AAAAGTAT
1 GTATATAGTATAAAGTATAAAACTATATAA-TATA-AGTATTAAAGTATAAAAGTATAAAAGTAT
* *
275320 TAAAGTAT-ATA--ATACA-A-AA-TATTAAAGTATTAAA
64 TAAAGTATAAAACTATAGATATAAGTATTAAAGTATTAAA
* *
275354 GTATATACTATAAAGTATAAAACTATATAATATAAGTATTAAAGTGTAAAAGTATAAAAGTATTA
1 GTATATAGTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAAAGTATAAAAGTATTA
*
275419 AAGTATAAAACTATAGATATAAGTATTAAAATATTAAA
66 AAGTATAAAACTATAGATATAAGTATTAAAGTATTAAA
275457 GTATATAGTATAAAGTATAAAACTATATAATATAAGTATTAAAG--T----GTAT--AAGTATTA
1 GTATATAGTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAAAGTATAAAAGTATTA
275514 AAGTATAAAACTATAGAATATAAGTATTAAAGTA-TATAA
66 AAGTATAAAACTATAG-ATATAAGTATTAAAGTATTA-AA
* * * * * *
275553 GTATTAAAGTATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTATAAAGGTATA
1 GTA-TATAGTA-TAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAAAGTATA
275611 CATATATATA
Statistics
Matches: 220, Mismatches: 14, Indels: 34
0.82 0.05 0.13
Matches are distributed among these distances:
93 7 0.03
94 12 0.05
95 48 0.22
96 25 0.11
97 26 0.12
98 32 0.15
100 5 0.02
101 2 0.01
102 2 0.01
103 57 0.26
104 4 0.02
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (103 bp):
GTATATAGTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAAAGTATAAAAGTATTA
AAGTATAAAACTATAGATATAAGTATTAAAGTATTAAA
Found at i:275557 original size:45 final size:45
Alignment explanation
Indices: 275450--275573 Score: 198
Period size: 45 Copynumber: 2.8 Consensus size: 45
275440 AGTATTAAAA
*
275450 TATTAAAGTATAT-AGTA-TAAAGTATAAAACTATATAATATAAG
1 TATTAAAGTATATAAGTATTAAAGTATAAAACTATAGAATATAAG
*
275493 TATTAAAGTGTATAAGTATTAAAGTATAAAACTATAGAATATAAG
1 TATTAAAGTATATAAGTATTAAAGTATAAAACTATAGAATATAAG
* *
275538 TATTAAAGTATATAAGTATTAAAGTATTAAAGTATA
1 TATTAAAGTATATAAGTATTAAAGTATAAAACTATA
275574 AAATTATAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
43 12 0.16
44 4 0.05
45 58 0.78
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (45 bp):
TATTAAAGTATATAAGTATTAAAGTATAAAACTATAGAATATAAG
Found at i:275592 original size:45 final size:44
Alignment explanation
Indices: 275450--275610 Score: 186
Period size: 45 Copynumber: 3.6 Consensus size: 44
275440 AGTATTAAAA
*
275450 TATTAAAGTATAT-AGTATAAAGTATAAAACTATATAATATAAG
1 TATTAAAGTATATAAGTATAAAGTATAAAACTATAAAATATAAG
* *
275493 TATTAAAGTGTATAAGTATTAAAGTATAAAACTATAGAATATAAG
1 TATTAAAGTATATAAGTA-TAAAGTATAAAACTATAAAATATAAG
* *
275538 TATTAAAGTATATAAGTATTAAAGTATTAAAGTATAAAAT-TATAG
1 TATTAAAGTATATAAGTA-TAAAGTATAAAACTATAAAATATA-AG
*
275583 -AATAGAAGTATGA-AAGTATAAAGGTATA
1 TATTA-AAGTAT-ATAAGTATAAA-GTATA
275611 CATATATATA
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
43 12 0.12
44 13 0.12
45 78 0.75
46 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.34
Consensus pattern (44 bp):
TATTAAAGTATATAAGTATAAAGTATAAAACTATAAAATATAAG
Found at i:275645 original size:22 final size:22
Alignment explanation
Indices: 275615--275678 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
275605 GGTATACATA
275615 TATATAAACTATAATGTATAAG
1 TATATAAACTATAATGTATAAG
* *
275637 TGTATAAACTATAAGTCTATAAG
1 TATATAAACTATAA-TGTATAAG
*
275660 TATAT-AA-TATAAAGTATAA
1 TATATAAACTATAATGTATAA
275679 TAAAAGTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.14
21 5 0.14
22 15 0.42
23 11 0.31
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
TATATAAACTATAATGTATAAG
Found at i:275694 original size:2 final size:2
Alignment explanation
Indices: 275687--275714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
275677 AATAAAAGTT
275687 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
275715 AAAGTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:275741 original size:15 final size:14
Alignment explanation
Indices: 275723--275805 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
275713 TAAAAGTAAT
275723 AAGTAATAAAGTATA
1 AAGT-ATAAAGTATA
*
275738 AAGTGTATATAATTATTA
1 AA--GTATA-AAGTA-TA
*
275756 AA-TATAAAATATA
1 AAGTATAAAGTATA
275769 TAAGTATATAAGTATTA
1 -AAGTATA-AAGTA-TA
*
275786 AA-TATAAAGTTTA
1 AAGTATAAAGTATA
275799 AAGTATA
1 AAGTATA
275806 TATAACTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
13 6 0.11
14 14 0.25
15 14 0.25
16 9 0.16
17 8 0.15
18 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (14 bp):
AAGTATAAAGTATA
Found at i:275776 original size:30 final size:29
Alignment explanation
Indices: 275277--275807 Score: 155
Period size: 29 Copynumber: 17.8 Consensus size: 29
275267 ATATAAACTA
*
275277 TAAACTATAAAGTATATAA-TATA-AAGTAT
1 TAAA-TATAAAATATA-AAGTATATAAGTAT
*
275306 TAAATA-AAAAGTATTAAAGTATATAA-TAC
1 TAAATATAAAA-TA-TAAAGTATATAAGTAT
* * *
275335 AAAATATTAAAGTATTAAAGTATAT-ACTA-
1 TAAATA-TAAAATA-TAAAGTATATAAGTAT
*
275364 TAAAGTATAAAACTATATA--ATATAAGTAT
1 TAAA-TATAAAA-TATAAAGTATATAAGTAT
*
275393 TAAAGTGTAAAAGTATAAAAGTAT-TAAAGTAT
1 TAAA-TATAAAA-TAT-AAAGTATAT-AAGTAT
* * *
275425 AAAACTAT-AGATAT-AAGTAT-TAAAATAT
1 TAAA-TATAAAATATAAAGTATAT-AAGTAT
* * * *
275453 TAAAGTATATAGTATAAAGTATAAAACTA-
1 TAAA-TATAAAATATAAAGTATATAAGTAT
* *
275482 TATAATAT-AAGTATTAAAGTGTATAAGTAT
1 TA-AATATAAAATA-TAAAGTATATAAGTAT
*
275512 TAAAGTATAAAACTAT--AGAATATAAGTAT
1 TAAA-TATAAAA-TATAAAGTATATAAGTAT
*
275541 TAAAGTATATAAGTATTAAAGTAT-TAAAGTAT
1 TAAA-TATA-AAATA-TAAAGTATAT-AAGTAT
* * *
275573 AAAATTATAGAATA-GAAGTATGA-AAGTA-
1 TAAA-TATAAAATATAAAGTAT-ATAAGTAT
* *
275601 TAAAGGTATACATATATATAAACTATA-ATGTA-
1 TAAA--TATA-A-A-ATATAAAGTATATAAGTAT
* * *
275633 TAAGTGTATAAACTAT-AAGTCTATAAGTA-
1 TAA--ATATAAAATATAAAGTATATAAGTAT
*
275662 TATAATATAAAGTATAATAAAAGTTTAT-A-TA-
1 TA-AATATAAA--AT-AT-AAAGTATATAAGTAT
* * * * *
275693 TATATATATATATATATA-TATAAAAGTAA
1 TAAATATA-AAATATAAAGTATATAAGTAT
* * *
275722 TAAGTAATAAAGTATAAAGTGTATATAATTAT
1 TAAAT-ATAAAATATAAA--GTATATAAGTAT
275754 TAAATATAAAATATATAAGTATATAAGTAT
1 TAAATATAAAATATA-AAGTATATAAGTAT
* *
275784 TAAATATAAAGTTTAAAGTATATA
1 TAAATATAAAATATAAAGTATATA
275808 TAACTATATA
Statistics
Matches: 379, Mismatches: 69, Indels: 108
0.68 0.12 0.19
Matches are distributed among these distances:
26 3 0.01
27 10 0.03
28 50 0.13
29 130 0.34
30 81 0.21
31 31 0.08
32 62 0.16
33 12 0.03
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (29 bp):
TAAATATAAAATATAAAGTATATAAGTAT
Found at i:275832 original size:47 final size:44
Alignment explanation
Indices: 275757--275849 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 44
275747 TAATTATTAA
*
275757 ATATAAAATATATAAGTATATAAGTATTAAATATAAAGTTTAAAGT
1 ATATAAAATATATAAGTATATAAGTATT-AATATAAA-TATAAAGT
* * *
275803 ATATATAACTATATAAGTATACTTA-TATTAATATTAATATAAAGT
1 ATATA-AAATATATAAGTATA-TAAGTATTAATATAAATATAAAGT
275848 AT
1 AT
275850 TAATTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 9 0.22
46 12 0.29
47 18 0.44
48 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (44 bp):
ATATAAAATATATAAGTATATAAGTATTAATATAAATATAAAGT
Found at i:275899 original size:18 final size:17
Alignment explanation
Indices: 275876--275933 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
275866 AATATATAAA
275876 TAAATATTTATAAAGTAT
1 TAAATA-TTATAAAGTAT
*
275894 TAAATA-TA-AGTA-TAT
1 TAAATATTATA-AAGTAT
275909 GTAAATATGTATAAAGTAT
1 -TAAATAT-TATAAAGTAT
275928 TAAATA
1 TAAATA
275934 AAACATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 4 0.12
16 9 0.28
18 15 0.47
19 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
TAAATATTATAAAGTAT
Found at i:275901 original size:14 final size:14
Alignment explanation
Indices: 275751--275906 Score: 62
Period size: 14 Copynumber: 11.2 Consensus size: 14
275741 TGTATATAAT
*
275751 TATTAAATATAAAA
1 TATTAAATATAAAG
*
275765 TATATAAGTATATAAG
1 TAT-TAAATATA-AAG
275781 TATTAAATATAAAG
1 TATTAAATATAAAG
275795 T-TTAAAGTAT--A-
1 TATTAAA-TATAAAG
*
275806 TA-TAACTATATAAG
1 TATTAAATATA-AAG
* *
275820 TA-TACTTATATTAA-
1 TATTA--AATATAAAG
275834 TATT-AATATAAAG
1 TATTAAATATAAAG
*
275847 TATTAATTATTAAA-
1 TATTAAATA-TAAAG
* *
275861 TATAAAATATATAAA
1 TATTAAATATA-AAG
* **
275876 TAAATATTTATAAAG
1 T-ATTAAATATAAAG
275891 TATTAAATAT-AAG
1 TATTAAATATAAAG
275904 TAT
1 TAT
275907 ATGTAAATAT
Statistics
Matches: 105, Mismatches: 20, Indels: 35
0.66 0.12 0.22
Matches are distributed among these distances:
10 3 0.03
11 4 0.04
12 7 0.07
13 18 0.17
14 34 0.32
15 25 0.24
16 14 0.13
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.40
Consensus pattern (14 bp):
TATTAAATATAAAG
Found at i:276639 original size:22 final size:22
Alignment explanation
Indices: 276614--276670 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
276604 CTTAATTCCC
*
276614 AAAT-CCCAAATCCATAAATCTT
1 AAATCCCCAAATCCAT-AACCTT
*
276636 AAATCCCCAAATCCCTAACCTT
1 AAATCCCCAAATCCATAACCTT
276658 AAATCCCCAAATC
1 AAATCCCCAAATC
276671 TTATACTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATCCCCAAATCCATAACCTT
Found at i:279591 original size:20 final size:20
Alignment explanation
Indices: 279565--279632 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
279555 TTGATCTTAC
*
279565 TTGATATTGCTTGATTTTGT
1 TTGATATTGCTTGATTCTGT
* * *
279585 TTTATATTGTTTGCTTCTGT
1 TTGATATTGCTTGATTCTGT
* * *
279605 TTGATATTTCTTAATTCTGC
1 TTGATATTGCTTGATTCTGT
279625 TTGATATT
1 TTGATATT
279633 TGTAAGGGTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.09, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGATATTGCTTGATTCTGT
Found at i:279757 original size:23 final size:23
Alignment explanation
Indices: 279729--279779 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
279719 ATACAGGATA
* *
279729 CTTGCTGAATTTATGCAATGATG
1 CTTGCTGAATTGATACAATGATG
279752 CTTGCTGAATTGATACAATGATG
1 CTTGCTGAATTGATACAATGATG
279775 CTTGC
1 CTTGC
279780 GAGTTGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (23 bp):
CTTGCTGAATTGATACAATGATG
Found at i:280720 original size:13 final size:13
Alignment explanation
Indices: 280702--280750 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
280692 CTTAACATGT
280702 TTAAAAATAAAAC
1 TTAAAAATAAAAC
280715 TT-AAAATAAAA-
1 TTAAAAATAAAAC
*
280726 -TGAAAATGAAAAC
1 TTAAAAAT-AAAAC
*
280739 TTAAAAAGAAAA
1 TTAAAAATAAAA
280751 TAAAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:280722 original size:12 final size:12
Alignment explanation
Indices: 280705--280744 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
280695 AACATGTTTA
280705 AAAATAAAACTT
1 AAAATAAAACTT
*
280717 AAAATAAAA-TG
1 AAAATAAAACTT
280728 AAAATGAAAACTT
1 AAAAT-AAAACTT
280741 AAAA
1 AAAA
280745 AGAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAATAAAACTT
Found at i:280755 original size:24 final size:24
Alignment explanation
Indices: 280705--280759 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
280695 AACATGTTTA
*
280705 AAAAT-AAAACTTAAAATAAAATG
1 AAAATGAAAACTTAAAAGAAAATG
280728 AAAATGAAAACTTAAAAAGAAAAT-
1 AAAATGAAAACTT-AAAAGAAAATG
280752 AAAA-GAAA
1 AAAATGAAA
280760 GAACTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.31
24 11 0.38
25 9 0.31
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (24 bp):
AAAATGAAAACTTAAAAGAAAATG
Found at i:281022 original size:27 final size:26
Alignment explanation
Indices: 280980--281032 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
280970 ATTTAGAAGG
*
280980 TGCTGACTAGATCTTCTAGAAAACTAC
1 TGCTGACTAGACCTTCTAG-AAACTAC
*
281007 TGCTGACTGGACCTTCTAGAAACTAC
1 TGCTGACTAGACCTTCTAGAAACTAC
281033 CATGTCAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (26 bp):
TGCTGACTAGACCTTCTAGAAACTAC
Found at i:287182 original size:68 final size:69
Alignment explanation
Indices: 287057--287241 Score: 270
Period size: 68 Copynumber: 2.7 Consensus size: 69
287047 TCTTTAACCG
* * * *
287057 TTCATCTAACTGGCC-TAATTGACACCTTTCTGTC-AATTCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTAGCCATGATTGACACATTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTA
287120 GCCT
66 GCCT
* *
287124 TTCATCTAACT-GCCATGATTGACACATGTCTATCAAATACACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTAGCCATGATTGACACATTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTA
287188 GCCT
66 GCCT
* *
287192 TTCATCTAACTAG-CATGATTGACACATTTCTGTCAAATGCACAATTAGGC
1 TTCATCTAACTAGCCATGATTGACACATTTCTGTCAAATACACAGTTAGGC
287242 ACTATAATAA
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
66 3 0.03
67 26 0.25
68 76 0.72
69 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (69 bp):
TTCATCTAACTAGCCATGATTGACACATTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTA
GCCT
Found at i:287303 original size:21 final size:21
Alignment explanation
Indices: 287270--287319 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
287260 AATATCAATG
*
287270 AACTCTCTCTCACTCATTATA
1 AACTCTATCTCACTCATTATA
* *
287291 AATTCTATCTCACTTATTATA
1 AACTCTATCTCACTCATTATA
287312 AACTCTAT
1 AACTCTAT
287320 ACTTTACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (21 bp):
AACTCTATCTCACTCATTATA
Found at i:288142 original size:58 final size:58
Alignment explanation
Indices: 287451--288133 Score: 967
Period size: 58 Copynumber: 11.8 Consensus size: 58
287441 TATATTTCCC
* * * * * *
287451 ATACAGAAATTCATACATTTAGAATGAATTTTTTAG--TTCTGCACACATAGTGCCC-
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
*
287506 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
** * * *
287564 ATACATAAATTCATACACTTAGTATGAATTTCTTAACTTTTTTCACACAAAGTGGCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
287622 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
287680 ATACGAAAATTCATACACTTAGTATGTATTTCTTAGCTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * *
287738 ATACGGAAATTCACACACTTAGTATGAATTTCTTATCTTTTTGCACATAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * * *
287796 AAACGGAAATTCACACACTTAGTATGAATTTCTTAGCTTTTTACACACAAAGTTCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * * * * *
287854 ATACAGAAATTTATACATTTAGTATGAATTTCATAACTTTTTGCGCACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * * * *
287912 ATACGAAAATTCATACACTTAGTATAAATTTCTTAGCCTTTTGCACATAAAGTGTCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
287970 ATACGGAAATTCACACACTTAGTATGAATTTCTTAGCTTTTTACACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * * *
288028 ATACGGAAATTTATACACTTAGTATCAATTTCTTAGCTTTTTACACACAAAGTGCCAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
288086 ATACGGAAATTCATACAATTAGTATGAATTTCTTATCTTTTTGCACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACAC
288134 TTAGTGCCAT
Statistics
Matches: 558, Mismatches: 67, Indels: 3
0.89 0.11 0.00
Matches are distributed among these distances:
55 32 0.06
57 16 0.03
58 510 0.91
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (58 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
Found at i:292738 original size:68 final size:68
Alignment explanation
Indices: 292607--292860 Score: 384
Period size: 68 Copynumber: 3.8 Consensus size: 68
292597 TCTTTAACCG
* * * * *
292607 TTCATCTAACTGGCCTAATGGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
292671 CCA
66 CCT
* *
292674 TTCATCTAACTGGCATGATTGACACCTATCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
292739 CCT
66 CCT
* *
292742 TTCATCTAACTGGCATGATTGACACATTTCTGCCAAATGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
292807 ACT
66 CCT
* *
292810 TTCATCTAACTGACATGATCGACACATTTCTGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCC
292861 ATTAATCTTG
Statistics
Matches: 171, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 30 0.18
68 141 0.82
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (68 bp):
TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:293712 original size:58 final size:58
Alignment explanation
Indices: 293076--293704 Score: 999
Period size: 58 Copynumber: 10.8 Consensus size: 58
293066 TATATTTCCC
*
293076 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
293134 ATACGGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTACCCA
1 ATACGG-AAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * *
293193 ATGCAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * *
293251 ATACAGAAATTCATACACATAGTATGAATTTCTTAGCTTTTTGCACACAATGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * * *
293309 ATACGGGAATTCACT-TACTTAGTATGAATTTCTTAGCTTTTTGCAAACAAAGTGCCTA
1 ATACGGAAATTCA-TACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* *
293367 ATACGGAAATTCACACACTTAGTATGAATTTCTTAGCTTTTTGTACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
** * * *
293425 ATACAAAAATTCATACACTTAGTATGAATTTTTTAACTTTTTGCACACAAATTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
* * *
293483 ATACAGAAATTCATACACTTAGTATGACTTTCTTAGCTTTTTCCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
*
293541 ATACGGAAATTCACACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
*
293599 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
*
293657 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTCCACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACAC
293705 TTAGTGCCAT
Statistics
Matches: 524, Mismatches: 44, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
58 470 0.90
59 54 0.10
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (58 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCA
Found at i:294080 original size:22 final size:20
Alignment explanation
Indices: 294036--294090 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
294026 TGGCCCTTTA
*
294036 GTATCGATACTCCTACCATG
1 GTATTGATACTCCTACCATG
*
294056 GTATTGATACTACCATACTATG
1 GTATTGATACT-CC-TACCATG
*
294078 GTACTGATACTCC
1 GTATTGATACTCC
294091 CTTTCGGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 4 0.13
22 16 0.53
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATTGATACTCCTACCATG
Found at i:296028 original size:21 final size:21
Alignment explanation
Indices: 296002--296049 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
295992 AAATTAGCTA
296002 AGCATGACAAAAGTCATACTT
1 AGCATGACAAAAGTCATACTT
296023 AGCATGACAAAAGTCATACTT
1 AGCATGACAAAAGTCATACTT
296044 AGCATG
1 AGCATG
296050 TTTAAAAATT
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:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
AGCATGACAAAAGTCATACTT
Found at i:296094 original size:19 final size:18
Alignment explanation
Indices: 296060--296099 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
296050 TTTAAAAATT
296060 AAACTTAAAATAAAAATGA
1 AAACTTAAAATAAAAA-GA
296079 AAACTTAAAA-AGAAAAGA
1 AAACTTAAAATA-AAAAGA
296097 AAA
1 AAA
296100 GAAAGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.15
Consensus pattern (18 bp):
AAACTTAAAATAAAAAGA
Found at i:296737 original size:20 final size:20
Alignment explanation
Indices: 296712--296761 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
296702 ATCTTAGAGC
296712 ATTTATTTTAACATAAATTT
1 ATTTATTTTAACATAAATTT
296732 ATTTATTTTAACATAAATTT
1 ATTTATTTTAACATAAATTT
296752 ATTTATTTTA
1 ATTTATTTTA
296762 GTTGATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATTTTAACATAAATTT
Found at i:298165 original size:15 final size:15
Alignment explanation
Indices: 298143--298178 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
298133 GTTACTTAGT
*
298143 CCGGTTCAATTTAAA
1 CCGGTTCAATCTAAA
*
298158 CTGGTTCAATCTAAA
1 CCGGTTCAATCTAAA
298173 CCGGTT
1 CCGGTT
298179 AAACCGCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (15 bp):
CCGGTTCAATCTAAA
Found at i:298489 original size:17 final size:16
Alignment explanation
Indices: 298458--298488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
298448 AATATTGAAA
*
298458 CTTGAACTCAAAAAAG
1 CTTGAACTAAAAAAAG
298474 CTTGAACTAAAAAAA
1 CTTGAACTAAAAAAA
298489 AAATTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTAAAAAAAG
Found at i:298560 original size:14 final size:14
Alignment explanation
Indices: 298541--298568 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
298531 AAATGAAAGA
298541 ATAGTTATATAATT
1 ATAGTTATATAATT
298555 ATAGTTATATAATT
1 ATAGTTATATAATT
298569 TTGTTATAAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:301385 original size:19 final size:21
Alignment explanation
Indices: 301363--301405 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
301353 CAATACCAGC
301363 ACTA-AAAAAGG-GTACCGAT
1 ACTAGAAAAAGGAGTACCGAT
* *
301382 ACTAGAAATAGGAGTATCGAT
1 ACTAGAAAAAGGAGTACCGAT
301403 ACT
1 ACT
301406 TCCCTTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 6 0.30
21 10 0.50
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (21 bp):
ACTAGAAAAAGGAGTACCGAT
Found at i:309889 original size:3 final size:3
Alignment explanation
Indices: 309883--309941 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
309873 AACAAAGCAA
309883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
309931 AAT AAT AAT AA
1 AAT AAT AAT AA
309942 ACCTAAAACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:312690 original size:3 final size:3
Alignment explanation
Indices: 312684--312731 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
312674 ATTATTTATT
* * *
312684 TAA TAA TAA TAA TAT TATA TAA TAA CAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
312729 TAA
1 TAA
312732 CTAAAACAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:312701 original size:19 final size:21
Alignment explanation
Indices: 312662--312713 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
312652 TGTAAAAATG
*
312662 TAATAATAATAAATTATTTATT
1 TAATAATAAT-AATTATTTATA
312684 TAATAATAATAA-TA-TTATA
1 TAATAATAATAATTATTTATA
*
312703 TAATAACAATA
1 TAATAATAATA
312714 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.50
20 2 0.07
21 2 0.07
22 10 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATAATAATTATTTATA
Found at i:313207 original size:113 final size:113
Alignment explanation
Indices: 313065--314076 Score: 1274
Period size: 113 Copynumber: 8.8 Consensus size: 113
313055 ATAGAGTCAT
* * * * * *
313065 GCAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTATTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
313130 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
* * * *
313178 ACAAAAAGTTTAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
313243 ATTATGAAC-TCCTTCTGGAAATGCTGAT-GAT-GATATGTCTCATTCTGTGATAGAGTCAT
66 ATTATGAACTTTC-TCTGGAAATGCTGATCCATCGA-ATG----A-----TG--A-ATTCAA
* * * * *
313302 GCAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *** *
313367 ATTATGAACTTTCTCTGGAAAAATTAATACTGATCTATCTCCTTCTGTGATAGAA-TCAT
66 ATTATGAACTTTCTCTGG----A--AATGCTGATCCA--T-C--GAATGAT-GAATTCAA
*
313426 G-AAAAAGATTGAACAAGTTCTTCTCATTATGAAGTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
313490 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCGAGTGATGAATTCAA
65 CATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
*
313539 GC-AAAAGATTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
313603 CATTATGAACTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAA
65 CATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
*
313651 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
313716 ATTATGAACTCT-TCTGGAAATGATGATCCATCGAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
313763 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
313828 ATTATGAACTCTAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
*
313876 GAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
313941 ATTATGAACTCTAC-CTGGAAATGCTGATCCATTGAATGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
313989 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
314054 ATTATGAACTCTAC-CTGGAAATG
66 ATTATGAACT-TTCTCTGGAAATG
314077 TTTTAAGAAA
Statistics
Matches: 800, Mismatches: 62, Indels: 74
0.85 0.07 0.08
Matches are distributed among these distances:
111 2 0.00
112 218 0.27
113 393 0.49
115 1 0.00
116 2 0.00
118 9 0.01
121 2 0.00
123 6 0.01
124 145 0.18
125 5 0.01
126 1 0.00
127 1 0.00
128 2 0.00
130 8 0.01
131 1 0.00
132 1 0.00
133 1 0.00
136 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
Found at i:314211 original size:75 final size:76
Alignment explanation
Indices: 314088--314264 Score: 277
Period size: 75 Copynumber: 2.3 Consensus size: 76
314078 TTTAAGAAAA
* * *
314088 AAACATTC-TGCACTGTAGGGCTTACAGCTGACCAGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCAGAAGGCTTTGAAAACATCAAAAAGCTCCCG
314152 AAGGC-TTTTGG
65 AAGGCTTTTTGG
**
314163 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCAGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
314228 AGGCTTTTTGG
66 AGGCTTTTTGG
*
314239 AAACATCATGCATTGTAGGACTTACA
1 AAACATCATGCACTGTAGGACTTACA
314265 TATGTGAGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
74 2 0.02
75 61 0.65
76 31 0.33
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCAGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:314970 original size:22 final size:22
Alignment explanation
Indices: 314945--315004 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
314935 AATAAAGCTT
*
314945 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
314967 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
314989 TCATCTTTGAAAAGAG
1 TCATCTTTGAAAAGAG
315005 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:316930 original size:18 final size:16
Alignment explanation
Indices: 316899--316933 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
316889 TATTTTTTTC
316899 AAAAAAAAAAACAAAA
1 AAAAAAAAAAACAAAA
316915 AAAAACAAATAAACAAAA
1 AAAAA-AAA-AAACAAAA
316933 A
1 A
316934 GCCAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAACAAAA
Found at i:323397 original size:31 final size:31
Alignment explanation
Indices: 323362--323424 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
323352 AGAGATGTGG
323362 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
323393 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
323424 T
1 T
323425 TTATATGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTGCAGAGTTGACAGAT
Found at i:325865 original size:17 final size:17
Alignment explanation
Indices: 325844--325895 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
325834 AATTTTCCTT
325844 TTTTTTC-TCATTTTTC
1 TTTTTTCATCATTTTTC
325860 TTTTTTCATCATTTTTC
1 TTTTTTCATCATTTTTC
*
325877 TTTTTTCTTC-TTTTTC
1 TTTTTTCATCATTTTTC
325893 TTT
1 TTT
325896 CTTTGCTAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 16 0.47
17 18 0.53
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTCATCATTTTTC
Found at i:332524 original size:3 final size:3
Alignment explanation
Indices: 332518--332565 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
332508 ATTATTTATT
* *
332518 TAA TAA TAA TAA T-A TAA T-A TAA TAA CAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
332563 TAA
1 TAA
332566 CTAAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:333974 original size:20 final size:20
Alignment explanation
Indices: 333951--334004 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
333941 ATGTAAAAAT
*
333951 AAGAAAAAACCGGTTAGGAA
1 AAGACAAAACCGGTTAGGAA
333971 AAGACAAAACCGGTTAGGAA
1 AAGACAAAACCGGTTAGGAA
333991 AAGACAAAACCGGT
1 AAGACAAAACCGGT
334005 AAAGAGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (20 bp):
AAGACAAAACCGGTTAGGAA
Found at i:334124 original size:202 final size:202
Alignment explanation
Indices: 333771--334166 Score: 580
Period size: 202 Copynumber: 2.0 Consensus size: 202
333761 GAAAAAATAT
* * ** * *
333771 GACAAAACCAGTCACGAAAAGACAAAACCGGTAAAGCGCTACCTGATATATTGCAAGTATCGCTA
1 GACAAAACCAGTCACGAAAAGACAAAACCGGTAAAGAGATACCAAATATATTGAAAGTATCGATA
* *
333836 CTTTAATATAAGTATCGACACATAGTGAATTTAAAGGAGAAGCAATTTTAGCGTCTATAAAGTGT
66 CTTTAATATAAGTATCGACACATAGTGAATTTAAAGGAGAAACAATTTTAGCGTCTATAAAGTAT
* *
333901 CGATTCTTTATAAATATGTATCGATCCACAACGATA-AAACATGTAAAAATAAGAAAAAACCGGT
131 CGATTCTTTATAAAAATGTATCGATCCACAACGATATAAA-AGGTAAAAATAAGAAAAAACCGGT
333965 TAGGAAAA
195 TAGGAAAA
* * * *
333973 GACAAAACCGGTTAGGAAAAGACAAAACCGGTAAAGAGATACCAAATATATTGAAAGTGTCGATA
1 GACAAAACCAGTCACGAAAAGACAAAACCGGTAAAGAGATACCAAATATATTGAAAGTATCGATA
* *
334038 CTTTAATATAAGTATCGACACATTGTGAATTTAAAGGAGAAACAGTTTTAGCG-CGTATAAAGTA
66 CTTTAATATAAGTATCGACACATAGTGAATTTAAAGGAGAAACAATTTTAGCGTC-TATAAAGTA
* * * *
334102 TCGATTCTTTATAAAAATGTATCGATCCATAACGGTATAAAAGGTAAAAATATGATAAAACCGGT
130 TCGATTCTTTATAAAAATGTATCGATCCACAACGATATAAAAGGTAAAAATAAGAAAAAACCGGT
334167 CTCTAAATGA
Statistics
Matches: 172, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
201 1 0.01
202 168 0.98
203 3 0.02
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (202 bp):
GACAAAACCAGTCACGAAAAGACAAAACCGGTAAAGAGATACCAAATATATTGAAAGTATCGATA
CTTTAATATAAGTATCGACACATAGTGAATTTAAAGGAGAAACAATTTTAGCGTCTATAAAGTAT
CGATTCTTTATAAAAATGTATCGATCCACAACGATATAAAAGGTAAAAATAAGAAAAAACCGGTT
AGGAAAA
Found at i:342509 original size:21 final size:21
Alignment explanation
Indices: 342485--342549 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
342475 AAGACAATCA
342485 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
342506 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
342527 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
342548 AG
1 AG
342550 GCATAAGGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.42, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:342647 original size:33 final size:33
Alignment explanation
Indices: 342583--342649 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
342573 AAATAGATGG
* * *
342583 AGTGGTGAAAGAAGTTAAGGTGTCGATGGGTGA
1 AGTGGTGAAAGAAGTTAAGATATCGAGGGGTGA
* *
342616 AGTGGTGAAAGAAGTTGAGATATTGAGGGGTGA
1 AGTGGTGAAAGAAGTTAAGATATCGAGGGGTGA
342649 A
1 A
342650 CTTAAGATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.01, G:0.42, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTAAGATATCGAGGGGTGA
Found at i:342856 original size:18 final size:18
Alignment explanation
Indices: 342833--342871 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
342823 AAAAAAATAT
342833 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
* *
342851 GAAGAAGAAAATATGGAG
1 GAAGAAGAAAAGAGGGAG
342869 GAA
1 GAA
342872 ATGAGGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGGAG
Found at i:344427 original size:19 final size:19
Alignment explanation
Indices: 344403--344451 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
344393 AATATAGAGT
344403 TAATTTTGTATA-AGATTTA
1 TAATTTTGTATACA-ATTTA
344422 TAATTTTGTATACAATTTA
1 TAATTTTGTATACAATTTA
344441 TAATTTTGTAT
1 TAATTTTGTAT
344452 GTGGATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATACAATTTA
Found at i:345032 original size:21 final size:21
Alignment explanation
Indices: 345002--345048 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
344992 CAGATAACGG
*
345002 GTCGATACATTTATTGAAAGT
1 GTCGAAACATTTATTGAAAGT
*
345023 TTCGAAACATTTATTGAAAGT
1 GTCGAAACATTTATTGAAAGT
345044 GTCGA
1 GTCGA
345049 TCCCAGAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (21 bp):
GTCGAAACATTTATTGAAAGT
Found at i:345397 original size:201 final size:199
Alignment explanation
Indices: 345018--345979 Score: 1106
Period size: 200 Copynumber: 4.8 Consensus size: 199
345008 ACATTTATTG
* * **
345018 AAAGTTTCGAAACATTTATTGAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* * * *
345083 ATAGGTAATTTTTCAATTTAACCGATATAACTAAACCGGTTTTATAAGAGAATAGGTCTACATAA
66 ATAGGTAATTTTTCAATGTAACCGGTATAA-TATACCGGTTTTATGAGAGAATAGGTCTACATAA
* * * *
345148 TGTATCGAAACTTCTGTAATTTGTGTCGATA-TTGTTTCTCCTGAAGGAATGCCCAAAAGGGTGC
130 TGTATCGACACTTGTGTAATTTGTGTCGATACTT-TTTGTCCAGAAGGAATGCCCAAAAGGGTGC
*
345212 ACGCAA
194 ACGCAT
* *
345218 AAAGTGTTGATACATTTATAAACAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTATAAA-AAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGT
* * ** *
345283 ACTAGGTAATTTTTCAATGTAACCGGTACACATATACCAATTTTATGAGAGAATAGGTGTACA-A
65 AATAGGTAATTTTTCAATGTAACCGGTATA-ATATACCGGTTTTATGAGAGAATAGGTCTACATA
*
345347 TATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGT
129 -ATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCC-AAAAGGGT
345412 GGC-C-CACT
192 -GCACGCA-T
*
345420 -AAGTGTCGATACATTTATACAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* * * * *
345484 ATAGATAATTTTGT-AATATAACCGATATAAATATACCAGTTTTATGTGAGAATAGGTCTACATA
66 ATAGGTAATTTT-TCAATGTAACCGGTAT-AATATACCGGTTTTATGAGAGAATAGGTCTACATA
* * * ** * * * *
345548 ATGTATCGACACTTTTTTATTTTGTGTCGATAAGTTTTGTCCAGAATGAATGCCCAAAATGATGA
129 ATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGC
*
345613 ACACAT
194 ACGCAT
* * * *
345619 AAAGTTTCGATATATTTATAAAAAGTGTCGATACTAGAAACATCGAAACCCATACA-TATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATA-ATTATAATGT
* * * *
345683 AATAGGTAAATTTACAATGTATCCAGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACA-A
65 AATAGGTAATTTTTCAATGTAACCGGTATAA-TATACCGGTTTTATGAGAGAATAGGTCTACATA
* * *
345747 TATGTATCGACACTTGTG-GATTTGGTGTCGATACTTTTTGTCCAAAAGGAA-GGCC-AAAGGGT
129 -ATGTATCGACACTTGTGTAATTT-GTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGG-
*
345809 TGCATGCAT
191 TGCACGCAT
* * * *
345818 AAAGTGTCGATACTTTTTTAAAAAGTTTCGATCCCA-AGAACATCGAAACCGATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGA-AACATCGAAACCCATAATTATAATGT
* * * * *
345882 AATAGGTAAATTTCCAATGTAACCGGTAAAAATATACCGATTTTATGAGAAAATAGGTC-ATCAT
65 AATAGGTAATTTTTCAATGTAACCGGT-ATAATATACCGGTTTTATGAGAGAATAGGTCTA-CAT
* * *
345946 AAAGTATCGACAATTAT-TAAATTTGTGTCGATAC
128 AATGTATCGACACTTGTGT-AATTTGTGTCGATAC
345980 CATTTTAAAT
Statistics
Matches: 648, Mismatches: 88, Indels: 53
0.82 0.11 0.07
Matches are distributed among these distances:
198 8 0.01
199 149 0.23
200 312 0.48
201 165 0.25
202 12 0.02
203 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
ATAGGTAATTTTTCAATGTAACCGGTATAATATACCGGTTTTATGAGAGAATAGGTCTACATAAT
GTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCAC
GCAT
Found at i:347465 original size:6 final size:6
Alignment explanation
Indices: 347454--347493 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
347444 CAAGAGGTCA
* * *
347454 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
347494 TTATTATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:347469 original size:12 final size:12
Alignment explanation
Indices: 347454--347493 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
347444 CAAGAGGTCA
*
347454 ATGAAGATGAAG
1 ATGACGATGAAG
347466 ATGACGATGAAG
1 ATGACGATGAAG
*
347478 ATGACGATGATG
1 ATGACGATGAAG
347490 ATGA
1 ATGA
347494 TTATTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:347475 original size:18 final size:18
Alignment explanation
Indices: 347454--347493 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
347444 CAAGAGGTCA
347454 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
347472 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
347490 ATGA
1 ATGA
347494 TTATTATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:348519 original size:25 final size:25
Alignment explanation
Indices: 348485--348536 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
348475 TCGTTGTGGG
348485 TACATTATTTGAACATTGCTATGTA
1 TACATTATTTGAACATTGCTATGTA
*
348510 TACATTATTTGAACATTGTTATGTA
1 TACATTATTTGAACATTGCTATGTA
348535 TA
1 TA
348537 AATTTCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (25 bp):
TACATTATTTGAACATTGCTATGTA
Found at i:348818 original size:15 final size:15
Alignment explanation
Indices: 348798--348836 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
348788 TCTCCATAAC
* *
348798 AAAGTTTTCATACAT
1 AAAGTTTCCAAACAT
*
348813 AAAGTTTCCAAACTT
1 AAAGTTTCCAAACAT
348828 AAAGTTTCC
1 AAAGTTTCC
348837 CATAAAGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (15 bp):
AAAGTTTCCAAACAT
Found at i:349336 original size:200 final size:198
Alignment explanation
Indices: 348837--349601 Score: 854
Period size: 201 Copynumber: 3.8 Consensus size: 198
348827 TAAAGTTTCC
* * * * *
348837 CATAAAGTGTCGATATAGTTTTAAAAAGTATCGATCCAGAAACATCGAAATCC-ATAAATATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAACATC-AAAACCGATAATTATAAT
* * * * *
348901 GTAATAGGTAAATTTACAATGTAACCAGTATAACTACACTGGTTTTATGAGAGAATAGGTCTACA
65 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACA
* ** * * * * * *
348966 TAATTTATCGACACTTCTGGAATTTTTGTCGATACTGTTTGTCCAGAAGGAATTCCCATAAGGGG
130 TAATGTATCGACACTT-TTTAATTTGTGTCGATACTTTTTGTACAGAATGAATGCCCA-AAAGGG
*
349031 TGCACT
193 TGCACA
* * *
349037 CATAAAGTGTCAAAACATTTTTAAAACA-TATCGATCCCAAAAACATCAAAACCTATAATTATAA
1 CATAAAGTGTCGATACATTTTTAAAA-AGTATCGAT-CCAAAAACATCAAAACCGATAATTATAA
* ** * * * * *
349101 TGTAATAGGTAATTTTGTAATATAA-CTGATATAAATATACCGGTTTTATGTGAGAATAGGTCTA
64 TGTAATAGGTAAATTTACAATGTAACCAG-TATAAATATACCGGTTTTATGAGAAAATAGGTCAA
* *
349165 CATAATATGTCGACACTTTTTAATGTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAAAAGG
128 CATAATGTATCGACACTTTTTAAT-TTGTGTCGATACTTTTTGTACAGAATGAATGCCCAAAAGG
* *
349230 GTGAACG
192 GTGCACA
* * *
349237 CATAAAGTGTGGATACATTTATAAAAAGTGTCGATCCCAAAAACATCAAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGAT-CCAAAAACATCAAAACCGATAATTATAAT
* ** ** *
349302 GTAATAGGTAAATTTACAATGGAACCAGTATAAATATATTGGTTTTATGTTAAAATAGGTGAACA
65 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACA
* * * *
349367 AAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTTCAAAATGAATG-CCAAAAGGGT
130 TAATGTATCGACACTTTTTA-ATTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAAAAGGG-
349431 TGCACA
193 TGCACA
* * **
349437 CATAAAGTGTCGATACATGTTTTAAAAAGTATCGATCCAAAAAGAATTAAAATTGATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCAAAAA-CATCAAAACCGATAATTATAA
* * * * *
349502 TATAATAGGTAAATTTACAATGTAACCGGTATAATTGTACCGGTTTTATGAGAAAATAGGTGAAC
64 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCAAC
* *
349567 ATTATGTATCGACACGTTTTAAATTTGTGTCGATA
129 ATAATGTATCGACAC-TTTTTAATTTGTGTCGATA
349602 GTTATAAATA
Statistics
Matches: 479, Mismatches: 74, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
199 10 0.02
200 229 0.48
201 236 0.49
202 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAACATCAAAACCGATAATTATAATG
TAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACAT
AATGTATCGACACTTTTTAATTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAAAAGGGTGC
ACA
Found at i:354487 original size:199 final size:198
Alignment explanation
Indices: 353711--354613 Score: 1040
Period size: 201 Copynumber: 4.5 Consensus size: 198
353701 ACCTAAATAC
* * *
353711 GTGTCAATACATTT-TCTAAAAGTATCGA-CCCAAAAAATATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * *
353774 TAGGTAAATTAACAATGTAACCGGTATAAATATACC-GATTAATTAGAAAATAGGTTAACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACATAAT
* * *
353838 GCATCGACACTTGTGTAATTTGTGTCGATACTTATTATCCAGAATGAATGCCCAAATGAGGTGCA
129 GTATCGACACTTAT-TAATTTGTGTCGATACTT-TTATCCAGAATGAATG-CCAAACGAGGTGCA
*
353903 CACATAAA
191 CGCATAAA
* *
353911 GTGTCGATACAATTATTAAAAGTATCAATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAAT
** ** *
353975 AGGTAAATTTACAATGTAACCGGTATAAATATACCCATTTTATGTTAAAATAGGTGAACATAATG
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACATAATG
* * * **
354040 TATCGACACGTT-TTATATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAA-AAGGTTTTA
130 TATCGACAC-TTATTA-ATTTGTGTCGATAC-TTTTATCCAGAATGAATGCCAAACGAGG-TGCA
*
354103 CGTATAAA
191 CGCATAAA
* * *
354111 GTGTCGATACATGTT-TTAAAAAGTATCGATCCAAAAAATATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACAT-TTATT-AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * * *
354175 TATGTAAATTTACAATGTAACCGGTATAAATATAACGGTTTTATGAGAAAATAGGTCATCATAAA
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACATAAT
* * *
354240 GTATCGATACTTATTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACG-GGTGCAC
129 GTATCGACACTTATT-AATTTGTGTCGATAC-TTTTATCCAGAATGAATGCCAAACGAGGTGCAC
354304 GCATAAA
192 GCATAAA
* * * * *
354311 GTGTCGATACATTTATTAAAACTATCGAGCCCAAAAACATCGATACCGATAATTACAATGTGATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
354376 GGTAAATTTACAATGTATCCGATAGAAATATACCGGTTTTATGAAAAAAATAGGTCTAA-ATAAT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATG-AGAAAATAGGT-TAACATAAT
* * * * *
354440 GTATTGACACTCT-TTAAGTTTATGTCGTTACTTGTT-TTCAGAATGAATGCCCAACGAGGTGCA
129 GTATCGACACT-TATTAA-TTTGTGTCGATACTT-TTATCCAGAATGAATGCCAAACGAGGTGCA
354503 CGCATAAA
191 CGCATAAA
* * * *
354511 GTGTCGATACATTTA--AAATTGTATCGATCCAAAAAACATCAAAACTGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* *
354574 AGGTAAATTTGCAATGTTACCGGTATAAATATACCGGTTT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
354614 ACTTATAAAA
Statistics
Matches: 603, Mismatches: 78, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
198 3 0.00
199 174 0.29
200 207 0.34
201 214 0.35
202 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACATAATGT
ATCGACACTTATTAATTTGTGTCGATACTTTTATCCAGAATGAATGCCAAACGAGGTGCACGCAT
AAA
Found at i:354733 original size:86 final size:86
Alignment explanation
Indices: 354633--354928 Score: 511
Period size: 86 Copynumber: 3.4 Consensus size: 86
354623 ATAGGTCAAG
*
354633 ATAAGCGCTACCTATTACATATATAAGCGCTGCCTAATATGTTATTGTACTTGATAATATTTCCG
1 ATAAGCGCTACCTATTACATATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
354698 GTTAAATGCCTATTTTATTAT
66 GTTAAATGCCTATTTTATTAT
*
354719 ATAAGCGCTACCTATTACATATATAAGCGCTATCTAATATGTTATTGTACTTGATAATATTTCCG
1 ATAAGCGCTACCTATTACATATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
354784 GTTAAATGCCTATTTTATTAT
66 GTTAAATGCCTATTTTATTAT
* *
354805 ATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTTATAATATTTCC
1 ATAAGCGCTACCTATTACA-TATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCC
354870 GGTTAAATGCCTATTTTATTAT
65 GGTTAAATGCCTATTTTATTAT
** *
354892 ATAAGCGCTACCTATTTTATTATATAAGAGCTACCTA
1 ATAAGCGCTACCTATTACA-TATATAAGCGCTACCTA
354929 TTAAATTACA
Statistics
Matches: 200, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
86 103 0.51
87 97 0.49
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (86 bp):
ATAAGCGCTACCTATTACATATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
GTTAAATGCCTATTTTATTAT
Found at i:354850 original size:23 final size:23
Alignment explanation
Indices: 354800--354844 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
354790 TGCCTATTTT
* *
354800 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCACTACCTAATAC
354823 ATTATATAAGCACTACCTAATA
1 ATTATATAAGCACTACCTAATA
354845 TGTTATTGTA
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:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCACTACCTAATAC
Found at i:354905 original size:23 final size:23
Alignment explanation
Indices: 354879--354951 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
354869 CGGTTAAATG
354879 CCTATTTTATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
*
354902 CCTATTTTATTATATAAGAGCTA
1 CCTATTTTATTATATAAGCGCTA
** * *
354925 CCTATTAAATTACATAAGCTCTA
1 CCTATTTTATTATATAAGCGCTA
354948 CCTA
1 CCTA
354952 ATATGTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (23 bp):
CCTATTTTATTATATAAGCGCTA
Found at i:359394 original size:2 final size:2
Alignment explanation
Indices: 359387--359415 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
359377 ATTCTCTAGT
359387 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 T
359416 GATTATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:375550 original size:45 final size:44
Alignment explanation
Indices: 375486--375593 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 44
375476 TCAAAAAAAT
*
375486 GTCTTATGAAATAAATTGGGTAATCTTGGTAATAGCTCCAACATA
1 GTCTTA-GAAATAAGTTGGGTAATCTTGGTAATAGCTCCAACATA
* *
375531 GTCTTAGGAAATAAGTTGGGTAATGTTGGTAATAGTTCCAACATA
1 GTCTTA-GAAATAAGTTGGGTAATCTTGGTAATAGCTCCAACATA
*
375576 GTGTTAGAAATAAGTTGG
1 GTCTTAGAAATAAGTTGG
375594 AAATCAACCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 12 0.21
45 46 0.79
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (44 bp):
GTCTTAGAAATAAGTTGGGTAATCTTGGTAATAGCTCCAACATA
Found at i:384830 original size:138 final size:139
Alignment explanation
Indices: 384598--384855 Score: 366
Period size: 138 Copynumber: 1.9 Consensus size: 139
384588 CGTGTATGAT
384598 AGTTATCGATCGATTATTATTAATGCATAACGGTGCATTTTTCGTATAAGCACTATGTGTACTTC
1 AGTTATCGATCGATTATTATTAATGCATAACGGTGCATTTTTCGTATAAGCACTATGTGTACTTC
* **
384663 AGGCACTAGATGTGCAATCATGGTATTCATAATGAGTTTATG-ATTTACCATTTCGATATAAAAA
66 AGGCACTAGATGTGCAATCATGGAATTCATAAAAAGTTTATGAATTT-CCATTTCGATATAAAAA
384727 AATGTATAAA
130 AATGTATAAA
* * *
384737 AGTTATCGATCGATT-TTGTTTAATGCATAACGGTGCATTTTT-GTATCAGTACTATGTGTACTT
1 AGTTATCGATCGATTATT-ATTAATGCATAACGGTGCATTTTTCGTATAAGCACTATGTGTAC-T
*
384800 TC-GGCACTATG-TGTGC-ATCCATGGAATTCATAAAAAGTTTGTGAATTTCCATTTCG
64 TCAGGCACTA-GATGTGCAAT-CATGGAATTCATAAAAAGTTTATGAATTTCCATTTCG
384856 GCACTTCGGT
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
137 2 0.02
138 59 0.55
139 46 0.43
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (139 bp):
AGTTATCGATCGATTATTATTAATGCATAACGGTGCATTTTTCGTATAAGCACTATGTGTACTTC
AGGCACTAGATGTGCAATCATGGAATTCATAAAAAGTTTATGAATTTCCATTTCGATATAAAAAA
ATGTATAAA
Found at i:384933 original size:95 final size:95
Alignment explanation
Indices: 384767--384963 Score: 367
Period size: 95 Copynumber: 2.1 Consensus size: 95
384757 TAATGCATAA
384767 CGGTGCATTTTTGTATCAGTACTATGTGTACTTTCGGCACTATGTGTGCATCCATGGAATTCATA
1 CGGTGCATTTTTGTATCAGTACTATGTGTACTTTCGGCACTATGTGTGCATCCATGGAATTCATA
384832 AAAAGTTTGTGAATTTCCATTTCGGCACTT
66 AAAAGTTTGTGAATTTCCATTTCGGCACTT
*
384862 CGGTGCATTTTTGTATCAGTACTATGTGTATTTTCGGCACTATGTGTGCATCCATGGAATTCATA
1 CGGTGCATTTTTGTATCAGTACTATGTGTACTTTCGGCACTATGTGTGCATCCATGGAATTCATA
* *
384927 ATAAGTTTGTGAATTTTCATTTCGGCACTT
66 AAAAGTTTGTGAATTTCCATTTCGGCACTT
384957 CGGTGCA
1 CGGTGCA
384964 ATGCATGTAC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (95 bp):
CGGTGCATTTTTGTATCAGTACTATGTGTACTTTCGGCACTATGTGTGCATCCATGGAATTCATA
AAAAGTTTGTGAATTTCCATTTCGGCACTT
Found at i:407408 original size:33 final size:32
Alignment explanation
Indices: 407285--407410 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 32
407275 AAGCTAAGTC
* * * *
407285 TATGATATGAGTTATTGCCATGGAAGTTCATGT
1 TATGATATAAGTT-TTGCCATGAAAGTTTACGT
* * * * *
407318 TATGGTATAAGTTTTTGCCGTAAAAGTATACAT
1 TATGATATAAG-TTTTGCCATGAAAGTTTACGT
* * * *
407351 TATGACATTAGTTTTGGCTTGAAAGTTTACGT
1 TATGATATAAGTTTTGCCATGAAAGTTTACGT
407383 TATGATATAAGTTCTTGCCATGAAAGTT
1 TATGATATAAGTT-TTGCCATGAAAGTT
407411 CATGCTAAGA
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
32 27 0.39
33 41 0.59
34 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (32 bp):
TATGATATAAGTTTTGCCATGAAAGTTTACGT
Found at i:408215 original size:17 final size:17
Alignment explanation
Indices: 408193--408228 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
408183 TATAATATAA
408193 AACTACAACTAAGTACC
1 AACTACAACTAAGTACC
408210 AACTACAACTAAGTACC
1 AACTACAACTAAGTACC
408227 AA
1 AA
408229 GTATCTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.17
Consensus pattern (17 bp):
AACTACAACTAAGTACC
Found at i:413783 original size:45 final size:45
Alignment explanation
Indices: 413699--413999 Score: 372
Period size: 45 Copynumber: 6.7 Consensus size: 45
413689 CCTCCATTTA
* * * * * **
413699 TGTTTATAATATACCCATATAAATTTTAACTATAGTATACTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
*
413744 TGTTGATAATGTACCCATATACATTTCAAC-CATAATATACTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTC-TAACATACTTTTC
413789 TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
* * * *
413834 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATAATTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
* * *
413879 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
* * * * **
413924 TATTGATAATGTACCCATACACATTTCAACT-AAAGTATGTTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTCTAA-CATACTTTTC
*
413969 TGTTGATAATGTACCCATTTACATTTCAACT
1 TGTTGATAATGTACCCATATACATTTCAACT
414000 ATGACATCCT
Statistics
Matches: 229, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
44 1 0.00
45 227 0.99
46 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (45 bp):
TGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTC
Found at i:414023 original size:135 final size:135
Alignment explanation
Indices: 413711--414038 Score: 342
Period size: 135 Copynumber: 2.4 Consensus size: 135
413701 TTTATAATAT
* * * *** * *
413711 ACCCATATAAATTTTAACTATAGTAT-ACTTTTCTGTTGATAATGTACCCATATACATTTCAACC
1 ACCCATATACATTTCAACTATAGCATAAC-TTTCTGCCAATAATGAACCCATATGCATTTCAACC
* * * *
413775 ATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAACATACTTTTCTGTTGA
65 ATAACATACTTTTCTATTGATAATGTACCCATACACATTTCAACTCAAACATACTTTTCTGTTGA
413840 TAATGC
130 TAATGC
* * * *** *
413846 ACCCATATGCATTTCAACTCTAGCATAATTTTCTGTTGATAATGCACCCATATGCATTTCAACTC
1 ACCCATATACATTTCAACTATAGCATAACTTTCTGCCAATAATGAACCCATATGCATTTCAAC-C
* * **
413911 -TAGCATACTTTTCTATTGATAATGTACCCATACACATTTCAACT-AAAGTATGTTTTTCTGTTG
65 ATAACATACTTTTCTATTGATAATGTACCCATACACATTTCAACTCAAA-CATACTTTTCTGTTG
*
413974 ATAATGT
129 ATAATGC
* *
413981 ACCCATTTACATTTCAACTAT-GACAT-CCTTTCATGCCAATAATGAACCCATATGCATT
1 ACCCATATACATTTCAACTATAG-CATAACTTTC-TGCCAATAATGAACCCATATGCATT
414039 AGCATTTTCA
Statistics
Matches: 162, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
134 7 0.04
135 153 0.94
136 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (135 bp):
ACCCATATACATTTCAACTATAGCATAACTTTCTGCCAATAATGAACCCATATGCATTTCAACCA
TAACATACTTTTCTATTGATAATGTACCCATACACATTTCAACTCAAACATACTTTTCTGTTGAT
AATGC
Found at i:414474 original size:20 final size:20
Alignment explanation
Indices: 414449--414490 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
414439 TTGGTTCTGA
* *
414449 AGTATCGATACTACTACCCT
1 AGTATCAATACTACTACACT
*
414469 AGTATCAATACTTCTACACT
1 AGTATCAATACTACTACACT
414489 AG
1 AG
414491 GGTACCGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (20 bp):
AGTATCAATACTACTACACT
Found at i:416731 original size:36 final size:36
Alignment explanation
Indices: 416684--416754 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
416674 TCAATTTCAA
416684 TCCCGACCTTCTTTTCAACATTATCAACATTCTTAT
1 TCCCGACCTTCTTTTCAACATTATCAACATTCTTAT
*
416720 TCCCGACCTTCTTTTCAACATTATCAATATTCTTA
1 TCCCGACCTTCTTTTCAACATTATCAACATTCTTA
416755 CCTTTATCCT
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:0.25, C:0.30, G:0.03, T:0.42
Consensus pattern (36 bp):
TCCCGACCTTCTTTTCAACATTATCAACATTCTTAT
Found at i:422015 original size:42 final size:42
Alignment explanation
Indices: 421969--422085 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 42
421959 ATTCTATAGG
*
421969 TGACTCCCCTTCGCAGGAAAGACATGTGAGATACACTTCGGA
1 TGACTCCCCTTCGCAGGAAAGTCATGTGAGATACACTTCGGA
* * * * *** *
422011 TGACTCTCATTCGCATGAAATTCATGTGAGATATTTTTTGGA
1 TGACTCCCCTTCGCAGGAAAGTCATGTGAGATACACTTCGGA
* *
422053 TGACTCCTCTTC-AAGAGAAAGTCATGTGAGATA
1 TGACTCCCCTTCGCAG-GAAAGTCATGTGAGATA
422086 TTATTCCAGC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (42 bp):
TGACTCCCCTTCGCAGGAAAGTCATGTGAGATACACTTCGGA
Found at i:423905 original size:137 final size:137
Alignment explanation
Indices: 423654--423918 Score: 365
Period size: 137 Copynumber: 1.9 Consensus size: 137
423644 GCCCTAAAAT
* * * * *
423654 ATGTTTGATCTCTACCATTGATCCATCTTAATCTGACGGTTATCCTTCATGTGGTGCTTTTACTA
1 ATGTTTGATCTCTACCATTGATCCATCTTAATCTGACGGCTATCATTCATGTGGTACTCTCACTA
* * *
423719 AGTTGGAAAACCCTAATCCTACTAGGTTAAGCAGATTTAGGCTCTTTGCTAGGCTTAGTGGATTT
66 AGTTGGAAAACCCTAATCCTACTAGGTCAAGCAGATTTAGGCTCCTTGCTAGGCCTAGTGGATTT
423784 GGGGTCC
131 GGGGTCC
* **
423791 ATGTTTGATCTCTTCTGTTGATCCATCTTAATCTGACGGCTATCATTCATGT-GTCACTCTCACT
1 ATGTTTGATCTCTACCATTGATCCATCTTAATCTGACGGCTATCATTCATGTGGT-ACTCTCACT
* *
423855 AAGTTGGAAAACCCTAATCCTACTGGGTC-AG-ACGAATTTGGGCTCCTTGCTAGGCCTAGTGGA
65 AAGTTGGAAAACCCTAATCCTACTAGGTCAAGCA-G-ATTTAGGCTCCTTGCTAGGCCTAGTGGA
423918 T
128 T
423919 GAGTTTGTTG
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
135 1 0.01
136 5 0.04
137 106 0.95
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (137 bp):
ATGTTTGATCTCTACCATTGATCCATCTTAATCTGACGGCTATCATTCATGTGGTACTCTCACTA
AGTTGGAAAACCCTAATCCTACTAGGTCAAGCAGATTTAGGCTCCTTGCTAGGCCTAGTGGATTT
GGGGTCC
Found at i:424516 original size:17 final size:18
Alignment explanation
Indices: 424494--424528 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
424484 TGAATAGTGT
*
424494 CATAACGT-CATTATAAA
1 CATAACGTAAATTATAAA
424511 CATAACGTAAATTATAAA
1 CATAACGTAAATTATAAA
424529 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (18 bp):
CATAACGTAAATTATAAA
Found at i:426096 original size:13 final size:14
Alignment explanation
Indices: 426078--426109 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
426068 GATTTTCTAA
426078 TTGAAAATCAT-TT
1 TTGAAAATCATGTT
426091 TTG-AAATCATGTT
1 TTGAAAATCATGTT
426104 TTGAAA
1 TTGAAA
426110 TTACTACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 8 0.47
14 2 0.12
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (14 bp):
TTGAAAATCATGTT
Found at i:426099 original size:12 final size:13
Alignment explanation
Indices: 426082--426110 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
426072 TTCTAATTGA
426082 AAATCAT-TTTTG
1 AAATCATGTTTTG
426094 AAATCATGTTTTG
1 AAATCATGTTTTG
426107 AAAT
1 AAAT
426111 TACTACCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (13 bp):
AAATCATGTTTTG
Found at i:428349 original size:22 final size:23
Alignment explanation
Indices: 428300--428357 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
428290 ACCCCGTGGA
*
428300 GGGTATCGGTACTCACTCAAAGG
1 GGGTATCGGTACCCACTCAAAGG
* *
428323 AGGTATCGGTACCCATTC-AAGG
1 GGGTATCGGTACCCACTCAAAGG
*
428345 GGGTATCGATACC
1 GGGTATCGGTACC
428358 TAGCGCCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGTATCGGTACCCACTCAAAGG
Found at i:434128 original size:19 final size:20
Alignment explanation
Indices: 434088--434128 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
434078 ATCTAACATA
*
434088 GGGGTATCGGTACCCTTTTG
1 GGGGTATCGGTACCCTTCTG
434108 GGGGTATCGGTACCC-TCTG
1 GGGGTATCGGTACCCTTCTG
434127 GG
1 GG
434129 TAATCTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.10, C:0.22, G:0.39, T:0.29
Consensus pattern (20 bp):
GGGGTATCGGTACCCTTCTG
Found at i:434570 original size:18 final size:18
Alignment explanation
Indices: 434529--434577 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
434519 ATTTTATACT
434529 TCTTAAATTAAATCCACA
1 TCTTAAATTAAATCCACA
* * *
434547 TATTAAATTAAATTCATA
1 TCTTAAATTAAATCCACA
434565 TCTTAACATTAAA
1 TCTTAA-ATTAAA
434578 AATATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTAAATTAAATCCACA
Found at i:434595 original size:25 final size:24
Alignment explanation
Indices: 434562--434626 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
434552 AATTAAATTC
434562 ATATCTTAACATTAAAAATATATTT
1 ATATCTTAACATTAAAAATATA-TT
* *
434587 TTATCTTAAC-TTATTAAATATATT
1 ATATCTTAACATTA-AAAATATATT
434611 ATATTCTTAA-ATTAAA
1 ATA-TCTTAACATTAAA
434627 TTATTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
24 8 0.24
25 25 0.76
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATCTTAACATTAAAAATATATT
Found at i:434631 original size:30 final size:30
Alignment explanation
Indices: 434592--434668 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
434582 TATTTTTATC
* *
434592 TTAACTTATTAAATATATTATATTCTTAAA
1 TTAAATTATTAAATATATTACATTCTTAAA
* **
434622 TTAAATTATTAAATATATTCCATTCTTACC
1 TTAAATTATTAAATATATTACATTCTTAAA
*
434652 TTAAACTATTAAATATA
1 TTAAATTATTAAATATA
434669 ATTTGTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAATTATTAAATATATTACATTCTTAAA
Found at i:434847 original size:31 final size:30
Alignment explanation
Indices: 434760--434861 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
434750 AAAATGTATA
* * * **
434760 TTTTATTTTTAATTTAAAAATATATTAAAT
1 TTTTATCTTAAATATAAAAATATATTTTAT
* *
434790 TTTTATCTTAACTACAAAAATATATTTTAT
1 TTTTATCTTAAATATAAAAATATATTTTAT
*
434820 TTTTATCTTAAATATAAAATATATATTTTAG
1 TTTTATCTTAAATATAAAA-ATATATTTTAT
434851 TTTTATCTTAA
1 TTTTATCTTAA
434862 TTTTAAAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 40 0.66
31 21 0.34
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTTATCTTAAATATAAAAATATATTTTAT
Found at i:434958 original size:24 final size:26
Alignment explanation
Indices: 434931--434983 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 26
434921 ATTTAATAAG
434931 TTAAGATAAGAATAAAATATATTTTTAA
1 TTAAGATAAGAATAAAATATA-TTTT-A
434959 GTTAAGATAAGAATAAAATATATTT
1 -TTAAGATAAGAATAAAATATATTT
434984 AATAAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (26 bp):
TTAAGATAAGAATAAAATATATTTTA
Found at i:434959 original size:59 final size:59
Alignment explanation
Indices: 434895--435011 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 59
434885 ATATAAAAAA
* * * *
434895 TTTAAGTTAGGGTCAGAACAAAATATATTTAATAAGTTAAGATA-AGAATAAAATATATT
1 TTTAAGTTAAGATAAGAACAAAATATATTTAATAAGTTAAAATACA-AATAAAATATATT
*
434954 TTTAAGTTAAGATAAGAATAAAATATATTTAATAAGTTAAAATACAAATAAAATATAT
1 TTTAAGTTAAGATAAGAACAAAATATATTTAATAAGTTAAAATACAAATAAAATATAT
435012 AATTCTAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 51 0.98
60 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (59 bp):
TTTAAGTTAAGATAAGAACAAAATATATTTAATAAGTTAAAATACAAATAAAATATATT
Found at i:434966 original size:29 final size:30
Alignment explanation
Indices: 434909--435011 Score: 156
Period size: 30 Copynumber: 3.5 Consensus size: 30
434899 AGTTAGGGTC
*
434909 AGAACAAAATATATTTAATAAGTTAAGATA
1 AGAATAAAATATATTTAATAAGTTAAGATA
*
434939 AGAATAAAATATATTT-TTAAGTTAAGATA
1 AGAATAAAATATATTTAATAAGTTAAGATA
*
434968 AGAATAAAATATATTTAATAAGTTAAAATA
1 AGAATAAAATATATTTAATAAGTTAAGATA
434998 CA-AATAAAATATAT
1 -AGAATAAAATATAT
435012 AATTCTAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
29 28 0.42
30 38 0.57
31 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (30 bp):
AGAATAAAATATATTTAATAAGTTAAGATA
Found at i:441771 original size:3 final size:3
Alignment explanation
Indices: 441763--441854 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
441753 TTTACCCTAA
441763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
441810 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
441855 GTACTTTTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.05
3 83 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:442150 original size:25 final size:27
Alignment explanation
Indices: 442101--442151 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
442091 AAAAAATGAG
442101 TTTTTTTTAAAATAATAATGCTTTTAAC
1 TTTTTTTTAAAATAATAAT-CTTTTAAC
442129 TTTTTTTTAAAATAA-AAT-TTTTA
1 TTTTTTTTAAAATAATAATCTTTTA
442152 GAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.22
27 3 0.13
28 15 0.65
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTTTTAAAATAATAATCTTTTAAC
Found at i:442367 original size:2 final size:2
Alignment explanation
Indices: 442354--442389 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
442344 ATTCATTTTA
*
442354 AT AT AC 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
442390 GTACATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:442496 original size:13 final size:13
Alignment explanation
Indices: 442480--442506 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
442470 AGATAAAACA
442480 AAGAACTAAATAT
1 AAGAACTAAATAT
442493 AAGAACTAAATAT
1 AAGAACTAAATAT
442506 A
1 A
442507 TACAACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
AAGAACTAAATAT
Found at i:443710 original size:3 final size:3
Alignment explanation
Indices: 443688--443756 Score: 66
Period size: 3 Copynumber: 21.0 Consensus size: 3
443678 ATTAAATATT
*
443688 TAA TATA TAA TAA GTAAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAT
1 TAA TA-A TAA TAA -T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
443737 TAA TATT TAA TATA TAA TAA
1 TAA TA-A TAA TA-A TAA TAA
443757 GTATATTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
3 41 0.73
4 13 0.23
5 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Done.